Search results for: molecular diversity

Authors: Fei Jia, Xingjian Bai, Xiaowei Zhang, Wenjie Yan, Ruitong Dai, Xingmin Li, Jozef Kokini

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Pseudomonas aeruginosa is a Gram-negative, aerobic, opportunistic human pathogen that is present in the soil, water, and food. This microbe has been recognized as a representative food-borne spoilage bacterium that can lead to many types of infections. Considering the casualties and property loss caused by P. aeruginosa, the development of a rapid and reliable technique for the detection of P. aeruginosa is crucial. The whole-cell aptasensor, an emerging biosensor using aptamer as a capture probe to bind to the whole cell, for food-borne pathogens detection has attracted much attention due to its convenience and high sensitivity. Here, a low-field magnetic resonance imaging (LF-MRI) aptasensor for the rapid detection of P. aeruginosa was developed. The basic detection principle of the magnetic relaxation switch (MRSw) nanosensor lies on the ‘T₂-shortening’ effect of magnetic nanoparticles in NMR measurements. Briefly speaking, the transverse relaxation time (T₂) of neighboring water protons get shortened when magnetic nanoparticles are clustered due to the cross-linking upon the recognition and binding of biological targets, or simply when the concentration of the magnetic nanoparticles increased. Such shortening is related to both the state change (aggregation or dissociation) and the concentration change of magnetic nanoparticles and can be detected using NMR relaxometry or MRI scanners. In this work, two different sizes of magnetic nanoparticles, which are 10 nm (MN₁₀) and 400 nm (MN₄₀₀) in diameter, were first immobilized with anti- P. aeruginosa aptamer through 1-Ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC)/N-hydroxysuccinimide (NHS) chemistry separately, to capture and enrich the P. aeruginosa cells. When incubating with the target, a ‘sandwich’ (MN₁₀-bacteria-MN₄₀₀) complex are formed driven by the bonding of MN400 with P. aeruginosa through aptamer recognition, as well as the conjugate aggregation of MN₁₀ on the surface of P. aeruginosa. Due to the different magnetic performance of the MN₁₀ and MN₄₀₀ in the magnetic field caused by their different saturation magnetization, the MN₁₀-bacteria-MN₄₀₀ complex, as well as the unreacted MN₄₀₀ in the solution, can be quickly removed by magnetic separation, and as a result, only unreacted MN₁₀ remain in the solution. The remaining MN₁₀, which are superparamagnetic and stable in low field magnetic field, work as a signal readout for T₂ measurement. Under the optimum condition, the LF-MRI platform provides both image analysis and quantitative detection of P. aeruginosa, with the detection limit as low as 100 cfu/mL. The feasibility and specificity of the aptasensor are demonstrated in detecting real food samples and validated by using plate counting methods. Only two steps and less than 2 hours needed for the detection procedure, this robust aptasensor can detect P. aeruginosa with a wide linear range from 3.1 ×10² cfu/mL to 3.1 ×10⁷ cfu/mL, which is superior to conventional plate counting method and other molecular biology testing assay. Moreover, the aptasensor has a potential to detect other bacteria or toxins by changing suitable aptamers. Considering the excellent accuracy, feasibility, and practicality, the whole-cell aptasensor provides a promising platform for a quick, direct and accurate determination of food-borne pathogens at cell-level.

Keywords: magnetic resonance imaging, meat spoilage, P. aeruginosa, transverse relaxation time

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Authors: Natalia C. E. S. Nascimento, Mercia L. Oliveira, Fernando R. A. Lima, Leonardo T. C. do Nascimento, Marina B. Silveira, Brigida G. A. Schirmer, Andrea V. Ferreira, Carlos Malamut, Juliana B. da Silva

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Tissue hypoxia is a common characteristic of solid tumors leading to decreased sensitivity to radiotherapy and chemotherapy. In the clinical context, tumor hypoxia assessment employing the positron emission tomography (PET) tracer ¹⁸F-fluoromisonidazole ([¹⁸F]FMISO) is helpful for physicians for planning and therapy adjusting. The aim of this work was to implement the synthesis of 18F-FMISO in a TRACERlab® MXFDG module and also to establish the quality control procedure. [¹⁸F]FMISO was synthesized at Centro de Desenvolvimento da Tecnologia Nuclear (CDTN/CNEN/Brazil) using an automated synthesizer (TRACERlab® MXFDG, GE) adapted for the production of [¹⁸F]FMISO. The FMISO chemical standard was purchased from ABX. 18O- enriched water was acquired from Center of Molecular Research. Reagent kits containing eluent solution, acetonitrile, ethanol, 2.0 M HCl solution, buffer solution, water for injections and [¹⁸F]FMISO precursor (dissolved in 2 ml acetonitrile) were purchased from ABX. The [¹⁸F]FMISO samples were purified by Solid Phase Extraction method. The quality requirements of [¹⁸F]FMISO are established in the European Pharmacopeia. According to that reference, quality control of [¹⁸F]FMISO should include appearance, pH, radionuclidic identity and purity, radiochemical identity and purity, chemical purity, residual solvents, bacterial endotoxins, and sterility. The duration of the synthesis process was 53 min, with radiochemical yield of (37.00 ± 0.01) % and the specific activity was more than 70 GBq/µmol. The syntheses were reproducible and showed satisfactory results. In relation to the quality control analysis, the samples were clear and colorless at pH 6.0. The spectrum emission, measured by using a High-Purity Germanium Detector (HPGe), presented a single peak at 511 keV and the half-life, determined by the decay method in an activimeter, was (111.0 ± 0.5) min, indicating no presence of radioactive contaminants, besides the desirable radionuclide (¹⁸F). The samples showed concentration of tetrabutylammonium (TBA) < 50μg/mL, assessed by visual comparison to TBA standard applied in the same thin layer chromatographic plate. Radiochemical purity was determined by high performance liquid chromatography (HPLC) and the results were 100%. Regarding the residual solvents tested, ethanol and acetonitrile presented concentration lower than 10% and 0.04%, respectively. Healthy female mice were injected via lateral tail vein with [¹⁸F]FMISO, microPET imaging studies (15 min) were performed after 2 h post injection (p.i), and the biodistribution was analyzed in five-time points (30, 60, 90, 120 and 180 min) after injection. Subsequently, organs/tissues were assayed for radioactivity with a gamma counter. All parameters of quality control test were in agreement to quality criteria confirming that [¹⁸F]FMISO was suitable for use in non-clinical and clinical trials, following the legal requirements for the production of new radiopharmaceuticals in Brazil.

Keywords: automatic radiosynthesis, hypoxic tumors, pharmacopeia, positron emitters, quality requirements

Procedia PDF Downloads 176

Authors: Elena Ionescu, Elena Iacob, Marie-Louise Ionescu, Carmen Elena Tebrencu, Oana Teodora Ciuperca

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Echinacea species (Asteraceae) has received a global attention because it is widely used for treatment of cold, flu and upper respiratory tract infections. Echinacea species contain a great variety of chemical components that contribute to their activity. The most important components responsible for the biological activity are those with high molecular-weight such as polysaccharides, polyacetylenes, highly unsaturated alkamides and caffeic acid derivatives. The principal factors that may influence the chemical composition of Echinacea include the species and the part of plant used (aerial parts or roots ). In recent years the market for Echinacea has grown rapidly and also the cases of adultery/replacement especially for Echinacea root. The identification of presence or absence of same biomarkers provide information for safe use of Echinacea species in food supplements industry. The aim of the study was the preliminary evaluation and fingerprinting by UV-VISIBLE spectroscopy of biomarkers in terms of content in phenolic derivatives of some Echinacea species (E. purpurea, E. angustifolia and E. pallida) for identification and authentication of the species. The steps of the study were: (1) samples (extracts) preparation from Echinacea species (non-hydrolyzed and hydrolyzed ethanol extracts); (2) samples preparation of reference substances (polyphenol acids: caftaric acid, caffeic acid, chlorogenic acid, ferulic acid; flavonoids: rutoside, hyperoside, isoquercitrin and their aglycones: quercitri, quercetol, luteolin, kaempferol and apigenin); (3) identification of specific absorption at wavelengths between 700-200 nm; (4) identify the phenolic compounds from Echinacea species based on spectral characteristics and the specific absorption; each class of compounds corresponds to a maximum absorption in the UV spectrum. The phytochemical compounds were identified at specific wavelengths between 700-200 nm. The absorption intensities were measured. The obtained results proved that ethanolic extract showed absorption peaks attributed to: phenolic compounds (free phenolic acids and phenolic acids derivatives) registrated between 220-280 nm, unsymmetrical chemical structure compounds (caffeic acid, chlorogenic acid, ferulic acid) with maximum absorption peak and absorption "shoulder" that may be due to substitution of hydroxyl or methoxy group, flavonoid compounds (in free form or glycosides) between 330-360 nm, due to the double bond in position 2,3 and carbonyl group in position 4 flavonols. UV spectra showed two major peaks of absorption (quercetin glycoside, rutin, etc.). The results obtained by UV-VIS spectroscopy has revealed the presence of phenolic derivatives such as cicoric acid (240 nm), caftaric acid (329 nm), caffeic acid (240 nm), rutoside (205 nm), quercetin (255 nm), luteolin (235 nm) in all three species of Echinacea. The echinacoside is absent. This profile mentioned above and the absence of phenolic compound echinacoside leads to the conclusion that species harvested as Echinacea angustifolia and Echinacea pallida are Echinacea purpurea also; It can be said that preliminary fingerprinting of Echinacea species through correspondence with the phenolic derivatives profile can be achieved by UV-VIS spectroscopic investigation, which is an adequate technique for preliminary identification and authentication of Echinacea in medicinal herbs.

