Biology subjects

Ahmed, M.

Publications and source records attributed to Ahmed, M..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

Phylogenomic Insights into the Evolution and Origin of Nematoda

The phylum Nematoda represents one of the most cosmopolitan and abundant metazoan groups on Earth. In this study, we reconstructed the phylogenomic tree for phylum Nematoda. A total of 60 genomes, belonging to eight nematode orders, were newly sequenced, providing the first low-coverage genomes for the orders Dorylaimida, Mononchida, Monhysterida, Chromadorida, Triplonchida, and Enoplida. The resulting phylogeny is well-resolved across most clades, with topologies remaining consistent across various reconstruction parameters. The subclass Enoplia is placed as a sister group to the rest of Nematoda, agrees with previous published phylogenies. While the order Triplonchida is monophyletic, it is not well-supported, and the order Enoplida is paraphyletic. Taxa possessing a stomatostylet form a monophyletic group; however, the superfamily Aphelenchoidea does not constitute a monophyletic clade. The genera Trichinella and Trichuris are inferred to have shared a common ancestor approximately 202 mya, a considerably later period than previously suggested. All stomatostylet-bearing nematodes are proposed to have originated [~]305 mya, corresponding to the transition from the Devonian to the Permian period. The genus Thornia is placed outside of Dorylaimina and Nygolaimina, disagreeing with its position in previous studies. Additionally, we tested the whole genome amplification method and demonstrated that it is a promising strategy for obtaining sufficient DNA for phylogenomic studies of microscopic eukaryotes. This study significantly expanded the current nematode genome dataset, and the well-resolved phylogeny enhances our understanding of the evolution of Nematoda.

genomics↗

bioRxiv2023

In silico optimization of DNA codons in genes encoded by various strains of Ebola Virus

Ebola hemorrhagic fever (HF) is a severe and often lethal disease that occurs in primates, including humans. It was first identified in 1976 during two outbreaks of fatal haemorrhagic fever in Central Africa. Due to its high fatality rate and lack of a widespread cure, Ebola HF poses a considerable challenge in treatment, making Ebola virus disease (EVD) one of the deadliest zoonotic diseases. The viral genome is [~]19kb long, linear, non-segmented, and negative single-stranded (-SS) RNA. The genome of the Ebola virus (EBOV) comprises seven genes, namely NP, GP, L, and VP (VP30, VP24, VP40, VP35), which encode nucleoprotein, glycoprotein, RNA polymerase, and viral proteins. By optimizing the DNA sequence through codon adaptation, we observed significant enhancements in the codon adaptation index (CAI) and the GC content compared to the wild-type strain. These findings demonstrate that optimized genes hold the potential for improved expression in the host organism without the production of truncated proteins. Further, these optimized genes can facilitate proper protein folding and function. In conclusion, these results have implications for vaccine production, as higher codon optimization enhances the expression of the genes, making them appropriate amounts for vaccine development.

bioinformatics↗

bioRxiv2023

Restoring adiponectin via rosiglitazone ameliorates tissue wasting in mice with lung cancer.

The cancer associated cachexia syndrome (CACS) is a systemic metabolic disorder resulting in loss of body weight due to skeletal muscle and adipose tissues atrophy. CACS is particularly prominent in lung cancer patients, where it contributes to poor quality of life and excess mortality. Using the Kras/Lkb1 (KL) mouse model, we found that CACS is associated with white adipose tissue (WAT) dysfunction that directly affects skeletal muscle homeostasis. WAT transcriptomes showed evidence of reduced adipogenesis, and, in agreement, we found low levels of circulating adiponectin. To preserve adipogenesis and restore adiponectin levels, we treated mice with the PPAR-{gamma} agonist, rosiglitazone. Rosiglitazone treatment increased serum adiponectin levels, delayed weight loss, and preserved skeletal muscle and adipose tissue mass, as compared to vehicle-treated mice. The preservation of muscle mass with rosiglitazone was associated with increases in AMPK and AKT activity. Similarly, activation of the adiponectin receptors in muscle cells increased AMPK activity, anabolic signaling, and protein synthesis. Our data suggest that PPAR-{gamma} agonists may be a useful adjuvant therapy to preserve tissue mass in lung cancer. Key points- The PPAR-{gamma} agonist, rosiglitazone, restores circulating adiponectin levels in mice with lung cancer. - Rosiglitazone preserves skeletal muscle and adipose tissue mass in mice with lung cancer. - The preservation of muscle mass with rosiglitazone is associated with increases in AMPK and AKT activity. - Stimulation of adiponectin signaling increases AMPK activity, anabolic signaling, and protein synthesis in muscle cell culture.

