Search results for: molecular electrocatalysts

Authors: Igor Vishnevskyi

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Introduction: The urinary bladder undergoes repeated strain during its working cycle, suggesting the presence of an efficient support system, force transmission, and mechanical amplification. The concept of a "hydrostatic skeleton" (HS) could contribute to our understanding of the functional relationships among bladder constituents. Methods: A multidisciplinary literature review was conducted to identify key features of the HS and to gather evidence supporting its applicability in urinary bladder biomechanics. The collected evidence was synthesized to propose a framework for understanding the potential hydrostatic properties of the urinary bladder based on existing knowledge and HS principles. Results: Our analysis revealed similarities in biomechanical features between living fluid-filled structures and the urinary bladder. These similarities include the geodesic arrangement of fibres, the role of enclosed fluid (urine) in force transmission, prestress as a determinant of stiffness, and the ability to maintain shape integrity during various activities. From a biomechanical perspective, urine may be considered an essential component of the bladder. The hydrostatic skeleton, with its autonomy and flexibility, may provide insights for researchers involved in bladder engineering. Discussion: The concept of a hydrostatic skeleton offers a holistic perspective for understanding bladder function by considering multiple mechanical factors as a single structure with emergent properties. Incorporating viewpoints from various fields on HS can help identify how this concept applies to live fluid-filled structures or organs and reveal its broader relevance to biological systems, both natural and artificial. Conclusion: The hydrostatic skeleton (HS) design principle can be applied to the urinary bladder. Understanding the bladder as a structure with HS can be instrumental in biomechanical modelling and engineering. Further research is required to fully elucidate the cellular and molecular mechanisms underlying HS in the bladder.

Keywords: hydrostatic skeleton, urinary bladder morphology, shape integrity, prestress, biomechanical modelling

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Authors: Sarmiza Stanca, Wolfgang Fritzsche, Christoph Krafft, Jürgen Popp

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Independent of the cell type a thin layer of a few nanometers thickness surrounds the cell interior as the cellular membrane. The transport of ions and molecules through the membrane is achieved in a very precise way by pores. Understanding the process of opening and closing the pores due to an electrochemical gradient across the membrane requires knowledge of the pore constitutive proteins. Recent reports prove the access to the molecular level of the cellular membrane by atomic force microscopy (AFM). This technique also permits an electrochemical study in the immediate vicinity of the tip. Specific molecules can be electrochemically localized in the natural cellular membrane. Our work aims to recognize the protein domains of the pores using an AFM probe as a miniaturized amperometric sensor, and to follow the protein behavior while changing the applied potential. The intensity of the current produced between the surface and the AFM probe is amplified and detected simultaneously with the surface imaging. The AFM probe plays the role of the working electrode and the substrate, a conductive glass on which the cells are grown, represent the counter electrode. For a better control of the electric potential on the probe, a third electrode Ag/AgCl wire is mounted in the circuit as a reference electrode. The working potential is applied between the electrodes with a programmable source and the current intensity in the circuit is recorded with a multimeter. The applied potential considers the overpotential at the electrode surface and the potential drop due to the current flow through the system. The reported method permits a high resolved electrochemical study of the protein domains on the living cell membrane. The amperometric map identifies areas of different current intensities on the pore depending on the applied potential. The reproducibility of this method is limited by the tip shape, the uncontrollable capacitance, which occurs at the apex and a potential local charge separation.

Keywords: AFM, sensor, membrane, pores, proteins

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Authors: Sandeep Vasaikar, Lary Obi

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Rapid and discriminative genotyping methods are useful for determining the clonality of the isolates in nosocomial or household outbreaks. Multilocus sequence typing (MLST) is a nucleotide sequence-based approach for characterising bacterial isolates. The genetic diversity and the clinical relevance of the drug-resistant Klebsiella isolates from Mthatha are largely unknown. For this reason, prospective, experimental study of the molecular epidemiology of Klebsiella isolates from patients being treated in Mthatha over a three-year period was analysed. Methodology: PCR amplification and sequencing of the drug-resistance-associated genes, and multilocus sequence typing (MLST) using 7 housekeeping genes mdh, pgi, infB, FusAR, phoE, gapA and rpoB were conducted. A total of 32 isolates were analysed. Results: The percentages of multidrug-resistant (MDR), extensively drug-resistance (XDR) and pandrug-resistant (PDR) isolates were; MDR 65.6 % (21) and XDR and PDR with 0 % each. In this study, K. pneumoniae was 19/32 (59.4 %). MLST results showed 22 sequence types (STs) were identified, which were further separated by Maximum Parsimony into 10 clonal complexes and 12 singletons. The most dominant group was Klebsiella pneumoniae with 23/32 (71.8 %) isolates, Klebsiella oxytoca as a second group with 2/32 (6.25 %) isolates, and a single (3.1 %) K. varricola as a third group while 6 isolates were of unknown sequences. Conclusions/significance: A phylogenetic analysis of the concatenated sequences of the 7 housekeeping genes showed that strains of K. pneumoniae form a distinct lineage within the genus Klebsiella, with K. oxytoca and K. varricola its nearest phylogenetic neighbours. With the analysis of 7 genes were determined 1 K. variicola, which was mistakenly identified as K. pneumoniae by phenotypic methods. Two misidentifications of K. oxytoca were found when phenotypic methods were used. No significant differences were observed between ESBL blaCTX-M, blaTEM and blaSHV groups in the distribution of Sequence types (STs) or Clonal complexes (CCs).

Keywords: phylogenetic analysis, phylogeny, klebsiella phylogenetic, klebsiella

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Authors: Vivek B. Ravindran, Aravind Surapaneni, Rebecca Traub, Sarvesh K. Soni, Andrew S. Ball

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Parasitic diseases have a devastating, long-term impact on human health and welfare. More than two billion people are infected with soil-transmitted helminths (STHs), including the roundworms (Ascaris), hookworms (Necator and Ancylostoma) and whipworm (Trichuris) with majority occurring in the tropical and subtropical regions of the world. Despite its low prevalence in developed countries, the removal of STHs from wastewater remains crucial to allow the safe use of sludge or recycled water in agriculture. Conventional methods such as incubation and optical microscopy are cumbersome; consequently, the results drastically vary from person-to-person observing the ova (eggs) under microscope. Although PCR-based methods are an alternative to conventional techniques, it lacks the ability to distinguish between viable and non-viable helminth ova. As a result, wastewater treatment industries are in major need for radically new and innovative tools to detect and quantify STHs eggs with precision, accuracy and being cost-effective. In our study, we focus on the following novel and innovative techniques: -Recombinase polymerase amplification and Surface enhanced Raman spectroscopy (RPA-SERS) based detection of helminth ova. -Use of metal nanoparticles and their relative nanozyme activity. -Colorimetric detection, differentiation and enumeration of genera of helminth ova using hydrolytic enzymes (chitinase and lipase). -Propidium monoazide (PMA)-qPCR to detect viable helminth ova. -Modified assay to recover and enumerate helminth eggs from fresh raw sewage. -Transcriptome analysis of ascaris ova in fresh raw sewage. The aforementioned techniques have the potential to replace current conventional and molecular methods thereby producing a standard protocol for the determination and enumeration of helminth ova in sewage sludge.