Keywords: Echinacea species, Fingerprinting, Phenolic compounds, UV-VIS spectroscopy

Procedia PDF Downloads 235

Authors: Aurica P. Chiriac, Vera Balan, Mihai Asandulesa, Elena Butnaru, Nita Tudorachi, Elena Stoleru, Loredana E. Nita, Iordana Neamtu, Alina Diaconu, Liliana Mititelu-Tartau

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The interest for studying ‘smart’ materials is entirely justified and in this context were realized investigations on poly(2-hydroxyethylmethacrylate-co-3, 9-divinyl-2, 4, 8, 10-tetraoxaspiro (5.5) undecane), which is a macromolecular compound with sensibility at pH and temperature, gel formation capacity, binding properties, amphilicity, good oxidative and thermal stability. Physico-chemical characteristics in terms of the molecular weight, temperature-sensitive abilities and thermal stability, as well rheological, dielectric and spectroscopic properties were evaluated in correlation with further coupling capabilities. Differential scanning calorimetry investigation indicated Tg at 36.6 °C and a melting point at Tm=72.8°C, for the studied copolymer, and up to 200oC two exothermic processes (at 99.7°C and 148.8°C) were registered with losing weight of about 4 %, respective 19.27%, which indicate just processes of thermal decomposition (and not phenomena of thermal transition) owing to scission of the functional groups and breakage of the macromolecular chains. At the same time, the rheological studies (rotational tests) confirmed the non-Newtonian shear-thinning fluid behavior of the copolymer solution. The dielectric properties of the copolymer have been evaluated in order to investigate the relaxation processes and two relaxation processes under Tg value were registered and attributed to localized motions of polar groups from side chain macromolecules, or parts of them, without disturbing the main chains. According to literature and confirmed as well by our investigations, β-relaxation is assigned with the rotation of the ester side group and the γ-relaxation corresponds to the rotation of hydroxy- methyl side groups. The fluorescence spectroscopy confirmed the copolymer structure, the spiroacetal moiety getting an axial conformation, more stable, with lower energy, able for specific interactions with molecules from environment, phenomena underlined by different shapes of the emission spectra of the copolymer. Also, the copolymer was used as template for indomethacin incorporation as model drug, and the biocompatible character of the complex was confirmed. The release behavior of the bioactive compound was dependent by the copolymer matrix composition, the increasing of 3, 9-divinyl-2, 4, 8, 10-tetraoxaspiro (5.5) undecane comonomer amount attenuating the drug release. At the same time, the in vivo studies did not show significant differences of leucocyte formula elements, GOT, GPT and LDH levels, nor immune parameters (OC, PC, and BC) between control mice group and groups treated just with copolymer samples, with or without drug, data attesting the biocompatibility of the polymer samples. The investigation of the physico-chemical characteristics of poly(2-hydrxyethyl methacrylate-co-3, 9-divinyl-2, 4, 8, 10-tetraoxaspiro (5.5) undecane) in terms of temperature-sensitive abilities, rheological and dielectrical properties, are bringing useful information for further specific use of this polymeric compound.

Keywords: bioapplications, dielectric and spectroscopic properties, dual sensitivity at pH and temperature, smart materials

Procedia PDF Downloads 268

Authors: Trevor C. Brown, David J. Miron

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Gas-solid physical adsorption methods are central to the characterization and optimization of the effective surface area, pore size and porosity for applications such as heterogeneous catalysis, and gas separation and storage. Properties such as adsorption uptake, capacity, equilibrium constants and Gibbs free energy are dependent on the composition and structure of both the gas and the adsorbent. However, challenges remain, in accurately calculating these properties from experimental data. Gas adsorption experiments involve measuring the amounts of gas adsorbed over a range of pressures under isothermal conditions. Various constant-parameter models, such as Langmuir and Brunauer-Emmett-Teller (BET) theories are used to provide information on adsorbate and adsorbent properties from the isotherm data. These models typically do not provide accurate interpretations across the full range of pressures and temperatures. The Langmuir adsorption isotherm is a simple approximation for modelling equilibrium adsorption data and has been effective in estimating surface areas and catalytic rate laws, particularly for high surface area solids. The Langmuir isotherm assumes the systematic filling of identical adsorption sites to a monolayer coverage. The BET model is based on the Langmuir isotherm and allows for the formation of multiple layers. These additional layers do not interact with the first layer and the energetics are equal to the adsorbate as a bulk liquid. This BET method is widely used to measure the specific surface area of materials. Both Langmuir and BET models assume that the affinity of the gas for all adsorption sites are identical and so the calculated adsorbent uptake at the monolayer and equilibrium constant are independent of coverage and pressure. Accurate representations of adsorption data have been achieved by extending the Langmuir and BET models to include pressure-varying uptake capacities and equilibrium constants. These parameters are determined using a novel regression technique called flexible least squares for time-varying linear regression. For isothermal adsorption the adsorption parameters are assumed to vary slowly and smoothly with increasing pressure. The flexible least squares for pressure-varying linear regression (FLS-PVLR) approach assumes two distinct types of discrepancy terms, dynamic and measurement for all parameters in the linear equation used to simulate the data. Dynamic terms account for pressure variation in successive parameter vectors, and measurement terms account for differences between observed and theoretically predicted outcomes via linear regression. The resultant pressure-varying parameters are optimized by minimizing both dynamic and measurement residual squared errors. Validation of this methodology has been achieved by simulating adsorption data for n-butane and isobutane on activated carbon at 298 K, 323 K and 348 K and for nitrogen on mesoporous alumina at 77 K with pressure-varying Langmuir and BET adsorption parameters (equilibrium constants and uptake capacities). This modeling provides information on the adsorbent (accessible surface area and micropore volume), adsorbate (molecular areas and volumes) and thermodynamic (Gibbs free energies) variations of the adsorption sites.

Keywords: Langmuir adsorption isotherm, BET adsorption isotherm, pressure-varying adsorption parameters, adsorbate and adsorbent properties and energetics

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Authors: Lachin Mikjtarnejad, Mohsen Farzaneh

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Various microbes, such as fungi and bacteria species, are naturally found in the fruit microbiota, and some of them act as a pathogen and result in fruit rot. Among non-pathogenic microbes, yeasts (single-celled microorganisms belonging to the fungi kingdom) can colonize fruit tissues and interact with them without causing any damage to them. Although yeasts are part of the plant microbiota, there is little information about their interactions with plants in comparison with bacteria and filamentous fungi. According to several existing studies, some yeasts can colonize different plant species and have the biological control ability to suppress some of the plant pathogens. It means those specific yeast-colonized plants are more resistant to some plant pathogens. The major objective of the present investigation is to isolate yeast strains from apple fruit and screen their ability to control Penicillium expansum, the causal agent of blue mold of fruits. In the present study, psychrotrophic and epiphytic yeasts were isolated from apple fruits that were stored at low temperatures (0–1°C). Totally, 42 yeast isolates were obtained and identified by molecular analysis based on genomic sequences of the D1/D2 and ITS1/ITS4 regions of their rDNA. All isolated yeasts were primarily screened by' in vitro dual culture assay against P. expansum by measuring the fungus' relative growth inhibition after 10 days of incubation. The results showed that the mycelial growth of P. expansum was reduced between 41–53% when challenged by promising yeast strains. The isolates with the strongest antagonistic activity belonged to Metschnikowia pulcherrima A13, Rhodotorula mucilaginosa A41, Leucosporidium Scottii A26, Aureobasidium pullulans A19, Pichia guilliermondii A32, Cryptococcus flavescents A25, and Pichia kluyveri A40. The results of seven superior isolates to inhibit blue mold decay on fruit showed that isolates A. pullulans A19, L. scottii A26, and Pi. guilliermondii A32 could significantly reduce the fruit rot and decay with 26 mm, 22 mm and 20 mm zone diameter, respectively, compared to the control sample with 43 mm. Our results show Pi. guilliermondii strain A13 was the most effective yeast isolates in inhibiting P. expansum on apple fruits. In addition, various biological control mechanisms of promising biological isolates against blue mold have been evaluated to date, including competition for nutrients and space, production of volatile metabolites, reduction of spore germination, production of siderophores and production of extracellular lytic enzymes such as chitinase and β-1,3-glucanase. However, the competition for nutrients and the ability to inhibit P. expansum spore growth have been introduced as the prevailing mechanisms among them. Accordingly, in our study, isolates A13, A41, A40, A25, A32, A19 and A26 inhibited the germination of P. expansum, whereas isolates A13 and A19 were the strongest inhibitors of P. expansum mycelia growth, causing 89.13% and 81.75 % reduction in the mycelial surface, respectively. All the promising isolates produced chitinase and β-1,3-glucanase after 3, 5 and 7 days of cultivation. Finally, based on our findings, we are proposing that, Pi. guilliermondiias as an effective biocontrol agent and alternative to chemical fungicides to control the blue mold of apple fruit.

Keywords: yeast, yeast enzymes, biocontrol, post harvest diseases

Procedia PDF Downloads 105

Authors: Sachin Mulmi Shrestha, Xin Fang, Hui Ye, Lihua Ren, Qinghua Ji, Ruihua Shi

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Background: Esophageal squamous cell carcinoma (ESCC) is a tumor arising from esophageal epithelial cells and is one of the major disease subtype in Asian countries, including China. Esophageal cancer is the 7th highest incidence based on the 2020 data of GLOBOCAN. The pathogenesis of cancer is still not well understood as many molecular and genetic basis of esophageal carcinogenesis has yet to be clearly elucidated. Circular RNAs are RNA molecules that are formed by back-splicing covalently joined 3′- and 5′-endsrather than canonical splicing, and recent data suggest circular RNAs could sponge miRNAs and are enriched with functional miRNA binding sites. Hence, we studied the mechanism of circular RNA, its biological function, and the relationship between microRNA in the carcinogenesis of ESCC. Methods: 4 pairs of normal and esophageal cancer tissues were collected in Zhongda hospital, affiliated to Southeast University, and high-throughput RNA sequencing was done. The result revealed that circ_0032746 was upregulated, and thus we selected circ_0032746 for further study. The backsplice junction of circRNA was validated by sanger sequence, and stability was determined by RNASE R assay. The binding site of circRNA and microRNA was predicted by circinteractome,mirandaand RNAhybrid database. Furthermore, circRNA was silenced by siRNA and then by lentivirus. The regulatory axis of circ0032746/miR4270 was validated by shRNA, mimic, and inhibitor transfection. Then, in vitro experiments were performed to assess the role of circ0032746 on proliferation (CCK-8 assay and colon formation assay), migration and invasion (Transewell assay), and apoptosis of ESCC. Results: The upregulated circ0032746 was validated in 9 pairs of tissues and 5 types of cell lines by qPCR, which showed high expression and was statistically significant (P<0.005) ). Upregulated circ0032746 was silenced by shRNA, which showed significant knockdown in KYSE 30 and TE-1 cell lines expression compared to control. Nuclear and cytoplasmic mRNA fraction experiment displayed the cytoplasmic location of circ0032746. The sponging of miR4270 was validated by co-transfection of sh-circ0032746 and mimic or inhibitor. Transfection with mimic showed the decreased expression of circ_0032746, whereas inhibitor inhibited the result. In vitro experiments showed that silencing of circ_0032746 inhibited the proliferation, migration, and invasion compared to the negative control group. The apoptosis was seen higher in a knockdown group than in the control group. Furthermore, 11 common mircoRNA target mRNAs were predicted by Targetscan, MirTarbase, and miRanda database, which may further play role in the pathogenesis. Conclusion: Our results showed that novel circ_0032746 is upregulated in ESCC and plays role in itsoncogenicity. Silencing of circ_0032746 inhibits the proliferation and migration of ESCC whereas increases the apoptosis of cancer cells. Hence, circ0032746 acts as an oncogene in ESCC by sponging with miR4270 and could be a potential biomarker in the diagnosis of ESCC in the future.