cancer biology↗

bioRxiv2023

PolyGR and polyPR knock-in mice reveal a conserved neuroprotective extracellular matrix signature in C9orf72 ALS/FTD neurons

A GGGGCC repeat expansion in C9orf72 is the most common genetic cause of ALS and FTD (C9ALS/FTD). The presence of dipeptide repeat (DPR) proteins, generated by translation of the expanded repeat, is a major pathogenic feature of C9ALS/FTD pathology, but their most relevant effects in a physiological context are not known. Here, we generated C9orf72 DPR knock-in mouse models characterised by physiological expression of 400 codon-optimised polyGR or polyPR repeats, and heterozygous C9orf72 reduction. (GR)400 and (PR)400 knock-in mice exhibit cortical neuronal hyperexcitability, age-dependent spinal motor neuron loss and progressive motor dysfunction, showing that they recapitulate key features of C9FTD/ALS. Quantitative proteomics revealed an increase in extracellular matrix (ECM) proteins in (GR)400 and (PR)400 spinal cord, with the collagen COL6A1 the most increased protein. This signature of increased ECM proteins was also present in C9ALS patient iPSC-motor neurons indicating it is a conserved feature of C9ALS/FTD. TGF-{beta}1 was one of the top predicted regulators of this ECM signature and polyGR expression in human iPSC-neurons was sufficient to induce TGF-{beta}1 followed by COL6A1, indicating TGF-{beta}1 is one driver of the ECM signature. Knockdown of the TGF-{beta}1 or COL6A1 orthologue in Drosophila dramatically and specifically exacerbated neurodegeneration in polyGR flies, showing that TGF-{beta}1 and COL6A1 protect against polyGR toxicity. Altogether, our physiological C9orf72 DPR knock-in mice have revealed a neuroprotective and conserved ECM signature in C9FTD/ALS.

neuroscience↗

bioRxiv2023

Gene editing of putative cAMP and Ca2+-regulated proteins using an efficient cloning-free CRISPR/Cas9 system in Trypanosoma cruzi

Trypanosoma cruzi, the agent of Chagas disease, must adapt to a diversity of environmental conditions that it faces during its life cycle. The adaptation to these changes is mediated by signaling pathways that coordinate the cellular responses to the new environmental settings. Cyclic AMP (cAMP) and Calcium (Ca2+) signaling pathways regulate critical cellular processes in this parasite, such as differentiation, osmoregulation, host cell invasion and cell bioenergetics. Although the use of CRISPR/Cas9 technology prompted reverse genetics approaches for functional analysis in T. cruzi, it is still necessary to expand the toolbox for genome editing in this parasite, as for example to perform multigene analysis. Here we used an efficient T7RNAP/Cas9 strategy to tag and delete three genes predicted to be involved in cAMP and Ca2+ signaling pathways: a putative Ca2+/calmodulin-dependent protein kinase (CAMK), Flagellar Member 6 (FLAM6) and Cyclic nucleotide-binding domain/C2 domain-containing protein (CC2CP). We endogenously tagged these three genes and determined the subcellular localization of the tagged proteins. Furthermore, the strategy used to knockout these genes allow us to presume that TcCC2CP is an essential gene in T. cruzi epimastigotes. Our results will open new venues for future research on the role of these proteins in T. cruzi.

