Search results for: evolutionary bioinformatics

Authors: Andreas Schomburg, Claire Le Bayon, Claire Guenat, Philip Brunner

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Numerous river restoration projects have been established in Switzerland in recent years after decades of human activity in floodplains. The success of restoration projects in terms of biodiversity and ecosystem functions largely depend on the development of the floodplain soil system. Plants and earthworms as ecosystem engineers are known to be able to build up a stable soil structure by incorporating soil organic matter into the soil matrix that creates water stable soil aggregates. Their engineering efficiency however largely depends on changing soil properties and frequent floods along an evolutive floodplain transect. This study, therefore, aims to quantify the effect of flood frequency and duration as well as of physico-chemical soil parameters on plants’ and earthworms’ engineering efficiency. It is furthermore predicted that these influences may have a different impact on one of the engineers that leads to a varying contribution to aggregate formation within the floodplain transect. Ecosystem engineers were sampled and described in three different floodplain habitats differentiated according to the evolutionary stages of the vegetation ranging from pioneer to forest vegetation in a floodplain restored 15 years ago. In addition, the same analyses were performed in an embanked adjacent pasture as a reference for the pre-restored state. Soil aggregates were collected and analyzed for their organic matter quantity and quality using Rock Eval pyrolysis. Water level and discharge measurements dating back until 2008 were used to quantify the return period of major floods. Our results show an increasing amount of water stable aggregates in soil with increasing distance to the river and show largest values in the reference site. A decreasing flood frequency and the proportion of silt and clay in the soil texture explain these findings according to F values from one way ANOVA of a fitted mixed effect model. Significantly larger amounts of labile organic matter signatures were found in soil aggregates in the forest habitat and in the reference site that indicates a larger contribution of plants to soil aggregation in these habitats compared to the pioneer vegetation zone. Earthworms’ contribution to soil aggregation does not show significant differences in the floodplain transect, but their effect could be identified even in the pioneer vegetation with its large proportion of coarse sand in the soil texture and frequent inundations. These findings indicate that ecosystem engineers seem to be able to create soil aggregates even under unfavorable soil conditions and under frequent floods. A restoration success can therefore be expected even in ecosystems with harsh soil properties and frequent external disturbances.

Keywords: ecosystem engineers, flood frequency, floodplains, river restoration, rock eval pyrolysis, soil organic matter incorporation, soil structuration

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Authors: Wayde Veldman, Ozlem T. Bishop, Igor Polikarpov

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In bacteria, mono and disaccharides are phosphorylated during uptake into the cell via the widely used phosphoenolpyruvate (PEP)-dependent phosphotransferase transport system. As an initial step in the phosphorylated disaccharide metabolism pathway, certain glycoside hydrolase family 1 (GH1) enzymes play a crucial role in releasing phosphorylated and non-phosphorylated monosaccharides. However, structural determinants for the specificity of these enzymes still need to be clarified. GH1 enzymes are known to have a wide array of functions. According to the CAZy database, there are twenty-one different enzymatic activities in the GH1 family. Here, the structure and substrate specificity of a GH1 enzyme from Bacillus licheniformis, hereafter known as BlBglH, was investigated. The sequence of the enzyme BlBglH was compared to the sequences of other characterized GH1 enzymes using sequence alignment, sequence identity calculations, phylogenetic analysis, and motif discovery. Through these various analyses, BlBglH was found to have sequence features characteristic of the 6-phospho-β-glucosidase activity enzymes. Additionally, motif and structure comparisons of the three most commonly studied GH1 enzyme-activities revealed a shared loop amongst the different structures that consist of different sequence motifs – this loop is thought to guide specific substrates (depending on activity) towards the active-site. To further affirm BlBglH enzyme activity, molecular docking and molecular dynamics simulations were performed. Docking was carried out using 6-phospho-β-glucosidase enzyme-activity positive (p-Nitrophenyl-beta-D-glucoside-6-phosphate) and negative (p-Nitrophenyl-beta-D-galactoside-6-phosphate) control ligands, followed by 400 ns molecular dynamics simulations. The positive-control ligand maintained favourable interactions within the active site until the end of the simulation. The negative-control ligand was observed exiting the enzyme at 287 ns. Binding free energy calculations showed that the positive-control complex had a substantially more favourable binding energy compared to the negative-control complex. Jointly, the findings of this study suggest that the BlBglH enzyme possesses 6-phospho-β-glucosidase enzymatic activity.

Keywords: 6-P-β-glucosidase, glycoside hydrolase 1, molecular dynamics, sequence analysis, substrate specificity

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Authors: Sundru Manjulata Devi, Prakash M. Halami

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The immemorial use of fermented foods from vegetables, dairy and other biological sources are of great demand in India because of their health benefits. However, the diversity of Lactobacillus plantarum group (LPG) of vegetable origin has not been revealed yet, particularly with reference to their probiotic functionalities. In the present study, the different species of probiotic Lactobacillus plantarum group (LPG) i.e., L. plantarum subsp. plantarum MTCC 5422 (from fermented cereals), L. plantarum subsp. argentoratensis FG16 (from fermented bamboo shoot) and L. paraplantarum MTCC 9483 (from fermented gundruk) (as characterized by multiplex recA PCR assay) were considered to investigate their relative expression of MUB domains of mub gene (mucin binding protein) by Real time PCR. Initially, the allelic variation in the mub gene was assessed and found to encode three different variants (Type I, II and III). All the three types had 8, 9 and 10 MUB domains respectively (as analysed by Pfam database) and were found to be responsible for adhesion of bacteria to the host intestinal epithelial cells. These domains either get inserted or deleted during speciation or evolutionary events and lead to divergence. The reverse transcriptase qPCR analysis with mubLPF1+R1 primer pair supported variation in amplicon sizes with 300, 500 and 700 bp among different LPG strains. The relative expression of these MUB domains significantly unregulated in the presence of 1% mucin in overnight grown cultures. Simultaneously, the mub gene expressed efficiently by 7 fold in the culture L. paraplantarum MTCC 9483 with 10 MUB domains. An increase in the expression levels for L. plantarum subsp. plantarum MTCC 5422 and L. plantarum subsp. argentoratensis FG16 (MCC 2974) with 9 and 8 repetitive domains was around 4 and 2 fold, respectively. The detection and expression of an integrase (int) gene in the upstream region of mub gene reveals the excision and integration of these repetitive domains. Concurrently, an in vitro adhesion assay to mucin and exclusion of pathogens (such as Listeria monocytogenes and Micrococcus leuteus) was investigated and observed that the L. paraplantarum MTCC 9483 with more adhesion domains has more ability to adhere to mucin and inhibited the growth of pathogens. The production and expression of plantaricin-like bacteriocin (plnNC8 type) in MTCC 9483 suggests the pathogen inhibition. Hence, the expression of MUB domains can act as potential biomarkers in the screening of a novel probiotic LPG strain with adherence property. The present study provides a platform for an easy, rapid, less time consuming, low-cost methodology for the detection of potential probiotic bacteria. It was known that the traditional practices followed in the preparation of fermented bamboo shoots/gundruk/cereals of Indian foods contain different kinds of neutraceuticals for functional food and novel compounds with health promoting factors. In future, a detailed study of these food products can add more nutritive value, consumption and suitable for commercialization.

Keywords: adhesion gene, fermented foods, MUB domains, probiotics

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Authors: Hannah Dean

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The growth ideology, and its association with progress, is an important construct in the narrative of modernity. This ideology is embedded in neoclassical economic growth theory which conceptualises growth as linear and predictable, and the entrepreneur as a rational economic manager. This conceptualisation has been critiqued for reinforcing the managerial discourse in entrepreneurship studies. Despite these critiques, both the neoclassical growth theory and its adjacent managerial discourse dominate entrepreneurship studies notably the literature on female entrepreneurs. The latter is the focus of this paper. Given this emphasis on growth, female entrepreneurs are portrayed as problematic because their growth lags behind their male counterparts. This image which ignores the complexity and diversity of female entrepreneurs’ experience persists in the literature due to the lack of studies that analyse the process and contextual factors surrounding female entrepreneurs’ experience. This study aims to address the subordination of female entrepreneurs by questioning the hegemonic logic of economic growth and the managerial discourse as a true representation for the entrepreneurial experience. This objective is achieved by drawing on Schumpeter’s theorising and narrative inquiry. This exploratory study undertakes in depth interviews to gain insights into female entrepreneurs’ experience and the impact of the economic growth model and the managerial discourse on their performance. The narratives challenge a number of assumptions about female entrepreneurs. The participants occupied senior positions in the corporate world before setting up their businesses. This is at odds with much writing which assumes that women underperform because they leave their career without gaining managerial experience to achieve work-life balance. In line with Schumpeter, who distinguishes the entrepreneur from the manager, the participants’ main function was innovation. They did not believe that the managerial paradigm governing their corporate careers was applicable to their entrepreneurial experience. Formal planning and managerial rationality can hinder their decision making process. The narratives point to the gap between the two worlds which makes stepping into entrepreneurship a scary move. Schumpeter argues that the entrepreneurial process is evolutionary and that failure is an integral part of it. The participants’ entrepreneurial process was in fact irregular. The performance of new combinations was not always predictable. They therefore relied on their initiative. The inhibition to deploy these traits had an adverse effect on business growth. The narratives also indicate that over-reliance on growth threaten the business survival as it faces competing pressures. The study offers theoretical and empirical contributions to (female) entrepreneurship studies by presenting Schumpeter’s theorising as an alternative theoretical framework to the neoclassical economic growth theory. The study also reduces entrepreneurs’ vulnerability by making them aware of the negative influence that the linear growth model and the managerial discourse hold upon their performance. The study has implications for policy makers as it generates new knowledge that incorporates the current social and economic changes in the context of entrepreneurs that can no longer be sustained by the linear growth models especially in the current economic climate.