Keywords: circRNA, esophageal squamous cell carcinoma, microRNA, upregulated

Procedia PDF Downloads 91

Authors: Deepak Loura

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Production and productivity of several crops in the country continue to be adversely affected by biotic (e.g., Insect-pests and diseases) and abiotic (e.g., water temperature and salinity) stresses. Over-dependence on pesticides and other chemicals is economically non-viable for the resource-poor farmers of our country. Further, pesticides can potentially affect human and environmental safety. While traditional breeding techniques and proper- management strategies continue to play a vital role in crop improvement, we need to judiciously use biotechnology approaches for the development of genetically modified crops addressing critical problems in the improvement of crop plants for sustainable agriculture. Modern biotechnology can help to increase crop production, reduce farming costs, and improve food quality and the safety of the environment. Genetic engineering is a new technology which allows plant breeders to produce plants with new gene combinations by genetic transformation of crop plants for improvement of agronomic traits. Advances in recombinant DNA technology have made it possible to have genes between widely divergent species to develop genetically modified or genetically engineered plants. Plant genetic engineering provides the strength to harness useful genes and alleles from indigenous microorganisms to enrich the gene pool for developing genetically modified (GM) crops that will have inbuilt (inherent) resistance to insect pests, diseases, and abiotic stresses. Plant biotechnology has made significant contributions in the past 20 years in the development of genetically engineered or genetically modified crops with multiple benefits. A variety of traits have been introduced in genetically engineered crops which include (i) herbicide resistance. (ii) pest resistance, (iii) viral resistance, (iv) slow ripening of fruits and vegetables, (v) fungal and bacterial resistance, (vi) abiotic stress tolerance (drought, salinity, temperature, flooding, etc.). (vii) quality improvement (starch, protein, and oil), (viii) value addition (vitamins, micro, and macro elements), (ix) pharmaceutical and therapeutic proteins, and (x) edible vaccines, etc. Multiple genes in transgenic crops can be useful in developing durable disease resistance and a broad insect-control spectrum and could lead to potential cost-saving advantages for farmers. The development of transgenic to produce high-value pharmaceuticals and the edible vaccine is also under progress, which requires much more research and development work before commercially viable products will be available. In addition, molecular-aided selection (MAS) is now routinely used to enhance the speed and precision of plant breeding. Newer technologies need to be developed and deployed for enhancing and sustaining agricultural productivity. There is a need to optimize the use of biotechnology in conjunction with conventional technologies to achieve higher productivity with fewer resources. Therefore, genetic modification/ engineering of crop plants assumes greater importance, which demands the development and adoption of newer technology for the genetic improvement of crops for increasing crop productivity.

Keywords: biotechnology, plant genetic engineering, genetically modified, biotic, abiotic, disease resistance

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Authors: Faheema Khan

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To investigate the ability of sensitive and tolerant genotype of Glycine max to adapt to a saline environment in a field, we examined the growth performance, water relation and activities of antioxidant enzymes in relation to photosynthetic rate, chlorophyll a fluorescence, photosynthetic pigment concentration, protein and proline in plants exposed to salt stress. Ten soybean genotypes (Pusa-20, Pusa-40, Pusa-37, Pusa-16, Pusa-24, Pusa-22, BRAGG, PK-416, PK-1042, and DS-9712) were selected and grown hydroponically. After 3 days of proper germination, the seedlings were transferred to Hoagland’s solution (Hoagland and Arnon 1950). The growth chamber was maintained at a photosynthetic photon flux density of 430 μmol m−2 s−1, 14 h of light, 10 h of dark and a relative humidity of 60%. The nutrient solution was bubbled with sterile air and changed on alternate days. Ten-day-old seedlings were given seven levels of salt in the form of NaCl viz., T1 = 0 mM NaCl, T2=25 mM NaCl, T3=50 mM NaCl, T4=75 mM NaCl, T5=100 mM NaCl, T6=125 mM NaCl, T7=150 mM NaCl. The investigation showed that genotype Pusa-24, PK-416 and Pusa-20 appeared to be the most salt-sensitive. genotypes as inferred from their significantly reduced length, fresh weight and dry weight in response to the NaCl exposure. Pusa-37 appeared to be the most tolerant genotype since no significant effect of NaCl treatment on growth was found. We observed a greater decline in the photosynthetic variables like photosynthetic rate, chlorophyll fluorescence and chlorophyll content, in salt-sensitive (Pusa-24) genotype than in salt-tolerant Pusa-37 under high salinity. Numerous primers were verified on ten soybean genotypes obtained from Operon technologies among which 30 RAPD primers shown high polymorphism and genetic variation. The Jaccard’s similarity coefficient values for each pairwise comparison between cultivars were calculated and similarity coefficient matrix was constructed. The closer varieties in the cluster behaved similar in their response to salinity tolerance. Intra-clustering within the two clusters precisely grouped the 10 genotypes in sub-cluster as expected from their physiological findings.Salt tolerant genotype Pusa-37, was further analysed by 2-Dimensional gel electrophoresis to analyse the differential expression of proteins at high salt stress. In the Present study, 173 protein spots were identified. Of these, 40 proteins responsive to salinity were either up- or down-regulated in Pusa-37. Proteomic analysis in salt-tolerant genotype (Pusa-37) led to the detection of proteins involved in a variety of biological processes, such as protein synthesis (12 %), redox regulation (19 %), primary and secondary metabolism (25 %), or disease- and defence-related processes (32 %). In conclusion, the soybean plants in our study responded to salt stress by changing their protein expression pattern. The photosynthetic, biochemical and molecular study showed that there is variability in salt tolerance behaviour in soybean genotypes. Pusa-24 is the salt-sensitive and Pusa-37 is the salt-tolerant genotype. Moreover this study gives new insights into the salt-stress response in soybean and demonstrates the power of genomic and proteomic approach in plant biology studies which finally could help us in identifying the possible regulatory switches (gene/s) controlling the salt tolerant genotype of the crop plants and their possible role in defence mechanism.

Keywords: glycine max, salt stress, RAPD, genomic and proteomic variability

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Authors: Ruolan Zhang, Ryo Imai, Naoko Senda, Tomoyuki Sakai

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Enzymes have attracted increasing attentions in industrial manufacturing for their applicability in catalyzing complex chemical reactions under mild conditions. Directed evolution has become a powerful approach to optimize enzymes and exploit their full potentials under the circumstance of insufficient structure-function knowledge. With the incorporation of cell-free synthetic biotechnology, rapid enzyme synthesis can be realized because no cloning procedure such as transfection is needed. Its open environment also enables direct enzyme measurement. These properties of cell-free biotechnology lead to excellent throughput of enzymes generation. However, the capabilities of current screening methods have limitations. Fluorescence-based assay needs applicable fluorescent label, and the reliability of acquired enzymatic activity is influenced by fluorescent label’s binding affinity and photostability. To acquire the natural activity of an enzyme, another method is to combine pre-screening step and high-performance liquid chromatography (HPLC) measurement. But its throughput is limited by necessary time investment. Hundreds of variants are selected from libraries, and their enzymatic activities are then identified one by one by HPLC. The turn-around-time is 30 minutes for one sample by HPLC, which limits the acquirable enzyme improvement within reasonable time. To achieve the real high-throughput enzyme screening, i.e., obtain reliable enzyme improvement within reasonable time, a widely applicable high-throughput measurement of enzymatic reactions is highly demanded. Here, a high-throughput screening method using broadband coherent anti-Stokes Raman spectroscopy (CARS) was proposed. CARS is one of coherent Raman spectroscopy, which can identify label-free chemical components specifically from their inherent molecular vibration. These characteristic vibrational signals are generated from different vibrational modes of chemical bonds. With the broadband CARS, chemicals in one sample can be identified from their signals in one broadband CARS spectrum. Moreover, it can magnify the signal levels to several orders of magnitude greater than spontaneous Raman systems, and therefore has the potential to evaluate chemical's concentration rapidly. As a demonstration of screening with CARS, alcohol dehydrogenase, which converts ethanol and nicotinamide adenine dinucleotide oxidized form (NAD+) to acetaldehyde and nicotinamide adenine dinucleotide reduced form (NADH), was used. The signal of NADH at 1660 cm⁻¹, which is generated from nicotinamide in NADH, was utilized to measure the concentration of it. The evaluation time for CARS signal of NADH was determined to be as short as 0.33 seconds while having a system sensitivity of 2.5 mM. The time course of alcohol dehydrogenase reaction was successfully measured from increasing signal intensity of NADH. This measurement result of CARS was consistent with the result of a conventional method, UV-Vis. CARS is expected to have application in high-throughput enzyme screening and realize more reliable enzyme improvement within reasonable time.

Keywords: Coherent Anti-Stokes Raman Spectroscopy, CARS, directed evolution, enzyme screening, Raman spectroscopy

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Authors: Leonid Zhukov, Dmytro Petrenko

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Optical thermometry has no alternative in many cases of industrial most effective continuous temperature control. Classical optical thermometry technologies can be used on available for pyrometers controlled objects with stable radiation characteristics and transmissivity of the intermediate medium. Without using temperature corrections, it is possible in the case of a “black” body for energy pyrometry and the cases of “black” and “grey” bodies for spectral ratio pyrometry or with using corrections – for any colored bodies. Consequently, with increasing the number of operating waves, optical thermometry possibilities to reduce methodical errors significantly expand. That is why, in recent 25-30 years, research works have been reoriented on more perfect spectral (multicolor) thermometry technologies. There are two physical material substances, i.e., substance (controlled object) and electromagnetic field (thermal radiation), to be operated in optical thermometry. Heat is transferred by radiation; therefore, radiation has the energy, entropy, and temperature. Optical thermometry was originating simultaneously with the developing of thermal radiation theory when the concept and the term "radiation temperature" was not used, and therefore concepts and terms "conditional temperatures" or "pseudo temperature" of controlled objects were introduced. They do not correspond to the physical sense and definitions of temperature in thermodynamics, molecular-kinetic theory, and statistical physics. Launched by the scientific thermometric society, discussion about the possibilities of temperature measurements of objects, including colored bodies, using the temperatures of their radiation is not finished. Are the information about controlled objects transferred by their radiation enough for temperature measurements? The positive and negative answers on this fundamental question divided experts into two opposite camps. Recent achievements of spectral thermometry develop events in her favour and don’t leave any hope for skeptics. This article presents the results of investigations and developments in the field of spectral thermometry carried out by the authors in the Department of Thermometry and Physics-Chemical Investigations. The authors have many-year’s of experience in the field of modern optical thermometry technologies. Innovative technologies of optical continuous temperature control have been developed: symmetric-wave, two-color compensative, and based on obtained nonlinearity equation of spectral emissivity distribution linear, two-range, and parabolic. Тhe technologies are based on direct measurements of physically substantiated and proposed by Prof. L. Zhukov, radiation temperatures with the next calculation of the controlled object temperature using this radiation temperatures and corresponding mathematical models. Тhe technologies significantly increase metrological characteristics of continuous contactless and light-guide temperature control in energy, metallurgical, ceramic, glassy, and other productions. For example, under the same conditions, the methodical errors of proposed technologies are less than the errors of known spectral and classical technologies in 2 and 3-13 times, respectively. Innovative technologies provide quality products obtaining at the lowest possible resource-including energy costs. More than 600 publications have been published on the completed developments, including more than 100 domestic patents, as well as 34 patents in Australia, Bulgaria, Germany, France, Canada, the USA, Sweden, and Japan. The developments have been implemented in the enterprises of USA, as well as Western Europe and Asia, including Germany and Japan.

