Risk perception of sun exposure and knowledge of vitamin D among the healthcare providers in a high-risk country: a cross-sectional study.

BACKGROUND: High levels of vitamin D deficiency are commonly reported even in regions with abundant sunshine. This necessitates a comprehensive understanding of the determinants that influence sun exposure practices. As the primary source of health-related knowledge for the general public, the attitude of the healthcare professionals towards sunlight and their awareness related to vitamin D deficiency can be critical in this regard. METHODS: A cross-sectional survey was conducted among 2,242 physicians, intern doctors, and senior medical students in Bangladesh from October 2019 to February 2020. A pre-tested structured questionnaire (containing twelve close-ended questions) was used. The perceptions of health risks due to sun exposure, and basic knowledge of the physiological and epidemiological aspects of vitamin D deficiency were tested. RESULTS: An overall negative attitude towards sunlight in the context of Bangladesh was highlighted - 68% participants thought regular sun exposure would be harmful or very harmful; 26% thought the level of UV radiation was very high; 44% recommended using sunscreen always; skin burns, heat stroke, and cancer were selected as potential consequences of regular sun exposure by 45%, 21%, and 30% respondents respectively. Overall knowledge regarding vitamin D deficiency appeared to be biased towards bone health; other symptoms and associated illnesses not having obvious link to Calcium-metabolism were identified much lesser frequently. Furthermore, 'sunrise to 10 am' was identified as the best time to get vitamin D by 69% participants; 60% believed < 30 min of weekly sun exposure would be sufficient for the Bangladeshi population; an only 33% identified that prevalence of vitamin D insufficiency in Bangladesh would be 50% or more. Taking vitamin D-rich food was suggested by more respondents over regular sun exposure (43% vs. 33%) as more effective remedial strategy to curb vitamin D deficiency in Bangladesh. CONCLUSION: In addition to highlighting some crucial knowledge gaps, results from this study provides a comprehensive baseline dataset for knowledge and attitude regarding the public health aspects of vitamin D deficiency among the healthcare providers in Bangladesh, which would be generalizable to other countries with similar socio-demographic context, and will facilitate taking more effective policies worldwide.

Fluorometric determination of lead(II) by using aptamer-functionalized upconversion nanoparticles and magnetite-modified gold nanoparticles.

A fluorescent nanoprobe for Pb(II) has been developed by employing aptamer-functionalized upconversion nanoparticles (UCNPs) and magnetic Fe3O4-modified (MNPs) gold nanoparticles (GNPs). First, aptamer-functionalized UCNPs and aptamer-functionalized magnetic GNPs were synthesized to obtained the fluorescent nanoprobe. The particles were combined by adding a complementary ssDNA. In the absence of Pb(II), the UCNPs, MNPs and GNPs are linked via complementary base pairing. This led to a decrease in the green upconversion fluorescence peaking at 547 nm (under 980 nm excitation). In the presence of Pb(II), the dsDNA between UCNPs and MNPs-GNPs is cleaved, and fluorescence recovers. This effect allows Pb(II) to be quantified, with a wide working range of 25-1400 nM and a lower detection limit of 5.7 nM. The nanoprobe gave satisfactory results when analyzing Pb(II) in tea and waste water. Graphical abstractSchematic representation of fluorescent nanoprobe based on fluorescence resonance energy transfer (FRET) between upconversion nanoparticles (UCNPs) and gold nanoparticles (GNPs)-Fe3O4 magnetic nanoparticles (MNPs) for detection of Pb2+.

Reflections on a journey: a retrospective of the ISCB Student Council symposium series.

This article describes the motivation, origin and evolution of the student symposia series organised by the ISCB Student Council. The meeting series started thirteen years ago in Madrid and has spread to four continents. The article concludes with the highlights of the most recent edition of annual Student Council Symposium held in conjunction with the 25th Conference on Intelligent Systems for Molecular Biology and the 16th European Conference on Computational Biology, in Prague, in July 2017.

Evolutionary, structural and functional analysis of the caleosin/peroxygenase gene family in the Fungi.