Keywords: economic growth, female entrepreneurs, managerial discourse, Schumpeter

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Authors: Chen Wang, Jared Evans, Yan Asmann

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With the quick evolvement of next-generation sequencing techniques, whole-exome or exome-panel data have become a cost-effective way for detection of small exonic mutations, but there has been a growing desire to accurately detect copy number variations (CNVs) as well. In order to address this research and clinical needs, we developed a sequencing coverage pattern-based method not only for copy number detections, data integrity checks, CNV calling, and visualization reports. The developed methodologies include complete automation to increase usability, genome content-coverage bias correction, CNV segmentation, data quality reports, and publication quality images. Automatic identification and removal of poor quality outlier samples were made automatically. Multiple experimental batches were routinely detected and further reduced for a clean subset of samples before analysis. Algorithm improvements were also made to improve somatic CNV detection as well as germline CNV detection in trio family. Additionally, a set of utilities was included to facilitate users for producing CNV plots in focused genes of interest. We demonstrate the somatic CNV enhancements by accurately detecting CNVs in whole exome-wide data from the cancer genome atlas cancer samples and a lymphoma case study with paired tumor and normal samples. We also showed our efficient reuses of existing exome sequencing data, for improved germline CNV calling in a family of the trio from the phase-III study of 1000 Genome to detect CNVs with various modes of inheritance. The performance of the developed method is evaluated by comparing CNV calling results with results from other orthogonal copy number platforms. Through our case studies, reuses of exome sequencing data for calling CNVs have several noticeable functionalities, including a better quality control for exome sequencing data, improved joint analysis with single nucleotide variant calls, and novel genomic discovery of under-utilized existing whole exome and custom exome panel data.

Keywords: bioinformatics, computational genetics, copy number variations, data reuse, exome sequencing, next generation sequencing

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Authors: Daniela E. Marin, Cornelia Braicu, Gina C. Pistol, Roxana Cojocneanu-Petric, Ioana Berindan Neagoe, Mihail A. Gras, Ionelia Taranu

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Aristolochic acid (AA) is a carcinogenic, mutagenic, and nephrotoxic compound commonly found in the Aristolochiaceae family of plants. AA is frequently associated with urothelial carcinoma of the upper urinary tract in human and animals and is considered as being responsible for Balkan Endemic Nephropathy. The pig provides a good animal model because the porcine urological system is very similar to that of humans, both in aspects of physiology and anatomy. MicroRNA (miRNA) are small non-coding RNAs that have an impact on a wide range of biological processes by regulating gene expression at post-transcriptional level. The objective of this study was to analyze the miRNA profiling in the kidneys of AA intoxicated swine. For this purpose, ten TOPIGS-40 crossbred weaned piglets, 4-week-old, male and females with an initial average body weight of 9.83 ± 0.5 kg were studied for 28 days. They were given ad libitum access to water and feed and randomly allotted to one of the following groups: control group (C) or aristolochic acid group (AA). They were fed a maize-soybean-meal-based diet contaminated or not with 0.25mgAA/kg. To profile miRNA in the kidneys of pigs, microarrays and bioinformatics approaches were applied to analyze the miRNA in the kidney of control and AA intoxicated pigs. After normalization, our results have shown that a total of 5 known miRNAs and 4 novel miRNAs had different profiling in the kidney of intoxicated animals versus control ones. Expression of miR-32-5p, miR-497-5p, miR-423-3p, miR-218-5p, miR-128-3p were up-regulated by 0.25mgAA/kg feed, while the expression of miR-9793-5p, miR-9835-3p, miR-9840-3p, miR-4334-5p was down-regulated. The microRNA profiling in kidney of intoxicated animals was associated with modified expression of target genes as: RICTOR, LASP1, SFRP2, DKK2, BMI1, RAF1, IGF1R, MAP2K1, WEE1, HDGF, BCL2, EIF4E etc, involved in cell division cycle, apoptosis, cell differentiation and cell migration, cell signaling, cancer etc. In conclusion, this study provides new data concerning the microRNA profiling in kidney after aristolochic acid intoxications with important implications for human and animal health.

Keywords: aristolochic acid, kidney, microRNA, swine

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Authors: D. Hammad, D. P. Tonge

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Rheumatoid arthritis (RA) is a disabling and common autoimmune disease during which the body's immune system attacks healthy tissues. This results in complicated and long-lasting actions being carried out by the immune system, which typically only occurs when the immune system encounters a foreign object. In the case of RA, the disease affects millions of people and causes joint inflammation, ultimately leading to the destruction of cartilage and bone. Interestingly, the disease mechanism still remains unclear. It is likely that RA occurs as a result of a complex interplay of genetic and environmental factors including an imbalance in the microorganism population inside our body. The human microbiome or microbiota is an extensive community of microorganisms in and on the bodies of animals, which comprises bacteria, fungi, viruses, and protozoa. Recently, the development of molecular techniques to characterize entire bacterial communities has renewed interest in the involvement of the microbiome in the development and progression of RA. We believe that an imbalance in some of the specific bacterial species in the gut, mouth and other sites may lead to atopobiosis; the translocation of these organisms into the blood, and that this may lead to changes in immune system status. The aim of this study was, therefore, to characterize the microbiome of RA serum samples in comparison to healthy control subjects using 16S rRNA gene amplification and sequencing. Serum samples were obtained from healthy control volunteers and from patients with RA both prior to, and following treatment. The bacterial community present in each sample was identified utilizing V4 region 16S rRNA amplification and sequencing. Bacterial identification, to the lowest taxonomic rank, was performed using a range of bioinformatics tools. Significantly, the proportions of the Lachnospiraceae, Ruminococcaceae, and Halmonadaceae families were significantly increased in the serum of RA patients compared with healthy control serum. Furthermore, the abundance of Bacteroides and Lachnospiraceae nk4a136_group, Lachnospiraceae_UGC-001, RuminococcaceaeUCG-014, Rumnococcus-1, and Shewanella was also raised in the serum of RA patients relative to healthy control serum. These data support the notion of a blood microbiome and reveal RA-associated changes that may have significant implications for biomarker development and may present much-needed opportunities for novel therapeutic development.

Keywords: blood microbiome, gut and oral bacteria, Rheumatoid arthritis, 16S rRNA gene sequencing

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Authors: Sheng-Yu Lee

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Aim: Opioid use disorder is often characterized by repetitive drug-seeking and drug-taking behaviors with severe public health consequences. Animal model showed that opioid-induced perturbations in the gut microbiota causally relate to neuroinflammation, deficits in reward responding, and opioid tolerance, possibly due to changes in gut microbiota. Therefore, we propose that the dysbiosis of gut microbiota can be associated with pathogenesis of opioid dependence. In this current study, we explored the differences in gut microbiota between patients and normal controls and in patients before and after initiation of methadone treatment program for 12 weeks. Methods: Patients with opioid use disorder between 20 and 65 years were recruited from the methadone maintenance outpatient clinic in 2 medical centers in the Southern Taiwan. Healthy controls without any family history of major psychiatric disorders (schizophrenia, bipolar disorder and major depressive disorder) were recruited from the community. After initial screening, 15 patients with opioid use disorder joined the study for initial evaluation (Week 0), 12 of them completed the 12-week follow-up while receiving methadone treatment and ceased heroin use (Week 12). Fecal samples were collected from the patients at baseline and the end of 12th week. A one-time fecal sample was collected from the healthy controls. The microbiota of fecal samples were investigated using 16S rRNA V3V4 amplicon sequencing, followed by bioinformatics and statistical analyses. Results: We found no significant differences in species diversity in opioid dependent patients between Week 0 and Week 12, nor compared between patients at both points and controls. For beta diversity, using principal component analysis, we found no significant differences between patients at Week 0 and Week 12, however, both patient groups showed significant differences compared to control (P=0.011). Furthermore, the linear discriminant analysis effect size (LEfSe) analysis was used to identify differentially enriched bacteria between opioid use patients and healthy controls. Compared to controls, the relative abundance of Lactobacillaceae Lactobacillus (L. Lactobacillus), Megasphaera Megasphaerahexanoica (M. Megasphaerahexanoica) and Caecibacter Caecibactermassiliensis (C Caecibactermassiliensis) were increased in patients at Week 0, while Coriobacteriales Atopobiaceae (C. Atopobiaceae), Acidaminococcus Acidaminococcusintestini (A. Acidaminococcusintestini) and Tractidigestivibacter Tractidigestivibacterscatoligenes (T. Tractidigestivibacterscatoligenes) were increased in patients at Week 12. Conclusion: In conclusion, we suggest that the gut microbiome community maybe linked to opioid use disorder, such differences may not be altered even after 12-week of cessation of opioid use.