Keywords: emissivity, radiation temperature, object temperature, spectral thermometry

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Authors: Todd H. Buxton, Yong G. Lai

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Temperature management in regulated rivers can involve significant expenditures of water to meet the cold-water requirements of species in summer. For this purpose, flows released from Lewiston Dam on the Trinity River in Northern California are 12.7 cms with temperatures around 11oC in July through September to provide adult spring Chinook cold water to hold in deep pools and mature until spawning in fall. The releases are more than double the flow and 10oC colder temperatures than the natural conditions before the dam was built. The high, cold releases provide springers the habitat they require but may suppress the stream food base and limit future populations of salmon by reducing the juvenile fish size and survival to adults via the positive relationship between the two. Field and modeling research was undertaken to explore whether lowering summer releases from Lewiston Dam may promote thermal stratification in river pools so that both the cold-water needs of adult salmon and warmer water requirements of other organisms in the stream biome may be met. For this investigation, a three-dimensional (3D) computational fluid dynamics (CFD) model was developed and validated with field measurements in two deep pools on the Trinity River. Modeling and field observations were then used to identify the flows and temperatures that may form and maintain thermal stratification under different meteorologic conditions. Under low flows, a pool was found to be well mixed and thermally homogenous until temperatures began to stratify shortly after sunrise. Stratification then strengthened through the day until shading from trees and mountains cooled the inlet flow and decayed the thermal gradient, which collapsed shortly before sunset and returned the pool to a well-mixed state. This diurnal process of stratification formation and destruction was closely predicted by the 3D CFD model. Both the model and field observations indicate that thermal stratification maintained the coldest temperatures of the day at ≥2m depth in a pool and provided water that was around 8oC warmer in the upper 2m of the pool. Results further indicate that the stratified pool under low flows provided almost the same daily average temperatures as when flows were an order of magnitude higher and stratification was prevented, indicating significant water savings may be realized in regulated streams while also providing a diversity in water temperatures the ecosystem requires. With confidence in the 3D CFD model, the model is now being applied to a dozen pools in the Trinity River to understand how pool bathymetry influences thermal stratification under variable flows and diurnal temperature variations. This knowledge will be used to expand the results to 52 pools in a 64 km reach below Lewiston Dam that meet the depth criteria (≥2 m) for spring Chinook holding. From this, rating curves will be developed to relate discharge to the volume of pool habitat that provides springers the temperature (<15.6oC daily average), velocity (0.15 to 0.4 m/s) and depths that accommodate the escapement target for spring Chinook (6,000 adults) under maximum fish densities measured in other streams (3.1 m3/fish) during the holding time of year (May through August). Flow releases that meet these goals will be evaluated for water savings relative to the current flow regime and their influence on indicator species, including the Foothill Yellow-Legged Frog, and aspects of the stream biome that support salmon populations, including macroinvertebrate production and juvenile Chinook growth rates.

Keywords: 3D CFD modeling, flow regulation, thermal stratification, chinook salmon, foothill yellow-legged frogs, water managment

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Authors: Mohammad Al-Refai, Majed Wakid

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Introduction: Soil-transmitted diseases (STD) are caused by intestinal worms that are transmitted via various routes into the human body resulting in various clinical manifestations. The intestinal worms causing these infections are known as soil transmitted helminths (STH), including Hook worms, Ascaris lumbricoides (A. lumbricoides), Trichuris trichiura (T. trichiura), and Strongyloides sterocoralis (S. sterocoralis). Objectives: The aim of this study was to investigate the prevalence of STH among newly arrived expatriate labors in Jeddah city, Saudi Arabia, using three different techniques (direct smears, sedimentation concentration, and real-time PCR). Methods: A total of 188 stool specimens were collected and investigated at the parasitology laboratory in the Special Infectious Agents Unit at King Fahd Medical Research Center, King Abdulaziz University in Jeddah, Saudi Arabia. Microscopic examination of wet mount preparations using normal saline and Lugols Iodine was carried out, followed by the formal ether sedimentation method. In addition, real-time PCR was used as a molecular tool to detect several STH and hookworm speciation. Results: Out of 188 stool specimens analyzed, in addition to STH parasite, several other types were detected. 9 samples (4.79%) were positive for Entamoeba coli, 7 samples (3.72%) for T. trichiura, 6 samples (3.19%) for Necator americanus, 4 samples (2.13%) for S. sterocoralis, 4 samples (2.13%) for A. lumbricoides, 4 samples (2.13%) for E. histolytica, 3 samples (1.60%) for Blastocystis hominis, 2 samples (1.06%) for Ancylostoma duodenale, 2 samples (1.06%) for Giardia lamblia, 1 sample (0.53%) for Iodamoeba buetschlii, 1 sample (0.53%) for Hymenolepis nana, 1 sample (0.53%) for Endolimax nana, and 1 sample (0.53%) for Heterophyes heterophyes. Out of the 35 infected cases, 26 revealed single infection, 8 with double infections, and only one triple infection of different STH species and other intestinal parasites. Higher rates of STH infections were detected among housemaids (11 cases) followed by drivers (7 cases) when compared to other occupations. According to educational level, illiterate participants represent the majority of infected workers (12 cases). The majority of workers' positive cases were from the Philippines. In comparison between laboratory techniques, out of the 188 samples screened for STH, real-time PCR was able to detect the DNA in (19/188) samples followed by Ritchie sedimentation technique (18/188), and direct wet smear (7/188). Conclusion: STH infections are a major public health issue to healthcare systems around the world. Communities must be educated on hygiene practices and the severity of such parasites to human health. As far as drivers and housemaids come to close contact with families, including children and elderlies. This may put family members at risk of developing serious side effects related to STH, especially as the majority of workers were illiterate, lacking the basic hygiene knowledge and practices. We recommend the official authority in Jeddah and around the kingdom of Saudi Arabia to revise the standard screening tests for newly arrived workers and enforce regular follow-up inspections to minimize the chances of the spread of STH from expatriate workers to the public.

Keywords: expatriate labors, Jeddah, prevalence, soil transmitted helminths

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Authors: Yi H. Wong, Li L. Chan, Chee O. Leong, Stephen Ambu, Joon W. Mak, Priyadashi S. Sahu

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Background: Acanthamoeba is a free-living opportunistic protist which is ubiquitously distributed in the environment. Virulent Acanthamoeba can cause fatal encephalitis in immunocompromised patients and potential blinding keratitis in immunocompetent contact lens wearers. Approximately 24 species have been identified but only the A. castellanii, A. polyphaga and A. culbertsoni are commonly associated with human infections. Until to date, the precise molecular basis for Acanthamoeba pathogenesis remains unclear. Previous studies reported that Acanthamoeba virulence can be diminished through prolonged axenic culture but revived through serial mouse passages. As no clear explanation on this reversible pathogenesis is established, hereby, we postulate that the epigenetic regulators, DNA-methyltransferases (DNMT) and histone-deacetylases (HDAC), could possibly be involved in granting the virulence plasticity of Acanthamoeba spp. Methods: Four rounds of mouse passages were conducted to revive the virulence potential of the virulence-attenuated Acanthamoeba castellanii strain (ATCC 50492). Briefly, each mouse (n=6/group) was inoculated intraperitoneally with Acanthamoebae cells (2x 105 trophozoites/mouse) and incubated for 2 months. Acanthamoebae cells were isolated from infected mouse organs by culture method and subjected to subsequent mouse passage. In vitro cytopathic, encystment and gelatinolytic assays were conducted to evaluate the virulence characteristics of Acanthamoebae isolates for each passage. PCR primers which targeted on the 2 members (DNMT1 and DNMT2) and 5 members (HDAC1 to 5) of the DNMT and HDAC gene families respectively were custom designed. Quantitative real-time PCR (qPCR) was performed to detect and quantify the relative expression of the two gene families in each Acanthamoeba isolates. Beta-tubulin of A. castellanii (Genbank accession no: XP_004353728) was included as housekeeping gene for data normalisation. PCR mixtures were also analyzed by electrophoresis for amplicons detection. All statistical analyses were performed using the paired one-tailed Student’s t test. Results: Our pathogenicity tests showed that the virulence-reactivated Acanthamoeba had a higher degree of cytopathic effect on vero cells, a better resistance to encystment challenge and a higher gelatinolytic activity which was catalysed by serine protease. qPCR assay showed that DNMT1 expression was significantly higher in the virulence-reactivated compared to the virulence-attenuated Acanthamoeba strain (p ≤ 0.01). The specificity of primers which targeted on DNMT1 was confirmed by sequence analysis of PCR amplicons, which showed a 97% similarity to the published DNA-methyltransferase gene of A. castellanii (GenBank accession no: XM_004332804.1). Out of the five primer pairs which targeted on the HDAC family genes, only HDAC4 expression was significantly difference between the two variant strains. In contrast to DNMT1, HDAC4 expression was much higher in the virulence-attenuated Acanthamoeba strain. Conclusion: Our mouse passages had successfully restored the virulence of the attenuated strain. Our findings suggested that DNA-methyltransferase (DNMT1) and histone deacetylase (HDAC4) expressions are associated with virulence potential of Acanthamoeba spp.

Keywords: acanthamoeba, DNA-methyltransferase, histone deacetylase, virulence-associated proteins

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Authors: Thiago E. Goto, Carla C. Lopes, Helena B. Nader, Anielle C. A. Silva, Noelio O. Dantas, José R. Siqueira Jr., Luciano Caseli

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Quantum dots (QD) are semiconductor nanocrystals that can be employed in biological research as a tool for fluorescence imagings, having the potential to expand in vivo and in vitro analysis as cancerous cell biomarkers. Particularly, cadmium selenide (CdSe) magic-sized quantum dots (MSQDs) exhibit stable luminescence that is feasible for biological applications, especially for imaging of tumor cells. For these facts, it is interesting to know the mechanisms of action of how such QDs mark biological cells. For that, simplified models are a suitable strategy. Among these models, Langmuir films of lipids formed at the air-water interface seem to be adequate since they can mimic half a membrane. They are monomolecular films formed at liquid-gas interfaces that can spontaneously form when organic solutions of amphiphilic compounds are spread on the liquid-gas interface. After solvent evaporation, the monomolecular film is formed, and a variety of techniques, including tensiometric, spectroscopic and optic can be applied. When the monolayer is formed by membrane lipids at the air-water interface, a model for half a membrane can be inferred where the aqueous subphase serve as a model for external or internal compartment of the cell. These films can be transferred to solid supports forming the so-called Langmuir-Blodgett (LB) films, and an ampler variety of techniques can be additionally used to characterize the film, allowing for the formation of devices and sensors. With these ideas in mind, the objective of this work was to investigate the specific interactions of CdSe MSQDs with tumorigenic and non-tumorigenic cells using Langmuir monolayers and LB films of lipids and specific cell extracts as membrane models for diagnosis of cancerous cells. Surface pressure-area isotherms and polarization modulation reflection-absorption spectroscopy (PM-IRRAS) showed an intrinsic interaction between the quantum dots, inserted in the aqueous subphase, and Langmuir monolayers, constructed either of selected lipids or of non-tumorigenic and tumorigenic cells extracts. The quantum dots expanded the monolayers and changed the PM-IRRAS spectra for the lipid monolayers. The mixed films were then compressed to high surface pressures and transferred from the floating monolayer to solid supports by using the LB technique. Images of the films were then obtained with atomic force microscopy (AFM) and confocal microscopy, which provided information about the morphology of the films. Similarities and differences between films with different composition representing cell membranes, with or without CdSe MSQDs, was analyzed. The results indicated that the interaction of quantum dots with the bioinspired films is modulated by the lipid composition. The properties of the normal cell monolayer were not significantly altered, whereas for the tumorigenic cell monolayer models, the films presented significant alteration. The images therefore exhibited a stronger effect of CdSe MSQDs on the models representing cancerous cells. As important implication of these findings, one may envisage for new bioinspired surfaces based on molecular recognition for biomedical applications.