BACKGROUND: Caleosin/peroxygenases, CLO/PXG, (designated PF05042 in Pfam) are a group of genes/proteins with anomalous distributions in eukaryotic taxa. We have previously characterised CLO/PXGs in the Viridiplantae. The aim of this study was to investigate the evolution and functions of the CLO/PXGs in the Fungi and other non-plant clades and to elucidate the overall origin of this gene family. RESULTS: CLO/PXG-like genes are distributed across the full range of fungal groups from the basal clades, Cryptomycota and Microsporidia, to the largest and most complex Dikarya species. However, the genes were only present in 243 out of 844 analysed fungal genomes. CLO/PXG-like genes have been retained in many pathogenic or parasitic fungi that have undergone considerable genomic and structural simplification, indicating that they have important functions in these species. Structural and functional analyses demonstrate that CLO/PXGs are multifunctional proteins closely related to similar proteins found in all major taxa of the Chlorophyte Division of the Viridiplantae. Transcriptome and physiological data show that fungal CLO/PXG-like genes have complex patterns of developmental and tissue-specific expression and are upregulated in response to a range of biotic and abiotic stresses as well as participating in key metabolic and developmental processes such as lipid metabolism, signalling, reproduction and pathogenesis. Biochemical data also reveal that the Aspergillus flavus CLO/PXG has specific functions in sporulation and aflatoxin production as well as playing roles in lipid droplet function. CONCLUSIONS: In contrast to plants, CLO/PXGs only occur in about 30% of sequenced fungal genomes but are present in all major taxa. Fungal CLO/PXGs have similar but not identical roles to those in plants, including stress-related oxylipin signalling, lipid metabolism, reproduction and pathogenesis. While the presence of CLO/PXG orthologs in all plant genomes sequenced to date would suggest that they have core housekeeping functions in plants, the selective loss of CLO/PXGs in many fungal genomes suggests more restricted functions in fungi as accessory genes useful in particular environments or niches. We suggest an ancient origin of CLO/PXG-like genes in the 'last eukaryotic common ancestor' (LECA) and their subsequent loss in ancestors of the Metazoa, after the latter had diverged from the ancestral fungal lineage.

Differential Evolution approach to detect recent admixture.

The genetic structure of human populations is extraordinarily complex and of fundamental importance to studies of anthropology, evolution, and medicine. As increasingly many individuals are of mixed origin, there is an unmet need for tools that can infer multiple origins. Misclassification of such individuals can lead to incorrect and costly misinterpretations of genomic data, primarily in disease studies and drug trials. We present an advanced tool to infer ancestry that can identify the biogeographic origins of highly mixed individuals. reAdmix can incorporate individual's knowledge of ancestors (e.g. having some ancestors from Turkey or a Scottish grandmother). reAdmix is an online tool available at http://chcb.saban-chla.usc.edu/reAdmix/.

Entropy-Based Emotion Recognition from Multichannel EEG Signals Using Artificial Neural Network.

Humans experience a variety of emotions throughout the course of their daily lives, including happiness, sadness, and rage. As a result, an effective emotion identification system is essential for electroencephalography (EEG) data to accurately reflect emotion in real-time. Although recent studies on this problem can provide acceptable performance measures, it is still not adequate for the implementation of a complete emotion recognition system. In this research work, we propose a new approach for an emotion recognition system, using multichannel EEG calculation with our developed entropy known as multivariate multiscale modified-distribution entropy (MM-mDistEn) which is combined with a model based on an artificial neural network (ANN) to attain a better outcome over existing methods. The proposed system has been tested with two different datasets and achieved better accuracy than existing methods. For the GAMEEMO dataset, we achieved an average accuracy ± standard deviation of 95.73% ± 0.67 for valence and 96.78% ± 0.25 for arousal. Moreover, the average accuracy percentage for the DEAP dataset reached 92.57% ± 1.51 in valence and 80.23% ± 1.83 in arousal.

Artificial microRNAs (amiRNAs) engineering - On how microRNA-based silencing methods have affected current plant silencing research.

In recent years, endogenous microRNAs have been described as important regulators of gene expression in eukaryotes. Artificial microRNAs (amiRNAs) represent a recently developed miRNA-based strategy to silence endogenous genes. amiRNAs can be created by exchanging the miRNA/miRNA(∗) sequence within a miRNA precursor with a sequence designed to match the target gene, this is possible as long as the secondary RNA structure of the precursor is kept intact. In this review, we summarize the basic methodologies to design amiRNAs and detail their applications in plants genetic functional studies as well as their potential for crops genetic improvement.

Roborovski hamster (Phodopus roborovskii) strain SH101 as a systemic infection model of SARS-CoV-2.