Keywords: opioid use disorder, gut microbiota, methadone treatment, follow up study

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Authors: Uraib Sharaha, Ahmad Salman, Eladio Rodriguez-Diaz, Elad Shufan, Klaris Riesenberg, Irving J. Bigio, Mahmoud Huleihel

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Antimicrobial drugs have an important role in controlling illness associated with infectious diseases in animals and humans. However, the increasing resistance of bacteria to a broad spectrum of commonly used antibiotics has become a global health-care problem. Rapid determination of antimicrobial susceptibility of a clinical isolate is often crucial for the optimal antimicrobial therapy of infected patients and in many cases can save lives. The conventional methods for susceptibility testing like disk diffusion are time-consuming and other method including E-test, genotyping are relatively expensive. Fourier transform infrared (FTIR) microscopy is rapid, safe, and low cost method that was widely and successfully used in different studies for the identification of various biological samples including bacteria. The new modern infrared (IR) spectrometers with high spectral resolution enable measuring unprecedented biochemical information from cells at the molecular level. Moreover, the development of new bioinformatics analyses combined with IR spectroscopy becomes a powerful technique, which enables the detection of structural changes associated with resistivity. The main goal of this study is to evaluate the potential of the FTIR microscopy in tandem with machine learning algorithms for rapid and reliable identification of bacterial susceptibility to antibiotics in time span of few minutes. The bacterial samples, which were identified at the species level by MALDI-TOF and examined for their susceptibility by the routine assay (micro-diffusion discs), are obtained from the bacteriology laboratories in Soroka University Medical Center (SUMC). These samples were examined by FTIR microscopy and analyzed by advanced statistical methods. Our results, based on 550 E.coli samples, were promising and showed that by using infrared spectroscopic technique together with multivariate analysis, it is possible to classify the tested bacteria into sensitive and resistant with success rate higher than 85% for eight different antibiotics. Based on these preliminary results, it is worthwhile to continue developing the FTIR microscopy technique as a rapid and reliable method for identification antibiotic susceptibility.

Keywords: antibiotics, E. coli, FTIR, multivariate analysis, susceptibility

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Authors: Gheorghe Braniste

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The management of the training process in sports is closely related to the awareness of the close connection between performance and the morphological, functional and psychological characteristics of the athlete's body. Achieving high results in Olympic sports is influenced, on the one hand, by the genetically determined characteristics of the body and, on the other hand, by the morphological, functional and motor abilities of the athlete. Taking into account the importance of properly understanding the evolutionary specificity of athletes to assess their competitive potential, this study provides a comparative analysis of the parameters that characterize the growth and development of the level of adaptation of sweeping rowers, considering the growth interval between 12 and 20 years. The study established that, in the multi-annual training process, the bodies of the targeted athletes register significant adaptive changes while analyzing parameters of the morphological, functional, psychomotor and sports-technical spheres. As a result of the influence of physical efforts, both specific and non-specific, there is an increase in the adaptability of the body, its transfer to a much higher level of functionality within the parameters, useful and economical adaptive reactions influenced by environmental factors, be they internal or external. The research was carried out for 7 years, on a group of 28 athletes, following their evolution and recording the specific parameters of each age stage. In order to determine the level of physical, morpho-functional, psychomotor development and technical training of rowers, the screening data were applied at the State University of Physical Education and Sports in the Republic of Moldova. During the research, measurements were made on the waist, in the standing and sitting position, arm span, weight, circumference and chest perimeter, vital capacity of the lungs, with the subsequent determination of the vital index (tolerance level to oxygen deficiency in venous blood in Stange and Genchi breath-taking tests that characterize the level of oxygen saturation, absolute and relative strength of the hand and back, calculation of body mass and morphological maturity indices (Kettle index), body surface area (body gait), psychomotor tests (Romberg test), test-tepping 10 s., reaction to a moving object, visual and auditory-motor reaction, recording of technical parameters of rowing on a competitive distance of 200 m. At the end of the study it was found that highly performance is sports is to be associated on the one hand with the genetically determined characteristics of the body and, on the other hand, with favorable adaptive reactions and energy saving, as well as morphofunctional changes influenced by internal and external environmental factors. The importance of the results obtained at the end of the study was positively reflected in obtaining the maximum level of training of athletes in order to demonstrate performance in large-scale competitions and mostly in the Olympic Games.

Keywords: olympics, parameters, performance, peak

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Authors: Samia Elfekih, Wee Tek Tay, Karl Gordon, Paul De Barro

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Invasive species represent an increasing threat to food biosecurity, causing significant economic losses in agricultural systems. An example is the sweet potato whitefly, Bemisia tabaci, which is a complex of morphologically indistinguishable species causing average annual global damage estimated at US$2.4 billion. The Bemisia complex represents an interesting model for evolutionary studies because of their extensive distribution and potential for invasiveness and population expansion. Within this complex, two species, Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) have invaded well beyond their home ranges whereas others, such as Indian Ocean (IO) and Australia (AUS), have not. In order to understand why some Bemisia species have become invasive, genome-wide sequence scans were used to estimate population dynamics over time and relate these to climate. The Bayesian Skyline Plot (BSP) method as implemented in BEAST was used to infer the historical effective population size. In order to overcome sampling bias, the populations were combined based on geographical origin. The datasets used for this particular analysis are genome-wide SNPs (single nucleotide polymorphisms) called separately in each of the following groups: Sub-Saharan Africa (Burkina Faso), Europe (Spain, France, Greece and Croatia), USA (Arizona), Mediterranean-Middle East (Israel, Italy), Middle East-Central Asia (Turkmenistan, Iran) and Reunion Island. The non-invasive ‘AUS’ species endemic to Australia was used as an outgroup. The main findings of this study show that the BSP for the Sub-Saharan African MED population is different from that observed in MED populations from the Mediterranean Basin, suggesting evolution under a different set of environmental conditions. For MED, the effective size of the African (Burkina Faso) population showed a rapid expansion ≈250,000-310,000 years ago (YA), preceded by a period of slower growth. The European MED populations (i.e., Spain, France, Croatia, and Greece) showed a single burst of expansion at ≈160,000-200,000 YA. The MEAM1 populations from Israel and Italy and the ones from Iran and Turkmenistan are similar as they both show the earlier expansion at ≈250,000-300,000 YA. The single IO population lacked the latter expansion but had the earlier one. This pattern is shared with the Sub-Saharan African (Burkina Faso) MED, suggesting IO also faced a similar history of environmental change, which seems plausible given their relatively close geographical distributions. In conclusion, populations within the invasive species MED and MEAM1 exhibited signatures of population expansion lacking in non-invasive species (IO and AUS) during the Pleistocene, a geological epoch marked by repeated climatic oscillations with cycles of glacial and interglacial periods. These expansions strongly suggested the potential of some Bemisia species’ genomes to affect their adaptability and invasiveness.

Keywords: whitefly, RADseq, invasive species, SNP, climate change

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Authors: Athanasios Raftopoulos

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In this paper, an attempt is made to explain the evolution or development of human’s representational arsenal from its humble beginnings to its modern abstract symbols. Representations are physical entities that represent something else. To represent a thing (in a general sense of “thing”) means to use in the mind or in an external medium a sign that stands for it. The sign can be used as a proxy of the represented thing when the thing is absent. Representations come in many varieties, from signs that perceptually resemble their representative to abstract symbols that are related to their representata through conventions. Relying the distinction among indices, icons, and symbols, it is explained how symbolic representations gradually emerged from indices and icons. To understand the development or evolution of our representational arsenal, the development of the cognitive capacities that enabled the gradual emergence of representations of increasing complexity and expressive capability should be examined. The examination of these factors should rely on a careful assessment of the available empirical neuroscientific and paleo-anthropological evidence. These pieces of evidence should be synthesized to produce arguments whose conclusions provide clues concerning the developmental process of our representational capabilities. The analysis of the empirical findings in this paper shows that Homo Erectus was able to use both icons and symbols. Icons were used as external representations, while symbols were used in language. The first step in the emergence of representations is that a sensory-motor purely causal schema involved in indices is decoupled from its normal causal sensory-motor functions and serves as a representation of the object that initially called it into play. Sensory-motor schemes are tied to specific contexts of the organism-environment interactions and are activated only within these contexts. For a representation of an object to be possible, this scheme must be de-contextualized so that the same object can be represented in different contexts; a decoupled schema loses its direct ties to reality and becomes mental content. The analysis suggests that symbols emerged due to selection pressures of the social environment. The need to establish and maintain social relationships in ever-enlarging groups that would benefit the group was a sufficient environmental pressure to lead to the appearance of the symbolic capacity. Symbols could serve this need because they can express abstract relationships, such as marriage or monogamy. Icons, by being firmly attached to what can be observed, could not go beyond surface properties to express abstract relations. The cognitive capacities that are required for having iconic and then symbolic representations were present in Homo Erectus, which had a language that started without syntactic rules but was structured so as to mirror the structure of the world. This language became increasingly complex, and grammatical rules started to appear to allow for the construction of more complex expressions required to keep up with the increasing complexity of social niches. This created evolutionary pressures that eventually led to increasing cranial size and restructuring of the brain that allowed more complex representational systems to emerge.

