Biology subjects

Islam, M. S.

Publications and source records attributed to Islam, M. S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Mutation profiling of KRAS and BRAF in primary tumors and circulating tumor cells of colorectal cancer patients using PNA-LNA molecular switch

Identifying KRAS and BRAF mutation status is essential for guiding targeted therapies and enhancing treatment outcomes in colorectal cancer (CRC). This study employs the "PNA-LNA molecular switch" to detect mutations in KRAS codon 12 (c.35G>T/G12V) and BRAF codon 600 (c.1799T>A/V600E) from primary tumours and circulating tumour cells (CTCs) in CRC patients, correlating mutation status with clinicopathological parameters. DNA was isolated from 71 primary tumours and 37 CTC samples. Mutation profiles were generated using the PNA-LNA molecular switch. KRAS mutations were detected in 26 primary tumours (36.6%) and 13 CTCs (26.8%), while BRAF mutations were observed in 19 primary tumours (26.8%) and 7 CTCs (19%). No significant correlation was observed between mutation status and clinicopathological parameters in primary tumours. However, KRAS G12V mutations in CTCs significantly correlated with lymph node metastasis (p=0.002), overall pathological stage (p=0.005), and lymphovascular invasion (p=0.034). BRAF V600E mutation status showed no significant clinicopathological associations. Validation of the PNA-LNA molecular switch against Next-Generation Sequencing (NGS) showed 89% concordance with p-values < 0.001 for both genes. This method is highly comparable to NGS for detecting KRAS and BRAF mutations and shows promise as a point-of-care diagnostic tool. Larger patient cohorts are required to confirm its clinical utility.

cancer biology↗

bioRxiv2025

Integrative Machine Learning Reveals Potential Signature Genes Using Transcriptomics in Colon Cancer

BackgroundColon cancer is a significant health burden in the world and the second leading cause of cancer-related deaths. Despite advancements in diagnosis and treatment, identifying robust biomarkers for early detection and therapeutic targets remains imperative. Materials and methodsThis study used an integrative approach combining transcriptomics and machine learning to identify signature genes and pathways associated with colon cancer. RNA-Seq data from The Cancer Genome Atlas-Colon Adenocarcinoma (TCGA-COAD) project, comprising 485 samples (444 tumors and 41 normal tissues), were analyzed. ResultsDifferential gene expression analysis revealed 657 upregulated and 8,566 downregulated genes. Notably, EPB41L3, TSPAN7, and ABI3BP were identified as highly upregulated, while LYVE1, PLPP1, and NFE2L3 were significantly downregulated in tumor samples. Gene Set Enrichment Analysis (GSEA) identified dysregulated pathways, including E2F targets, MYC targets, and G2M checkpoints, underscoring cell cycle regulation and metabolic reprogramming alterations in colon cancer. Machine learning models-Random Forest, Neural Networks, and Logistic Regression-achieved high classification accuracy (97-99%) and near-perfect Area Under the Receiver Operating Characteristic Curve (AUC-ROC) values (approximately 1.00), validating their predictive capabilities. Key genes consistently identified across these models highlight their potential translational relevance as biomarkers. This study integrates differential expression analysis, pathway enrichment, and machine learning to uncover critical insights into colon cancer biology. ConclusionThe findings lay the groundwork for developing diagnostic and therapeutic strategies, with the identified genes and pathways serving as promising candidates for future validation and clinical applications. This approach exemplifies the potential of precision medicine to advance colon cancer research and improve patient outcomes.

cancer biology↗

bioRxiv2025

Modulation of cellular ageing regulates Integrated Stress Response signalling to control blood cell homeostasis