Keywords: biomembrane, langmuir monolayers, quantum dots, surfaces

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Authors: Lewis J. Woollin, Robert I. Davidson, Paul Watson, Philip J. Hyde

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Introduction: In-vitro testing of arthroplasty materials is of paramount importance when ensuring that they can withstand the performance requirements encountered in-vivo. One common machine used for in-vitro testing is a pin-on-plate tribometer, an early stage screening device that generates data on the wear characteristics of arthroplasty bearing materials. These devices test vertically loaded rotating cylindrical pins acting against reciprocating plates, representing the bearing surfaces. In this study, a pin-on-plate machine has been developed that provides several improvements over current technology, thereby progressing arthroplasty bearing research. Historically, pin-on-plate tribometers have been used to investigate the performance of arthroplasty bearing materials under conditions commonly encountered during a standard gait cycle; nominal operating pressures of 2-6 MPa and an operating frequency of 1 Hz are typical. There has been increased interest in using pin-on-plate machines to test more representative in-vivo conditions, due to the drive to test 'beyond compliance', as well as their testing speed and economic advantages over hip simulators. Current pin-on-plate machines do not accommodate the increased performance requirements associated with more extreme kinematic conditions, therefore a next-generation pin-on-plate tribometer has been developed to bridge the gap between current technology and future research requirements. Methodology: The design was driven by several physiologically relevant requirements. Firstly, an increased loading capacity was essential to replicate the peak pressures that occur in the natural hip joint during running and chair-rising, as well as increasing the understanding of wear rates in obese patients. Secondly, the introduction of mid-cycle load variation was of paramount importance, as this allows for an approximation of the loads present in a gait cycle to be applied and to test the fatigue properties of materials. Finally, the rig must be validated against previous-generation pin-on-plate and arthroplasty wear data. Results: The resulting machine is a twelve station device that is split into three sets of four stations, providing an increased testing capacity compared to most current pin-on-plate tribometers. The loading of the pins is generated using a pneumatic system, which can produce contact pressures of up to 201 MPa on a 3.2 mm² round pin face. This greatly exceeds currently achievable contact pressures in literature and opens new research avenues such as testing rim wear of mal-positioned hip implants. Additionally, the contact pressure of each set can be changed independently of the others, allowing multiple loading conditions to be tested simultaneously. Using pneumatics also allows the applied pressure to be switched ON/OFF mid-cycle, another feature not currently reported elsewhere, which allows for investigation into intermittent loading and material fatigue. The device is currently undergoing a series of validation tests using Ultra-High-Molecular-Weight-Polyethylene pins and 316L Stainless Steel Plates (polished to a Ra < 0.05 µm). The operating pressures will be between 2-6 MPa, operating at 1 Hz, allowing for validation of the machine against results reported previously in the literature. The successful production of this next-generation pin-on-plate tribometer will, following its validation, unlock multiple previously unavailable research avenues.

Keywords: arthroplasty, mechanical design, pin-on-plate, total joint replacement, wear testing

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Authors: Guillaume Bélanger, Jean-Philippe Fontaine, Clémence Hauduc

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There is an undeniable thirst from organic chemists and from the pharmaceutical industry to access complex alkaloids with short syntheses. While medicinal chemists are interested in the fascinating wide range of biological properties of alkaloids, synthetic chemists are rather interested in finding new routes to access these challenging natural products of often low availability from nature. To synthesize complex polycyclic cores of natural products, reaction cascades or sequences performed one-pot offer a neat advantage over classical methods for their rapid increase in molecular complexity in a single operation. In counterpart, reaction cascades need to be run on substrates bearing all the required functional groups necessary for the key cyclizations. Chemoselectivity is thus a major issue associated with such a strategy, in addition to diastereocontrol and regiocontrol for the overall transformation. In the pursuit of synthetic efficiency, our research group developed an innovative one-pot transformation of linear substrates into bi- and tricyclic adducts applied to the construction of Aspidospermatan-type alkaloids. The latter is a rich class of indole alkaloids bearing a unique bridged azatricyclic core. Despite many efforts toward the synthesis of members of this family, efficient and versatile synthetic routes are still coveted. Indeed, very short, non-racemic approaches are rather scarce: for example, in the cases of aspidospermidine and aspidospermine, syntheses are all fifteen steps and over. We envisaged a unified approach to access several members of the Aspidospermatan alkaloids family. The key sequence features a highly chemoselective formamide activation that triggers a Vilsmeier-Haack cyclization, followed by an azomethine ylide generation and intramolecular cycloaddition. Despite the high density and variety of functional groups on the substrates (electron-rich and electron-poor alkenes, nitrile, amide, ester, enol ether), the sequence generated three new carbon-carbon bonds and three rings in a single operation with good yield and high chemoselectivity. A detailed study of amide, nucleophile, and dipolarophile variations to finally get to the successful combination required for the key transformation will be presented. To complete the indoline fragment of the natural products, we developed an original approach. Indeed, all reported routes to Aspidospermatan alkaloids introduce the indoline or indole early in the synthesis. In our work, the indoline needs to be installed on the azatricyclic core after the key cyclization sequence. As a result, typical Fischer indolization is not suited since this reaction is known to fail on such substrates. We thus envisaged a unique photocatalyzed decarboxylative radical cyclization. The development of this reaction as well as the scope and limitations of the methodology, will also be presented. The original Vilsmeier-Haack and azomethine ylide cyclization sequence as well as the new photocatalyzed decarboxylative radical cyclization will undoubtedly open access to new routes toward polycyclic indole alkaloids and derivatives of pharmaceutical interest in general.

Keywords: Aspidospermatan alkaloids, azomethine ylide cycloaddition, decarboxylative radical cyclization, indole and indoline synthesis, one-pot sequential cyclizations, photocatalysis, Vilsmeier-Haack Cyclization

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Authors: Juliana A. B. Silva, Caio H. T. L. Albuquerque, Leonardo L. dos Santos, Cristiane K. Oliveira, Ivani Malvestiti, Fernando Hallwass, Ricardo L. Longo

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Complexes with lanthanide ions have been extensively studied due to their applications as luminescent, magnetic and catalytic materials as molecular or extended crystals, thin films, glasses, polymeric matrices, ionic liquids, and in solution. NMR chemical shift data in solution have been reported and suggest fluxional structures in a wide range of coordination compounds with rare earth ions. However, the fluxional mechanisms for these compounds are still not established. This structural fluxionality may affect the photophysical, catalytic and magnetic properties in solution. Thus, understanding the structural interconversion mechanisms may aid the design of coordination compounds with, for instance, improved (electro)luminescence, catalytic and magnetic behaviors. The [Eu(btfa)₃bipy] complex, where btfa= 4,4,4-trifluoro-1-phenyl-1,3-butanedionate and bipy= 2,2’-bipiridyl, has a well-defined X-ray crystallographic structure and preliminary 1H NMR data suggested a structural fluxionality. Thus, we have investigated a series of coordination compounds with lanthanide ions [Ln(btfa)₃L], where Ln = La, Eu, Gd or Yb and L= bipy or phen (phen=1,10-phenanthroline) using a combined theoretical-experimental approach. These complexes were synthesized and fully characterized, and detailed NMR measurements were obtained. They were also studied by quantum chemical computational methods (DFT-PBE0). The aim was to determine the relevant factors in the structure of these compounds that favor or not the fluxional behavior. Measurements of the 1H NMR signals at variable temperature in CD₂Cl₂ of the [Eu(btfa)₃L] complexes suggest that these compounds have a fluxional structure, because the crystal structure has non-equivalent btfa ligands that should lead to non-equivalent hydrogen atoms and thus to more signals in the NMR spectra than those obtained at room temperature, where all hydrogen atoms of the btfa ligands are equivalent, and phen ligand has an effective vertical symmetry plane. For the [Eu(btfa)₃bipy] complex, the broadening of the signals at –70°C provides a lower bound for the coalescence temperature, which indicates the energy barriers involved in the structural interconversion mechanisms are quite small. These barriers and, consequently, the coalescence temperature are dependent upon the radii of the lanthanide ion as well as to their paramagnetic effects. The PBE0 calculated structures are in very good agreement with the crystallographic data and, for the [Eu(btfa)₃bipy] complex, this method provided several distinct structures with almost the same energy. However, the energy barrier for structural interconversion via dissociative pathways were found to be quite high and could not explain the experimental observations. Whereas the pseudo-rotation pathways, involving the btfa and bipy ligands, have very small activation barriers, in excellent agreement with the NMR data. The results also showed an increase in the activation barrier along the lanthanide series due to the decrease of the ionic radii and consequent increase of the steric effects. TD-DFT calculations showed a dependence of the ligand donor state energy with different structures of the complex [Eu(btfa)₃phen], which can affect the energy transfer rates and the luminescence. The energy required to promote the structural fluxionality may also enhance the luminescence quenching in solution. These results can aid in the design of more luminescent compounds and more efficient devices.

Keywords: computational chemistry, lanthanide-based compounds, NMR, structural fluxionality

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Authors: Maddalena Arigoni, Maria Luisa Ratto, Raffaele A. Calogero, Luca Alessandri

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The presence of tumor heterogeneity, where distinct cancer cells exhibit diverse morphological and phenotypic profiles, including gene expression, metabolism, and proliferation, poses challenges for molecular prognostic markers and patient classification for targeted therapies. Understanding the causes and progression of cancer requires research efforts aimed at characterizing heterogeneity, which can be facilitated by evolving single-cell sequencing technologies. However, analyzing single-cell data necessitates computational methods that often lack objective validation. Therefore, the establishment of benchmarking datasets is necessary to provide a controlled environment for validating bioinformatics tools in the field of single-cell oncology. Benchmarking bioinformatics tools for single-cell experiments can be costly due to the high expense involved. Therefore, datasets used for benchmarking are typically sourced from publicly available experiments, which often lack a comprehensive cell annotation. This limitation can affect the accuracy and effectiveness of such experiments as benchmarking tools. To address this issue, we introduce omics benchmark experiments designed to evaluate bioinformatics tools to depict the heterogeneity in single-cell tumor experiments. We conducted single-cell RNA sequencing on six lung cancer tumor cell lines that display resistant clones upon treatment of EGFR mutated tumors and are characterized by driver genes, namely ROS1, ALK, HER2, MET, KRAS, and BRAF. These driver genes are associated with downstream networks controlled by EGFR mutations, such as JAK-STAT, PI3K-AKT-mTOR, and MEK-ERK. The experiment also featured an EGFR-mutated cell line. Using 10XGenomics platform with cellplex technology, we analyzed the seven cell lines together with a pseudo-immunological microenvironment consisting of PBMC cells labeled with the Biolegend TotalSeq™-B Human Universal Cocktail (CITEseq). This technology allowed for independent labeling of each cell line and single-cell analysis of the pooled seven cell lines and the pseudo-microenvironment. The data generated from the aforementioned experiments are available as part of an online tool, which allows users to define cell heterogeneity and generates count tables as an output. The tool provides the cell line derivation for each cell and cell annotations for the pseudo-microenvironment based on CITEseq data by an experienced immunologist. Additionally, we created a range of pseudo-tumor tissues using different ratios of the aforementioned cells embedded in matrigel. These tissues were analyzed using 10XGenomics (FFPE samples) and Curio Bioscience (fresh frozen samples) platforms for spatial transcriptomics, further expanding the scope of our benchmark experiments. The benchmark experiments we conducted provide a unique opportunity to evaluate the performance of bioinformatics tools for detecting and characterizing tumor heterogeneity at the single-cell level. Overall, our experiments provide a controlled and standardized environment for assessing the accuracy and robustness of bioinformatics tools for studying tumor heterogeneity at the single-cell level, which can ultimately lead to more precise and effective cancer diagnosis and treatment.