Keywords: colorimetry, helminth, PMA-QPCR, nanoparticles, RPA, viable

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Authors: Mark Andrew

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Geopolitical tensions are at a thirty-year high, and the pace of technological innovation is driving asymmetry in force capabilities between nation states and between non-state actors. Technology futures are a vital component of defence capability growth, and investments in technology futures need to be informed by accurate and reliable forecasts of the options for ‘systems of systems’ innovation, development, and deployment. This paper describes a method for forecasting technology futures developed through an analysis of four key systems’ development stages, namely: technology domain categorisation, scanning results examining novel systems’ signals and signs, potential system-of systems’ implications in warfare theatres, and political ramifications in terms of funding and development priorities. The method has been applied to several technology domains, including physical systems (e.g., nano weapons, loitering munitions, inflight charging, and hypersonic missiles), biological systems (e.g., molecular virus weaponry, genetic engineering, brain-computer interfaces, and trans-human augmentation), and information systems (e.g., sensor technologies supporting situation awareness, cyber-driven social attacks, and goal-specification challenges to proliferation and alliance testing). Although the current application of the method has been team-centred using paper-based rapid prototyping and iteration, the application of autonomous language models (such as GPT-3) is anticipated as a next-stage operating platform. The importance of forecasting accuracy and reliability is considered a vital element in guiding technology development to afford stronger contingencies as ideological changes are forecast to expand threats to ecology and earth systems, possibly eclipsing the traditional vulnerabilities of nation states. The early results from the method will be subjected to ground truthing using longitudinal investigation.

Keywords: forecasting, technology futures, uncertainty, complexity

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Authors: Vishal V. R. Nandigana, Mohammad Heiranian, Narayana R. Aluru

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Graphene material has found tremendous applications in water desalination, DNA sequencing and energy storage. Multiple nanopores are etched to create opening for water desalination and energy storage applications. The nanopores created are of the order of 3-5 nm allowing multiple ions to transport through the pore. In this paper, we present for the first time, molecular dynamics study of single ion transport, where only one ion passes through the graphene nanopore. The diameter of the graphene nanopore is of the same order as the hydration layers formed around each ion. Analogous to single electron transport resulting from ionic transport is observed for the first time. The current-voltage characteristics of such a device are similar to single electron transport in quantum dots. The current is blocked until a critical voltage, as the ions are trapped inside a hydration shell. The trapped ions have a high energy barrier compared to the applied input electrical voltage, preventing the ion to break free from the hydration shell. This region is called “Coulomb blockade region”. In this region, we observe zero transport of ions inside the nanopore. However, when the electrical voltage is beyond the critical voltage, the ion has sufficient energy to break free from the energy barrier created by the hydration shell to enter into the pore. Thus, the input voltage can control the transport of the ion inside the nanopore. The device therefore acts as a binary storage unit, storing 0 when no ion passes through the pore and storing 1 when a single ion passes through the pore. We therefore postulate that the device can be used for fluidic computing applications in chemistry and biology, mimicking a computer. Furthermore, the trapped ion stores a finite charge in the Coulomb blockade region; hence the device also acts a super capacitor.

Keywords: graphene nanomembrane, single ion transport, Coulomb blockade, nanofluidics

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Authors: Fabio T. Costa, Sergio E. Moya, Marcelo H. Sousa

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Nanocomposites designed by embedding magnetic nanoparticles into a polymeric matrix stand out as ideal magnetic-hybrid and magneto-responsive materials as sorbents for removal of pollutants in environmental applications. Covalent coupling is often desired for the immobilization of species on these nanocomposites, in order to keep them permanently bounded, not desorbing or leaching over time. Moreover, unwanted adsorbates can be separated by successive washes/magnetic separations, and it is also possible to recover the adsorbate covalently bound to the nanocomposite surface through detaching/cleavage protocols. Thus, in this work, we describe the preparation and characterization of highly-magnetizable chloromethylated polystyrene-based nanocomposite beads for selective covalent coupling in environmental applications. For synthesis optimization, acid resistant core-shelled maghemite (γ-Fe₂O₃) nanoparticles were coated with oleate molecules and directly incorporated into the organic medium during a suspension polymerization process. Moreover, the cross-linking agent ethylene glycol dimethacrylate (EGDMA) was utilized for co-polymerization with the 4-vinyl benzyl chloride (VBC) to increase the resistance of microbeads against leaching. After characterizing samples with XRD, ICP-OES, TGA, optical, SEM and TEM microscopes, a magnetic composite consisting of ~500 nm-sized cross-linked polymeric microspheres embedding ~8 nm γ-Fe₂O₃ nanoparticles was verified. This nanocomposite showed large room temperature magnetization (~24 emu/g) due to the high content in maghemite (~45 wt%) and resistance against leaching even in acidic media. Moreover, the presence of superficial chloromethyl groups, probed by FTIR and XPS spectroscopies and confirmed by an amination test can selectively adsorb molecules through the covalent coupling and be used in molecular separations as shown for the selective removal of 4-aminobenzoic acid from a mixture with benzoic acid.

Keywords: nanocomposite, magnetic nanoparticle, covalent separation, pollutant removal

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Authors: Hany M. Fayed, Rehab F. Abdel-Rahman, Alyaa F. Hessin, Hanan A. Ogaly, Gihan F. Asaad, Abeer A. A. Salama, Sahar Abdelrahman, Mahmoud S. Arbid, Marwan Abd Elbaset Mohamed

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Liver fibrosis is a serious global health problem that occurs as a result of a variety of chronic liver disorders. Apigenin, a flavonoid found in many plants, has several pharmacological properties. The aim of this study was to evaluate the antifibrotic efficacy of apigenin (APG) against experimentally induced hepatic fibrosis in rats via using thioacetamide (TAA) and to explore the possible underlying mechanisms. TAA (100 mg/kg, i.p.) was given three times each week for two weeks to induce liver fibrosis. After TAA injections, APG was given orally (5 and 10 mg/kg) daily for two weeks. Biochemical, molecular, histological and immunohistochemical analyses were performed on blood and liver tissue samples. The functioning of the liver, oxidative stress, inflammation, and liver fibrosis indicators were all evaluated. The findings showed that TAA markedly increased the activities of aspartate aminotransferase (AST) and alanine aminotransferase (ALT), as well as the levels of malondialdehyde (MDA), focal adhesion kinase (FAK), hypoxia-inducible factor-1 (HIF-1), nuclear factor-κB (NF-κB), transforming growth factor-beta (TGF-β), tumor necrosis factor-alpha (TNF-α) and interleukin-1β (IL-1β) with a reduction in albumin, total protein, A/G ratio, GSH content and interleukin-10 (IL-10). Moreover, TAA elevated the content of collagen I, α -smooth muscle actin (α-SMA), and hydroxyproline in the liver. The treatment with APG in a dose-dependent manner has obviously prevented these alterations and amended the harmful effects induced by TAA. The histopathological and immunohistochemical observations supported this biochemical evidence. The higher dose of APG produced the most significant antifibrotic effect. As a result of these data, APG appears to be a promising antifibrotic drug and could be used as a new herbal medication or dietary supplement in the future for the treatment of liver fibrosis. This effect might be related to the inhibition of the HIF-1/FAK signaling pathway.

