Biology subjects

Ahmad, A.

Publications and source records attributed to Ahmad, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Quantitative differences in anaerobic growth and metabolism of three different E. coli strains using 13C-Metabolic Flux Analysis

Escherichia coli are model organisms for biotechnological research owing to their abilities to grow on defined media and consume a variety of carbon sources, as well as a vast knowledge base and tools available for their manipulation. Several E. coli strains and their derivatives are available. However, the quantitative metabolic differences between the strains could be better characterized. In this study, we investigated the differences in the intracellular flux distribution between three commonly used strains of E. coli (K-12 MG1655, C, and W) using 13C-Metabolic flux analysis (13C-MFA), the gold standard in fluxomics. The labeling data was analyzed using FluxPyt, our previously developed Python-based tool. Threefold differences in the growth rates of these strains were observed when growing anaerobically on glucose in M9 medium, with E. coli W being the fastest ( = 0.62 {+/-} 0.01 h-1) and E. coli C the slowest ( = 0.22 {+/-} 0.01 h-1). The strains growth rates correlate with glucose uptake and flux through the oxidative pentose phosphate pathway. Interestingly, succinate was a major product in E. coli C only. 13C-MFA revealed that under these conditions, Entner-Doudoroff (ED) pathway was active in E. coli C and E. coli W but not in E. coli K-12 MG1655. In E. coli K-12 MG1655 and E. coli C, the Tricarboxylic Acid (TCA) cycle ran incompletely. Also, the glyoxylate shunt was inactive in all three strains. Growth, xylose intake rates, and product profiles on xylose mirrored those of glucose. Thus, this study has highlighted significant differences in the growth and metabolism of the E. coli strains on glucose and xylose. This will form a basis for identifying the best strain for a particular application.

systems biology↗

bioRxiv2024

Optically active, paper-based scaffolds for 3D cardiac tissue engineering

In this work, we report the design and fabrication of a light-addressable, paper-based, nanocomposite scaffold for optical modulation and read-out of in vitro grown cardiac tissue. The scaffold consists of paper cellulose microfibers functionalized with gold nanorods (GNRs) and semiconductor quantum dots (QDs), embedded into a cell-permissive collagen matrix. The GNRs enable cardiomyocyte activity modulation through local temperature gradients induced by near-infrared (NIR) laser illumination, with the local temperature changes reported by the temperature-dependent QD photoluminescence (PL). The micrometer size paper fibers promote the tubular organization of HL-1 cardiac muscle cells, while the NIR plasmonic stimulation modulates reversibly their activity. Given its high spatial resolution, NIR modulation offers an excellent alternative to electrode-based methods for cell activity modulation and is more compatible with 3D tissue constructs. As such, optical platforms based on nanocomposite scaffolds will have a significant impact on the progress of drug screening, toxicity studies, and heart disease modeling.

bioengineering↗

bioRxiv2023

A Framework for Fast, Large-scale, Semi-Automatic Inference of Animal Behavior from Monocular Videos

An automatic, quick, accurate, and scalable method for animal behavior inference using only videos of animals offers unprecedented opportunities to understand complex biological phenomena and answer challenging ecological questions. The advent of sophisticated machine learning techniques now allows the development and implementation of such a method. However, apart from developing a network model that infers animal behavior from video inputs, the key challenge is to obtain sufficient labeled (annotated) data to successfully train that network - a laborious task that needs to be repeated for every species and/or animal system. Here, we propose solutions for both problems, i) a novel methodology for rapidly generating large amounts of annotated data of animals from videos and ii) using it to reliably train deep neural network models to infer the different behavioral states of every animal in each frame of the video. Our methods workflow is bootstrapped with a relatively small amount of manually-labeled video frames. We develop and implement this novel method by building upon the open-source tool Smarter-LabelMe, leveraging deep convolutional visual detection and tracking in combination with our behavior inference model to quickly produce large amounts of reliable training data. We demonstrate the effectiveness of our method on aerial videos of plains and Grevys Zebras (Equus quagga and Equus grevyi). We fully open-source the code1 of our method as well as provide large amounts of accurately-annotated video datasets2 of zebra behavior using our method. A video abstract of this paper is available here3.

animal behavior and cognition↗

bioRxiv2023

The piRNA protein Asz1 is essential for germ cell and gonad development in in zebrafish and exhibits differential necessities in distinct types of RNP granules

