Biology subjects

Rahman, M. M.

Publications and source records attributed to Rahman, M. M..

At least 55 records · Page 3Linked to original sources

bioRxiv2022

Bacterial communities associated with the surfaces of the fresh fruits sold around Dhaka Medical College and Hospital and their anti-microbial profiles

BackgroundNow-a-days, fresh fruits are popular sources of healthy diets with low energy density. Since they are consumed raw, it may act as a source of foodborne disease and a reservoir for antibiotic resistant organisms. This study aimed to determine microbial prevalence among the fruits sold outside Dhaka Medical College Hospital (DMCH) along with their antimicrobial profiles and to detect antimicrobial resistance genes among the resistant organisms. MethodsThirty-five different types of fruits were bought from around DMCH and analyzed for the presence of bacteria. Antibiotic sensitivity was done and ESBL, AmpC {beta}-lactamase, and MBL positive strains were identified by standard methods followed by PCR to detect ESBL, AmpC {beta}-lactamase, and MBL genes. FindingsTwenty seven different organisms were isolated and identified which were-Klebsiella spp (33{middle dot}33%), Citrobacter spp (29{middle dot}64%), Enterobacter spp (22{middle dot}22%), Escherichia coli (11{middle dot}11%), and Staphylococcus aureus (3{middle dot}70%). Among them 48{middle dot}15% organisms were resistant to different antibiotics. Only one organism (Citrobacter spp) produced ESBL phenotypically (7{middle dot}69%). Two (15{middle dot}38%) were positive for AmpC {beta}-lactamase and one of these (Enterobacter spp) possessed both SHV and CTX-M15A genes by PCR. Imipenem resistance was 84{middle dot}62% of the antibiotic resistant organisms, and 10 (90{middle dot}91%) were phenotypically MBL positive by CD test, DDS test, and MHT. By PCR, one Enterobacter spp had MBL encoding gene OXA-48. InterpretationFresh fruits, contaminated with pathogens, might be a source of transmission of resistant organisms and attribute to public health issues. FundingThe office of Directorate General of Health Service, Ministry of Health and Family Welfare, Bangladesh. ImportanceFruits sold around Dhaka Medical College and Hospital (DMCH) are usually consumed by patients, patients attendant and Health care worker. This investigation emphasized not only on the extent of bacterial contamination but also attempted to measure the anti-microbial profile of these organisms isolated from the fruits commonly available and readily consumed in and around DMCH.

microbiology↗

bioRxiv2022

The Caenorhabditis elegans centrosome is surrounded by a membrane reticulum, the centriculum, that affects centrosome size and function

Centrosomes are membraneless organelles that nucleate microtubules. At their core is a pair of centrioles that recruit pericentriolar material (PCM), a phase-separated condensate. In many cell types, including human cells, centrosomes are surrounded by endoplasmic reticulum-derived membranes of unknown structure and function. Using volume electron microscopy, we show that the C. elegans centrosome is surrounded by a membrane reticulum that we call the centriculum, for centrosome-associated membrane reticulum. Increasing centriculum size by genetic means led to expansion of the PCM and increased microtubule nucleation capacity, an unexpected finding given that the PCM is a membraneless condensate. We provide evidence that the centriculum serves as a microtubule "filter" by limiting the number of microtubules that can elongate fully. We also show the centriculum fuses with the nuclear envelope during mitosis. We propose that this fusion contributes to nuclear envelope breakdown by transducing forces from the elongating spindle to the nuclear membranes.

cell biology↗

bioRxiv2021

PplD is a de-N-acetylase of the cell wall linkage unit of streptococcal rhamnopolysaccharides

The cell wall of the human bacterial pathogen Group A Streptococcus (GAS) consists of peptidoglycan decorated with the Lancefield group A carbohydrate (GAC). GAC is a promising target for the development of GAS vaccines. In this study, employing chemical, compositional, and NMR methods, we show that GAC is attached to peptidoglycan via glucosamine 1-phosphate. This structural feature makes the GAC-peptidoglycan linkage highly sensitive to cleavage by nitrous acid and resistant to mild acid conditions. Using this characteristic of the GAS cell wall, we identify PplD as a protein required for deacetylation of linkage N-acetylglucosamine (GlcNAc). X-ray structural analysis indicates that PplD performs catalysis via a modified acid/base mechanism. Genetic surveys in silico together with functional analysis indicate that PplD homologs deacetylate the polysaccharide linkage in many streptococcal species. We further demonstrate that introduction of positive charges to the cell wall by GlcNAc deacetylation protects GAS against host cationic antimicrobial proteins.