Severe acute respiratory syndrome CoV-2 (SARS-CoV-2) is currently causing a worldwide threat with its unusually high transmission rates and rapid evolution into diverse strains. Unlike typical respiratory viruses, SARS-CoV-2 frequently causes systemic infection by breaking the boundaries of the respiratory systems. The development of animal models recapitulating the clinical manifestations of COVID-19 is of utmost importance not only for the development of vaccines and antivirals but also for understanding the pathogenesis. However, there has not been developed an animal model for systemic infection of SARS-CoV-2 representing most aspects of the clinical manifestations of COVID-19 with systemic symptoms. Here we report that a Roborovski hamster strain SH101, a laboratory inbred hamster strain of P. roborovskii, displayed most symptoms of systemic infection upon SARS-CoV-2 infection as in the case of the human counterpart, unlike current COVID-19 animal models. Roborovski hamster strain SH101 post-infection of SARS-CoV-2 represented most clinical symptoms of COVID-19 such as snuffling, labored breathing, dyspnea, cough, hunched posture, progressive weight loss, ruffled fur, and high fever following shaking chills. Histological examinations also revealed initial right-predominated pneumonia as well as slight organ damages in the brain and liver, manifesting systemic COVID-19 cases. Considering the merit of a small animal as well as its clinical manifestations of SARS-CoV-2 infection in human, this hamster model seems to provide an ideal tool to investigate COVID-19.

Mesoporous silica supported orderly-spaced gold nanoparticles SERS-based sensor for pesticides detection in food.

In this study, a novel sensor fabricated with compactly arranged gold nanoparticles (AuNPs) templated from mesoporous silica film (MSF) via air-water interface has been confirmed as a promising surface-enhanced Raman scattering (SERS) substrate for detecting trace levels of 2,4-dichlorophenoxyacetic acid (2,4-D), pymetrozine and thiamethoxam. The densely arranged AuNPs@MSF had an average AuNPs size of 5.15 nm with small nanogaps (<2nm) between AuNPs, and exhibited a high SERS performance. SERS spectra of pesticides were collected after their adsorption on the AuNPs@MSF. The results showed that the concentration of 2,4-D, pymetrozine and thiamethoxam gave a good linear relationship with SERS intensity. Moreover, the designed SERS-based sensor (AuNPs@MSF) was stable for 3 months with ca. 3% relative standard deviation (RSD) and was applied successfully for the analysis of 2,4-D extraction from both environmental and food samples. The proposed SERS-based sensor was further validated by HPLC and showed satisfactory result (p > 0.05).

Evolutionary and genomic analysis of the caleosin/peroxygenase (CLO/PXG) gene/protein families in the Viridiplantae.

Bioinformatics analyses of caleosin/peroxygenases (CLO/PXG) demonstrated that these genes are present in the vast majority of Viridiplantae taxa for which sequence data are available. Functionally active CLO/PXG proteins with roles in abiotic stress tolerance and lipid droplet storage are present in some Trebouxiophycean and Chlorophycean green algae but are absent from the small number of sequenced Prasinophyceaen genomes. CLO/PXG-like genes are expressed during dehydration stress in Charophyte algae, a sister clade of the land plants (Embryophyta). CLO/PXG-like sequences are also present in all of the >300 sequenced Embryophyte genomes, where some species contain as many as 10-12 genes that have arisen via selective gene duplication. Angiosperm genomes harbour at least one copy each of two distinct CLO/PX isoforms, termed H (high) and L (low), where H-forms contain an additional C-terminal motif of about 30-50 residues that is absent from L-forms. In contrast, species in other Viridiplantae taxa, including green algae, non-vascular plants, ferns and gymnosperms, contain only one (or occasionally both) of these isoforms per genome. Transcriptome and biochemical data show that CLO/PXG-like genes have complex patterns of developmental and tissue-specific expression. CLO/PXG proteins can associate with cytosolic lipid droplets and/or bilayer membranes. Many of the analysed isoforms also have peroxygenase activity and are involved in oxylipin metabolism. The distribution of CLO/PXG-like genes is consistent with an origin >1 billion years ago in at least two of the earliest diverging groups of the Viridiplantae, namely the Chlorophyta and the Streptophyta, after the Viridiplantae had already diverged from other Archaeplastidal groups such as the Rhodophyta and Glaucophyta. While algal CLO/PXGs have roles in lipid packaging and stress responses, the Embryophyte proteins have a much wider spectrum of roles and may have been instrumental in the colonisation of terrestrial habitats and the subsequent diversification as the major land flora.

The Peroxygenase Activity of the Aspergillus flavus Caleosin, AfPXG, Modulates the Biosynthesis of Aflatoxins and Their Trafficking and Extracellular Secretion via Lipid Droplets.