Organismal ageing is associated with a decline in cellular and molecular functions. One of the hallmarks of ageing is stem cell exhaustion which occurs due to dynamic changes in the stem cell - niche microenvironment. Ageing affects stem cell potency impacting self-renewal and differentiation trajectories. Blood cell homeostasis in the hematopoietic system is tightly regulated by a fine balance between stemness and differentiation. Here, we employ the Drosophila hematopoietic organ, the larval lymph gland (LG) to investigate the impact of modulating cellular ageing on organ homeostasis. LG consists of a Posterior Signalling Center (PSC) that acts as a stem cell niche and maintains the prohemocytes housed in the Medullary Zone (MZ). Cortical Zone (CZ) consists of differentiated hemocytes namely plasmatocytes, crystal cells and lamellocytes. Intricate signalling networks active in the PSC and MZ orchestrate and regulate homeostasis. In this study, we characterize the effect of genetic perturbation of the molecular circuitry of ageing locally and systemically to investigate its effect on LG blood cell homeostasis. Genetic modulation of cellular ageing displays traditional hallmarks of ageing validating our model in the LG. Our results indicate that induction of accelerated ageing both locally and systemically leads to a reduction in stem cell niche size, DNA damage accumulation and increased progenitor differentiation whereas decelerated ageing shows an opposite trend. We show that the Integrated Stress Response (ISR) pathway is activated upon inducing accelerated ageing in the LG hemocytes possibly to recoup back to homeostatic conditions. Furthermore, LGs of ISR pathway mutants or upon perturbation of ISR pathway components in prohemocytes show increased blood cell differentiation indicating disruption of homeostasis. Genetic epistasis analysis shows that ectopic over-expression of ISR pathway genes in an accelerated ageing scenario over and above the existing levels can rescue the defects in blood cell homeostasis. Overall, our study explores how modulation of cellular aging locally or systemically can impact tissue homeostasis. Our research paves way to understand the cellular mechanisms underlying an aged versus young stem cell-niche microenvironment and how its abrogation may lead to onset of disease.

developmental biology↗

bioRxiv2024

Antimicrobial resistance, pathogenicity and virulence patterns of Escherichia coli isolated from cockroaches (Blattella germanica) across diverse environments: a public health concern

This investigation explores the prevalence and antimicrobial resistance (AMR) of Escherichia coli isolated from Blattella germanica (cockroaches) from diverse locations, including homes, kitchens, and laboratories, over the course of six months, from August 2022 to January 2023. A total of 125 cockroaches were analyzed, yielding 67 (53%) of positive E. coli isolates, with kitchen environments having the highest incidence (57.77%). The existence of virulence genes (stx1, stx2, and rfbO157) was confirmed by pathogenicity assessments carried out on mouse model, which led to a considerable increase in morbidity and mortality. 82.08% of isolates showed evidence of resistance to at least one antibiotic, according to the antimicrobial susceptibility test with {beta}-lactams displaying the highest rates of resistance. Remarkably, complex resistance patterns were observed in 77.61% of the isolates, which were categorized as multidrug-resistant. Multiple antibiotic resistance genes (ARGs) were found by molecular analysis, particularly blaTEM and tetA as well as virulence-associated genes (VAGs) linked to extraintestinal pathogenic E. coli. Phylogenetic grouping indicated that 90.38% of the MDR isolates belonged to virulent groups B2 and D. These findings highlight the role of cockroaches as potential reservoirs for pathogenic E. coli, raising significant public health concerns regarding AMR. The study underscores the imperative need for thorough investigation and feasible control strategies to ease the dissemination of AMR in diverse contexts.

microbiology↗

bioRxiv2024

Pairwise interactions, feedback rule changes, and deliberative decisions underlie honeybee inflight group coordination