microbiology↗

bioRxiv2021

An RNAi screen for genes that affect nuclear morphology in Caenorhabditis elegans reveals the involvement of unexpected processes

Aberration in nuclear morphology is one of the hallmarks of cellular transformation. However, the processes that, when mis-regulated, result aberrant nuclear morphology are poorly understood. In this study we carried out a systematic, high-throughput RNAi screen for genes that affect nuclear morphology in Caenorhabditis elegans embryos. The screen employed over 1700 RNAi constructs against genes required for embryonic viability. Nuclei of early embryos are typically spherical and their NPCs are evenly distributed. The screen was performed on early embryos expressing a fluorescently tagged component of the nuclear pore complex (NPC), allowing visualization of nuclear shape as well as the distribution of NPCs around the nuclear envelope. Our screen uncovered 182 genes whose down-regulation resulted in one or more abnormal nuclear phenotypes, including multiple nuclei, micronuclei, abnormal nuclear shape, anaphase bridges and abnormal NPC distribution. Many of these genes fall into common functional groups, including some that were not previously known to affect nuclear morphology, such as genes involved in mitochondrial function, the vacuolar ATPase and the CCT chaperonin complex. The results of this screen add to our growing knowledge of processes that affect nuclear morphology and that may be altered in cancer cells that exhibit abnormal nuclear shape.

cell biology↗

bioRxiv2021

Convergent loss of the necroptosis pathway in disparate mammalian lineages shapes virus countermeasures

Programmed cell death is a vital process in the life cycle of an organism. Necroptosis, an evolutionary restricted form of programmed necrosis, contributes to the innate immune response by killing pathogen-infected cells. This virus-host interaction pathway is organized around two key components: the receptor-interacting protein kinase 3 (RIPK3), which recruits and phosphorylates the mixed lineage kinase-like protein (MLKL), thus inducing cellular plasma membrane rupture and cell death. Critically, the presence of necroptotic inhibitors in viral genomes validates necroptosis as an important host defense mechanism. Here, we show, counterintuitively, that in different mammalian lineages of mammalian, central components of the necroptotic pathway, such as RIPK3 and MLKL genes, are deleted or display inactivating mutations. Frameshifts or premature stop codons are observed in all the studied species of cetaceans and leporids. In carnivores genomes, the MLKL gene is deleted, while in a small number of species from afrotheria and rodentia premature stop codons are observed in RIPK3 and/or MLKL. Interestingly, we also found a strong correlation between the disruption of necroptosis in leporids and cetaceans and the absence of the C-terminal domain of E3-like homologs (responsible for necroptosis inhibition) in their naturally infecting poxviruses. Overall, our study provides the first comprehensive picture of the molecular evolution of necroptosis in mammals. The loss of necroptosis multiple times during mammalian evolution highlights the importance of gene/pathway loss for species adaptation and suggests that necroptosis is not required for normal mammalian development. Moreover, this study highlights a co-evolutionary relationship between poxviruses and their hosts, emphasizing the role of host adaptation in shaping virus evolution.

evolutionary biology↗

bioRxiv2021

Multi-animal pose estimation and tracking with DeepLabCut

Estimating the pose of multiple animals is a challenging computer vision problem: frequent interactions cause occlusions and complicate the association of detected keypoints to the correct individuals, as well as having extremely similar looking animals that interact more closely than in typical multi-human scenarios. To take up this challenge, we build on DeepLabCut, a popular open source pose estimation toolbox, and provide high-performance animal assembly and tracking--features required for robust multi-animal scenarios. Furthermore, we integrate the ability to predict an animals identity directly to assist tracking (in case of occlusions). We illustrate the power of this framework with four datasets varying in complexity, which we release to serve as a benchmark for future algorithm development.

animal behavior and cognition↗

bioRxiv2021

Remodeling of oxygen-transporting tracheoles drives intestinal regeneration and tumorigenesis