Keywords: mental representations, iconic representations, symbols, human evolution

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Authors: Aidin Foroutan, David S. Wishart, Leluo L. Guan, Carolyn Fitzsimmons

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Maximizing efficiency and growth potential of beef cattle requires not only genetic selection (i.e. residual feed intake (RFI)) but also adequate nutrition throughout all stages of growth and development. Nutrient restriction during gestation has been shown to negatively affect post-natal growth and development as well as fertility of the offspring. This, when combined with RFI may affect progeny traits. This study aims to investigate the impact of selection for divergent genetic potential for RFI and maternal nutrition during early- to mid-gestation, on bull calf traits such as fertility and muscle development using multiple ‘omics’ approaches. Comparisons were made between High-diet vs. Low-diet and between High-RFI vs. Low-RFI animals. An epigenetics experiment on semen samples identified 891 biomarkers associated with growth and development. A gene expression study on Longissimus thoracis muscle, semimembranosus muscle, liver, and testis identified 4 genes associated with muscle development and immunity of which Myocyte enhancer factor 2A [MEF2A; induces myogenesis and control muscle differentiation] was the only differentially expressed gene identified in all four tissues. An initial metabolomics experiment on serum samples using nuclear magnetic resonance (NMR) identified 4 metabolite biomarkers related to energy and protein metabolism. Once all the biomarkers are identified, bioinformatics approaches will be used to create a database covering all the ‘omics’ data collected from this project. This database will be broadened by adding other information obtained from relevant literature reviews. Association analyses with these data sets will be performed to reveal key biological pathways affected by RFI and maternal nutrition. Through these association studies between the genome and metabolome, it is expected that candidate biomarker genes and metabolites for feed efficiency, fertility, and/or muscle development are identified. If these gene/metabolite biomarkers are validated in a larger animal population, they could potentially be used in breeding programs to select superior animals. It is also expected that this work will lead to the development of an online tool that could be used to predict future traits of interest in an animal given its measurable ‘omics’ traits.

Keywords: biomarker, maternal nutrition, omics, residual feed intake

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Authors: Oshma Chakoory, Sophie Comtet-Marre, Pierre Peyret

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Metagenomic classifiers are widely used for the taxonomic profiling of metagenomic data and estimation of taxa relative abundance. Small subunit rRNA genes are nowadays a gold standard for the phylogenetic resolution of complex microbial communities, although the power of this marker comes down to its use as full-length. We benchmarked the performance and accuracy of rRNA-specialized versus general-purpose read mappers, reference-targeted assemblers and taxonomic classifiers. We then built a pipeline called RiboTaxa to generate a highly sensitive and specific metataxonomic approach. Using metagenomics data, RiboTaxa gave the best results compared to other tools (Kraken2, Centrifuge (1), METAXA2 (2), PhyloFlash (3)) with precise taxonomic identification and relative abundance description, giving no false positive detection. Using real datasets from various environments (ocean, soil, human gut) and from different approaches (metagenomics and gene capture by hybridization), RiboTaxa revealed microbial novelties not seen by current bioinformatics analysis opening new biological perspectives in human and environmental health. In a study focused on corals’ health involving 20 metagenomic samples (4), an affiliation of prokaryotes was limited to the family level with Endozoicomonadaceae characterising healthy octocoral tissue. RiboTaxa highlighted 2 species of uncultured Endozoicomonas which were dominant in the healthy tissue. Both species belonged to a genus not yet described, opening new research perspectives on corals’ health. Applied to metagenomics data from a study on human gut and extreme longevity (5), RiboTaxa detected the presence of an uncultured archaeon in semi-supercentenarians (aged 105 to 109 years) highlighting an archaeal genus, not yet described, and 3 uncultured species belonging to the Enorma genus that could be species of interest participating in the longevity process. RiboTaxa is user-friendly, rapid, allowing microbiota structure description from any environment and the results can be easily interpreted. This software is freely available at https://github.com/oschakoory/RiboTaxa under the GNU Affero General Public License 3.0.

Keywords: metagenomics profiling, microbial diversity, SSU rRNA genes, full-length phylogenetic marker

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Authors: Miranda E. Karban

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A distinctive pattern of occipital squama convexity, known as the occipital bun or chignon, has traditionally been considered a derived Neandertal trait. However, some early modern and extant Homo sapiens share similar occipital bone morphology, showing pronounced internal and external occipital squama curvature and paralambdoidal flattening. It has been posited that these morphological patterns are homologous in the two groups, but this claim remains disputed. Many developmental hypotheses have been proposed, including assertions that the chignon represents a developmental response to a long and narrow cranial vault, a narrow or flexed basicranium, or a prognathic face. These claims, however, remain to be metrically quantified in a large subadult sample, and little is known about the feature’s developmental, functional, or evolutionary significance. This study assesses patterns of chignon development and covariation in a comparative sample of extant human growth study cephalograms. Cephalograms from a total of 549 European-derived North American subjects (286 male, 263 female) were scored on a 5-stage ranking system of chignon prominence. Occipital squama shape was found to exist along a continuum, with 34 subjects (6.19%) possessing defined chignons, and 54 subjects (9.84%) possessing very little occipital squama convexity. From this larger sample, those subjects represented by a complete radiographic series were selected for metric analysis. Measurements were collected from lateral and posteroanterior (PA) cephalograms of 26 subjects (16 male, 10 female), each represented at 3 longitudinal age groups. Age group 1 (range: 3.0-6.0 years) includes subjects during a period of rapid brain growth. Age group 2 (range: 8.0-9.5 years) includes subjects during a stage in which brain growth has largely ceased, but cranial and facial development continues. Age group 3 (range: 15.9-20.4 years) includes subjects at their adult stage. A total of 16 landmarks and 153 sliding semi-landmarks were digitized at each age point, and geometric morphometric analyses, including relative warps analysis and two-block partial least squares analysis, were conducted to study covariation patterns between midsagittal occipital bone shape and other aspects of craniofacial morphology. A convex occipital squama was found to covary significantly with a low, elongated neurocranial vault, and this pattern was found to exist from the youngest age group. Other tested patterns of covariation, including cranial and basicranial breadth, basicranial angle, midcoronal cranial vault shape, and facial prognathism, were not found to be significant at any age group. These results suggest that the chignon, at least in this sample, should not be considered an independent feature, but rather the result of developmental interactions relating to neurocranial elongation. While more work must be done to quantify chignon morphology in fossil subadults, this study finds no evidence to disprove the developmental homology of the feature in modern humans and Neandertals.

Keywords: chignon, craniofacial covariation, human cranial development, longitudinal growth study, occipital bun

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Authors: Saneeya Qureshi

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This paper reports doctoral research into the impact of Special Educational Needs Coordinators (SENCOs) on teachers in England, UK. Since 1994, it has been compulsory for all mainstream schools in the UK to have a SENCO who co-ordinates assessment and provision for supporting pupils with Special Educational Needs (SEN), helping teachers to develop and implement optimal SEN planning and resources. SENCOs’ roles have evolved as various policies continually redefined SEN provision, impacting their positioning within the school hierarchical structure. SENCOs in England are increasingly recognised as key members of school senior management teams. In this paper, It will be argued that despite issues around the transformative ‘professionalisation’ of their role, and subsequent conflict around boundaries and power relations, SENCOs enhance teachers’ abilities in terms of delivering optimal SEN provision. There is a significant international dimension to the issue: a similar role in respect of SEN management already exists in countries such as Ireland, Finland and Singapore, whilst in other countries, such as Italy and India, the introduction of a role similar to that of a SENCO is currently under discussion. The research question addressed is: do SENCOs enhance teachers’ abilities to be effective teachers of children with Special Educational Needs? The theoretical framework of the project is that of interpretivism, as it is acknowledged that there are contexts and realities are social constructions. The study applied a mixed method approach consisting of two phases. The first phase involved a purposive survey (n=42) of 223 primary school SENCOs, which enabled a deeper insight into SENCOs’ perceptions of their roles in relation to teachers. The second phase consisted of semi-structured interviews (n=36) of SENCOs, teachers and head teachers, in addition to school SEN-related documentation scrutiny. ‘Trustworthiness’ was accomplished through data and methodological triangulation, in addition to a rigorous process of coding and thematic analysis. The research was informed by an Ethical Code as per national guidelines. Research findings point to the evolutionary aspect of the SENCO role having engendered a culture of expectations amongst practitioners, as SENCOs transition from being ‘fixers’ to being ‘enablers’ of teachers. Outcomes indicate that SENCOs can empower teaching staff through the dissemination of specialist knowledge. However, there must be resources clearly identified for such dissemination to take place. It is imperative that both SENCOs and teachers alike address the issue of absolution of responsibility that arises when the ownership and accountability for the planning and implementation of SEN provision are not clarified so as to ensure the promotion of a positive school ethos around inclusive practices. Optimal outcomes through effective SEN interventions and teaching practices are positively correlated with the inclusion of teachers in the planning and execution of SEN provisions. An international audience can consider how the key findings are being manifest in a global context, with reference to their own educational settings. Research outcomes can aid the development of specific competencies needed to shape optimal inclusive educational settings in accordance with the official global priorities pertaining to inclusion.