Aflatoxins (AF) are highly detrimental to human and animal health. We recently demonstrated that the Aspergillus flavus caleosin, AfPXG, had peroxygenase activity and mediated fungal development and AF accumulation. We now report the characterization of an AfPXG-deficient line using reference strain NRRL3357. The resulting fungal phenotype included a severe decrease in mycelium growth, failure to sporulate, and reduced AF production. Increasing cellular oxidative status by administration of hydrogen peroxide and cumene hydroperoxide did not restore the AfPXG-deficient phenotype, which suggests that AfPXG-deficiency is not directly related to oxidative stress. To investigate possible alternative roles of AfPXG, a gain of function approach was used to overexpress AfPXG, with the reporter gene Gfp, in an AfPXG-deficient line, termed AfPXG+ . The resulting phenotype included elevated numbers of stable lipid droplets (LDs) plus enhanced AF production. Highly purified LDs from AfPXG+ cultures sequestered AF and this ability was positively correlated with overall LD number. Site-specific mutagenesis of AfPXG to delete Histidine 85 (AfPXGHis85), a residue essential for its catalytic activity, or deletion of the putative LD targeting domain (AfPXGD126-140), showed that AfPXG-peroxygenase activity was required for AF biosynthesis and that integration of AF into LDs was required for their export via a LD-dependent pathway. Ectopic expression in fungal cells of the plant LD-associated protein, oleosin, also resulted in both additional LD accumulation and enhanced AF secretion. These results suggest that both fungal LDs and their associated caleosin proteins are intimately involved in the biosynthesis, trafficking, and secretion of AF.

Highlights of the 2 (nd) Bioinformatics Student Symposium by ISCB RSG-UK.

Following the success of the 1 (st) Student Symposium by ISCB RSG-UK, a 2 (nd) Student Symposium took place on 7 (th) October 2015 at The Genome Analysis Centre, Norwich, UK. This short report summarizes the main highlights from the 2 (nd) Bioinformatics Student Symposium.

Rice Germosprout Extract Protects Erythrocytes from Hemolysis and the Aorta, Brain, Heart, and Liver Tissues from Oxidative Stress In Vitro.

Identifying dietary alternatives for artificial antioxidants capable of boosting antihemolytic and antioxidative defense has been an important endeavor in improving human health. In the present study, we studied antihemolytic and antioxidative effects of germosprout (i.e., the germ part along with sprouted stems plus roots) extract prepared from the pregerminated rice. The extract contained considerable amounts of antioxidant ß-carotene (414 ± 12 ng/g of extract) and phytochemicals such as total polyphenols (12.0 ± 1.1 mg gallic acid equivalent/g of extract) and flavonoids (11.0 ± 1.4 mg catechin equivalent/g of extract). The antioxidant potential of the extract was assessed by its DPPH- (2,2-diphenyl-1-picrylhydrazyl-) free radical scavenging activity where we observed that germosprout extract had considerable antioxidative potentials. To evaluate antihemolytic effect of the extract, freshly prepared erythrocytes were incubated with either peroxynitrite or Fenton's reagent in the absence or presence of the extract. We observed that erythrocytes pretreated with the extract exhibited reduced degree of in vitro hemolysis. To support the proposition that germosprout extract could act as a good antioxidative agent, we also induced in vitro oxidative stress in erythrocyte membranes and in the aorta, brain, heart, and liver tissue homogenates in the presence of the extract. As expected, germosprout extract decreased oxidative stress almost to the same extent as that of vitamin E, as measured by lipid peroxide levels, in all the mentioned tissues. We conclude that rice germosprout extract could be a good natural source of antioxidants to reduce oxidative stress-induced hemolysis and damage of blood vessels and other tissues.

Specific Caleosin/Peroxygenase and Lipoxygenase Activities Are Tissue-Differentially Expressed in Date Palm (Phoenix dactylifera L.) Seedlings and Are Further Induced Following Exposure to the Toxin 2,3,7,8-tetrachlorodibenzo-p-dioxin.

Two caleosin/peroxygenase isoforms from date palm, Phoenix dactylifera L., PdCLO2 and PdCLO4, were characterized with respect to their tissue expression, subcellular localization, and oxylipin pathway substrate specificities in developing seedlings. Both PdCLO2 and PdCLO4 had peroxygenase activities that peaked at the mid-stage (radicle length of 2.5 cm) of seedling growth and were associated with the lipid droplet (LD) and microsomal fractions. Recombinant PdCLO2 and PdCLO4 proteins heterologously expressed in yeast cells were localized in both LD and microsomal fractions. Each of the purified recombinant proteins exhibited peroxygenase activity but they were catalytically distinct with respect to their specificity and product formation from fatty acid epoxide and hydroxide substrates. We recently showed that date palm CLO genes were upregulated following exposure to the potent toxin, 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) (Hanano et al., 2016), and we show here that transcripts of 9- and 13-lipoxygenase (LOX) genes were also induced by TCDD exposure. At the enzyme level, 9-LOX and 13-LOX activities were present in a range of seedling tissues and responded differently to TCDD exposure, as did the 9- and 13-fatty acid hydroperoxide reductase activities. This demonstrates that at least two branches of the oxylipin pathway are involved in responses to the environmental organic toxin, TCDD in date palm.