The Drosophila tracheal system, as the functional equivalent of mammalian blood vessels, responds to hypoxia and transports oxygen throughout the body. Although the signaling pathways involved in tracheal development and the hypoxic response are well-studied, how adult tracheae interact with their target tissues is largely unknown. Here we show that the tracheae that serve the adult intestine are dynamic and respond to enteric infection, oxidative agents, and the development of gut tumors with increased terminal branching. Increased tracheation is necessary for efficient damage-induced intestinal stem cell (ISC)-mediated midgut regeneration and sufficient to drive ISC proliferation in the absence of damage. Gut damage or tumors induce Hif-1/Sima, which, in turn, stimulates tracheole branching via the FGF(Brachless/Bnl)/FGFR(Breathless/Btl) signaling cascade. Bnl/Btl signaling is required both in the intestinal epithelium and the tracheal system for efficient damage-induced tracheal remodeling and ISC proliferation. We show that chemical or Pseudomonas-generated ROS directly affect the trachea and are necessary for branching and intestinal regeneration. Similarly, tracheole branching and the resulting increase in oxygen supply are essential for tumor growth in the midgut. Thus, we have identified a novel mechanism of visceral tracheal-intestinal tissue communication, whereby oxidative damage and tumors induce neo-tracheogenesis in adult Drosophila. This process is reminiscent of cancer-induced neo-angiogenesis in mammals.

cell biology↗

bioRxiv2021

Large scale genomic and evolutionary study reveals SARS-CoV-2 virus isolates from Bangladesh strongly correlate with European origin and not with China.

RationaleThe global public health is in serious crisis due to emergence of SARS-CoV-2 virus. Studies are ongoing to reveal the genomic variants of the virus circulating in various parts of the world. However, data generated from low- and middle-income countries are scarce due to resource limitation. This study was focused to perform whole genome sequencing of 151 SARS-CoV-2 isolates from COVID-19 positive Bangladeshi patients. The goal of this study was to identify the genomic variants among the SARS-CoV-2 virus isolates in Bangladesh, to determine the molecular epidemiology and to develop a relationship between host clinical trait with the virus genomic variants. MethodSuspected patients were tested for COVID-19 using one step commercial qPCR kit for SARS-CoV-2 Virus. Viral RNA was extracted from positive patients, converted to cDNA which was amplified using Ion AmpliSeq SARS-CoV-2 Research Panel. Massive parallel sequencing was carried out using Ion AmpliSeq Library Kit Plus. Assembly of raw data is done by aligning the reads to a pre-defined reference genome (NC_045512.2) while retaining the unique variations of the input raw data by creating a consensus genome. A random forest-based association analysis was carried out to correlate the viral genomic variants with the clinical traits present in the host. ResultAmong the 151 viral isolates, we observed the 413 unique variants. Among these 8 variants occurred in more than 80 % of cases which include 241C to T, 1163A to T, 3037C to T,14408C to T, 23403A to G, 28881G to A, 28882 G to A, and finally the 28883G to C. Phylogenetic analysis revealed a predominance of variants belonging to GR clade, which have a strong geographical presence in Europe, indicating possible introduction of the SARS-CoV-2 virus into Bangladesh through a European channel. However, other possibilities like a route of entry from China cannot be ruled out as viral isolate belonging to L clade with a close relationship to Wuhan reference genome was also detected. We observed a total of 37 genomic variants to be strongly associated with clinical symptoms such as fever, sore throat, overall symptomatic status, etc. (Fishers Exact Test p-value<0.05). The most mention-worthy among those were the 3916CtoT (associated with causing sore throat, p-value 0.0005), the 14408C to T (associated with protection from developing cough, p-value= 0.027), and the 28881G to A, 28882G to A, and 28883G to C variant (associated with causing chest pain, p-value 0.025). ConclusionTo our knowledge, this study is the first large scale phylogenomic studies of SARS-CoV-2 virus circulating in Bangladesh. The observed epidemiological and genomic features may inform future research platform for disease management, vaccine development and epidemiological study.

genetics↗

bioRxiv2021

Unfolding the Apoptotic Mechanism of Antioxidant Enriched-Leaves of Tabebuia pallida in EAC Cells