Keywords: inclusion, school professionals, school leadership, special educational needs (SEN), special educational needs coordinators (SENCOs)

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Authors: Yuna Lee

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In the current policy process, there has been a growing interest in more open approaches that incorporate creativity and innovation based on the forecasting groups composed by the public and experts together into scientific data-driven foresight methods to implement more effective policymaking. Especially, citizen participation as collective intelligence in policymaking with design and deep scale of innovation at the global level has been developed and human-centred design thinking is considered as one of the most promising methods for strategic foresight. Yet, there is a lack of a common theoretical foundation for a comprehensive approach for the current situation of and post-COVID-19 era, and substantial changes in policymaking practice are insignificant and ongoing with trial and error. This project hypothesized that rigorously developed policy systems and tools that support strategic foresight by considering the public understanding could maximize ways to create new possibilities for a preferable future, however, it must involve a better understating of Behavioural Insights, including individual and cultural values, profit motives and needs, and psychological motivations, for implementing holistic and multilateral foresight and creating more positive possibilities. To what extent is the policymaking system theoretically possible that incorporates the holistic and comprehensive foresight and policy process implementation, assuming that theory and practice, in reality, are different and not connected? What components and environmental conditions should be included in the strategic foresight system to enhance the capacity of decision from policymakers to predict alternative futures, or detect uncertainties of the future more accurately? And, compared to the required environmental condition, what are the environmental vulnerabilities of the current policymaking system? In this light, this research contemplates the question of how effectively policymaking practices have been implemented through the synthesis of scientific, technology-oriented innovation with the strategic design for tackling complex societal challenges and devising more significant insights to make society greener and more liveable. Here, this study conceptualizes the notions of a new collaborative way of strategic foresight that aims to maximize mutual benefits between policy actors and citizens through the cooperation stemming from evolutionary game theory. This study applies mixed methodology, including interviews of policy experts, with the case in which digital transformation and strategic design provided future-oriented solutions or directions to cities’ sustainable development goals and society-wide urgent challenges such as COVID-19. As a result, artistic and sensual interpreting capabilities through strategic design promote a concrete form of ideas toward a stable connection from the present to the future and enhance the understanding and active cooperation among decision-makers, stakeholders, and citizens. Ultimately, an improved theoretical foundation proposed in this study is expected to help strategically respond to the highly interconnected future changes of the post-COVID-19 world.

Keywords: policymaking, strategic design, sustainable innovation, evolution of cooperation

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Authors: Md. Fazlul Karim, Ashik Sharfaraz, Aysha Ferdoushi

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Background: Computational medicinal chemistry approaches are used for designing and identifying new drug-like molecules, predicting properties and pharmacological activities, and optimizing lead compounds in drug development. SIRT7, a nicotinamide adenine dinucleotide (NAD+)-dependent deacylase which regulates aging, is an emerging target for cancer therapy with mounting evidence that SIRT7 downregulation plays important roles in reversing cancer phenotypes and suppressing tumor growth. Activation or altered expression of SIRT7 is associated with the progression and invasion of various cancers, including liver, breast, gastric, prostate, and non-small cell lung cancer. Objectives: The goal of this work was to identify potent and selective bioactive candidate inhibitors of SIRT7 by in silico screening of small molecule compounds obtained from Nigella sativa (N. sativa). Methods: SIRT7 structure was retrieved from The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB), and its active site was identified using CASTp and metaPocket. Molecular docking simulation was performed with PyRx 0.8 virtual screening software. Drug-likeness properties were tested using SwissADME and pkCSM. In silico toxicity was evaluated by Osiris Property Explorer. Bioactivity was predicted by Molinspiration software. Antitumor activity was screened for Prediction of Activity Spectra for Substances (PASS) using Way2Drug web server. Molecular dynamics (MD) simulation was carried out by Desmond v3.6 package. Results: A total of 159 bioactive compounds from the N. Sativa were screened against the SIRT7 enzyme. Five bioactive compounds: chrysin (CID:5281607), pinocembrin (CID:68071), nigellidine (CID:136828302), nigellicine (CID:11402337), and epicatechin (CID:72276) were identified as potent SIRT7 anti-cancer candidates after docking score evaluation and applying Lipinski's Rule of Five. Finally, MD simulation identified Chrysin as the top SIRT7 anti-cancer candidate molecule. Conclusion: Chrysin, which shows a potential inhibitory effect against SIRT7, can act as a possible anti-cancer drug candidate. This inhibitor warrants further evaluation to check its pharmacokinetics and pharmacodynamics properties both in vitro and in vivo.

Keywords: SIRT7, antitumor, molecular docking, molecular dynamics simulation

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Authors: Chang Liang, Weizhi Gong, Yan Zhang

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Purpose: Hepatocellular carcinoma (HCC) is a malignant tumor with a high mortality rate and poor prognosis worldwide. Murine double minute 2 (MDM2) regulates the tumor suppressor p53, increasing cancer risk and accelerating tumor progression. Speckle-type POX virus and zinc finger protein (SPOP), a key of subunit of Cullin-Ring E3 ligase, inhibits tumor genesis and progression by the ubiquitination of its downstream substrates. This study aimed to clarify whether SPOP and MDM2 are mutually regulated in HCC and the correlation between SPOP and MDM2 and the prognosis of HCC patients. Methods: First, the expression of SPOP and MDM2 in HCC tissues were detected by TCGA database. Then, 53 paired samples of HCC tumor and adjacent tissues were collected to evaluate the expression of SPOP and MDM2 using immunohistochemistry. Chi-square test or Fisher’s exact test were used to analyze the relationship between clinicopathological features and the expression levels of SPOP and MDM2. In addition, Kaplan‒Meier curve analysis and log-rank test were used to investigate the effects of SPOP and MDM2 on the survival of HCC patients. Last, the Multivariate Cox proportional risk regression model analyzed whether the different expression levels of SPOP and MDM2 were independent risk factors for the prognosis of HCC patients. Results: Bioinformatics analysis revealed the low expression of SPOP and high expression of MDM2 were related to worse prognosis of HCC patients. The relationship between the expression of SPOP and MDM2 and tumor stem-like features showed an opposite trend. The immunohistochemistry showed the expression of SPOP protein was significantly downregulated while MDM2 protein significantly upregulated in HCC tissue compared to that in para-cancerous tissue. Tumors with low SPOP expression were related to worse T stage and Barcelona Clinic Liver Cancer (BCLC) stage, but tumors with high MDM2 expression were related to worse T stage, M stage, and BCLC stage. Kaplan–Meier curves showed HCC patients with high SPOP expression and low MDM2 expression had better survival than those with low SPOP expression and high MDM2 expression (P < 0.05). A multivariate Cox proportional risk regression model confirmed that a high MDM2 expression level was an independent risk factor for poor prognosis in HCC patients (P <0.05). Conclusion: The expression of SPOP protein was significantly downregulated, while the expression of MDM2 significantly upregulated in HCC. The low expression of SPOP and high expression. of MDM2 were associated with malignant progression and poor prognosis of HCC patients, indicating a potential therapeutic target for HCC patients.

Keywords: hepatocellular carcinoma, murine double minute 2, speckle-type POX virus and zinc finger protein, ubiquitination

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

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The concept of organic agriculture has been accepted as novelty in Indian society, but there is no data available on the human pathogens colonizing plant parts due to such practices. Also, the pattern and mechanism of their colonization need to be understood in order to devise possible strategies for their prevention. In the present study, human pathogenic bacteria were isolated from organically grown tomato plants and five of them were identified as Klebsiella pneumoniae, Enterobacter ludwigii, Serratia fonticola, Stenotrophomonas maltophilia and Chryseobacterium jejuense. Tomato plants were grown in controlled aseptic conditions with 25±1˚C, 70% humidity and 12 hour L/D photoperiod. Six weeks old plants were divided into 6 groups of 25 plants each and treated as follows: Group 1: K. pneumonia, Group 2: E. ludwigii, Group 3: S. fonticola, Group 4: S. maltophilia, Group 5: C. jejuense, Group 6: Sterile distilled water (control). The inoculums for all treatments were prepared by overnight growth with uniform concentration of 108 cells/ml. Leaf samples from above groups were collected at 0.5, 2, 4, 6 and 24 hours post inoculation for the colony forming unit counts (CFU/cm2 of leaf area) of individual pathogens using leaf impression method. These CFU counts were used for the in vivo colonization assay and adherence assay of individual pathogens. Also, resistance of these pathogens to at least 12 antibiotics was studied. Based on these findings S. fonticola was found to be most prominently colonizing the phylloplane of tomato and was further studied. Tomato plants grown in controlled aseptic conditions same as mentioned above were divided into 2 groups of 25 plants each and treated as follows: Group 1: S. fonticola, Group 2: Sterile distilled water (control). Leaf samples from above groups were collected at 0, 24, 48, 72 and 96 hours post inoculation and homogenized in suitable buffers for surface and cell wall protein isolation. Protein samples thus obtained were subjected to isocratic SDS-gel electrophoresis and analyzed. It was observed that presence of S. fonticola could induce the expression of at least 3 additional cell wall proteins at different time intervals. Surface proteins also showed variation in the expression pattern at different sampling intervals. Further identification of these proteins by MALDI-MS and bioinformatics tools revealed the gene(s) involved in the interaction of S. fonticola with tomato phylloplane.