Keywords: apigenin, FAK, HIF-1, liver fibrosis, rat, thioacetamide

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Authors: Benjaporn Buranrat, Nootchanat Mairuae

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Cratoxylum formosum (Jack) Dyer (CF) has been used for the traditional medicines in South East Asian and Thailand. Normally, northeast Thai vegetables have proven cytotoxic to many cancer cells. Therefore, the present study aims to explore the molecular mechanisms underlying CF-induced cancer cell death and apoptosis on breast and liver cancer cells. The cytotoxicity and antiproliferative effects of CF on the human breast MCF-7 and liver HepG2 cancer cell lines were evaluated using sulforhodamine B assay and colony formation assay. Cell migration assay was measured using wound healing assay. The apoptosis induction mechanisms were investigated through reactive oxygen species formation, caspase 3 activity, and JC-1 activity. Gene expression by real-time PCR and apoptosis related protein levels by Western blot analysis. CF induced MCF-7 and HepG2 cell death by time- and dose-dependent manner. Furthermore, CF had the greater cytotoxic potency on MCF-7 more than HepG2 cells with IC50 values of 85.70+4.52 μM and 219.03±9.96 μM respectively, at 24 h. Treatment with CF also caused a dose-dependent decrease in colony forming ability and cell migration, especially on MCF-7 cells. CF induced ROS formation, increased caspase 3 activities, and decreased the mitochondrial membrane potential, and causing apoptotic body production and DNA fragmentation. CF significantly decreased expression of the cell cycle regulatory protein RAC1 and downstream proteins, cdk6. Additionally, CF enhanced p21 and reduced cyclin D1 protein levels. CF leaf extract induced cell death, apoptosis, antimigration in both of MCF-7 and HepG2 cells. CF could be useful for developing to anticancer drug candidate for breast and liver cancer therapy.

Keywords: cratoxylum formosum (jack) dyer, breast cancer, liver cancer, cell death

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Authors: Azar Sharafianpor, Hossein Rassi, Fahimeh Nemati Mansur

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Cardiovascular diseases (CVD) are the most important cause of death in industrialized and developing countries such as Iran. The most important risk factors for the CVD, genetic factors and chronic infectious agents, such as Helicobacter pylori, can be mentioned. The TNFα gene is one of the most important anti-inflammatory cytokines that can affect the sensitivity, efficacy, and ability of the immune response to chronic infections. Some TNF-α gene polymorphisms, including the replacement of the G nucleotide G with A at position 308 in the promoter region of TNF-α, increase the transcription of cytokines in the target cells and thus predispose a person to chronic infections. This study examines the TNF-α 308 polymorphism and its association with Helicobacter pylori infection in this disease. This study was a case-control study in which 154 patients were examined as cases or patients with symptoms of myocardial infarction or angina and 160 as controls or healthy subjects. All of the subjects at different ages were given venous blood and age, BMI, cholesterol, LDL, and HDL were determined. DNA was extracted from the specimens, and the cagA gene from H. pylori and the TNF-α-308 polymorphism were determined by PCR in patients and healthy subjects. Statistical analysis was performed with Epi Info software. The results showed that the frequency of H. pylori infection in the patients and healthy group were 53.23% (82 out of 154) and 47.5% (76 out of 160). There was no significant difference in H. pylori outbreak between the two groups. The frequencies of TNF-α-308 genotype for GG, GA, and AA in patients were 0.17, 0.49, and 0.34, respectively, whereas for controls 0.47, 0.35, and 0.18 for GG, GA, and AA, respectively. The frequency of genotype analysis of TNF-α-308 polymorphisms in both patients and healthy groups showed that there was a significant difference in the frequency of genotypes and the AA genotype was higher in the affected individuals. Also, there was a significant relationship between the genotype and the contamination with H. pylori and changes in cholesterol, LDL, and HDL levels were observed. The results of the study indicate that H. pylori detection in individuals with AA genotype in people under 50 years of age can play an important role in early diagnosis and treatment of cardiovascular disease.

Keywords: Helicobacter pylori, TNFα gene, cardiovascular diseases, TNFα-308 polymorphism

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Authors: El Montassir Dahmane, Nadia Eladlani, Aziz Ouahrouch, Mohammed Rhazi, Moha Taourirte

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The present study was aimed to approximate the optimal conditions to chromium recovery from wastewater by nanoparticles and whiskers of chitosan. Chitosan with an average molecular weight of 63 kDa and a 96% deacetylation degree was prepared according to our previous study. Chromium recovery is influenced by different parameters. In our search, we determined the appropriate range of pH to form chitosan–Cr(III), nanoparticles Cr(III), and whiskers– Cr(III) complex. We studied also the influence of chromium concentration and the nature of chitosan-based materials on the complexation process. Our main aim is to approximate the optimal conditions to remove chromium(III) from the tanning bath, recuperated from tannery wastewater of Marrakech in Morocco. A Perkin Elmer optima 2000 Inductively Coupled Plasma- Optical Emission Spectrometer (ICP-OES), was used to determine the quantity of chromium persistent in tannery wastewater after complexation phenomenon. To the best of our knowledge, this is the first report interested in the optimal conditions for chromium recovery from wastewater by nanoparticles and whiskers of chitosan. From our research, we found that in chromium solution, the appropriate range of pH to form complex is between 5.6 and 6.7. Also, the complexation of Cr(III) is depending on the nature of complexing ligand and chromium concentration. The obtained results reveal that nanoparticles present an excellent adsorption capacity regardless of chromium concentration. In addition, after a critical chromium concentration (250 mg/l), our ligand becomes saturated, that requires an increase of ligand mass for increasing chromium concentration in order to have a better adsorption capacity. Hence, in the same conditions, we used chitosan, its nanoparticles, whiskers, and chitosan based films to remove Cr(III) from tannery wastewater. The pH of this effluent was around 6, and its chromium concentration was 300 mg/l. The results expose that the sequence of complexing ligand in the effluent is the same in chromium solution, determined via our previous study. However, the adsorbed quantity is less due to the presence of other metallic ions in tannery wastewater. We conclude that the best complexing ligand-based chitosan is chitosan nanoaprticles whether it’s in chromium solution or in tannery wastewater. Nanoparticles are the best complexing ligand after 24 h of contact nanoparticles can remove 70% of chromium from this tannery wastewater.