Keywords: single cell omics, benchmark, spatial transcriptomics, CITEseq

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Authors: Ekaterina Zvorykina

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Nowadays, Arctic and Antarctic regions are distinguished to be one of the most important strategic resources for global development. Nonetheless, living conditions in Arctic regions still demand certain improvements. As soon as the region is rarely populated, one of the main points of interest is health accommodation of the people, who migrate to Arctic region for permanent and shift work. At Arctic and Antarctic latitudes, personnel face polar day and polar night conditions during the time of the year. It means that they are deprived of natural sunlight in winter season and have continuous daylight in summer. Firstly, the change in light intensity during 24-hours period due to migration affects circadian rhythms. Moreover, the controlled artificial light in winter is also an issue. The results of the recent studies on night shift medical professionals, who were exposed to permanent artificial light, have already demonstrated higher risks in cancer, depression, Alzheimer disease. Moreover, people exposed to frequent time zones change are also subjected to higher risks of heart attack and cancer. Thus, our main goals are to understand how high latitude work and living conditions can affect human health and how it can be prevented. In our study, we analyze molecular and cellular factors, which play important role in circadian rhythm change and distinguish main risk groups in people, migrating to high latitudes. The main well-studied index of circadian timing is melatonin or its metabolite 6-sulfatoxymelatonin. In low light intensity melatonin synthesis is disturbed and as a result human organism requires more time for sleep, which is still disregarded when it comes to working time organization. Lack of melatonin also causes shortage in serotonin production, which leads to higher depression risk. Melatonin is also known to inhibit oncogenes and increase apoptosis level in cells, the main factors for tumor growth, as well as circadian clock genes (for example Per2). Thus, people who work in high latitudes can be distinguished as a risk group for cancer diseases and demand more attention. Clock/Clock genes, known to be one of the main circadian clock regulators, decrease sensitivity of hypothalamus to estrogen and decrease glucose sensibility, which leads to premature aging and oestrous cycle disruption. Permanent light exposure also leads to accumulation superoxide dismutase and oxidative stress, which is one of the main factors for early dementia and Alzheimer disease. We propose a new screening system adjusted for people, migrating from middle to high latitudes and accommodation therapy. Screening is focused on melatonin and estrogen levels, sleep deprivation and neural disorders, depression level, cancer risks and heart and vascular disorders. Accommodation therapy includes different types artificial light exposure, additional melatonin and neuroprotectors. Preventive procedures can lead to increase of migration intensity to high latitudes and, as a result, the prosperity of Arctic region.

Keywords: circadian rhythm, high latitudes, melatonin, neuroprotectors

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Authors: Vladimir A. Basiuk, Laura J. Flores-Sanchez, Victor Meza-Laguna, Jose O. Flores-Flores, Lauro Bucio-Galindo, Elena V. Basiuk

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Noncovalent nanohybrid materials combining carbon nanotubes (CNTs) with phthalocyanines (Pcs) is a subject of increasing research effort, with a particular emphasis on the design of new heterogeneous catalysts, efficient organic photovoltaic cells, lithium batteries, gas sensors, field effect transistors, among other possible applications. The possibility of using unsubstituted Pcs for CNT functionalization is very attractive due to their very moderate cost and easy commercial availability. However, unfortunately, the deposition of unsubstituted Pcs onto nanotube sidewalls through the traditional liquid-phase protocols turns to be very problematic due to extremely poor solubility of Pcs. On the other hand, unsubstituted free-base H₂Pc phthalocyanine ligand, as well as many of its transition metal complexes, exhibit very high thermal stability and considerable volatility under reduced pressure, which opens the possibility for their physical vapor deposition onto solid surfaces, including nanotube sidewalls. In the present work, we show the possibility of simple, fast and efficient noncovalent functionalization of single-walled carbon nanotubes (SWNTs) with a series of 3d metal(II) phthalocyanines Me(II)Pc, where Me= Co, Ni, Cu, and Zn. The functionalization can be performed in a temperature range of 400-500 °C under moderate vacuum and requires about 2-3 h only. The functionalized materials obtained were characterized by means of Fourier-transform infrared (FTIR), Raman, UV-visible and energy-dispersive X-ray spectroscopy (EDS), scanning and transmission electron microscopy (SEM and TEM, respectively) and thermogravimetric analysis (TGA). TGA suggested that Me(II)Pc weight content is 30%, 17% and 35% for NiPc, CuPc, and ZnPc, respectively (CoPc exhibited anomalous thermal decomposition behavior). The above values are consistent with those estimated from EDS spectra, namely, of 24-39%, 27-36% and 27-44% for CoPc, CuPc, and ZnPc, respectively. A strong increase in intensity of D band in the Raman spectra of SWNT‒Me(II)Pc hybrids, as compared to that of pristine nanotubes, implies very strong interactions between Pc molecules and SWNT sidewalls. Very high absolute values of binding energies of 32.46-37.12 kcal/mol and the highest occupied and lowest unoccupied molecular orbital (HOMO and LUMO, respectively) distribution patterns, calculated with density functional theory by using Perdew-Burke-Ernzerhof general gradient approximation correlation functional in combination with the Grimme’s empirical dispersion correction (PBE-D) and the double numerical basis set (DNP), also suggested that the interactions between Me(II) phthalocyanines and nanotube sidewalls are very strong. The authors thank the National Autonomous University of Mexico (grant DGAPA-IN200516) and the National Council of Science and Technology of Mexico (CONACYT, grant 250655) for financial support. The authors are also grateful to Dr. Natalia Alzate-Carvajal (CCADET of UNAM), Eréndira Martínez (IF of UNAM) and Iván Puente-Lee (Faculty of Chemistry of UNAM) for technical assistance with FTIR, TGA measurements, and TEM imaging, respectively.

Keywords: carbon nanotubes, functionalization, gas-phase, metal(II) phthalocyanines

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Authors: Palak V. Patel, Jessica Pixley, Steven R. Feldman

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Introduction: Basal cell carcinoma (BCC) is the most common skin cancer worldwide and requires substantial resources to treat. When choosing between indicated therapies, providers consider their associated adverse effects, efficacy, cosmesis, and function preservation. The patient’s tumor burden, infiltrative risk, and risk of tumor recurrence are also considered. Treatment cost is often left out of these discussions. This can lead to financial toxicity, which describes the harm and quality of life reductions inflicted by high care costs. Methods: We studied the guidelines set forth by the American Academy of Dermatology for the treatment of BCC. A PubMed literature search was conducted to identify the costs of each recommended therapy. We discuss costs alongside treatment efficacy and side-effect profile. Results: Surgical treatment for BCC can be cost-effective if the appropriate treatment is selected for the presenting tumor. Curettage and electrodesiccation can be used in low-grade, low-recurrence tumors in aesthetically unimportant areas. The benefits of cost-conscious care are not likely to be outweighed by the risks of poor cosmesis or tumor return ($471 BCC of the cheek). When tumor burden is limited, MMS offers better cure rates and lower recurrence rates than surgical excision, and with comparable costs (MMS $1263; SE $949). Surgical excision with permanent sections may be indicated when tumor burden is more extensive or if molecular testing is necessary. The utility of surgical excision with frozen sections, which costs substantially more than MMS without comparable outcomes, is less clear (SE with frozen sections $2334-$3085). Less data exists on non-surgical treatments for BCC. These techniques cost less, but recurrence-risk is high. Side-effects of nonsurgical treatment are limited to local skin reactions, and cosmesis is good. Cryotherapy, 5-FU, and MAL-PDT are all more affordable than surgery, but high recurrence rates increase risk of secondary financial and psychosocial burden (recurrence rates 21-39%; cost $100-270). Radiation therapy offers better clearance rates than other nonsurgical treatments but is associated with similar recurrence rates and a significantly larger financial burden ($2591-$3460 BCC of the cheek). Treatments for advanced or metastatic BCC are extremely costly, but few patients require their use, and the societal cost burden remains low. Vismodegib and sonidegib have good response rates but substantial side effects, and therapy should be combined with multidisciplinary care and palliative measures. Expert-review has found sonidegib to be the less expensive and more efficacious option (vismodegib $128,358; sonidegib $122,579). Platinum therapy, while not FDA-approved, is also effective but expensive (~91,435). Immunotherapy offers a new line of treatment in patients intolerant of hedgehog inhibitors ($683,061). Conclusion: Dermatologists working within resource-compressed practices and with resource-limited patients must prudently manage the healthcare dollar. Surgical therapies for BCC offer the lowest risk of recurrence at the most reasonable cost. Non-surgical therapies are more affordable, but high recurrence rates increase the risk of secondary financial and psychosocial burdens. Treatments for advanced BCC are incredibly costly, but the low incidence means the overall cost to the system is low.