molecular biology↗

bioRxiv2023

Modelling the Effect of Allopregnanolone on the Resolution of Spike-Wave Discharges

ObjectiveChildhood absence epilepsy (CAE) is a paediatric generalized epilepsy disorder with a confounding feature of resolving in adolescence in a majority of cases. In this study, we modelled how the small-scale (synapse-level) effect of progesterone metabolite allopregnanolone induces a large-scale (network-level) effect on a thalamocortical circuit associated with this disorder. In particular, our goal was to understand the role of sex steroid hormones in the spontaneous remission of CAE. MethodsThe conductance-based computational model consisted of single-compartment cortical pyramidal, cortical interneurons, thalamic reticular and thalamocortical relay neurons, each described by a set of ordinary differential equations. Excitatory and inhibitory synapses were mediated by AMPA, GABAa and GABAb receptors. The model was implemented using the NetPyne modelling tool and the NEURON simulator. ResultsThe action of allopregnanolone on individual GABAa-receptor mediated synapses has an ameliorating effect on spike-wave discharges (SWDs) associated with absence seizures. This effect is region-specific and most significant in the thalamus, particularly the synapses between thalamic reticular neurons. SignificanceThe remedying effect of allopregnanolone on SWDs may possibly be true only for individuals that are predisposed to remission due to intrinsic connectivity differences or differences in tonic inhibition. These results are a useful first-step and prescribe directions for further investigation into the role of ALLO together with these differences to distinguish between models for CAE-remitting and non-remitting individuals.

neuroscience↗

bioRxiv2023

Synapses without tension fail to fire in an in vitro network of hippocampal neurons.

Neurons in the brain communicate with each other at their synapses. It has long been understood that this communication occurs through biochemical processes. Here, we reveal a previously unrecognized paradigm wherein mechanical tension in neurons is essential for communication. Using in vitro rat hippocampal neurons, we find that (1) neurons become tout/tensed after forming synapses resulting in a contractile neural network, and (2) without this contractility, neurons fail to fire. To measure time evolution of network contractility in 3D (not 2D) extracellular matrix, we developed an ultra-sensitive force sensor with 1 nN resolution. We employed Multi-Electrode Array (MEA) and iGluSnFR, a glutamate sensor, to quantify neuronal firing at the network and at the single synapse scale, respectively. When neuron contractility is relaxed, both techniques show significantly reduced firing. Firing resumes when contractility is restored. Neural contractility may play a crucial role in memory, learning, cognition, and various neuropathologies.

neuroscience↗

bioRxiv2023

Identification of 30 transition fibre proteins reveals a complex and dynamic structure with essential roles in ciliogenesis

Transition fibres are appendages that surround the distal end of mature basal bodies (also called distal appendages) and are essential for ciliogenesis, but only a small number of proteins have been identified and functionally characterised. Here, through genome-wide analysis, we have identified 30 additional transition fibre proteins (TFPs) in the flagellated eukaryote Trypanosoma brucei and mapped the arrangement of the molecular components. We discovered TFPs recruited to the basal body pre- and post-initiation of ciliogenesis with differential expression of TFPs at the assembling new flagellum compared to the existing old flagellum. Knockdown by RNAi of 17 TFPs revealed 6 were necessary for ciliogenesis and a further 3 were necessary for normal flagellum length. We identified 9 TFPs that had a detectable orthologue in at least one basal body-forming eukaryotic organism outside of the kinetoplastid parasites. Our work demonstrates that transition fibres are complex and dynamic in their composition throughout the cell cycle which relates to their essential roles in ciliogenesis and length regulation.

cell biology↗

bioRxiv2023

memo-eQTL: DNA methylation modulated genetic variant effect on gene transcriptional regulation