Systematic descriptions of the underlying interaction rules that insects use to support group and swarm flight has the potential to contribute to mathematics, biology, and robotics, including aerial swarming under sensory and computational limitations. This study analyzes 1,000 trajectories of flying honeybees in crowded conditions approaching a moving stimulus and finds how during this stimulus, honeybees coordinate flight through pairwise interactions involving a novel three-zone decision-making process. The experimental setup consists of 3-D position reconstructions via a high speed camera system recording honeybee foragers returning to a hive entrance actuated to move robotically. The analysis consists of neighborhood identification through three methods (cross-correlation, distance threshold, and average distance threshold), which reveals the dominant interaction is pairwise. The individual leader-follower pair interactions are then tested against three regulation candidates: optic flow, relative velocity, and optical expansion rate, based on minimizing root mean square error. The results show that each follower demonstrates a three stage process involving a feedback rule change, linked by an intermediate observation/decision phase. During the initial "lock" phase, an insect maintains a consistent optical expansion rate until inter-agent distance closes to 10 cm. The regulation candidates then undergo large variations during a relatively long observation/decision zone, with 1.04 seconds being the average time in the decision zone. 79% of the paired insect entries into the decision zone result in subsequent re-engagement to track the same initial leader, while 21% result in disengagement from the group behavior. Visual regulation candidate comparison in the third stage indicates that upon re-engagement, the follower relative velocity is regulated to provide consistent velocity matching between agents. The third stages velocity tracking is consistent with a closed-loop feedback proportional-integral (PI) controller regulating velocity tracking error. Across the insect population studied, the proportional gain remained showed minimal variability over individuals, a derivative gain was considered and found negligible, and the integral gain varied by individual. Collectively, these findings underscore the existence of an alternative swarm architecture, highlighting individual decision-making capabilities, feedback regulation target changes, and the presence of reactive, deliberative, and moderate (PI control) timescale interaction rules contained within aerial groups.

animal behavior and cognition↗

bioRxiv2024

MDRepo - an open environment for data warehousing and knowledge discovery from molecular dynamics simulations

BackgroundMolecular Dynamics (MD) simulation of biomolecules provides important insights into conformational changes and dynamic behavior, revealing critical information about folding and interactions with other molecules. This enables advances in drug discovery and the design of therapeutic interventions. The collection of simulations stored in computers across the world holds immense potential to serve as training data for future Machine Learning models that will transform the prediction of structure, dynamics, drug interactions, and more. A needIdeally, there should exist an open access repository that enables scientists to submit and store their MD simulations of proteins and protein-drug interactions, and to find, retrieve, analyze, and visualize simulations produced by others. However, despite the ubiquity of MD simulation in structural biology, no such repository exists; as a result, simulations are instead stored in scattered locations without uniform metadata or access protocols. A solutionHere, we introduce MDRepo, a robust infrastructure that supports a relatively simple process for standardized community contribution of simulations, activates common downstream analyses on stored data, and enables search, retrieval, and visualization of contributed data. MDRepo is built on top of the open-source CyVerse research cyberinfrastructure, and is capable of storing petabytes of simulations, while providing high bandwidth upload and download capabilities and laying a foundation for cloud-based access to its stored data.

biochemistry↗

bioRxiv2024

The Ubiquitin Ligase RBX2/SAG Regulates Mitochondrial Ubiquitination and Mitophagy

Clearance of damaged mitochondria via mitophagy is crucial for cellular homeostasis. While the role of ubiquitin (Ub) ligase PARKIN in mitophagy has been extensively studied, increasing evidence suggests the existence of PARKIN-independent mitophagy in highly metabolically active organs such as the heart. Here, we identify a crucial role for Cullin-RING Ub ligase 5 (CRL5) in basal mitochondrial turnover in cardiomyocytes. CRL5 is a multi-subunit Ub ligase comprised by the catalytic RING box protein RBX2 (also known as SAG), scaffold protein Cullin 5 (CUL5), and a substrate-recognizing receptor. Analysis of the mitochondrial outer membrane-interacting proteome uncovered a robust association of CRLs with mitochondria. Subcellular fractionation, immunostaining, and immunogold electron microscopy established that RBX2 and Cul5, two core components of CRL5, localizes to mitochondria. Depletion of RBX2 inhibited mitochondrial ubiquitination and turnover, impaired mitochondrial membrane potential and respiration, and increased cell death in cardiomyocytes. In vivo, deletion of the Rbx2 gene in adult mouse hearts suppressed mitophagic activity, provoked accumulation of damaged mitochondria in the myocardium, and disrupted myocardial metabolism, leading to rapid development of dilated cardiomyopathy and heart failure. Similarly, ablation of RBX2 in the developing heart resulted in dilated cardiomyopathy and heart failure. Notably, the action of RBX2 in mitochondria is not dependent on PARKIN, and PARKIN gene deletion had no impact on the onset and progression of cardiomyopathy in RBX2-deficient hearts. Furthermore, RBX2 controls the stability of PINK1 in mitochondria. Proteomics and biochemical analyses further revealed a global impact of RBX2 deficiency on the mitochondrial proteome and identified several mitochondrial proteins as its putative substrates. These findings identify RBX2-CRL5 as a mitochondrial Ub ligase that controls mitophagy under physiological conditions in a PARKIN-independent, PINK1-dependent manner, thereby regulating cardiac homeostasis.