Keywords: cell wall proteins, human pathogenic bacteria, phylloplane, solanum lycopersicum

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Authors: Vijaya Dixit Aasheesh Dixit

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Shipbuilding industry operates in Engineer Procure Construct (EPC) context. Product mix of a shipyard comprises of various types of ships like bulk carriers, tankers, barges, coast guard vessels, sub-marines etc. Each order is unique based on the type of ship and customized requirements, which are engineered into the product right from design stage. Thus, to execute every new project, a shipyard needs to upgrade its production expertise. As a result, over the long run, holistic learning occurs across different types of projects which contributes to the knowledge base of the shipyard. Simultaneously, in the short term, during execution of a project comprising of multiple sister ships, repetition of similar tasks leads to learning at activity level. This research aims to capture above learnings of a shipyard and incorporate learning curve effect in project scheduling and materials procurement to improve project performance. Extant literature provides support for the existence of such learnings in an organization. In shipbuilding, there are sequences of similar activities which are expected to exhibit learning curve behavior. For example, the nearly identical structural sub-blocks which are successively fabricated, erected, and outfitted with piping and electrical systems. Learning curve representation can model not only a decrease in mean completion time of an activity, but also a decrease in uncertainty of activity duration. Sister ships have similar material requirements. The same supplier base supplies materials for all the sister ships within a project. On one hand, this provides an opportunity to reduce transportation cost by batching the order quantities of multiple ships. On the other hand, it increases the inventory holding cost at shipyard and the risk of obsolescence. Further, due to learning curve effect the production scheduled of each consequent ship gets compressed. Thus, the material requirement schedule of every next ship differs from its previous ship. As more and more ships get constructed, compressed production schedules increase the possibility of batching the orders of sister ships. This work aims at integrating materials management with project scheduling of long duration projects for manufacturing of multiple sister ships. It incorporates the learning curve effect on progressively compressing material requirement schedules and addresses the above trade-off of transportation cost and inventory holding and shortage costs while satisfying budget constraints of various stages of the project. The activity durations and lead time of items are not crisp and are available in the form of probabilistic distribution. A Stochastic Mixed Integer Programming (SMIP) model is formulated which is solved using evolutionary algorithm. Its output provides ordering dates of items and degree of order batching for all types of items. Sensitivity analysis determines the threshold number of sister ships required in a project to leverage the advantage of learning curve effect in materials management decisions. This analysis will help materials managers to gain insights about the scenarios: when and to what degree is it beneficial to treat a multiple ship project as an integrated one by batching the order quantities and when and to what degree to practice distinctive procurement for individual ship.

Keywords: learning curve, materials management, shipbuilding, sister ships

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Authors: Tracey Woods

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In the ever-evolving landscape of academia, the traditional role of the librarian has undergone a remarkable transformation. Once considered as custodians of books and gatekeepers of information, librarians have the potential to take on the vital role of facilitators of cross and inter-disciplinary projects. This shift is driven by the growing recognition of the value of interdisciplinary collaboration in addressing complex research questions in pursuit of novel solutions to real-world problems. This paper shall explore the potential of the academic librarian’s role in facilitating innovative, multi-disciplinary projects, both recognising and validating the vital role that the librarian plays in a somewhat underplayed profession. Academic libraries support teaching, the strengthening of knowledge discourse, and, potentially, the development of innovative practices. As the role of the library gradually morphs from a quiet repository of books to a community-based information hub, a potential opportunity arises. The academic librarian’s role is to build knowledge across a wide span of topics, from the advancement of AI to subject-specific information, and, whilst librarians are generally not offered the research opportunities and funding that the traditional academic disciplines enjoy, they are often invited to help build research in support of the academic. This identifies that one of the primary skills of any 21st-century librarian must be the ability to collaborate and facilitate multi-disciplinary projects. In universities seeking to develop research diversity and academic performance, there is an increasing awareness of the need for collaboration between faculties to enable novel directions and advancements. This idea has been documented and discussed by several researchers; however, there is not a great deal of literature available from recent studies. Having a team based in the library that is adept at creating effective collaborative partnerships is valuable for any academic institution. This paper outlines the development of such a project, initiated within and around an identified library-specific need: the replication of fragile special collections for object-based learning. The research was developed as a multi-disciplinary project involving the faculties of engineering (digital twins lab), architecture, design, and education. Centred around methods for developing a fragile archive into a series of tactile objects furthers knowledge and understanding in both the role of the library as a facilitator of projects, chairing and supporting, alongside contributing to the research process and innovating ideas through the bank of knowledge found amongst the staff and their liaising capabilities. This paper shall present the method of project development from the initiation of ideas to the development of prototypes and dissemination of the objects to teaching departments for analysis. The exact replication of artefacts is also balanced with the adaptation and evolutionary speculations initiated by the design team when adapted as a teaching studio method. The dynamic response required from the library to generate and facilitate these multi-disciplinary projects highlights the information expertise and liaison skills that the librarian possesses. As academia embraces this evolution, the potential for groundbreaking discoveries and innovative solutions across disciplines becomes increasingly attainable.

Keywords: Liaison librarian, multi-disciplinary collaborations, library innovations, librarian stakeholders

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Authors: Noury Bakrim

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When dealing with motivation/arbitrariness, forming form (Forma Formans) and morphodynamics are to be grasped as relevant implications of enunciation/enactment, schematization within the specificity of language as sound/meaning articulation. Thus, the fact that a language is a form does not contradict stasis/dynamic enunciation (reflexivity vs double articulation). Moreover, some languages exemplify the role of the forming form, uttering, and schematization (roots in Semitic languages, the Chinese case). Beyond the evolutionary biosemiotic process (form/substance bifurcation, the split between realization/representation), non-isomorphism/asymmetry between linguistic form/norm and linguistic realization (phonetics for instance) opens up a new horizon problematizing the role of Brain – sensorimotor contribution in the continuous forming form. Therefore, we hypothesize biotization as both process/trace co-constructing motivation/forming form. Henceforth, referring to our findings concerning distribution and motivation patterns within Berber written texts (pulse based obstruents and nasal-lateral levels in poetry) and oral storytelling (consonant intensity clustering in quantitative and semantic/prosodic motivation), we understand consonant clustering, motivation and schematization as a complex phenomenon partaking in patterns of oral/written iconic prosody and reflexive metalinguistic representation opening the stable form. We focus our inquiry on both Amazigh and English clusters (/spl/, /spr/) and iconic consonant iteration in [gnunnuy] (to roll/tumble), [smummuy] (to moan sadly or crankily). For instance, the syllabic structures of /splaeʃ/ and /splaet/ imply an anamorphic representation of the state of the world: splash, impact on aquatic surfaces/splat impact on the ground. The pair has stridency and distribution as distinctive features which specify its phonetic realization (and a part of its meaning) /ʃ/ is [+ strident] and /t/ is [+ distributed] on the vocal tract. Schematization is then a process relating both physiology/code as an arthron vocal/bodily, vocal/practical shaping of the motor-articulatory system, leading to syntactic/semantic thematization (agent/patient roles in /spl/, /sm/ and other clusters or the tense uvular /qq/ at the initial position in Berber). Furthermore, the productivity of serial syllable sequencing in Berber points out different expressivity forms. We postulate two Components of motivated formalization: i) the process of memory paradigmatization relating to sequence modeling under sensorimotor/verbal specific categories (production/perception), ii) the process of phonotactic selection - prosodic unconscious/subconscious distribution by virtue of iconicity. Basing on multiple tests including a questionnaire, phonotactic/visual recognition and oral/written reproduction, we aim at patterning/conceptualizing consonant schematization and motivation among EFL and Amazigh (Berber) learners and speakers integrating biolinguistic hypotheses.