Targeting apoptosis is a promising approach to inhibit the abnormal cell proliferation of cancer progression. Existing anti-apoptotic drugs, many derived from chemical substances, have often failed to combat cancer development and progression. Therefore, identification of apoptosis-inducing anticancer agents from plant-derived sources has become a key aim in cancer research. The present study was designed to explore the regulation of apoptosis by Tabebuia pallida (T. pallida) using an Ehrlich Ascites Carcinoma (EAC) mouse model and compositional analysis by LC-ESI-MS/MS. Dried and powdered T. pallida leaves (TPL), stem bark (TPSB), root bark (TPRB) and flowers (TPF) were extracted with 80% methanol. Using cultured EAC cells and EAC-bearing mice with and without these extracts, anticancer activities were studied by assessing cytotoxicity and tumor cell growth inhibition, changes in life span of mice, and hematological and biochemical parameters. Apoptosis was analyzed by microscopy and expression of selected apoptosis-related genes (Bcl-2, Bcl-xL, NF{kappa}-B, PARP-1, p53, Bax, caspase-3 and -8) using RT-PCR. LC-ESI-MS analysis was performed to identify the major compounds from the most active extracts. In EAC mice compared with untreated controls, the TPL extract exhibited the highest cytotoxicity with significant tumor cell growth inhibition (p< 0.001), reduced ascites by body weight (p< 0.01), increased the life span (p<0.001), normalized blood parameters (RBC/WBC counts), and increased the levels of superoxide dismutase and catalase. TPL-treated EAC cells showed apoptotic characteristics of membrane blebbing, chromatin condensation and nuclear fragmentation, and caspase-3 activation, compared with untreated EAC cells. Moreover, annexin V-FITC and propidium iodide signals were greatly enhanced in response to TPL treatment, indicating apoptosis induction. Pro- and anti-apoptotic signaling after TPL treatment demonstrated up-regulated p53, Bax and PARP-1, and down-regulated NF{kappa}-B, Bcl-2 and Bcl-xL expression, suggesting that TPL shifts the balance of pro- and anti-apoptotic genes towards cell death. LC-ESI-MS data of TPL showed a mixture of glycosides, lapachol, and quercetin antioxidant and its derivatives that were significantly linked to cancer cell targets. In conclusion, the TPL extract of T. pallida possesses significant anticancer activity. The tumor suppressive mechanism is due to apoptosis induced by activation of antioxidant enzymes and caspases and mediated by a change in the balance of pro- and anti-apoptotic genes that promotes cell death. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/426226v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@1112faaorg.highwire.dtl.DTLVardef@1505d1dorg.highwire.dtl.DTLVardef@1115a2aorg.highwire.dtl.DTLVardef@36a915_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2020

Host autophagy mediates organ wasting and nutrient mobilization for tumor growth

During tumor growth - when nutrient and anabolic demands are high - autophagy supports tumor metabolism and growth through lysosomal organelle turnover and nutrient recycling1. Ras-driven tumors additionally invoke non-autonomous autophagy in the microenvironment to support tumor growth, in part through transfer of amino acids2-4. Here we uncover a third critical role of autophagy in mediating systemic organ wasting and nutrient mobilization for tumor growth using a well-characterized malignant tumor model in Drosophila melanogaster. Micro-computed X-ray tomography and metabolic profiling reveal that RasV12; scrib-/- tumors grow 10-fold in volume, while systemic organ wasting unfolds with progressive muscle atrophy, loss of body mass, -motility, -feeding and eventually death. Tissue wasting is found to be mediated by autophagy and results in host mobilization of amino acids and sugars into circulation. Natural abundance Carbon 13 tracing demonstrates that tumor biomass is increasingly derived from host tissues as a nutrient source as wasting progresses. We conclude that host autophagy mediates organ wasting and nutrient mobilization that is utilized for tumor growth.

cell biology↗

bioRxiv2020

Molecular characterization of SARS-CoV-2 from Bangladesh: Implications in genetic diversity, possible origin of the virus, and functional significance of the mutations