Germ cells are essential for fertility, embryogenesis, and reproduction. Germline development requires distinct types of RNA-protein (RNP) granules, including germ plasm in embryos, piRNA granules in gonadal germ cells, and the Balbiani body (Bb) in oocytes. However, the regulation of RNP assemblies in zebrafish germline development are still poorly understood. Asz1 is a piRNA protein in Drosophila and mice. Zebrafish Asz1 localizes to both piRNA and Bb granules, with yet unknown functions. Here, we hypothesized that Asz1 functions in RNP granule assemblies and germline development in zebrafish. We generated asz1 mutant fish to determine the roles of Asz1 in germ cell development. We show that Asz1 is dispensable for somatic development, but essential for germ cell and gonad development. asz1-/- fish developed exclusively as sterile males with severely underdeveloped testes that lacked germ cells, demonstrating that Asz1 is essential for spermatogenesis. Mechanistically, we provide evidence to conclude that zygotic Asz1 is not required for primordial germ cell specification or migration to the gonad, but is essential for germ cell survival during post-embryonic gonad development, likely by suppressing the expression of germline transposons. Increased transposon expression and morphologically mis-organized piRNA granules in asz1 mutants, argues that zebrafish Asz1 functions in the piRNA pathway. We generated asz1;tp53 fish to partially rescue ovarian development, revealing underdeveloped mutant ovaries with defective oocytes, and that Asz1 is also essential for oogenesis. We further showed that in contrast with piRNA granules, Asz1 is dispensable for Bb granule formation, as shown by normal Bb localization of Buc and dazl. By uncovering Asz1 as an essential regulator of germ cell survival and gonadogenesis in zebrafish, and determining its differential necessity in distinct RNP granule types, our work advances our understanding of the developmental genetics of reproduction and fertility, as well as of RNP granule biology. Author SummaryGerm cells undergo a highly dynamic developmental program that begins in the early embryo and continues through juvenile and adult life. Identifying functional regulators and deciphering the developmental mechanisms of germ cells are critical for advancing our understanding of fertility and reproduction, as well as their associated diseases. Here, we identified Asz1 as an essential regulator of germ cell and gonad development in zebrafish. We demonstrate that zygotic Asz1 is dispensable for the specification and migration of primordial germ cells in the embryo, but is necessary for germ cell survival in the developing gonad, likely by protecting them from transposable elements. Upon loss of asz1, expression of germline transposons was induced, and piRNA granules were mis-organized, suggesting a conserved role for zebrafish Asz1 in the piRNA pathway. We show that Asz1 is required for both spermatogenesis and oogenesis. However, unlike RNA-protein (RNP) granules of the piRNA pathway, Asz1 was not required for RNP granules of the Balbiani body in differentiating oocytes, revealing its differential necessity in distinct types of germline RNP granules. In mice, Asz1 was shown to be essential for spermatogenesis but not oogenesis, but its functions in human gonads are unclear. Our work reports the functional requirements of Asz1 in both sexes in zebrafish, contributes to our knowledge of developmental reproduction biology, and sheds new light on the complexity of RNP granule assemblies.

developmental biology↗

bioRxiv2023

Extrasynaptic localization is essential for α5GABAA receptor modulation of dopamine system function

Dopamine system dysfunction, observed in animal models with psychosis-like symptomatology, can be restored by targeting Gamma-Aminobutyric Acid type A receptors (GABAAR) containing the 5, but not 1, subunit in the ventral hippocampus (vHipp). The reason for this discrepancy in efficacy remains elusive; however, one key difference is that 1GABAARs are primarily located in the synapse, whereas 5GABAARs are mostly extrasynaptic. To test whether receptor location is responsible for this difference in efficacy, we injected a small interfering ribonucleic acid (siRNA) into the vHipp to knock down radixin, a scaffolding protein that holds 5GABAARs in the extrasynaptic space. We then administered GL-II-73, a positive allosteric modulator of 5GABAARs (5-PAM) known to reverse shock-induced deficits in dopamine system function, to determine if shifting 5GABAARs from the extrasynaptic space to the synapse would prevent the effects of 5-PAM on dopamine system function. As expected, knockdown of radixin significantly decreased radixin-associated 5GABAARs and increased the proportion of synaptic 5GABAARs, without changing the overall expression of 5GABAARs. Importantly, GL-II-73 was no longer able to modulate dopamine neuron activity in radixin-knockdown rats, indicating that the extrasynaptic localization of 5GABAARs is critical for hippocampal modulation of the dopamine system. These results may have important implications for clinical use of GL-II-73, as periods of high hippocampal activity appear to favor synaptic 5GABAARs, thus efficacy may be diminished in conditions where aberrant hippocampal activity is present. Significance StatementDopamine activity is known to be altered in both psychosis patients and in animal models, with promising new antipsychotics restoring normal dopamine system function. One such drug is GL-II-73, a positive allosteric modulator of 5GABAARs (5-PAM). Interestingly, previous research has shown that a positive allosteric modulator of 1GABAARs (1-PAM) does not share this ability, even when directly given to the ventral hippocampus, a region known to modulate dopamine activity. One potential explanation for this difference we examined in this study is that 1GABAARs are primarily located in the synapse, whereas 5GABAARs are mostly extrasynaptic. Determining the mechanism of this differential efficacy could lead to the refinement of antipsychotic treatment and improve patient outcomes overall.

neuroscience↗

bioRxiv2023

Validation of σ2R/TMEM97 as a neuropathic pain target: Specificity, human expression and mechanism of action.