Keywords: consonant motivation and prosody, language and order of life, anamorphic representation, represented representation, biotization, sensori-motor and brain representation, form, formalization and schematization

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Authors: Ramin Mehdiabadi, Neda Menbari, Mohammad Nazir Menbari

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As a pressing public health concern, breast cancer stands as the predominant oncological diagnosis and principal cause of cancer-related mortality among women globally, accounting for 11.7% of new cancer incidences and 6.9% of cancer-related deaths. The annual figures indicate that approximately 230,480 women are diagnosed with breast cancer in the United States alone, with 39,520 succumbing to the disease. While developed economies have reported a deceleration in both incidence and mortality rates across various forms of cancer, including breast cancer, emerging and low-income economies manifest a contrary escalation, largely attributable to lifestyle-mediated risk factors such as tobacco usage, physical inactivity, and high caloric intake. Breast cancer is distinctly characterized by molecular heterogeneity, manifesting in specific subtypes delineated by biomarkers—Estrogen Receptors (ER), Progesterone Receptors (PR), and Human Epidermal Growth Factor Receptor 2 (HER2). These subtypes, comprising Luminal A, Luminal B, HER2-enriched, triple-negative/basal-like, and normal-like, necessitate nuanced, subtype-specific therapeutic regimens, thereby challenging the applicability of generalized treatment protocols. Within this molecular complexity, the transcription factor Forkhead Box M1 (FoxM1) has garnered attention as a significant driver of cellular proliferation, tumorigenesis, metastatic progression, and treatment resistance in a spectrum of human malignancies, including breast cancer. Concurrently, microRNAs (miRs), specifically miR-216b-5p, have been identified as post-transcriptional gene expression regulators and potential tumor suppressors. The overarching objective of this academic investigation is to explicate the multifaceted interrelationship between FoxM1 and miR-216b-5p across the disparate molecular subtypes of breast cancer. Employing a methodologically rigorous, interdisciplinary research design that incorporates cutting-edge molecular biology techniques, sophisticated bioinformatics analytics, and exhaustive meta-analyses of extant clinical data, this scholarly endeavor aims to unveil novel biomarker-specific therapeutic pathways. By doing so, this research is positioned to make a seminal contribution to the advancement of personalized, efficacious, and minimally toxic treatment paradigms, thus profoundly impacting the global efforts to ameliorate the burden of breast cancer.

Keywords: breast cancer, fox m1, microRNAs, mir-216b-5p, gene expression

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Authors: Angela U. Makolo

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Protein-coding and Non-coding regions determine the biology of a sequenced transcriptome. Research advances have shown that Non-coding regions are important in disease progression and clinical diagnosis. Existing bioinformatics tools have been targeted towards Protein-coding regions alone. Therefore, there are challenges associated with gaining biological insights from transcriptome sequence data. These tools are also limited to computationally intensive sequence alignment, which is inadequate and less accurate to identify both Protein-coding and Non-coding regions. Alignment-free techniques can overcome the limitation of identifying both regions. Therefore, this study was designed to develop an efficient sequence alignment-free model for identifying both Protein-coding and Non-coding regions in sequenced transcriptomes. Feature grouping and randomization procedures were applied to the input transcriptomes (37,503 data points). Successive iterations were carried out to compute the gradient vector that converged the developed Protein-coding and Non-coding Region Identifier (PNRI) model to the approximate coefficient vector. The logistic regression algorithm was used with a sigmoid activation function. A parameter vector was estimated for every sample in 37,503 data points in a bid to reduce the generalization error and cost. Maximum Likelihood Estimation (MLE) was used for parameter estimation by taking the log-likelihood of six features and combining them into a summation function. Dynamic thresholding was used to classify the Protein-coding and Non-coding regions, and the Receiver Operating Characteristic (ROC) curve was determined. The generalization performance of PNRI was determined in terms of F1 score, accuracy, sensitivity, and specificity. The average generalization performance of PNRI was determined using a benchmark of multi-species organisms. The generalization error for identifying Protein-coding and Non-coding regions decreased from 0.514 to 0.508 and to 0.378, respectively, after three iterations. The cost (difference between the predicted and the actual outcome) also decreased from 1.446 to 0.842 and to 0.718, respectively, for the first, second and third iterations. The iterations terminated at the 390th epoch, having an error of 0.036 and a cost of 0.316. The computed elements of the parameter vector that maximized the objective function were 0.043, 0.519, 0.715, 0.878, 1.157, and 2.575. The PNRI gave an ROC of 0.97, indicating an improved predictive ability. The PNRI identified both Protein-coding and Non-coding regions with an F1 score of 0.970, accuracy (0.969), sensitivity (0.966), and specificity of 0.973. Using 13 non-human multi-species model organisms, the average generalization performance of the traditional method was 74.4%, while that of the developed model was 85.2%, thereby making the developed model better in the identification of Protein-coding and Non-coding regions in transcriptomes. The developed Protein-coding and Non-coding region identifier model efficiently identified the Protein-coding and Non-coding transcriptomic regions. It could be used in genome annotation and in the analysis of transcriptomes.

Keywords: sequence alignment-free model, dynamic thresholding classification, input randomization, genome annotation

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Authors: Carmela Nardelli, Laura Iaffaldano, Valentina Capobianco, Antonietta Tafuto, Maddalena Ferrigno, Angela Capone, Giuseppe Maria Maruotti, Maddalena Raia, Rosa Di Noto, Luigi Del Vecchio, Pasquale Martinelli, Lucio Pastore, Lucia Sacchetti

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Maternal obesity and nutrient excess in utero increase the risk of future metabolic diseases in the adult life. The mechanisms underlying this process are probably based on genetic, epigenetic alterations and changes in foetal nutrient supply. In mammals, the placenta is the main interface between foetus and mother, it regulates intrauterine development, modulates adaptive responses to sub optimal in uterus conditions and it is also an important source of human amniotic mesenchymal stem cells (hA-MSCs). We previously highlighted a specific microRNA (miRNA) profiling in amnion from obese (Ob) pregnant women, here we compared the miRNA expression profile of hA-MSCs isolated from (Ob) and control (Co) women, aimed to search for any alterations in metabolic pathways that could predispose the new-born to the obese phenotype. Methods: We isolated, at delivery, hA-MSCs from amnion of 16 Ob- and 7 Co-women with pre-pregnancy body mass index (mean/SEM) 40.3/1.8 and 22.4/1.0 kg/m2, respectively. hA-MSCs were phenotyped by flow cytometry. Globally, 384 miRNAs were evaluated by the TaqMan Array Human MicroRNA Panel v 1.0 (Applied Biosystems). By the TargetScan program we selected the target genes of the miRNAs differently expressed in Ob- vs Co-hA-MSCs; further, by KEGG database, we selected the statistical significant biological pathways. Results: The immunophenotype characterization confirmed the mesenchymal origin of the isolated hA-MSCs. A large percentage of the tested miRNAs, about 61.4% (232/378), was expressed in hA-MSCs, whereas 38.6% (146/378) was not. Most of the expressed miRNAs (89.2%, 207/232) did not differ between Ob- and Co-hA-MSCs and were not further investigated. Conversely, 4.8% of miRNAs (11/232) was higher and 6.0% (14/232) was lower in Ob- vs Co-hA-MSCs. Interestingly, 7/232 miRNAs were obesity-specific, being expressed only in hA-MSCs isolated from obese women. Bioinformatics showed that these miRNAs significantly regulated (P<0.001) genes belonging to several metabolic pathways, i.e. MAPK signalling, actin cytoskeleton, focal adhesion, axon guidance, insulin signaling, etc. Conclusions: Our preliminary data highlight an altered miRNA profile in Ob- vs Co-hA-MSCs and suggest that an epigenetic miRNA-based mechanism of gene regulation could affect pathways involved in placental growth and function, thereby potentially increasing the newborn’s risk of metabolic diseases in the adult life.

Keywords: hA-MSCs, obesity, miRNA, biosystem

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Authors: Alexander A. Stakheev, Larisa V. Samokhvalova, Sergey K. Zavriev

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Fusarium fungi are among the most devastating plant pathogens distributed all over the world. Significant reduction of grain yield and quality caused by Fusarium leads to multi-billion dollar annual losses to the world agricultural production. These organisms can also cause infections in immunocompromised persons and produce the wide range of mycotoxins, such as trichothecenes, fumonisins, and zearalenone, which are hazardous to human and animal health. Identification of Fusarium fungi based on the morphology of spores and spore-forming structures, colony color and appearance on specific culture media is often very complicated due to the high similarity of these features for closely related species. Modern Fusarium taxonomy increasingly uses data of crossing experiments (biological species concept) and genetic polymorphism analysis (phylogenetic species concept). A number of novel Fusarium sibling species has been established using DNA barcoding techniques. Species recognition is best made with the combined phylogeny of intron-rich protein coding genes and ribosomal DNA sequences. However, the internal transcribed spacer of (ITS), which is considered to be universal DNA barcode for Fungi, is not suitable for genus Fusarium, because of its insufficient variability between closely related species and the presence of non-orthologous copies in the genome. Nowadays, the translation elongation factor 1 alpha (TEF1α) gene is the “gold standard” of Fusarium taxonomy, but the search for novel informative markers is still needed. In this study, we used two novel DNA markers, frataxin (FXN) and heat shock protein 90 (HSP90) to discover phylogenetic relationships between Fusarium species. Multilocus phylogenetic analysis based on partial sequences of TEF1α, FXN, HSP90, as well as intergenic spacer of ribosomal DNA (IGS), beta-tubulin (β-TUB) and phosphate permease (PHO) genes has been conducted for 120 isolates of 19 Fusarium species from different climatic zones of Russia and neighboring countries using maximum likelihood (ML) and maximum parsimony (MP) algorithms. Our analyses revealed that FXN and HSP90 genes could be considered as informative phylogenetic markers, suitable for evolutionary and taxonomic studies of Fusarium genus. It has been shown that PHO gene possesses more variable (22 %) and parsimony informative (19 %) characters than other markers, including TEF1α (12 % and 9 %, correspondingly) when used for elucidating phylogenetic relationships between F. avenaceum and its closest relatives – F. tricinctum, F. acuminatum, F. torulosum. Application of novel DNA barcodes confirmed the fact that F. arthrosporioides do not represent a separate species but only a subspecies of F. avenaceum. Phylogeny based on partial PHO and FXN sequences revealed the presence of separate cluster of four F. avenaceum strains which were closer to F. torulosum than to major F. avenaceum clade. The strain F-846 from Moldova, morphologically identified as F. poae, formed a separate lineage in all the constructed dendrograms, and could potentially be considered as a separate species, but more information is needed to confirm this conclusion. Variable sites in PHO sequences were used for the first-time development of specific qPCR-based diagnostic assays for F. acuminatum and F. torulosum. This work was supported by Russian Foundation for Basic Research (grant № 15-29-02527).