Highlights from the ISCB Student Council Symposia in 2016.

This editorial provides a brief overview of the 12th International Society for Computational Biology (ISCB) Student Council Symposium and the 4th European Student Council Symposium held in Florida, USA and The Hague, Netherlands, respectively. Further, the role of the ISCB Student Council in promoting education and networking in the field of computational biology is also highlighted.

ISCB-Student Council Narratives: Strategical development of the ISCB-Regional Student Groups in 2016.

Regional Student Groups are groups established and managed by the ISCB-Student Council in different regions of the world. The article highlights some of the initiatives and management lessons from our 'top-performing' Spotlight Regional Student Groups (RSGs), RSG-Argentina and RSG-UK, for the current year (2016). In addition, it details some of the operational hurdles faced by RSGs and possible solutions.

Highlights of the 1st Student Symposium of the ISCB RSG UK.

This short report summarises the scientific content and activities of a student-led event, the 1st student symposium by the UK Regional Student Group of the International Society for Computational Biology. The event took place on the 8th of October 2014.

Oral Administration of Ganoderma lucidum to Lead-Exposed Rats Protects Erythrocytes against Hemolysis: Implicates to Anti-Anemia.

We studied the effect of chronic oral exposure to lead acetate (PbA) on the sensitivity of RBC to hemolysis and whether the sensitivity could be decreased by feeding the rats with extract of medicinal mushroom Ganoderma lucidum. Three groups of rats, control, PbA-exposed, and G. lucidum (Gl)+PbA, were used. PbA (3 mM) was administered via drinking water and G. lucidum extract by gavage at 300 mg/Kg BW/day for 12 weeks. Afterwards, the rats were killed and washed RBCs were subjected to hemolysis in the presence of Fenton's reagents. Hemolysis was determined by estimating the amount of released hemoglobin. The levels of lipid peroxide (LPO) and GSH were determined from RBC membranes and whole RBCs, respectively. The levels of TNFα and LPO also were determined from hepatic tissues. The RBCs of PbA-exposed rats displayed significantly higher sensitivity to hemolysis than those of the Gl+PbA rats. The levels of LPO increased and GSH decreased in the RBCs, with concomitant increases in the levels of hepatic TNFα and LPO in the PbA-exposed rats. The degree of hemolysis was significantly low in the RBCs of Gl+PbA rats, concurrently with amelioration of hepatic parameters. Finally, the study suggests that PbA-induced-hemolysis and related oxidative-toxicity might be minimized by consumption of G. lucidum.

Tumor suppressors status in cancer cell line Encyclopedia.

Tumor suppressors play a major role in the etiology of human cancer, and typically achieve a tumor-promoting effect upon complete functional inactivation. Bi-allelic inactivation of tumor suppressors may occur through genetic mechanisms (such as loss of function mutation, copy number (CN) loss, or loss of heterozygosity (LOH)), epigenetic mechanisms (such as promoter methylation or histone modification), or a combination of the two. We report systematically derived status of 69 known or putative tumor suppressors, across 799 samples of the Cancer Cell Line Encyclopedia. In order to generate such resource we constructed a novel comprehensive computational framework for the assessment of tumor suppressor functional "status". This approach utilizes several orthogonal genomic data types, including mutation data, copy number, LOH and expression. Through correlation with additional data types (compound sensitivity and gene set activity) we show that this integrative method provides a more accurate assessment of tumor suppressor status than can be inferred by expression, copy number, or mutation alone. This approach has the potential for a more realistic assessment of tumor suppressor genes for both basic and translational oncology research.

NPEST: a nonparametric method and a database for transcription start site prediction.

In this paper we present NPEST, a novel tool for the analysis of expressed sequence tags (EST) distributions and transcription start site (TSS) prediction. This method estimates an unknown probability distribution of ESTs using a maximum likelihood (ML) approach, which is then used to predict positions of TSS. Accurate identification of TSS is an important genomics task, since the position of regulatory elements with respect to the TSS can have large effects on gene regulation, and performance of promoter motif-finding methods depends on correct identification of TSSs. Our probabilistic approach expands recognition capabilities to multiple TSS per locus that may be a useful tool to enhance the understanding of alternative splicing mechanisms. This paper presents analysis of simulated data as well as statistical analysis of promoter regions of a model dicot plant Arabidopsis thaliana. Using our statistical tool we analyzed 16520 loci and developed a database of TSS, which is now publicly available at www.glacombio.net/NPEST.