pathology↗

bioRxiv2024

Comparative analyses of adsorbed circulating proteins in the PMMA and PES hemodiafilters in patients on predilution online hemodiafiltration

Acute and chronic inflammation are common in patients with end-stage kidney disease (ESKD). So, the adsorption of pro-inflammatory cytokines by the hollow fiber has been expected to modify the inflammatory dysregulation in ESKD patients. However, it remains to be determined in detail what molecules of fiber materials can preferably adsorb proteins from the circulating circuit. We aimed this study to analyze directly the adsorbed proteins in the polymethyl methacrylate (PMMA) and polyethersulfone (PES) membranes in patients on predilution online hemodiafiltration (OL-HDF). To compare the adsorbed proteins in the PMMA and PES hemodiafilters membrane, we initially performed predilution OL-HDF using the PES (MFX-25Seco) membrane while then switched to the PMMA (PMF-A) membrane under the same condition in three patients. We extracted proteins from the collected hemodiafilters by extraction, then SDS-PAGE of the extracted sample, protein isolation, in-gel tryptic digestion, and nano-LC MS/MS analyses. The concentrations of adsorbed proteins from the PMMA and PES membrane extracts were 35.6{+/-}7.9 {micro}g/{micro}L and 26.1{+/-}9.2 {micro}g/{micro}L. SDS-PAGE analysis revealed distinct variations of adsorbed proteins mainly in the molecular weight between 10 to 25 kDa. By tryptic gel digestion and mass spectrometric analysis, the PMMA membrane exhibited higher adsorptions of {beta}2 microglobulin, dermcidin, retinol-binding protein-4, and lambda-1 light chain than those from the PES membrane. In contrast, amyloid A-1 protein was adsorbed more potently in the PES membrane. Western blot analyses revealed that the PMMA membrane adsorbed interleukin-6 (IL-6) approximately 5 to 118 times compared to the PES membrane. These findings suggest that PMMA-based OL-HDF therapy may be useful in controlling inflammatory status in ESKD patients.

pathology↗

bioRxiv2023

Identification of Natural Antiviral Drug Candidates Against Tilapia Lake Virus: Computational Drug Design Approaches

Tilapia Lake Virus (TiLV) is a disease that affects tilapia fish, causing a high rate of sudden death at any stage of their growth. Unfortunately, there are currently no effective antiviral drugs or vaccines to control the progression of this disease. Researchers have discovered that the CRM1 protein plays a critical function in the development and spreading of animal viruses. By inhibiting CRM1, the viruss spread in commercial fish farms can be suppressed. With this in mind, this study intended to identify potential antiviral drugs from two different tropical mangrove plants from tropical regions: Heritiera fomes and Ceriops candolleana. To identify promising compounds that target the CRM1 protein, a computer-aided drug discovery approach is employed containing molecular docking, ADME (absorption, distribution, metabolism and excretion) analysis, toxicity assessment as well as molecular dynamics (MD) simulation. To estimate binding affinities of all phytochemicals, molecular docking is used and the top three candidate compounds with the highest docking scores were selected, which are CID107876 (-8.3), CID12795736 (-8.2), and CID12303662 (-7.9). We also evaluated the ADME and toxicity properties of these compounds. Finally, molecular dynamics simulation was conducted to analyze the stability of the protein-ligand complex structures and confirm the suitability of these compounds. The computational study demonstrated that the phytochemicals found in H. fomes and C. candolleana could potentially serve as important inhibitors of TiLV, offering practical utility. However, further in vivo investigations are necessary to investigate the effectiveness of these compounds as antiviral drugs against the virus TiLV.