In a try to understand the pathogenesis, evolution and epidemiology of the SARS-CoV-2 virus, scientists from all over the world are tracking its genomic changes in real-time. Genomic studies can be helpful in understanding the disease dynamics. We have downloaded 324 complete and near complete SARS-CoV-2 genomes submitted in GISAID database from Bangladesh which were isolated between 30 March to 7 September, 2020. We then compared these genomes with Wuhan reference sequence and found 4160 mutation events including 2253 missense single nucleotide variations, 38 deletions and 10 insertions. The C>T nucleotide change was most prevalent (41% of all muations) possibly due to selective mutation pressure to reduce CpG sites to evade CpG targeted host immune response. The most frequent mutation that occurred in 98% isolates was 3037C>T which is a synonymous change that almost always accompanied 3 other mutations that include 241C>T, 14408C>T (P323L in RdRp) and 23403A>G (D614G in spike protein). The P323L was reported to increase mutation rate and D614G is associated with increased viral replication and currently most prevalent variant circulating all over the world. We identified multiple missense mutations in B-cell and T-cell predicted epitope regions and/or PCR target regions (including R203K and G204R that occurred in 86% of the isolates) that may impact immunogenicity and/or RT-PCR based diagnosis. Our analysis revealed 5 large deletion events in ORF7a and ORF8 gene products that may be associated with less severity of the disease and increased viral clearance. Our phylogeny analysis identified most of the isolates belonged to the Nextstrain clade 20B (86%) and GISAID clade GR (88%). Most of our isolates shared common ancestors either directly with European countries or jointly with middle eastern countries as well as Australia and India. Interestingly, the 19B clade (GISAID S clade) was unique to Chittagong which was originally prevalent in China. This reveals possible multiple introduction of the virus in Bangladesh via different routes. Hence more genome sequencing and analysis with related clinical data is needed to interpret functional significance and better predict the disease dynamics that may be helpful for policy makers to control the COVID-19 pandemic in Bangladesh.

bioinformatics↗

bioRxiv2020

Post-intervention Epidemiology of STH in Bangladesh: data to sustain the gains

IntroductionIn 2008, Bangladesh initiated Preventive Chemotherapy (PCT) for school-age children (SAC) through bi-annual school-based mass drug administration (MDA) to control Soil-Transmitted Helminth (STH) infections. In 2016, the Ministry of Health and Family Welfares Program on Lymphatic Filariasis Elimination and STH (ELFSTH) initiated district-level community impact assessments with Children Without Worms (CWW) using standardized, population-based sampling to measure the post-intervention STH burden across all ages ([≥] 1 yr) for the three STH species. Methods & Principal FindingsThe Integrated Community-based Survey for Program Monitoring (ICSPM) was developed by CWW and was used to survey 12 districts in Bangladesh from 2017 - 2020. We combined the individual demographic and parasite-specific characteristics from 10 districts and linked them with the laboratory data for collective analysis. Our analysis identified district-specific epidemiologic findings, important for program decisions. Of the 17,874 enrolled individuals, 10,824 (61%) provided stool samples. Overall, the prevalence of any STH species was substantially reduced to 14% from 79.8% in 2005. The impact was similar across all ages. STH prevalence was below 10% in 10 districts collectively, but remained high in 4 districts, despite their high reported PCT coverage in previous years. Among all, Bhola district was unique because it was the only district with high Trichuris prevalence. ConclusionBangladesh successfully lowered STH prevalence across all ages despite targeting SAC only. Data from the survey indicate significant number of adults and pre-school age children (PSAC) were self-deworming with purchased pills. This may account for the flat impact curve across all ages. Overall prevalence varied across surveyed districts, with persistent high transmission in the northeastern districts and a district in the central flood zone, indicating possible service and ecological factors. Discrepancies in the impact between districts highlight the need for district-level data to evaluate program implementation after consistent high PCT coverage. Authors SummaryBangladesh government conducted school-based mass drug administration (MDA) for over 10 years to control soil-transmitted helminth (STH) infections. School-based evaluations of MDA indicate a reduction in STH burden among school-aged children (SAC). To further assess the impact on the community, Children Without Worms and the Ministry of Health and Family Welfares Program on Lymphatic Filariasis Elimination and STH (ELFSTH) initiated district-level community impact surveys in 12 districts. We share the results from the latter 10 districts here. Our analysis of 10,824 interviews and stool samples from 10 districts showed an estimated 14% of community members infected with at least one species of STH. This finding is substantially lower than the baseline STH prevalence (79.8%) estimated in 2005. Bangladeshs successful impact was achieved across all ages despite only treating SAC. Deworming source data showed significant numbers of adults and pre-school age children (PSAC) self-dewormed with locally purchased pills. Prevalence varied across the surveyed districts, with persistent high transmission in the northeastern districts and a district in the central flood zone, indicating possible ecological and service factors contributing to persistent infections. Discrepancies in the impact across districts highlights the need for sub-national level data to evaluate program performance fllowing consistent high intervention.

scientific communication and education↗

bioRxiv2020

Entelon(R) (vitis vinifera seed extract) reduces inflammation and calcification in a beagle dog model of intravascular bovine pericardium implantation