Keywords: nanoparticles, whiskers, chitosan, chromium

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Authors: W. Stawiński, A. Wegrzyn, O. M. Freitas, S. A. Figueiredo

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Water is a life supporting resource, crucial for humanity and essential for natural ecosystems, which have been endangered by developing industry and increasing human population. Dyes are common in effluents discharged by various industries such as paper, plastics, food, cosmetics, and textile. They produce toxic effects on animals and disturb natural biological processes in receiving waters. Having complex molecular structure and resistance to biological decomposition they are problematic and difficult to be treated by conventional methods. In the search of efficient and sustainable method, sorption has been getting more interest in application to wastewaters treatment. Clays are minerals that have a layer structure based on phyllosilicate sheets that may carry a charge, which is balanced by ions located between the sheets. These charge-balancing ions can be exchanged resulting in very good ion-exchange properties of the material. Modifications of clays enhance their properties, producing a good and inexpensive sorbent for the removal of pollutants from wastewaters. The presented work proves that the treatment of a clay, vermiculite, with nitric acid followed by washing in citric acid strongly increases the sorption of two cationic dyes, methylene blue (C.I. 52015) and astrazon red (C.I. 110825). Desorption studies showed that the best eluent for regeneration is a solution of NaCl in ethanol. Cycles of sorption and desorption in column system showed no significant deterioration of sorption capacity and proved that the material shows a very good performance as sorbent, which can be recycled and reused. The results obtained open new possibilities of further modifications on vermiculite and modifications of other materials in order to get very efficient sorbents useful for wastewater treatment.

Keywords: cationic dyestuffs, sorption and regeneration, vermiculite, wastewater treatment

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Authors: Sina Moradi, Sanly Liu, Christopher W. K. Chow, John Van Leeuwen, David Cook, Mary Drikas, Soha Habibi, Rose Amal

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In recent years, chloramine has been widely used for both primary and secondary disinfection. However, a major concern with the use of chloramine as a secondary disinfectant is the decay of chloramine and nitrification occurrence. The management of chloramine decay and the prevention of nitrification are critical for water utilities managing chloraminated drinking water distribution systems. The detection and monitoring of nitrification episodes is usually carried out through measuring certain water quality parameters, which are commonly referred to as indicators of nitrification. The approach taken in this study was to collect water samples from different sites throughout a drinking water distribution systems, Tailem Bend – Keith (TBK) in South Australia, and analyse the samples by high performance size exclusion chromatography (HPSEC). We investigated potential association between the water qualities from HPSEC analysis with chloramine decay and/or nitrification occurrence. MATLAB 8.4 was used for data processing of HPSEC data and chloramine decay. An increase in the absorbance signal of HPSEC profiles at λ=230 nm between apparent molecular weights of 200 to 1000 Da was observed at sampling sites that experienced rapid chloramine decay and nitrification while its absorbance signal of HPSEC profiles at λ=254 nm decreased. An increase in absorbance at λ=230 nm and AMW < 500 Da was detected for Raukkan CT (R.C.T), a location that experienced nitrification and had significantly lower chloramine residual (<0.1 mg/L). This increase in absorbance was not detected in other sites that did not experience nitrification. Moreover, the UV absorbance at 254 nm of the HPSEC spectra was lower at R.C.T. than other sites. In this study, a chloramine residual index (C.R.I) was introduced as a new indicator of chloramine decay and nitrification occurrence, and is defined based on the ratio of area underneath the HPSEC spectra at two different wavelengths of 230 and 254 nm. The C.R.I index is able to indicate DS sites that experienced nitrification and rapid chloramine loss. This index could be useful for water treatment and distribution system managers to know if nitrification is occurring at a specific location in water distribution systems.

Keywords: nitrification, HPSEC, chloramine decay, chloramine residual index

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Authors: Uzaira Rafique, Kousar Parveen

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The discharge volume and composition of Textile effluents gains scientific concern due to its hazards and biotoxcity of azo dyes. Azo dyes are non-biodegradable due to its complex molecular structure and recalcitrant nature. Serious attempts have been made to synthesize and develop new materials to combat the environmental problems. The present study is designed for removal of a range of azo dyes (Methyl orange, Congo red and Basic fuchsine) from synthetic aqueous solutions and real textile effluents. For this purpose, Metal (cobalt) doped alumina hybrids are synthesized and applied as adsorbents in the batch experiment. Two different aluminium precursor (aluminium nitrate and spent aluminium foil) and glucose are mixed following sol gel method to get hybrids. The synthesized materials are characterized for surface and bulk properties using FTIR, SEM-EDX and XRD techniques. The characterization of materials under FTIR revealed that –OH (3487-3504 cm-1), C-H (2935-2985 cm-1), Al-O (~ 800 cm-1), Al-O-C (~1380 cm-1), Al-O-Al (659-669 cm-1) groups participates in the binding of dyes onto the surface of hybrids. Amorphous shaped particles and elemental composition of carbon (23%-44%), aluminium (29%-395%), and oxygen (11%-20%) is demonstrated in SEM-EDX micrograph. Time-dependent batch-experiments under identical experimental parameters showed 74% congo red, 68% methyl orange and 85% maximum removal of basic fuchsine onto the surface of cobalt doped alumina hybrids probably through the ion-exchange mechanism. The experimental data when treated with adsorption models is found to have good agreement with pseudo second order kinetic and freundlich isotherm for adsorption process. The present study concludes the successful synthesis of novel and efficient cobalt doped alumina hybrids providing environmental friendly and economical alternative to the commercial adsorbents for the treatment of industrial effluents.

Keywords: alumina hybrid, adsorption, dopant, isotherm, kinetic

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Authors: Wasim Sajjad, Manzoor Ahmad, Sundas Qadir, Muhammad Rafiq, Fariha Hasan, Richard Tehan, Kerry L. McPhail, Aamer Ali Shah

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Aim: This study aims to investigate the possible radiation protective role of a compatible solute in the tolerance of radio-halophilic bacterium against stresses, like desiccation and exposure to ionizing radiation. Methods and Results: Nine different radio-resistant bacteria were isolated from desert soil, where strain WMA-LM19 was chosen for detailed studies on the basis of its high tolerance for ultraviolet radiation among all these isolates. 16S rRNA gene sequencing indicated that the bacterium was closely related to Stenotrophomonas sp. (KT008383). A bacterial milking strategy was applied for extraction of intracellular compatible solutes in 70% (v/v) ethanol, which were purified by high-performance liquid chromatography (HPLC). The compound was characterized as ectoine by 1H and 13C nuclear magnetic resonance (NMR), and mass spectrometry (MS). Ectoine demonstrated more efficient preventive activity (54.80%) to erythrocyte membranes and also inhibited oxidative damage to proteins and lipids in comparison to the standard ascorbic acid. Furthermore, a high level of ectoine-mediated protection of bovine serum albumin against ionizing radiation (1500-2000 Jm-2) was observed, as indicated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis. Conclusion: The results indicated that ectoine can be used as a potential mitigator and radio-protective agent to overcome radiation- and salinity-mediated oxidative damage in extreme environments. Significance and Impact of the Study: This study shows that ectoine from radio-halophiles can be used as a potential source in topical creams as sunscreen. The investigation of ectoine as UV protectant also changes the prospective that radiation resistance is specific only to molecular adaptation.