pharmacology and toxicology↗

bioRxiv2023

UBL3 interaction with α-synuclein is downregulated by silencing MGST3

Ubiquitin-like 3 (UBL3) is a membrane-anchored protein that has been discovered to function as a protein post-translational modifier, helping to sort proteins into small extracellular vesicles (sEVs). Aggregations of alpha-synuclein (-syn) are associated with the pathology of neurodegenerative diseases such as Parkinsons disease (PD). The aggregation and toxicity of -syn can be influenced by its interactions with specific proteins. Recently, the interactions between UBL3 and -syn was uncovered. It is believed to play a role in eliminating excess -syn from neurons, or in the spread of -syn pathology in the brain associated with neurodegenerative diseases. However, the regulator that can mediate the interaction between UBL3 and -syn remains unclear. In this study, we employed the split gaussian luciferase complementation assay and RNA interference (RNAi) technology to discover that QSOX2, HTATIP2, UBE3C, MGST3, NSF, HECTD1, SAE1 and ATG3 are involved in downregulating the interaction between UBL3 and -syn. Among these proteins, silencing MGST3 had the most significant impact on the UBL3--syn interaction (with a fold change log2 of less than - 1). MGST3 is a part of the antioxidant system, and silencing MGST3 is believed to contribute to oxidative stress. We used hydrogen peroxide (H2O2) to induce oxidative stress and observed its effect on the UBL3--syn interaction. Our finding showed that an 800M concentration of H2O2 could also downregulate this interaction. However, the effect of oxidative stress caused by 800M H2O2 on the UBL3--syn interaction did not be enhanced by silencing MGST3. In conclusion, the interaction between UBL3 and -syn is downregulated by silencing MGST3.

molecular biology↗

bioRxiv2022

Genomic diversity of Streptococcus uberis isolated from clinical mastitis of cattle in selected areas of Bangladesh

Streptococci are the major etiology in mastitis, a cause of huge economic losses in the dairy industries. Streptococcus (S.) agalactiae, S. dysagalactiae and S. uberis are mostly encountered in bovine mastitis; however, data on the diversity and characteristics of Streptococcus in clinical mastitis of cattle in Bangladesh is lacking. Thus, the present study was aimed to determine the diversity and antimicrobial resistance pattern of Streptococcus spp. isolated from clinical mastitis of cattle reared in Bangladesh. A total of 105 milk samples comprising eighty (80) from cattle with clinical mastitis (CCM) and twenty-five (25) from apparently healthy cattle (AHC) in four prominent dairy farms and one dairy community were purposively collected and examined in this study. Milk samples were enriched in Luria Bertani broth (LB) and Streptococcus spp. was isolated on Modified Edwards Medium and identified by 16S rRNA gene sequencing. Among eighty (80) clinical samples, eighteen (18) were positive for Streptococcus spp. while none of the milk from AHC revealed Streptococcus by cultural and molecular examination. Sequencing and phylogenetic analysis identified 55.6%, 33.3%, 5.6% and 5.6% of the Streptococcus isolates as S. uberis, S. agalactiae, S. hyovaginalis and S. urinalis, respectively. Antibiotic sensitivity testing with antimicrobials commonly used to treat clinical mastitis revealed 100%, 100%, and 30% of the S. agalactiae, S. hyovaginalis, and S. uberis as multidrug-resistant, respectively. Molecular characterization through whole genome sequencing of five (5) S. uberis isolates identified at least two novel ST types of S. uberis circulating in the study areas with one ST (4/5 isolates) clustered with the isolates from China, India and Thailand, and the other (1/5) with UK, Ireland and Australia. Pan-genome analysis and phylogeny of the core genome sequences also clustered the isolates into two sub-clusters, indicating the presence of at least two different subtypes of S. uberis in the study area. On virulence profiling, all the isolates of this study were found to harbor at least 35 virulence and putative virulence genes probably associated with intramammary infection (IMI) indicating all the S. uberis isolated in this study as potential pathogen. From the overall findings it was evident that Strepococcus occurring in bovine mastitis are diverse and S. uberis genome carries an array of putative virulence factors which need to be investigated genotypically and phenotypically to identify a specific trait or determinant governing the virulence and fitness of this bacterium. Moreover, Streptococcus isolated in this study carried multidrug resistance which needs careful consideration during the selection of a treatment regimen for mastitis.