ObjectiveInflammation and calcification are major factors responsible for failure of bioprosthetic valve and other substitute heart valve implantations. The objective of this study was to evaluate the anti-inflammatory and anti-calcification effects of Entelon150(R) (consisting of grape-seed extract) in a beagle dog model of intravascular bovine pericardium implantation. MethodsIn total, 8 healthy male beagle dogs were implanted with a bovine pericardium bilaterally in the external jugular veins and divided into two groups. Animals in the Entelon150(R) group (n = 4) were treated with 150 mg of Entelon150(R) twice daily for six weeks after surgery. The negative control (NC) group (n = 4) was treated with 5 ml of saline using the same method. After six weeks, we measured the calcium content, performed histological examination, and performed molecular analysis. ResultsThe calcium content of implanted tissue in the Entelon150(R) group (0.56{+/-}0.14 mg/g) was significantly lower than that in the NC group (1.48{+/-}0.57 mg/g) (p < 0.05). Histopathological examination showed that infiltration of chronic inflammatory cells, such as fibroblasts and macrophages, occurred around the graft in all groups; however, the inflammation level of the implanted tissue in the Entelon150(R) group was significantly lower than that in the NC group. Both immunohistochemical and western blot analyses revealed that bone morphogenetic protein 2 expression was significantly attenuated in the Entelon150(R) group. ConclusionsOur results indicate that Entelon150(R) significantly attenuates post-implantation inflammation and degenerative calcification of the bovine pericardium in dogs. Therefore, Entelon150(R) may increase the longevity of the bovine pericardium after intravascular implantation.

bioengineering↗

bioRxiv2020

Genetic analysis of SARS-CoV-2 isolates collected from Bangladesh: insights into the origin, mutation spectrum, and possible pathomechanism

As the coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), rages across the world, killing hundreds of thousands and infecting millions, researchers are racing against time to elucidate the viral genome. Some Bangladeshi institutes are also in this race, sequenced a few isolates of the virus collected from Bangladesh. Here, we present a genomic analysis of 14 isolates. The analysis revealed that SARS-CoV-2 isolates sequenced from Dhaka and Chittagong were the lineage of Europe and the Middle East, respectively. Our analysis identified a total of 42 mutations, including three large deletions, half of which were synonymous. Most of the missense mutations in Bangladeshi isolates found to have weak effects on the pathogenesis. Some mutations may lead the virus to be less pathogenic than the other countries. Molecular docking analysis to evaluate the effect of the mutations on the interaction between the viral spike proteins and the human ACE2 receptor, though no significant interaction was observed. This study provides some preliminary insights into the origin of Bangladeshi SARS-CoV-2 isolates, mutation spectrum and its possible pathomechanism, which may give an essential clue for designing therapeutics and management of COVID-19 in Bangladesh.

genomics↗

bioRxiv2020

Novel insights into the structure and transport mechanisms of TAPT1

Transmembrane anterior-posterior transformation protein 1 (TAPT1), encoded by the TAPT1 gene expressed in the basal ciliary body, plays a crucial role in cilia formation as well as axial skeletal patterning. Mutations in this gene have been reported to cause several ciliopathies and osteo-related diseases. Unfortunately, the cellular and molecular pathogenic mechanisms are still unclear also due to the lack of X-ray crystallographic structure and further characterization of TAPT1 protein. In this study, we attempted to characterize this protein by in silico techniques. A 3D structure of TAPT1 was generated by the ab initio method, which was further used for the analysis of the substrate-binding site, to determine pore size and for the prediction of the possible substrate(s). Validation by using different software packages revealed a reliable 3D model of TAPT1. Topology modeling revealed that TAPT1 has eight transmembrane helices with a total number of 27 helices in secondary structure. The amino acid residues H235, R323, K443, N446, S447, L450, K453, S454, Y457, K511, N513, D533, K535, D536, and T538 were found to form the pore surface as well as involved in the binding interaction with the substrate(s). This study predicted flavonoids as the possible substrate for TAPT1, which could further be confirmed by ingenuity pathway analysis. Moreover, our analysis indicated that TAPT1 might localize in the mitochondrial membrane in addition to the ciliary basal body. Our study gives novel insights for TAPT1 structure and its function.

biochemistry↗

bioRxiv2020

A novel RNA virus, Macrobrachium rosenbergii Golda virus (MrGV), linked to mass mortalities of the larval giant freshwater prawn in Bangladesh