Keywords: DNA barcode, fusarium, identification, phylogenetics, taxonomy

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Authors: Tugba Altin

Abstract:

In a time characterized by escalating climate change impacts, communities globally face extreme events with deep-reaching tangible and intangible consequences. At the intersection of these phenomena lies the profound impact on the cultural and emotional connections that individuals forge with their environments. This study casts a spotlight on the Lytton Creek Fire of 2021, showcasing it as an exemplar of both the visible destruction brought by such events and the more covert yet deeply impactful disturbances to place attachment (PA). Defined as the emotional and cognitive bond individuals form with their surroundings, PA is critical in comprehending how such catastrophic events reshape cultural identity and the bond with the land. Against the stark backdrop of the Lytton Creek Fire's devastation, the research seeks to unpack the multilayered dynamics of PA amidst the tangible wreckage and the intangible repercussions such as emotional distress and disrupted cultural landscapes. Delving deeper, it examines how affected populations renegotiate their affiliations with these drastically altered environments, grappling with both the tangible loss of their homes and the intangible challenges to solace, identity, and community cohesion. This exploration is instrumental in the broader climate change narrative, as it offers crucial insights into how these personal-place relationships can influence and shape climate adaptation and recovery strategies. Departing from traditional data collection methodologies, this study adopts an interpretive phenomenological approach enriched by hermeneutic insights and places the experiences of the Lytton community and its co-researchers at its core. Instead of conventional interviews, innovative methods like walking audio sessions and photo elicitation are employed. These techniques allow participants to immerse themselves back into the environment, reviving and voicing their memories and emotions in real-time. Walking audio captures reflections on spatial narratives after the trauma, whereas photo voices encapsulate the intangible emotions, presenting a visual representation of place-based experiences. Key findings emphasize the indispensability of addressing both the tangible and intangible traumas in community recovery efforts post-disaster. The profound changes to the cultural landscape and the subsequent shifts in PA underscore the need for holistic, culturally attuned, and emotionally insightful adaptation strategies. These strategies, rooted in the lived experiences and testimonies of the affected individuals, promise more resonant and effective recovery efforts. The research further contributes to climate change discourse, highlighting the intertwined pathways of tangible reconstruction and the essentiality of emotional and cultural rejuvenation. Furthermore, the use of participatory methodologies in this inquiry challenges traditional research paradigms, pointing to potential evolutionary shifts in qualitative research norms. Ultimately, this study underscores the need for a more integrative approach in addressing the aftermath of environmental disasters, ensuring that both physical and emotional rebuilding are given equal emphasis.

Keywords: place attachment, community recovery, disaster reponse, sensory responses, intangible traumas, visual methodologies

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Authors: Margaret Boone Rappaport, Christopher J. Corbally

Abstract:

The ancient ape ancestral population from which living great ape and human species evolved had demographic features affecting their evolution. The population was large, had great genetic variability, and natural selection was effective at honing adaptations. The emerging populations of chimpanzees and humans were affected more by founder effects and genetic drift because they were smaller. Natural selection did not disappear, but it was not as strong. Consequences of the 'population crash' and the human effective population size are introduced briefly. The history of the ancient apes is written in the genomes of living humans and great apes. The expansion of the brain began before the human line emerged. Coalescence times for some genes are very old – up to several million years, long before Homo sapiens. The mismatch between gene trees and species trees highlights the anthropoid speciation processes, and gives the human genome history a fuzzy, probabilistic quality. However, it suggests traits that might form a foundation for capacities emerging later. A theoretical model is presented in which the genomes of early ape populations provide the substructure for the emergence of religious capacity later on the human line. The model does not search for religion, but its foundations. It suggests a course by which an evolutionary line that began with prosimians eventually produced a human species with biologically based religious capacity. The model of the sequential emergence of religious capacity relies on cognitive science, neuroscience, paleoneurology, primate field studies, cognitive archaeology, genomics, and population genetics. And, it emphasizes five trait types: (1) Documented, positive selection of sensory capabilities on the human line may have favored survival, but also eventually enriched human religious experience. (2) The bonobo model suggests a possible down-regulation of aggression and increase in tolerance while feeding, as well as paedomorphism – but, in a human species that remains cognitively sharp (unlike the bonobo). The two species emerged from the same ancient ape population, so it is logical to search for shared traits. (3) An up-regulation of emotional sensitivity and compassion seems to have occurred on the human line. This finds support in modern genetic studies. (4) The authors’ published model of morality's emergence in Homo erectus encompasses a cognitively based, decision-making capacity that was hypothetically overtaken, in part, by religious capacity. Together, they produced a strong, variable, biocultural capability to support human sociability. (5) The full flowering of human religious capacity came with the parietal expansion and smaller face (klinorhynchy) found only in Homo sapiens. Details from paleoneurology suggest the stage was set for human theologies. Larger parietal lobes allowed humans to imagine inner spaces, processes, and beings, and, with the frontal lobe, led to the first theologies composed of structured and integrated theories of the relationships between humans and the supernatural. The model leads to the evolution of a small population of African hominins that was ready to emerge with religious capacity when the species Homo sapiens evolved two hundred thousand years ago. By 50-60,000 years ago, when human ancestors left Africa, they were fully enabled.

Keywords: genetic drift, genomics, parietal expansion, religious capacity

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Authors: Sebastian Kehne, Alexander Epple, Werner Herfs

Abstract:

A new method for optimal selection of components for multi-axes forward-feed drive systems is proposed in which the choice of motors, gear boxes and ball screw drives is optimized. Essential is here the synchronization of electrical and mechanical frequency behavior of all axes because even advanced controls (like H∞-controls) can only control a small part of the mechanical modes – namely only those of observable and controllable states whose value can be derived from the positions of extern linear length measurement systems and/or rotary encoders on the motor or gear box shafts. Further problems are the unknown processing forces like cutting forces in machine tools during normal operation which make the estimation and control via an observer even more difficult. To start with, the open source Modelica Feed Drive Library which was developed at the Laboratory for Machine Tools, and Production Engineering (WZL) is extended from one axis design to the multi axes design. It is capable to simulate the mechanical, electrical and thermal behavior of permanent magnet synchronous machines with inverters, different gear boxes and ball screw drives in a mechanical system. To keep the calculation time down analytical equations are used for field and torque producing equivalent circuit, heat dissipation and mechanical torque at the shaft. As a first step, a small machine tool with a working area of 635 x 315 x 420 mm is taken apart, and the mechanical transfer behavior is measured with an impulse hammer and acceleration sensors. With the frequency transfer functions, a mechanical finite element model is built up which is reduced with substructure coupling to a mass-damper system which models the most important modes of the axes. The model is modelled with Modelica Feed Drive Library and validated by further relative measurements between machine table and spindle holder with a piezo actor and acceleration sensors. In a next step, the choice of possible components in motor catalogues is limited by derived analytical formulas which are based on well-known metrics to gain effective power and torque of the components. The simulation in Modelica is run with different permanent magnet synchronous motors, gear boxes and ball screw drives from different suppliers. To speed up the optimization different black-box optimization methods (Surrogate-based, gradient-based and evolutionary) are tested on the case. The objective that was chosen is to minimize the integral of the deviations if a step is given on the position controls of the different axes. Small values are good measures for a high dynamic axes. In each iteration (evaluation of one set of components) the control variables are adjusted automatically to have an overshoot less than 1%. It is obtained that the order of the components in optimization problem has a deep impact on the speed of the black-box optimization. An approach to do efficient black-box optimization for multi-axes design is presented in the last part. The authors would like to thank the German Research Foundation DFG for financial support of the project “Optimierung des mechatronischen Entwurfs von mehrachsigen Antriebssystemen (HE 5386/14-1 | 6954/4-1)” (English: Optimization of the Mechatronic Design of Multi-Axes Drive Systems).

Keywords: ball screw drive design, discrete optimization, forward feed drives, gear box design, linear drives, machine tools, motor design, multi-axes design

Procedia PDF Downloads 255