Keywords: ectoine, anti-oxidant, stenotrophomonas sp., ultraviolet radiation

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Authors: Walid Tawfik

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The interaction of intense short nano- and picosecond laser pulses with plasma leads to reach variety of important applications, including time-resolved laser induced breakdown spectroscopy (LIBS), soft x-ray lasers, and laser-driven accelerators. The progress in generating of femtosecond down to sub-10 fs optical pulses has opened a door for scientists with an essential tool in many ultrafast phenomena, such as femto-chemistry, high field physics, and high harmonic generation (HHG). The advent of high-energy laser pulses with durations of few optical cycles provided scientists with very high electric fields, and produce coherent intense UV to NIR radiation with high energy which allows for the investigation of ultrafast molecular dynamics with femtosecond resolution. In this work, we could experimentally achieve the generation of a two-octave-wide supercontinuum ultrafast pulses extending from ultraviolet at 3.5 eV to the near-infrared at 1.3 eV in neon-filled capillary fiber. These pulses are created due to nonlinear self-phase modulation (SPM) in neon as a nonlinear medium. The measurements of the generated pulses were performed using spectral phase interferometry for direct electric-field reconstruction. A full characterization of the output pulses was studied. The output pulse characterization includes the pulse width, the beam profile, and the spectral bandwidth. Under optimization conditions, the reconstructed pulse intensity autocorrelation function was exposed for the shorts possible pulse duration to achieve transform-limited pulses with energies up to 600µJ. Furthermore, the effect of variation of neon pressure on the pulse-width was studied. The nonlinear SPM found to be increased with the neon pressure. The obtained results may give an opportunity to monitor and control ultrafast transit interaction in femtosecond chemistry.

Keywords: femtosecond laser, ultrafast, supercontinuum, ultra-broadband

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Authors: Ahmad Rasyadan Arshad, A. Rahman A. Jamal, N. Mohamed Ibrahim, Nor Azian Abdul Murad

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Introduction: Parkinson’s disease (PD) is a complex and asymptomatic disease where patients are usually diagnosed at late stage where about 70% of the dopaminergic neurons are lost. Therefore, identification of molecular biomarkers is crucial for early diagnosis of PD. MicroRNA (miRNA) is a short nucleotide non-coding small RNA which regulates the gene expression in post-translational process. The involvement of these miRNAs in neurodegenerative diseases includes maintenance of neuronal development, necrosis, mitochondrial dysfunction and oxidative stress. Thus, miRNA could be a potential biomarkers for diagnosis of PD. Objective: This study aim to identify the miRNA involved in Late Onset PD (LOPD) and Early Onset PD (EOPD) compared to the controls. Methods: This is a case-control study involved PD patients in the Chancellor Tunku Muhriz Hospital at the UKM Medical Centre. miRNA samples were extracted using miRNeasy serum/plasma kit from Qiagen. The quality of miRNA extracted was determined using Agilent RNA 6000 Nano kit in the Bioanalyzer. miRNA expression was performed using GeneChip miRNA 4.0 chip from Affymetrix. Microarray was performed in EOPD (n= 7), LOPD (n=9) and healthy control (n=11). Expression Console and Transcriptomic Analyses Console were used to analyze the microarray data. Result: miR-129-5p was significantly downregulated in EOPD compared to LOPD with -4.2 fold change (p = <0.050. miR-301a-3p was upregulated in EOPD compared to healthy control (fold = 10.3, p = <0.05). In LOPD versus healthy control, miR-486-3p (fold = 15.28, p = <0.05), miR-29c-3p (fold = 12.21, p = <0.05) and miR-301a-3p (fold = 10.01, p =< 0.05) were upregulated. Conclusion: Several miRNA have been identified to be differentially expressed in EOPD compared to LOPD and PD versus control. These miRNAs could serve as the potential biomarkers for early diagnosis of PD. However, these miRNAs need to be validated in a larger sample size.

Keywords: early onset PD, late onset PD, microRNA (miRNA), microarray

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Authors: Maryam Beiranvand, Sajad Yaghoubi

Abstract:

Background: Some microbes can colonize plants’ inner tissues without causing obvious damage and can even produce useful bioactive substances. In the present study, the diversity of the endophytic bacteria associated with medicinal plants from Iran was investigated by culturing techniques, molecular gene identification, as well as measuring them for antibacterial activity. Results: In the spring season from 2013 to 2014, 35 herb pharmacology samples were collected, sterilized, meshed, and then cultured on selective media culture. A total of 199 endophytic bacteria were successfully isolated from 35 tissue cultures of medical plants, and sixty-seven out of 199 bacterial isolates were subjected to identification by the 16S rRNA gene sequence analysis method. Based on the sequence similarity gene and phylogenetic analyses, these isolates were grouped into five classes, fourteen orders, seventeen families, twenty-one genera, and forty strains. The most abundant group of endophytic bacteria was actinobacterial, consisting of thirty-two (47%) out of 67 bacterial isolates. Ten (22.3%) out of 67 bacterial isolates remained unidentified and classified at the genus level. The signature of the 16S rRNA gene formed a distinct line in a phylogenetic tree showing that they might be new species of bacteria. One (5.2%) out of 67 bacterial isolates was still not well categorized. Forty-two out of 67 strains were candidates for antimicrobial activity tests. Nineteen (45%) out of 42 strains showed antimicrobial activity multidrug resistance (MDR); thirteen (68%) out of 19 strains were allocated to classes actinobacteria. Four (21%) out of 19 strains belonged to the Bacillaceae family, one (5.2%) out of 19 strains was the Paenibacillaceae family, and one (5.2%) out of 19 strains belonged to the Pseudomonadaceae family. The other twenty-three strains did not show inhibitory activities. Conclusions: Our research showed a high-level phylogenetic diversity and the intoxicating antibiotic activity of endophytic bacteria in the herb pharmacology of Iran.

Keywords: Antibacterial activity, endophytic bacteria, multidrug-resistant bacteria, whole genom sequencing

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Authors: ZhenlinJu, Christopher P. Vellano, RehanAkbani, Yiling Lu, Gordon B. Mills

Abstract:

The epithelial–mesenchymal transition (EMT) is a process by which epithelial cells acquire mesenchymal characteristics, such as profound disruption of cell-cell junctions, loss of apical-basolateral polarity, and extensive reorganization of the actin cytoskeleton to induce cell motility and invasion. A hallmark of EMT is its capacity to promote metastasis, which is due in part to activation of several transcription factors and subsequent downregulation of E-cadherin. Unfortunately, current approaches have yet to uncover robust protein marker sets that can classify tumors as possessing strong EMT signatures. In this study, we utilize reverse phase protein array (RPPA) data and consensus clustering methods to successfully classify a subset of cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) tumors into an EMT protein signaling group (EMT group). The overall survival (OS) of patients in the EMT group is significantly worse than those in the other Hormone and PI3K/AKT signaling groups. In addition to a shrinkage and selection method for linear regression (LASSO), we applied training/test set and Monte Carlo resampling approaches to identify a set of protein markers that predicts the EMT status of CESC tumors. We fit a logistic model to these protein markers and developed a classifier, which was fixed in the training set and validated in the testing set. The classifier robustly predicted the EMT status of the testing set with an area under the curve (AUC) of 0.975 by Receiver Operating Characteristic (ROC) analysis. This method not only identifies a core set of proteins underlying an EMT signature in cervical cancer patients, but also provides a tool to examine protein predictors that drive molecular subtypes in other diseases.