microbiology↗

bioRxiv2022

Reverse genetics identifies proteins regulating lipid droplet biogenesis via amphipathic helices

Lipid droplets (LDs) are storage organelles for neutral lipids. Our knowledge about fungal LD biogenesis is limited to budding yeast. Moreover, the regulation of LD in multinucleated filamentous fungi with considerable metabolic activity is unknown. Here, 19 LD-associated proteins were identified in Aspergillus oryzae using colocalization screening of a previously established Enhanced green fluorescent protein (EGFP) fusion proteins library. Following a functional screening, 12 candidates have been identified as lipid droplet regulating (LDR) proteins, the loss of which resulted in aberrant LD biogenesis. Four LDR proteins localize to LD via the putative amphipathic helices (AHs), as demonstrated with bioinformatics, targeted mutagenesis, and imaging. Further analysis revealed that LdrA with Opi1 domain is essential for cytoplasmic and nuclear LD biogenesis via this novel AH. Phylogenetic analysis demonstrated the pattern of their evolution, which was predominantly based-on gene duplication. Our study provides substantial molecular and evolutionary insights into LD biogenesis and creates a breakthrough in using reverse genetics for identifying LD-regulating proteins.

cell biology↗

bioRxiv2022

Comparative Phylogenetic Analysis and Transcriptomic Profiling of Dengue (DENV-3 genotype I) Outbreak in 2021 in Bangladesh

ObjectivesThe lack of a dengue disease animal model and the complex immune interaction in dengue infection hinders the study of host response and immunopathogenesis. The development of next-generation sequencing (NGS) technology allowed the researchers to study the transcriptomic profiles of human in-depth. We, therefore, implicated phylodynamic and transcriptomic approaches through NGS technology to know the origin of dengue virus (DENV) and their host response in infected patients with dengue fever. MethodsTo determine the whole genome sequences of the dengue virus and their transcriptomic profiles, RNA was extracted from the serum samples of 3 healthy, and 21 dengue patients. These samples were custom performed at phylogenetic, phylodynamic, differential express gene (DEG), and gene ontology (GO) using respective bioinformatics tools. ResultsThe whole genome sequence analysis revealed that the total number of nucleotide ranges on these serum RNA samples were in between 10647 and 10707. Phylogenetic tree analysis showed that these strains were belonged to DENV-3 genotype I. Phylodynamic analysis showed that the 2021 epidemic isolates were clade shifted and maintained as a new clade in compared to 2019 epidemic. Transcriptome analysis mapped a total of 19267 expressed genes. Of them, there were higher expression of genes in dengue-positive samples (n = 17375) with a count of 6953 unique genes in comparison to healthy controls (n = 12314) with a count of 1892 unique genes. A total of 2686 DEGs were identified in a host factor-independent manner in dengue patients with a q-value < 0.05. DESeq2 plot counts function of the top 24 genes with the smallest q-values of differential gene expression of RNA-seq data showed that 11 genes were upregulated, whereas 13 genes were downregulated. GO analysis showed a significant upregulation (p = <0.001) in a process of multicellular organismal, nervous system, sensory perception of chemical stimulus, and G protein-coupled receptor signalling pathways in the dengue patients. However, there were a significant downregulation (p = < 0.001) of intracellular component, cellular anatomical entity, and protein-containing complex in dengue patients. Most importantly, there was significant increase of a classes of immunity protein (Cytokines especially TGF-{beta}1, chemokines, inflammasome, and factors for blood coagulations) in dengue patients in compared to the healthy controls, with increased GO of immune system process. In addition, upregulation of toll receptor (TLR) signalling pathways were also initiated in the patients infected with dengue virus. These TLR pathways were particularly involved for the activation of innate in couple with adaptive immune system that probably involved the rapid elimination of dengue virus infected cells. These differentially expressed genes could be further investigated for target based prophylactic interventions for dengue. ConclusionThis is a first report to document the complete genomic features of dengue, and differentially expressed genes in patients with dengue virus in Bangladesh. These genes may have diagnostic and therapeutic values for dengue infection. Continual genomic surveillance is required to further investigate the shift in dominant genotypes in relation to viral pathogenesis.