Expression quantitative trait locus (eQTL) analysis has become an important tool in understanding the link between genetic variants and gene expression, ultimately helping to bridge the gap between risk SNPs and associated diseases. Recently, we identified and validated a specific case where the methylation of a CpG site can affect the relationship between the genetic variant and gene expression. To systematically evaluate this regulatory mechanism, we developed an extended eQTL mapping method named DNA methylation modulated eQTL (memo-eQTL). We performed memo-eQTL mapping in 128 normal prostate samples and discovered 1,731 memo-eQTLs, a vast majority of which have not been reported as eQTLs. We found that the methylation of the memo-eQTL CpG sites can either enhance or insulate the interaction between SNP and Gene expression by altering CTCF-based chromatin 3D structure. This study demonstrated the prevalence of memo-eQTLs, which can enable the identification of novel causal genes for traits or diseases associated with genetic variations.

bioinformatics↗

bioRxiv2023

Hacking brain development to test models of sensory coding

Animals can discriminate myriad sensory stimuli but can also generalize from learned experience. You can probably distinguish the favorite teas of your colleagues while still recognizing that all tea pales in comparison to coffee. Tradeoffs between detection, discrimination, and generalization are inherent at every layer of sensory processing. During development, specific quantitative parameters are wired into perceptual circuits and set the playing field on which plasticity mechanisms play out. A primary goal of systems neuroscience is to understand how material properties of a circuit define the logical operations-- computations--that it makes, and what good these computations are for survival. A cardinal method in biology--and the mechanism of evolution--is to change a unit or variable within a system and ask how this affects organismal function. Here, we make use of our knowledge of developmental wiring mechanisms to modify hard-wired circuit parameters in the Drosophila melanogaster mushroom body and assess the functional and behavioral consequences. By altering the number of expansion layer neurons (Kenyon cells) and their dendritic complexity, we find that input number, but not cell number, tunes odor selectivity. Simple odor discrimination performance is maintained when Kenyon cell number is reduced and augmented by Kenyon cell expansion.

neuroscience↗

bioRxiv2023

A shift in the mechanisms controlling hippocampal engram formation during brain maturation

The ability to form precise, episodic memories develops with age, with young children only able to form gist-like memories that lack precision. The cellular and molecular events in the developing hippocampus that underlie the emergence of precise, episodic-like memory formation are unclear. In mice, the absence of a competitive neuronal engram allocation process in the immature hippocampus precluded the formation of sparse engrams and precise memories until the fourth postnatal week, when inhibitory circuits in the hippocampus mature. This age-dependent shift in precision of episodic-like memories involved the functional maturation of parvalbumin-expressing interneurons in subfield CA1 by extracellular perineuronal nets which is necessary and sufficient for the onset of competitive neuronal allocation, sparse engram formation, and memory precision. One-Sentence SummaryEpisodic-like memory precision requires maturation of hippocampal inhibitory interneurons by the extracellular matrix.

neuroscience↗

bioRxiv2022

Re-implementation of an algorithm to integrate transcriptome and ChIP-seq data

Transcription factor binding to a gene regulatory region induces or represses its expression. Binding and expression target analysis (BETA) integrates the binding and gene expression data to predict this function. First, the regulatory potential of the factor is modeled based on the distance of its binding sites from the transcription start sites in a decay function. Then the differential expression statistics from an experiment where this factor was perturbed represent the binding effect. The rank product of the two values is employed to order in importance. This algorithm was originally implemented in Python. We reimplemented the algorithm in R to take advantage of existing data structures and other tools for downstream analyses. Here, we attempted to replicate the findings in the original BETA paper. We applied the new implementation to the same datasets using default and varying inputs and cutoffs. We successfully replicated the original results. Moreover, we showed that the method was appropriately influenced by varying the input and was robust to choices of cutoffs in statistical testing.

bioinformatics↗

bioRxiv2022

Occurrence and Antimicrobial Resistance Pattern of E. coli O157:H7 Isolated from Foods of Bovine Origin in Dessie and Kombolcha Towns, Ethiopia