Keywords: consensus clustering, TCGA CESC, Silhouette, Monte Carlo LASSO

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Authors: Salma H. Abu Hafsa, A. Mendonca, B. Brehm-Stecher, A. A. Hassan, S. A. Ibrahim

Abstract:

Enterococci are important inhabitants of the animal intestine and are widely used in probiotic products. A probiotic strain is expected to possess several desirable properties in order to exert beneficial effects. Therefore, the objective of this study was to isolate and characterize strains of Enterococcus sp. from chicken cecal and fecal samples to determine potential probiotic properties. Enterococci were isolated from thirty one chicken cecal and fecal samples collected from a local farm. In vitro studies were performed to assess antibacterial activity (using agar well diffusion and cell free supernatant broth technique against Salmonella enterica serotype Enteritidis), susceptibility to antibiotics (amoxycillin, cotrimoxazole, chloramphenicol, cefuroxime, ceftriaxone, ciprofloxacin, and nalidixic acid), survival in acidic conditions, resistance to bile salts, and their survival during simulated gastric juice conditions at pH 2.5. Isolates were identified using biochemical and molecular assays (API 50 CHL, and API ZYM kits followed by 16S rDNA gene sequence analysis). Two strains were identified, of which, Enteroccocus faecium was capable of inhibiting the growth of S. enteritidis and was susceptible to a wide range of antibiotics. In addition, the isolated strain exhibited significant resistance under highly acidic conditions (pH=2.5) for 8 hours and survived well in bile salt at 0.2% for 24 hours and showing ability to survive in the presence of simulated gastric juice at pH 2.5. Based on these results, the E. faecium isolate fulfills some of the criteria to be considered as a probiotic strain and therefore, could be used as a feed additive with good potential for controlling S. enteritidis in chickens. However, in vivo studies are needed to determine the safety of the strain.

Keywords: acid tolerance, antimicrobial activity, Enterococcus faecium, probiotic

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Authors: Neha Bhadauria, Indu Gaur, Shilpi Shilpi, Susmita Goswami, Prabir K. Paul

Abstract:

The aerial surface of plants colonized by Human Enteric Pathogens ()has been implicated in outbreaks of enteric diseases in humans. Practice of organic farming primarily using animal dung as manure and sewage water for irrigation are the most significant source of enteric pathogens on the surface of leaves, fruits and vegetables. The present work aims to have an insight into the molecular mechanism of interaction of Human Enteric Pathogens or their metabolites with cell wall receptors in plants. Tomato plants grown under aseptic conditions at 12 hours L/D photoperiod, 25±1°C and 75% RH were inoculated individually with S. fonticola and K. pneumonia. The leaves from treated plants were sampled after 24 and 48 hours of incubation. The cell wall and cytoplasmic proteins were extracted and isocratically separated on 1D SDS-PAGE. The sampled leaves were also subjected to formaldehyde treatment prior to isolation of cytoplasmic proteins to study protein-protein interactions induced by Human Enteric Pathogens. Protein bands extracted from the gel were subjected to MALDI-TOF-TOF MS analysis. The foremost interaction of Human Enteric Pathogens on the plant surface was found to be cell wall bound receptors which possibly set ups a wave a critical protein-protein interaction in cytoplasm. The study revealed the expression and suppression of specific cytoplasmic and cell wall-bound proteins, some of them being important components of signaling pathways. The results also demonstrated HEP induced rearrangement of signaling pathways which possibly are crucial for adaptation of these pathogens to plant surface. At the end of the study, it can be concluded that controlling the over-expression or suppression of these specific proteins rearrange the signaling pathway thus reduces the outbreaks of food-borne illness.

Keywords: cytoplasmic protein, cell wall-bound protein, Human Enteric Pathogen (HEP), protein-protein interaction

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Authors: Yuxi Liu, Boris Belousov, Mehrzad Esmaeili Charkhab, Oliver Tessmann

Abstract:

This paper presents a computational solution for designing reconfigurable interlocking structures that are fully assembled with SL Blocks. Formed by S-shaped and L-shaped tetracubes, SL Block is a specific type of interlocking puzzle. Analogous to molecular self-assembly, the aggregation of SL blocks will build a reversible hierarchical and discrete system where a single module can be numerously replicated to compose semi-interlocking components that further align, wrap, and braid around each other to form complex high-order aggregations. These aggregations can be disassembled and reassembled, responding dynamically to design inputs and changes with a unique capacity for reconfiguration. To use these aggregations as architectural structures, we developed computational tools that automate the configuration of SL blocks based on architectural design objectives. There are three critical phases in our work. First, we revisit the hierarchy of the SL block system and devise a top-down-type design strategy. From this, we propose two key questions: 1) How to translate 3D polyominoes into SL block assembly? 2) How to decompose the desired voxelized shapes into a set of 3D polyominoes with interlocking joints? These two questions can be considered the Hamiltonian path problem and the 3D polyomino tiling problem. Then, we derive our solution to each of them based on two methods. The first method is to construct the optimal closed path from an undirected graph built from the voxelized shape and translate the node sequence of the resulting path into the assembly sequence of SL blocks. The second approach describes interlocking relationships of 3D polyominoes as a joint connection graph. Lastly, we formulate the desired shapes and leverage our methods to achieve their reconfiguration within different levels. We show that our computational strategy will facilitate the efficient design of hierarchical interlocking structures with a self-replicating geometric module.

Keywords: computational design, SL-blocks, 3D polyomino puzzle, combinatorial problem

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Authors: Maryam Beiranvand, Sajad Yaghoubi

Abstract:

Background: Some microbes can colonize plants’ inner tissues without causing obvious damage and can even produce useful bioactive substances. In the present study, the diversity of the endophytic bacteria associated with medicinal plants from Iran was investigated by culturing techniques, molecular gene identification, as well as measuring them for antibacterial activity. Results: In the spring season from 2013 to 2014, 35 herb pharmacology samples were collected, sterilized, meshed, and then cultured on selective media culture. A total of 199 endophytic bacteria were successfully isolated from 35 tissue cultures of medical plants, and sixty-seven out of 199 bacterial isolates were subjected to identification by the 16S rRNA gene sequence analysis method. Based on the sequence similarity gene and phylogenetic analyses, these isolates were grouped into five classes, fourteen orders, seventeen families, twenty-one genera, and forty strains. The most abundant group of endophytic bacteria was actinobacterial, consisting of thirty-two (47%) out of 67 bacterial isolates. Ten (22.3%) out of 67 bacterial isolates remained unidentified and classified at the genus level. The signature of the 16S rRNA gene formed a distinct line in a phylogenetic tree showing that they might be new species of bacteria. One (5.2%) out of 67 bacterial isolates was still not well categorized. Forty-two out of 67 strains were candidates for antimicrobial activity tests. Nineteen (45%) out of 42 strains showed antimicrobial activity multidrug-resistance (MDR); thirteen (68%) out of 19 strains were allocated to classes actinobacteria. Four (21%) out of 19 strains belonged to the Bacillaceae family, one (5.2%) out of 19 strains was the Paenibacillaceae family, and one (5.2%) out of 19 strains belonged to the Pseudomonadaceae family. The other twenty-three strains did not show inhibitory activities. Conclusions: Our research showed a high-level phylogenetic diversity and the intoxicating antibiotic activity of endophytic bacteria in the herb pharmacology of Iran.