evolutionary biology↗

bioRxiv2022

Molecular characterization of enolase from Haemaphysalis longicornis tick

Withdrawal StatementThe authors have withdrawn their manuscript owing to for more improvement in our research work and need to revise our manuscript. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

molecular biology↗

bioRxiv2022

Insect visuomotor delay adjustments in group flightsupport swarm cohesion

Flying insects routinely demonstrate coordinated flight in groups. How they achieve this with very limited communication, vision, and neural systems remains an open question. We measured the visual reaction time in flying honeybees while they chased a moving target, and compared in-flight reaction times for solo animals with those flying in groups. Across 425 insects, the solo honeybees show diverse reaction times (an average of 30ms and a standard deviation of 50ms). The reaction times in groups are significantly more uniform (an average of 15ms and a standard deviation of only 7ms), indicating that honeybees in group flight adjust their reaction times to match their neighbors. To investigate the role of this adjustment, we curve fit the reaction time distributions and analyzed them in a mathematical model of swarming, finding that the reaction time increases the stable region of a cohesive swarm. To verify the stabilizing effect was not an artifact of curve fitting, we then inserted the measured delays in a swarm simulation, which breaks apart under the solo reaction times and achieves stable formations for the group reaction times. Together, our findings highlight how flying animals can synchronize their reaction times in group flights to improve group cohesion.

animal behavior and cognition↗

bioRxiv2022

Experimental identification of individual insect visual tracking delays in free flight and their effects on visual swarm patterns

Insects are model systems for swarming robotic agents, yet engineered descriptions do not fully explain the mechanisms by which they provide onboard sensing and feedback to support such motions; in particular, the exact value and population distribution of visuomotor processing delays are not yet quantified, nor the effect of such delays on a visually-interconnected swarm. This study measures untethered insects performing a solo in-flight visual tracking task and applies system identification techniques to build an experimentally-consistent model of the visual tracking behaviors, and then integrates the measured experimental delay and its variation into a visually interconnected swarm model to develop theoretical and simulated solutions and stability limits. The experimental techniques include the development of a moving visual stimulus and real-time multi camera based tracking system called VISIONS1 providing the capability to recognize and simultaneously track both a visual stimulus (input) and an insect at a frame rate of 60-120 Hz. A frequency domain analysis of honeybee tracking trajectories is conducted via fast Fourier and Chirp Z transforms, identifying a coherent linear region and its model structure. The model output is compared in time and frequency domain simulations. The experimentally measured delays are then related to probability density functions, and both the measured delays and their distribution are incorporated as inter-agent interaction delays in a second order swarming dynamics model. Linear stability and bifurcation analysis on the long range asymptotic behavior is used to identify delay distributions leading to a family of solutions with stable and unstable swarm center of mass (barycenter) locations. Numerical simulations are used to verify these results with both continuous and modeled distributions. The results of this experiment quantify a model structure and temporal lag (transport delay) in the closed loop dynamics, and show that this delay varies across 50 individuals from 5-110ms, with an average delay of 22ms and a standard deviation of 40ms. When analyzed within the swarm model, the measured delays support a diversity of solutions and indicate an unstable barycenter.