E. coli are frequently isolated food-borne pathogens from meat, milk, and their products. Moreover, there has been a significant rise in the antimicrobial resistance patterns of E. coli O157:H7 to commonly used antibiotics. A cross-sectional study was conducted from October, 2019 to July, 2021 to estimate prevalence and identify associated factors of E. coli and E. coli O157:H7 and to determine antibiotic resistance pattern of E. coli O157:H7 from foods of bovine origin in Dessie and Kombolcha towns. A total of 384 samples were collected. Systematic and simple random sampling techniques were employed for sampling carcasses and milking cows, respectively. E. coli and E. coli O157:H7 were detected according to recommended bacteriological protocols. E. coli O157:H7 strains were evaluated for in vitro antimicrobial susceptibility using agar disk diffusion method. Both descriptive and inferential statistical techniques were applied to analyze the data. Overall prevalence rates of E. coli and E. coli O157:H7 were 54.7% and 6.5%, respectively. Highest prevalence rates of E. coli (79.6%) and E. coli O157:H7 (16.7%) were obtained from carcass swab and milk tank samples, respectively. Unlike E. coli O157:H7, a statistically significant difference in the E. coli prevalence (P<0.05) was observed among the different sample types. Multidrug resistance was observed among all isolates of E. coli O157:H7. All E. coli O157:H7 isolates (100.0%) were susceptible to Ampicillin, Sulfamethoxazole-trimethoprim, and Norfloxacin. On the contrary, all of the isolates (100%) were resistant to Penicillin G, Vancomycin, and Oxacillin. The current study indicated that different foods of bovine origin in the study area were unsafe for human consumption. Hence, good hygienic production methods should be employed to ensure the safety of foods of bovine origin.

microbiology↗

bioRxiv2022

Long Noncoding RNA MALAT1 is Dynamically Regulated in Leader Cells during Collective Cancer Invasion

Cancer cells invade collectively with leader-follower organization. However, how leader cells are regulated during the dynamic invasion process remains poorly understood. Using a FRET nanobiosensor that tracks lncRNA dynamics in live single cells, we monitored the spatiotemporal distribution of lncRNA during collective cancer invasion. We show that lncRNA MALAT1 is dynamically regulated in the invading fronts of cancer cells and patient-derived organoids. The abundance, diffusivity, and distribution of MALAT1 transcripts are distinct between leader and follower cells. MALAT1 expression increases when a cell acquires the leader cell role and decreases when the migration process stops. Transient knockdown of MALAT1 prevents the formation of leader cells and abolishes the migration of cancer cells. Taken together, our single cell analysis suggests MALAT1 dynamically regulates leader cells during collective cancer invasion.

cancer biology↗

bioRxiv2022

Physical confinement promotes mesenchymal trans-differentiation of invading transformed cells in vivo

Metastasis is tightly linked with poor cancer prognosis, yet it is not clear how transformed cells become invasive carcinomas. We previously discovered that single KRasV12-transformed cells can invade directly from the epithelium by basal cell extrusion. During this process, cells de-differentiate by mechanically pinching off their epithelial determinants, but how they trans-differentiate into a migratory, mesenchymal phenotype is not known. Here, we demonstrate that basally extruded KRasV12-expressing cells become significantly deformed as they invade the zebrafish body. Decreasing the confinement that cells experience after they invade reduces the percentage of KRasV12 cells that trans-differentiate into mesenchymal cell types, while higher confinement increases this percentage. Additionally, increased confinement promotes accumulation of internal masses over time. Altogether, our results suggest that mechanical forces drive not only de-differentiation of KRasV12-transformed epithelial cells as they invade but also contribute to their re-differentiation into mesenchymal phenotypes that contribute to distant metastases.

cancer biology↗

bioRxiv2022

Mapping fetal myeloid differentiation in airway samples from premature neonates with single-cell profiling