Keywords: nonmelanoma skin cancer, basal cell skin cancer, squamous cell skin cancer, cost of care

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Authors: V. Cesaroni, C. Girometta, A. Bernicchia, M. Brusoni, F. Corana, R. M. Baiguera, C. M. Cusaro, M. L. Guglielminetti, B. Mannucci, H. Kawagishi, C. Perini, A. M. Picco, P. Rossi, E. Salerni, E. Savino

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Fungi of the genus Hericium contain various compounds with antibacterial activity, cytotoxic effect on cancer cells and bioactive molecules. Some of the active metabolites stimulate the synthesis of the Nerve Growth Factor (NGF). Recently, the effect of dietary supplement based on Hericium erinaceus on recognition memory and on hippocampal mossy fiber-CA3 neurotransmission was published. The aim of this study was to investigate the presence of Hericium species on Italian territory in order to isolate the strains for further studies and applications. The first step was to collect Hericium sporophores in Tuscany: H. alpestre Pers., H. coralloides (Scop.) Pers. and H. erinaceus (Bull.) Pers. were the species present. The strains of H. alpestre (H.a.1), H. coralloides (H.c.1) and H. erinaceus (H.e.1 & H.e.2) have been isolated in pure culture and preserved in the collection of the University of Pavia (MicUNIPV). The DNA sequences obtained from the strains were compared to other sequences found in international databases. Therefore, it was possible to construct a phylogenetic tree that highlights the clear separation in clades of the sequences and the molecular identification of our strains with the species of Hericium considered. The second step was to cultivate indoor and outdoor H. erinaceus in order to obtain as many sporophores as possible for further chemical analysis. All the procedures for H. erinaceus cultivation have been followed. Among the available recipes for indoor H. erinaceus cultivation, it was used a substrate formulation contained 70% oak sawdust, 20% rice bran, 10% wheat straw, 1% CaCO3 and 1% sucrose. The bioactive compounds present in the mycelia and in the sporophores of H. erinaceus were chemically analyzed in collaboration with the Centro Grandi Strumenti of the University of Pavia using high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS/MS). The materials to be analyzed were previously freeze-dried and then extracted with an alcoholic procedure. Preliminary chromatographic analysis revealed the presence of potentially bioactive and structurally different secondary metabolites such as polysaccharides, erinacins, ericenones, steroids and other terpenoids. Ericenones C and D (in sporophores) and erinacin A (in mycelium) have been identified by comparison with the respective standards. These molecules are known to have effects on the Central Nervous System (CNS) cells, which is the main objective of our studies. Thanks to the high sensitivity in the detection of bioactive compounds of H. erinaceus, it will be possible to use the To obtain lyophilized mycelium and the respective culture broth, 4 small pieces (about 5 mm2) of the respective H.e.1 or H.c.1 strains, taken from the margin of growing cultures (MEA), were inoculated into 1 liter of 2% ME (malt extract, Biokar Diagnostics). The static liquid cultures were kept at 24 °C in the dark chamber and fungi grew for one month. 10 replicates for each strain have been done. The method proposed as an analytical screening protocol to determine the optimal growth conditions of the fungus and to improve the production chain of H. erinaceus. These results encourage to carry out chemical analyzes also on H. alpestre and H. coralloides in order to evaluate the presence of bioactive compounds in these two species.

Keywords: Hericium species, Hercium erinaceus bioactive compounds, medicinal mushrooms, mushroom cultivation

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Authors: Hao Huang

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INTRODUCTION: The Association of American Colleges and Universities (AACU) recommends the development of ‘high-impact practices,’ in an effort to increase rates of student retention and student engagement at undergraduate institutions. To achieve these goals, the Scripps College Humanities Institute and HI Fellows Seminar not only featured distinguished academics presenting their scholarship about current immigration policy and its consequences in the USA and around the world but integrated socially significant community leaders and creative activists/artivists in public talks, student workshops and collaborative art events. Students participated in experiential learning that involved guest personal presentations and discussions, oral history interviews that applied standard oral history methodologies, detailed cultural documentation, collaborative artistic interventions, and weekly posts in Internet Digital Learning Environment Sakai collaborative course forums and regular responses to other students’ comments. Our teaching pedagogies addressed the four learning styles outlined in Kolb’s Learning Style Inventory. PROJECT DESCRIPTION: Over the academic year 2017-18, the Scripps College Humanities Institute and HI Fellows Seminar presented a Fall 2017 topic, ‘The World at Our Doorsteps: Immigration and Deportation in Los Angeles’. Our purpose was to address how current federal government anti-immigration measures have affected many students of color, some of whom are immigrants, many of whom are related to and are friends with people who are impacted by the attitudes as well as the practices of the U.S. Citizenship and Immigration Services. In Spring 2018, we followed with the topic, ‘Exclusive Nationalisms: Global Migration and Immigration’. This addresses the rise of white supremacists who have ascended to position of power worldwide, in America, Europe, Russia, and xenophobic nationalisms in China, Myanmar and the Philippines. Recent scholarship has suggested the existence of categories of refugees beyond the political or social, who fit into the more inclusive category of migrants. ASSESSMENT METHODOLOGIES: Assessment methodologies not only included qualitative student interviews and quantitative student evaluations in standard rubric format, but also Outcome Assessments, Formative Evaluations, and Outside Guest Teacher feedback. These indicated that the most effective educational practices involved collaborative inquiry in undergraduate research, community-based learning, and capstone projects. Assessments of E-portfolios, written and oral coursework, and final creative projects with associated 10-12 page analytic paper revealed that students developed their understanding of how government and social organizations work; they developed communication skills that enhanced working with others from different backgrounds; they developed their ability to thoughtfully evaluate their course performance by adopting reflective practices; they gained analytic and interpretive skills that encouraged self-confidence and self- initiative not only academically, but also with regards to independent projects. CONCLUSION: Most importantly, the Scripps Humanities Institute experiential learning project spurred on real-world actions by our students, such as a public symposium on how to cope with bigots, a student tutoring program for immigrant staff children, student negotiations with the administration to establish meaningful, sustainable diversity and inclusion programs on-campus. Activism is not only to be taught to and for our students– it has to be enacted by our students.

Keywords: immigration, migration, human rights, learning assessment

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Authors: Zdravko Trivic, John Chye Fung, Ruzica Bozovic-Stamenovic

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Within the context of rapidly ageing population in Singapore and the pressing demands on both caregivers and care providers, an integrated approach to ageing-friendly and ability-sensitive enabling environment becomes an imperative. This particularly applies to nursing home environments and their immediate surroundings, as they are becoming one of the main available options of long-term care for many senior adults who are unable to age at home. Yet, despite the considerable efforts to break the still predominant clinical approach to eldercare and to introduce more home-like design and person-centric care model, nursing homes keep being stigmatised and perceived as not so desirable environments to grow old in. The challenges are further emphasised by the associated physical, sensorial, psychological and cognitive declines that are the common consequences of ageing. Such declines have an immense impact on almost all aspects of older adults’ daily functioning, including problems with mobility and spatial orientation, difficulties in communication, withdrawal from social interaction, higher level of depression and decreased sense of independence and autonomy. However, typical nursing home designs tend to neglect the full capacities of balanced and carefully integrated multisensory stimuli as active component of care and ability building. This paper outlines part of a larger multi-disciplinary study of six nursing homes in Singapore, with overarching objectives to create new models of supportive nursing home environments that go beyond the clinical care model and encourage community integration with the nursing home settings. The paper focuses on the largely neglected aspects of sensorial comfort and multi-sensorial properties of nursing homes, including both indoor and immediate outdoor spaces (boundaries). The objective was to investigate the sensory rhythms and explore their role in nursing home users’ daily routine and therapeutic capacities. Socio-sensory rhythms were captured and analysed through a combination of on-site sensory recordings of “objective” quantitative sensory data (air temperature and humidity, sound level and luminance) using multi-function environment meter, perceived experienced data, spatial mapping, first-person observations of nursing home users’ activity patterns, and interviews. This was done in addition to employment of available assessment tools, such as Wisconsin Person Directed Care assessment tool, Dementia Quality of Life [DQoL] instrument, and Resident Environment Impact Scale [REIS], as these tools address the issues of sensorial experience insufficiently and selectively. Key findings indicate varied levels of sensory comfort, as well as diversity, intensity, and customisation of multi-sensory conditions within different nursing home spaces. Sensory stimulation is typically concentrated in communal living areas of the nursing homes or in the areas that often provide controlled or limited access, including specifically designed sensory rooms and outdoor green spaces (gardens and terraces). Opportunities for sensory stimulation are particularly limited for bed-bound senior residents and within more functional areas, such as corridors. This suggests that the capacities of nursing home designs to provide more diverse and better integrated pleasant sensory conditions as integrated “therapeutic devices” to build nursing home residents’ physical and mental abilities, encourage activity and improve wellbeing are far from exhausted.

Keywords: ageing-supportive environment, enabling design, multi-sensory assessment, nursing home environment

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Authors: Hannah R. Devens, Phillip L. Davidson, Dione Deaker, Kathryn E. Smith, Gregory A. Wray, Maria Byrne

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Marine invertebrate species with calcifying larvae are especially vulnerable to ocean acidification (OA) caused by rising atmospheric CO₂ levels. Acidic conditions can delay development, suppress metabolism, and decrease the availability of carbonate ions in the ocean environment for skeletogenesis. These stresses often result in increased larval mortality, which may lead to significant ecological consequences including alterations to the larval settlement, population distribution, and genetic connectivity. Importantly, many of these physiological and developmental effects are caused by genetic and molecular level changes. Although many studies have examined the effect of near-future oceanic pH levels on gene expression in marine invertebrates, little is known about the impact of OA on gene expression in a developmental context. Here, we performed mRNA-sequencing to investigate the impact of environmental acidity on gene expression across three developmental stages in the sea urchin Heliocidaris erythrogramma. We collected RNA from gastrula, early larva, and 1-day post-metamorphic juvenile sea urchins cultured at present-day and predicted future oceanic pH levels (pH 8.1 and 7.7, respectively). We assembled an annotated reference transcriptome encompassing development from egg to ten days post-metamorphosis by combining these data with datasets from two previous developmental transcriptomic studies of H. erythrogramma. Differential gene expression and time course analyses between pH conditions revealed significant alterations to developmental transcription that are potentially associated with pH stress. Consistent with previous investigations, genes involved in biomineralization and ion transport were significantly upregulated under acidic conditions. Differences in gene expression between the two pH conditions became more pronounced post-metamorphosis, suggesting a development-dependent effect of OA on gene expression. Furthermore, many differences in gene expression later in development appeared to be a result of broad downregulation at pH 7.7: of 539 genes differentially expressed at the juvenile stage, 519 of these were lower in the acidic condition. Time course comparisons between pH 8.1 and 7.7 samples also demonstrated over 500 genes were more lowly expressed in pH 7.7 samples throughout development. Of the genes exhibiting stage-dependent expression level changes, over 15% of these diverged from the expected temporal pattern of expression in the acidic condition. Through these analyses, we identify novel candidate genes involved in development, metabolism, and transcriptional regulation that are possibly affected by pH stress. Our results demonstrate that pH stress significantly alters gene expression dynamics throughout development. A large number of genes differentially expressed between pH conditions in juveniles relative to earlier stages may be attributed to the effects of acidity on transcriptional regulation, as a greater proportion of mRNA at this later stage has been nascent transcribed rather than maternally loaded. Also, the overall downregulation of many genes in the acidic condition suggests that OA-induced developmental delay manifests as suppressed mRNA expression, possibly from lower transcription rates or increased mRNA degradation in the acidic environment. Further studies will be necessary to determine in greater detail the extent of OA effects on early developing marine invertebrates.