bioengineering↗

bioRxiv2022

Genomic characteristics, virulence and antimicrobial resistance in avian pathogenic Escherichia coli MTR_BAU02 strain isolated from layer farms in Bangladesh

BackgroundColibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most significant infectious diseases affecting poultry worldwide. APEC is one of the leading causes of mortality and morbidity associated with significant economic losses in the poultry industry. ObjectiveThis study was aimed to determine the genomic diversity, virulence factor genes (VFGs) and antimicrobial resistance (AMR) genes in the APEC isolated from layer chickens using whole-genome sequencing (WGS). MethodAPEC MTR_BAU02 strain was isolated from the sick and dead birds. Genomic DNA from APEC MTR_BAU02 strain was extracted using commercial DNA extraction kit, WGS libraries were prepared using the Nextera DNA Flex Library Prep Kit, and finally, paired-end (2 x 250) WGS performed using Illumina MiSeq sequencer. ResultsThe genome size of strain APEC MTR_BAU02 is 4,924,680 bp with a GC content of 51.1% and 4,681 protein-coding sequences. Among the annotated WGS reads, 99.71% reads mapped to Enterobacteriaceae genomes. Based on the phylogenetic analysis of the APEC MTR_BAU02 genome and 99 reference genomes of E. coli, the APEC MTR_BAU02 genome showed sequence similarities with enterotoxigenic E. coli strains isolated from infections of different clinical severity. Metabolic functional annotations detected 380 SEED subsystems including genes coding for carbohydrate metabolism (17.34%), amino acid and derivatives (14.20%), protein metabolism (10.64%), cofactors, vitamins, prosthetic groups and pigments (7.49%), respiration (4.72%), membrane transport (4.49%), stress response (4.47%), motility and chemotaxis (4.46%), and virulence, disease and defense (2.22%). We also detected 92 VFGs and 122 AMR genes in the APEC MTR_BAU02 strain. ConclusionAssessment of these genomic features with functional genomic validation in commonly occurring serogroups of APEC will increase our understanding of the molecular pathogenesis, pave the way to early diagnosis and more effective control of colibacillosis, and improved animal welfare.

genomics↗

bioRxiv2022

Structure of a bacterial ribonucleoprotein complex central to the control of cell envelope biogenesis

The biogenesis of the essential precursor of the bacterial cell envelope, glucosamine-6-phosphate (GlcN6P), is controlled through intricate post-transcription networks mediated by GlmZ, a small regulatory RNA (sRNA). GlmZ stimulates translation of the mRNA encoding GlcN6P synthetase in Escherichia coli, but when bound by the protein RapZ, it becomes inactivated through cleavage by the endoribonuclease RNase E. Here we report the cryoEM structure of the RapZ:GlmZ complex, revealing a complementary match of the protein tetrameric quaternary structure to an imperfect structural repeat in the RNA. The RNA is contacted mostly through a highly conserved domain of RapZ that shares deep evolutionary relationship with phosphofructokinase and suggests links between metabolism and riboregulation. We also present the structure of a pre-cleavage encounter intermediate formed between the binary RapZ:GlmZ complex and RNase E that reveals how GlmZ is presented and recognised for cleavage. The structures suggest how other encounter complexes might guide recognition and action of endoribonucleases on target transcripts, and how structured substrates in polycistronic precursors are recognised for processing.

molecular biology↗