Single-cell genomic technologies hold great potential to advance our understanding of development and disease. A major limitation lies in isolating intact cells from primary tissues for profiling. Sampling methods compatible with current clinical interventions could enable longitudinal studies, the enrollment of large cohorts, and even the development of novel diagnostics. To explore single-cell RNA-seq (scRNA-seq) profiling of the cell types present at birth in the airway lumen of extremely premature (<28 weeks gestation) neonates, we isolated cells from endotracheal aspirates collected from intubated neonates within the first hour after birth. We generated data on 10 subjects, providing a rich view of airway luminal biology at a critical developmental period. Our results show that cells present in the airways of premature neonates primarily represent a continuum of myeloid differentiation, including fetal monocytes (25% of all cells), intermediate myeloid populations (48% of cells), and macrophages (2.6% of cells). To our knowledge, this is the first single-cell transcriptomic characterization of human monocytes in the neonatal airway isolated within an hour of birth. Applying trajectory analysis to the premature neonate myeloid populations, we identified two trajectories consistent with the developmental stages of interstitial and alveolar macrophages, as well as a third trajectory presenting a potential alternative pathway bridging these terminal macrophage states. While the three trajectories share many dynamic genes (5,451), they also have distinct transcriptional changes (259 alveolar-specific genes, 666 interstitial-specific genes, and 285 bridging-specific genes). Overall, our results define high quality single-cell data from cells isolated within the so-called "golden hour of birth" in extremely premature neonate airways representing complex lung biology and can be utilized in studies of human development and disease.

developmental biology↗

bioRxiv2022

Abdominal movements in insect flight reshape the role of non-aerodynamic structures for flight maneuverability I: Model predictive control for flower tracking

Research on insect flight control has focused primarily on the role of wings. Yet abdominal deflections during flight can potentially influence the dynamics of flight. This paper assesses the role of airframe deformations in flight, and asks to what extent the abdomen contributes to flight maneuverability. To address this, we use a combination of both a Model Predictive Control (MPC)-inspired computational inertial dynamics model, and free flight experiments in the hawkmoth, Manduca sexta. We explored both underactuated (i.e. number of outputs are greater than the number of inputs) and fully actuated (equal number of outputs and inputs) systems. Using metrics such as the non-dimensionalized tracking error and cost of transport to evaluate flight performance of the inertial dynamics model, we show that fully actuated simulations minimized the tracking error and cost of transport. Additionally, we tested the effect of restricted abdomen movement on free flight in live hawkmoths by fixing a carbon fiber rod over the thoracic-abdomen joint. Moths with a restricted abdomen performed worse than sham treatment moths. This study finds that abdominal motions contribute to flight control and maneuverability. Such motions of non-aerodynamic structures, found in all flying taxa, can inform the development of multi-actuated micro air vehicles.

physiology↗

bioRxiv2022

How do Protein Contaminants Influence DDA and DIA Proteomics

Mass spectrometry-based proteomics is constantly challenged by the presence of contaminant background signals. In particular, protein contaminants from reagents and sample handling are often abundant and almost impossible to avoid. For data-dependent acquisition (DDA) proteomics, exclusion list can be used to reduce the influence of protein contaminants. However, protein contamination has not been evaluated and is rarely addressed in data-independent acquisition (DIA). How protein contaminants influence proteomics data is also unclear. In this study, we established protein contaminant FASTA and spectral libraries that are applicable to all proteomic workflows and evaluated the impact of protein contaminants on both DDA and DIA proteomics. We demonstrated that including our contaminant libraries can reduce false discoveries and increase protein identifications, without influencing the quantification accuracy in various proteomic software platforms. With the pressing need to standardize proteomic workflow in the research community, we highly recommend including our contaminant FASTA and spectral libraries in all bottom-up proteomics workflow. Our contaminant libraries and a step-by-step tutorial to incorporate these libraries in different DDA and DIA data analysis platforms can be valuable resources for proteomics researchers, which are freely accessible at https://github.com/HaoGroup-ProtContLib.

systems biology↗