1Mass mortalities of the larval stage of the giant freshwater prawn, Macrobrachium rosenbergii, have been occurring in Bangladesh since 2011. Mortalities can reach 100% and have resulted in an 80% decline in the number of hatcheries actively producing M. rosenbergii. To investigate a causative agent for the mortalities, a disease challenge was carried out using infected material from a hatchery experiencing mortalities. Moribund larvae from the challenge were prepared for metatranscriptomic sequencing. De novo virus assembly revealed a 29 kb single-stranded positive-sense RNA virus with similarities in key protein motif sequences to yellow head virus (YHV), an RNA virus that causes mass mortalities in marine shrimp aquaculture, and other viruses in the Nidovirales order. Primers were designed against the novel virus and used to screen cDNA from larvae sampled from hatcheries in the South of Bangladesh from two consecutive years. Larvae from all hatcheries screened from both years were positive by PCR for the novel virus, including larvae from a hatchery that at the point of sampling appeared healthy, but later experienced mortalities. These screens suggest that the virus is widespread in M. rosenbergii hatchery culture in southern Bangladesh, and that early detection of the virus can be achieved by PCR. The hypothesised protein motifs of MrGV suggest that it is likely to be a new species within the Nidovirales order. Biosecurity measures should be taken in order to mitigate global spread through the movement of post-larvae within and between countries, which has previously been linked to other virus outbreaks in crustacean aquaculture.

molecular biology↗

bioRxiv2020

Evaluation of Neuropharmacological Effects of Different Chemical Extracts of Flemingia Stricta (Roxb.) Leaves.

BackgroundTraditional preparation of the leaf of Flemingia stricta (Fabaceae) Roxb., a medicinal plant of the Indian subcontinent, has been used for treatment of different diseases as herbal preparation. Our purpose was to analyze Neuropharmacological effects of different chemical extracts of Flemingia stricta Roxb. as particular form of behavioral inhibition that occurs in response to novel environmental events. MethodsIn present study, the anxiogenic activity of crude extracts of Flemingia stricta leaves was determined using standard animal behavioral models, such as hole cross and open field; Sedative property and anxiolytic potential were assessed by conducting thiopental sodium induced sleeping times tests and elevated plus maze test respectively. ResultsThe crude extracts at both dose (200 and 400mg/kg) exhibited a significant (P<0.05, P<0.01) dose-dependent suppression of motor activity and exploratory activity of mice in both open field and hole cross test. In anxiolytic study, extracts displayed increased percentage of entry into open arm at the dose of 200 and 400mg/kg. Extracts produced a significant (P<0.05, P<0.01) increase in sleeping duration and reduction of onset of sleep compared to sodium thiopental at both doses (200 and 400mg/kg). ConclusionThis study demonstrates that the treated extracts have significant central nervous system depressant effect. Further studies on the active constituent of the extract can provide approaches for therapeutic intervention.

pharmacology and toxicology↗

bioRxiv2020

Prediction of Motor Imagery Tasks from Multi-Channel EEG Data for Brain-Computer Interface Applications

The classification of motor imagery electroencephalogram (MI-EEG) is a pivotal part of the biosignal classification in the brain-computer interface (BCI) applications. Currently, this bio-engineering based technology is being employed by researchers in various fields to develop cutting edge applications. The classification of real-time MI-EEG signal is the core computing and challenging task in these applications. It is well-known that the existing classification methods are not so accurate due to the high dimensionality and dynamic behaviors of the real-time EEG data. To improve the classification performance of real-time BCI applications, this paper presents a clustering-based ensemble technique and a developed brain game that distinguishes different human thoughts. At first, we have gathered the brain signals, extracted and selected informative features from these signals to generate training and testing sets. After that, we have constructed several classifiers using Artificial Neural Network (ANN), Support Vector Machine (SVM), naive Bayes, Decision Tree (DT), Random Forest, Bagging, AdaBoost and compared the performance of these existing approaches with suggested clustering-based ensemble technique. On average, the proposed ensemble technique improved the classification accuracy of roughly 5 to 15% compared to the existing methods. Finally, we have developed the targeted brain game employing our suggested ensemble technique. In this game, real-time EEG signal classification and prediction tabulation through animated ball are controlled via threads. By playing this game, users can control the movements of the balls via the brain signals of motor imagery movements without using any traditional input devices. All relevant codes are available via open repository at: https://github.com/mrzResearchArena/MI-EEG.

bioengineering↗