Keywords: medical plant, endophytic bacteria, antimicrobial activity, whole genome sequencing analysis

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Authors: Yahia Massinissa, Yahia Mouloud

Abstract:

Cystic fibrosis (CF), the most common lethal genetic disease in the Europe population, is caused by mutations in the transmembrane conductance regulator gene (CFTR). It affects most organs including an epithelial tissue, base of hydroelectrolytic transepithelial transport, notably that aerial ways, the pancreas, the biliary ways, the intestine, sweat glands and the genital tractus. The gene whose anomalies are responsible of the cystic fibrosis codes for a protein Cl channel named CFTR (cystic fibrosis transmembrane conductance regulator) that exercises multiple functions in the cell, one of the most important in control of sodium and chlorine through epithelia. The deficient function translates itself notably by an abnormal production of viscous secretion that obstructs the execrator channels of this target organ: one observes then a dilatation, an inflammation and an atrophy of these organs. It also translates itself by an increase of the concentration in sodium and in chloride in sweat, to the basis of the sweat test. In order to do a phenotypical and genotypical diagnosis at a part of the Algerian population, our survey has been carried on 16 patients with evocative symptoms of the cystic fibrosis at that the clinical context has been confirmed by a sweat test. However, anomalies of the CFTR gene have been determined by electrophoresis in gel of polyacrylamide of the PCR products (polymerase chain reaction), after enzymatic digestion, then visualized to the ultraviolet (UV) after action of the ethidium bromide. All mutations detected at the time of our survey have already been identified at patients attained by this pathology in other populations of the world. However, the important number of found mutation with regard to the one of the studied patients testifies that the origin of this big clinical variability that characterizes the illness in the consequences of an enormous diversity of molecular defects of the CFTR gene.

Keywords: cystic fibrosis, CFTR gene, polymorphism, algerian population, sweat test, genotypical diagnosis

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Authors: Maryam Monazzah, Ronak Samadpour, Mehdi Nasr-esfahani, Fatemeh Qalavand, Marziye Motamedi

Abstract:

Bipolaris sorokiniana, and Heterodera filipjevi, are important wheat diseases that lead to yield losses worldwide. Identifying novel resistant sources helps us combat these devastating diseases. In this study, we studied the role of Cre3 gene and antioxidant enzymes in the immune responses of wheat genotypes to H. filipjevi and B. sorokiniana. Therefore, real-time PCR analysis using Cre3 gene marker, a resistant gene to cereal cyst nematodes, was conducted on leaves and roots, along with changes ‎in the activity of antioxidant enzymes, peroxidase, and catalase. Enzyme activity assay was performed on roots attacked by nematode and in leaves infected with Bipolaris. Wheat accessions including “Bam” (resistant), “Parsi” (moderately-resistant), “Azar2”, “Ohadi”, “Homa” (highly-susceptible) were previously screened against both stresses under greenhouse and field conditions. Results showed that Cre3 expression against cyst nematodes was significantly higher in resistant cultivars compared to susceptible cultivars. Cre3 was used in marker-assisted selection programs to identify genotypes carrying resistant genes to cyst nematodes. Interestingly, Cre3 was also up-regulated in both tissues of resistant cultivars to B. sorokiniana. Therefore, Cre3 in wheat similarly modulates immunity against B. sorokiniana and might be one of the central components of the induced immune system in wheat. The activity of antioxidant enzymes also indicated the highest increase in resistant genotypes upon both stresses that subsequently neutralize oxidative stress in tissues and decrease damage. Further studies on these resistance components may help us gain insight into the molecular basis of resistance and shed new light on the interaction and overlap between different forms of stress.

Keywords: Bipolaris sorokiniana, Heterodera filipjevi, resistant gene expression, wheat

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Authors: Sharique Ahmed, Khushtar Anwar Salman

Abstract:

Alpha-1-antitrypsin (AAT) is a major plasma serine protease inhibitor (SERPIN). Hereditary AAT deficiency is one of the common diseases in some part of the world. AAT is mainly produced in the liver and functions to protect the lung against proteolytic damage (e.g., from neutrophil elastase) acting as the major inhibitor for neutrophil elastase. α (1)-Antitrypsin (AAT) deficiency is an under recognized genetic condition that affects approximately 1 in 2,000 to 1 in 5,000 individuals and predisposes to liver disease and early-onset emphysema. Not only does α-1-antitrypsin deficiency lead to disabling syndrome of pulmonary emphysema, there are other disorders too which include ANCA (antineutrophilic cytoplasmic antibody) positive Wegener's granulomatosis, diffuse bronchiectasis, necrotizing panniculitis in α-1-antitrypsin phenotype (S), idiopathic pulmonary fibrosis and steroid dependent asthma. Augmentation therapy with alpha-1 antitrypsin (AAT) from human plasma has been available for specific treatment of emphysema due to AAT deficiency. Apart from this several observations have also suggested a role for endogenous suppressors of HIV-1, alpha-1 antitrypsin (AAT) has been identified to be one of those. In view of its varied important role in humans, serum from a mammalian source was chosen for the isolation and purification. Studies were performed on the homogeneous fraction. This study suggests that the buffalo serum α-1-antritrypsin has characteristics close to ovine, dog, horse and more importantly to human α-1-antritrypsin in terms of its hydrodynamic properties such as molecular weight, carbohydrate content, etc. The similarities in the hydrodynamic properties of buffalo serum α-1-antitrypsin with other sources of mammalian α-1-antitrypsin mean that it can be further studied and be a potential source for "augmentation therapy", as well as a source of AAT replacement therapy to raise serum levels above the protective threshold. Other parameters like the amino acid sequence, the effect of denaturants, and the thermolability or thermostability of the inhibitor will be the interesting basis of future studies on buffalo serum alpha-1 antitrypsin (AAT).