Keywords: development, gene expression, ocean acidification, RNA-sequencing, sea urchins

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Authors: Olga Smilevska Spasova, Katerina Boshkovska, Gorica Popova, Mirjana Popovska

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Introduction: Pneumonia is an infection of the pulmonary parenchyma. HPIV 3 is one of four viruses that is a member of the Paramyxoviridae family designated types 1-4 that have a nonsegmented, single-stranded RNA genome with a lipid-containing envelope. They are spread from the respiratory tract by aerosolized secretions or by direct contact with secretions. Type 3 is endemic and can cause serious illness in immunocompromised patients. Illness caused by parainfluenza occurs shortly after inoculation with the virus. The level of immunoglobulin A antibody in serum is the best predictor of susceptibility to infection. Streptococcus pneumonia or pneumococcus is a Gram-positive, spherical bacteria, usually found in pairs and it is a member of the genus Streptococcus. Streptococcus pneumonia resides asymptomatically in healthy carriers typically colonizing the respiratory tract, sinuses, and nasal cavity. In individuals with weaker immune systems like young infants, pneumococcal bacterium is the most common cause of community-acquired pneumonia in the world. Case Report: The aim is to present a case of lower respiratory tract infection in an infant caused by parainfluenza virus 3, S. pneumonia and undifferentiated gram-negative bacteria that was successfully treated. The infant is with a history of recurrent episodes of wheezing in the past 3mounts.Infant of 10months presents 2weeks before admittance with high fever, runny nose, and cough. The primary pediatrician prescribed oral cefpodoxime for 10days and inhaled salbutamol. Two days before admittance in hospital the infant with high fever, cough, and difficulty breathing. At admittance, infant is pale, anxious with rapid respirations, cough, wheezing and tachycardia. On auscultation: vesicular breathing sounds with high pitched wheezing and on the right coarse crackles. Investigations: Blood analysis: RBC: 4, 7 x1012L, WBC: 8,3x109L: Neut: 42.73% Lym: 41.57%, Hgb: 9.38 g/dl MCV: 62.7fl, MCH: 20.0pg MCHC: 31.8 g/dl RDW: 18.7% Plt-307.9 x109LCRP: 2,5mg/l, serum iron-7.92umol/l, O2sat-97% on blood gas analysis, puls-125/min.X-ray of chest with hyperinflationand right pericardial consolidation. Microbiological analysis of sputum sample is positive for undifferentiated gram-negative bacteria (colonizer)–resistant to cefotaxime, ampicillin, cefoxitin, sulfamet.+trimetoprim and sensitive to amikacin, gentamicin, and ciprofloxacin. Molecular multiplex RT-PCR for 19 viruses and multiplex PCR for 7 bacteria test for respiratory pathogens positive for Parainfluenza virus 3(Ct=22.73), Streptococcus pneumonia (Ct=26.75).IED: IgG-9.31g/l, IgA-0.351g/l, IgM-0.86g/l. Therapy: Treatment was started with inhaled salbutamol, intravenous antibiotic cefotaxime as well as systemic corticosteroids. On day 7 because of slow clinical resolution of chest auscultation findings and an etiologic clue with a positive sputum sample for resistant undifferentiated gram negative bacteria, a second intravenous antibiotic was administered amikacin. The infant is discharged on day 14 with resolution of clinical findings. Conclusion: Mixed co-infections with respiratory viruses and bacteria in immunocompromised infants are likely to lead to a more severe form of community acquired pneumonia that will need hospitalization.

Keywords: HPIV- 3, infant, pneumonia, S. pneumonia, x-ray chest

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Authors: Isabelle Barrett

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Natural watercourses provide a range of vital ecosystem services, notably freshwater provision. They also offer highly heterogeneous habitat which supports an extreme diversity of aquatic life. Exploitation of rivers, changing land use and flood prevention measures have led to habitat degradation and subsequent biodiversity loss; indeed, freshwater species currently face a disproportionate rate of extinction compared to their terrestrial and marine counterparts. Large woody debris (LWD) encompasses the trees, large branches and logs which fall into watercourses, and is responsible for important habitat characteristics. Historically, natural LWD has been removed from streams under the assumption that it is not aesthetically pleasing and is thus ecologically unfavourable, despite extensive evidence contradicting this. Restoration efforts aim to replace lost LWD in order to reinstate habitat heterogeneity. This paper aims to assess the current state of such restoration schemes for improving fluvial ecological health in the UK. A detailed review of the scientific literature was conducted alongside a meta-analysis of 25 UK-based projects involving LWD restoration. Projects were chosen for which sufficient information was attainable for analysis, covering a broad range of budgets and scales. The most effective strategies for river restoration encompass ecological success, stakeholder engagement and scientific advancement, however few projects surveyed showed sensitivity to all three; for example, only 32% of projects stated biological aims. Focus tended to be on stakeholder engagement and public approval, since this is often a key funding driver. Consequently, there is a tendency to focus on the aesthetic outcomes of a project, however physical habitat restoration does not necessarily lead to direct biodiversity increases. This highlights the significance of rivers as highly heterogeneous environments with multiple interlinked processes, and emphasises a need for a stronger scientific presence in project planning. Poor scientific rigour means monitoring is often lacking, with varying, if any, definitions of success which are rarely pre-determined. A tendency to overlook negative or neutral results was apparent, with unjustified focus often put on qualitative results. The temporal scale of monitoring is typically inadequate to facilitate scientific conclusions, with only 20% of projects surveyed reporting any pre-restoration monitoring. Furthermore, monitoring is often limited to a few variables, with biotic monitoring often fish-focussed. Due to their longer life cycles and dispersal capability, fish are usually poor indicators of environmental change, making it difficult to attribute any changes in ecological health to restoration efforts. Although the potential impact of LWD restoration may be positive, this method of restoration could simply be making short-term, small-scale improvements; without addressing the underlying symptoms of degradation, for example water quality, the issue cannot be fully resolved. Promotion of standardised monitoring for LWD projects could help establish a deeper understanding of the ecology surrounding the practice, supporting movement towards adaptive management in which scientific evidence feeds back to practitioners, enabling the design of more efficient projects with greater ecological success. By highlighting LWD, this study hopes to address the difficulties faced within river management, and emphasise the need for a more holistic international and inter-institutional approach to tackling problems associated with degradation.

Keywords: biological monitoring, ecological health, large woody debris, river management, river restoration

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Authors: Artem Kim, Clara Savary, Christele Dubourg, Wilfrid Carre, Houda Hamdi-Roze, Valerie Dupé, Sylvie Odent, Marie De Tayrac, Veronique David

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Holoprosencephaly (HPE) is a rare congenital brain malformation resulting from the incomplete separation of the two cerebral hemispheres. It is characterized by a wide phenotypic spectrum and a high degree of locus heterogeneity. Genetic defects in 16 genes have already been implicated in HPE, but account for only 30% of cases, suggesting that a large part of genetic factors remains to be discovered. HPE has been recently redefined as a complex multigenic disorder, requiring the joint effect of multiple mutational events in genes belonging to one or several developmental pathways. The onset of HPE may result from accumulation of the effects of multiple rare variants in functionally-related genes, each conferring a moderate increase in the risk of HPE onset. In order to decipher the genetic basis of HPE, unconventional patterns of inheritance involving multiple genetic factors need to be considered. The primary objective of this study was to uncover possible disease causing combinations of multiple rare variants underlying HPE by performing trio-based Whole Exome Sequencing (WES) of familial cases where no molecular diagnosis could be established. 39 families were selected with no fully-penetrant causal mutation in known HPE gene, no chromosomic aberrations/copy number variants and without any implication of environmental factors. As the main challenge was to identify disease-related variants among a large number of nonpathogenic polymorphisms detected by WES classical scheme, a novel variant prioritization approach was established. It combined WES filtering with complementary gene-level approaches: transcriptome-driven (RNA-Seq data) and clinically-driven (public clinical data) strategies. Briefly, a filtering approach was performed to select variants compatible with disease segregation, population frequency and pathogenicity prediction to identify an exhaustive list of rare deleterious variants. The exome search space was then reduced by restricting the analysis to candidate genes identified by either transcriptome-driven strategy (genes sharing highly similar expression patterns with known HPE genes during cerebral development) or clinically-driven strategy (genes associated to phenotypes of interest overlapping with HPE). Deeper analyses of candidate variants were then performed on a family-by-family basis. These included the exploration of clinical information, expression studies, variant characteristics, recurrence of mutated genes and available biological knowledge. A novel bioinformatics pipeline was designed. Applied to the 39 families, this final integrated workflow identified an average of 11 candidate variants per family. Most of candidate variants were inherited from asymptomatic parents suggesting a multigenic inheritance pattern requiring the association of multiple mutational events. The manual analysis highlighted 5 new strong HPE candidate genes showing recurrences in distinct families. Functional validations of these genes are foreseen.

Keywords: complex genetic disorder, holoprosencephaly, multiple rare variants, whole exome sequencing

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Authors: Shuo Li, Yannick Coffinier, Chann Lagadec, Fabrizio Cleri, Katsuhiko Nishiguchi, Akira Fujiwara, Soo Hyeon Kim, Nicolas Clément

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The need for single cell detection and analysis techniques has increased in the past decades because of the heterogeneity of individual living cells, which increases the complexity of the pathogenesis of malignant tumors. In the search for early cancer detection, high-precision medicine and therapy, the technologies most used today for sensitive detection of target analytes and monitoring the variation of these species are mainly including two types. One is based on the identification of molecular differences at the single-cell level, such as flow cytometry, fluorescence-activated cell sorting, next generation proteomics, lipidomic studies, another is based on capturing or detecting single tumor cells from fresh or fixed primary tumors and metastatic tissues, and rare circulating tumors cells (CTCs) from blood or bone marrow, for example, dielectrophoresis technique, microfluidic based microposts chip, electrochemical (EC) approach. Compared to other methods, EC sensors have the merits of easy operation, high sensitivity, and portability. However, despite various demonstrations of low limits of detection (LOD), including aptamer sensors, arrayed EC sensors for detecting single-cell have not been demonstrated. In this work, a new technique based on 20-nm-thick nanopillars array to support cells and keep them at ideal recognition distance for redox-labeled aptamers grafted on the surface. The key advantages of this technology are not only to suppress the false positive signal arising from the pressure exerted by all (including non-target) cells pushing on the aptamers by downward force but also to stabilize the aptamer at the ideal hairpin configuration thanks to a confinement effect. With the first implementation of this technique, a LOD of 13 cells (with5.4 μL of cell suspension) was estimated. In further, the nanosupported cell technology using redox-labeled aptasensors has been pushed forward and fully integrated into a single-cell electrochemical aptasensor array. To reach this goal, the LOD has been reduced by more than one order of magnitude by suppressing parasitic capacitive electrochemical signals by minimizing the sensor area and localizing the cells. Statistical analysis at the single-cell level is demonstrated for the recognition of cancer cells. The future of this technology is discussed, and the potential for scaling over millions of electrodes, thus pushing further integration at sub-cellular level, is highlighted. Despite several demonstrations of electrochemical devices with LOD of 1 cell/mL, the implementation of single-cell bioelectrochemical sensor arrays has remained elusive due to their challenging implementation at a large scale. Here, the introduced nanopillar array technology combined with redox-labeled aptamers targeting epithelial cell adhesion molecule (EpCAM) is perfectly suited for such implementation. Combining nanopillar arrays with microwells determined for single cell trapping directly on the sensor surface, single target cells are successfully detected and analyzed. This first implementation of a single-cell electrochemical aptasensor array based on Brownian-fluctuating redox species opens new opportunities for large-scale implementation and statistical analysis of early cancer diagnosis and cancer therapy in clinical settings.

Keywords: bioelectrochemistry, aptasensors, single-cell, nanopillars

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