Keywords: α-1-antitrypsin, augmentation therapy , hydrodynamic properties, serine protease inhibitor

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Authors: Arun Kharate, Sarata Kumar Sahu, Susen Kumar Panda, Niranjan Sahoo, H. K. Panda

Abstract:

In the present study, an attempt has been made for isolation and identification of feline panleukopaenia virus (FPLV) from wild felids of Nandankanan zoo, Odisha, India, along with prevalence study of FPLV. Fecal samples collected from wild felids (26 tigers, 22 lions, 5 leopards, 3 hyenas, 1 jaguar, 2 foxes and 1 wild cat) were subjected to hemagglutinnation test and fluorescent antibody test. In hemagglutinnation test 13 (50%) samples from tiger, 14 (63.63%) samples from lions, 1 (20%) sample from leopards, 1 (50%) from fox, 3 (100%) samples from hyenas and 1 (100%) sample from wild cat were positive. On fluorescent antibody test (FAT), 15 (57.69%) samples from tiger, 18 (81.81%) from lions, 2 (40%) from leopards, 1 (50%) from fox, 3 (100%) from hyenas and 1 (100%) from wild cat were positive. FPLV was isolated using MDBK cell line and preliminary characterization was done on the basis of characteristic cytopathic effect. The virus samples were quantified through titration in MDBK cells. Serological confirmation of FPLV isolates was carried out by HI test, micro-SNT and indirect-ELISA. Physico-chemical characters like pH and temperature resistance along molecular identification using specific FPLV primers was carried out. Seroprevalence study of 36 serum samples employing HI test, micro SNT and indirect-ELISA revealed prevalence of 38.8, 44.4 and 72.2% respectively. During study period an adult tigress and a tiger cub died suspected of feline panleukopenia. The necropsy findings in both animals showed hemorrhagic gastroenteritis. The cytological examination revealed presence of intranuclear inclusion bodies in the intestinal epithelial cells. Spleen, mesenteric lymph node and intestine were positive for feline panleukopenia by FAT. The investigation revealed that feline panleukopenia was prevalent in wild felines of Nandankanan zoo.

Keywords: Feline panleukopenia, fluorescent antibody test, hemagglutination test, indirect-ELISA, Nandankanan zoo

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Authors: Manar Makhoul, Buthainah Alsalamah, Salam Lawand, Hassan Azzam

Abstract:

The major storage proteins in endosperm of 33 cultivated and wild barley genotypes (H.vulgare, H. spontaneum, H. bulbosum, H. murinum, H. marinum) were analyzed to demonstrate the variation in the hordein polypeptides encoded by multigene families in grains. The SDS-PAGE revealed 13 and 17 alleles at the Hor1 and the Hor2 loci respectively, with frequencies from 0.83 to 14 and 0.56 to 13.41% respectively, while seven alleles at the Hor3 locus with frequencies from 3.63 to 30.91% were recognized. The phylogenetic analysis indicated to relevance of the polymorphism in hordein patterns as successful tool in identifying the individual genotypes and discriminating the species according to genome type. We also reported in this research complete nucleotide sequence B-hordein genes of seven wild and cultivated barley genotypes. A 152bp upstream sequence of B-hordein promoter contained a TATA box, CATC box, AAAG motif, N-motif and E-motif. In silico analysis of B-Hordein sequences demonstrated that the coding regions were not interrupted by any intron, and included the complete ORF which varied between 882 and 906 bp, and encoded mature proteins with 293-301 residues characterized by high contents of glutamine (29%), and proline (18%). Comparison of the predicted polypeptide sequences with the published ones suggested that all S-rich prolamins genes are descended from common ancestor. The sequence started at N-terminal with a signal peptide, and then followed directly by two domains; a repetitive one based on the repetition of the repeat unit PQQPFPQQ and C-terminal domain. Also, it was found that positions of the eight cysteine residues were highly conserved in all the B-hordein sequences, but Hordeum bulbosum had additional unpaired one. The phylogenetic tree of B-hordein polypeptide separated the genotypes in distinct seven subgroups. In general, the high homology between B-hordeins and LMW glutenin subunits suggests similar bread-making influences for these B-hordeins.

Keywords: hordeum, phylogenetic tree, sequencing, storage protein

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Authors: Hediyeh Talebi, Shokoofeh Ghiam, Changiz Eslahchi

Abstract:

Traditionally, Alzheimer’s disease research has focused on genes with significant fold changes, potentially neglecting subtle but biologically important alterations. Our study introduces an integrative approach that highlights genes crucial to underlying biological processes, regardless of their fold change magnitude. Alzheimer's Single-cell RNA-seq data related to the peripheral blood mononuclear cells (PBMC) was extracted from the Gene Expression Omnibus (GEO). After quality control, normalization, scaling, batch effect correction, and clustering, differentially expressed genes (DEGs) were identified with adjusted p-values less than 0.05. These DEGs were categorized based on cell-type, resulting in four datasets, each corresponding to a distinct cell type. To distinguish between cells from healthy individuals and those with Alzheimer's, an adversarial autoencoder with a classifier was employed. This allowed for the separation of healthy and diseased samples. To identify the most influential genes in this classification, the weight matrices in the network, which includes the encoder and classifier components, were multiplied, and focused on the top 20 genes. The analysis revealed that while some of these genes exhibit a high fold change, others do not. These genes, which may be overlooked by previous methods due to their low fold change, were shown to be significant in our study. The findings highlight the critical role of genes with subtle alterations in diagnosing Alzheimer's disease, a facet frequently overlooked by conventional methods. These genes demonstrate remarkable discriminatory power, underscoring the need to integrate biological relevance with statistical measures in gene prioritization. This integrative approach enhances our understanding of the molecular mechanisms in Alzheimer’s disease and provides a promising direction for identifying potential therapeutic targets.

Keywords: alzheimer's disease, single-cell RNA-seq, neural networks, blood biomarkers

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Authors: Stephanie Boue, Nicolas Sierro, Julia Hoeng, Manuel C. Peitsch

Abstract:

Systems biology relies on large numbers of data points and sophisticated methods to extract biologically meaningful signal and mechanistic understanding. For example, analyses of transcriptomics and proteomics data enable to gain insights into the molecular differences in tissues exposed to diverse stimuli or test items. Whereas the interpretation of endpoints specifically measuring a mechanism is relatively straightforward, the interpretation of big data is more complex and would benefit from comparing results obtained with diverse analysis methods. The sbv IMPROVER project was created to implement solutions to verify systems biology data, methods, and conclusions. Computational challenges leveraging the wisdom of the crowd allow benchmarking methods for specific tasks, such as signature extraction and/or samples classification. Four challenges have already been successfully conducted and confirmed that the aggregation of predictions often leads to better results than individual predictions and that methods perform best in specific contexts. Whenever the scientific question of interest does not have a gold standard, but may greatly benefit from the scientific community to come together and discuss their approaches and results, datathons are set up. The inaugural sbv IMPROVER datathon was held in Singapore on 23-24 September 2016. It allowed bioinformaticians and data scientists to consolidate their ideas and work on the most promising methods as teams, after having initially reflected on the problem on their own. The outcome is a set of visualization and analysis methods that will be shared with the scientific community via the Garuda platform, an open connectivity platform that provides a framework to navigate through different applications, databases and services in biology and medicine. We will present the results we obtained when analyzing data with our network-based method, and introduce a datathon that will take place in Japan to encourage the analysis of the same datasets with other methods to allow for the consolidation of conclusions.

Keywords: big data interpretation, datathon, systems toxicology, verification

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