The Sigma 2 receptor ({sigma}2R) was described pharmacologically more than three decades ago, but its molecular identity remained obscure until recently when it was identified as transmembrane protein 97 (TMEM97). We and others have shown that {sigma}2R/TMEM97 ligands alleviate mechanical hypersensitivity in mouse neuropathic pain models with a time course wherein maximal anti-nociceptive effect is approximately 24 hours following dosing. We sought to understand this unique anti-neuropathic pain effect by addressing two key questions: do these {sigma}2R/TMEM97 compounds act selectively via the receptor, and what is their downstream mechanism on nociceptive neurons? Using male and female conventional knockout (KO) mice for Tmem97, we find that a new {sigma}2R/TMEM97 binding compound, FEM-1689, requires the presence of the gene to produce anti-nociception in the spared nerve injury model in mice. Using primary mouse dorsal root ganglion (DRG) neurons, we demonstrate that FEM-1689 inhibits the integrated stress response (ISR) and promotes neurite outgrowth via a {sigma}2R/TMEM97-specific action. We extend the clinical translational value of these findings by showing that FEM-1689 reduces ISR and p-eIF2 levels in human sensory neurons and that it alleviates the pathogenic engagement of ISR by methylglyoxal. We also demonstrate that {sigma}2R/TMEM97 is expressed in human nociceptors and satellite glial cells. These results validate {sigma}2R/TMEM97 as a promising target for further development for the treatment of neuropathic pain. Significance StatementNeuropathic pain is a major medical problem that is poorly treated with existing therapeutics. Our findings demonstrate that targeting {sigma}2R/TMEM97 with a newly described modulator reduces pain hypersensitivity in a mouse model with exquisite selectivity. We also identify integrated stress response (ISR) inhibition as a potential mechanism of action that links the receptor to cellular signaling events that have preclinical and clinical validation for pain relief. Our work suggests that {sigma}2R/TMEM97 can be selectively engaged by specific small molecules to produce ISR inhibition in a subset of cells that are critical for neuropathic pain. {sigma}2R/TMEM97-targeted therapeutics thus have the potential to offer effective pain relief without engagement of opioid receptors.

neuroscience↗

bioRxiv2023

Protease-Activated Receptor 2 (PAR2) expressed in sensory neurons contributes to signs of pain and neuropathy in paclitaxel treated mice

Background and PurposeChemotherapy-Induced Peripheral Neuropathy (CIPN) is a common, dose-limiting side effect of cancer therapy. Protease-activated receptor 2 (PAR2) is implicated in a variety of pathologies, including CIPN. In this study, we demonstrate the role of PAR2 expressed in sensory neurons in a paclitaxel (PTX)-induced model of CIPN in mice. Experimental ApproachCIPN was induced in both PAR2 knockout/WT mice and mice with PAR2 ablated in sensory neurons via the intraperitoneal injection of paclitaxel. In vivo behavioral studies were done in mice using von Frey filaments and the Mouse Grimace Scale. We then examined immunohistochemical staining of dorsal root ganglion (DRG) and hind paw skin samples from CIPN mice to measure satellite cell gliosis and intra-epidermal nerve fiber (IENF) density. Pharmacological reversal of CIPN pain was tested with the PAR2 antagonist C781 Key ResultsMechanical allodynia caused by paclitaxel treatment was alleviated in PAR2 knockout mice of both sexes. In the PAR2 sensory neuronal conditional knockout (cKO) mice, both mechanical allodynia and facial grimacing were attenuated in mice of both sexes. In the dorsal root ganglion of the paclitaxel-treated PAR2 cKO mice, satellite glial cell activation was reduced compared to control mice. IENF density analysis of the skin showed that the paclitaxel-treated control mice have a reduction in nerve fiber density while the PAR2 cKO mice had a comparable skin innervation as the vehicle-treated animals. Similar results were seen with satellite cell gliosis in the DRG where gliosis induced by PTX was absent in PAR cKO mice. Finally, C781 was able to transiently reverse established PTX-evoked mechanical allodynia. Conclusions and ImplicationsOur work demonstrates that PAR2 expressed in sensory neurons plays a key role in paclitaxel-induced mechanical allodynia, spontaneous pain and signs of neuropathy, suggesting PAR2 as a possible therapeutic target in multiple aspects of paclitaxel CIPN.

neuroscience↗

bioRxiv2023

Microevolution and phylogenomic characterization with perspectives in the 2022-2023 outbreak of child Respiratory Syncytial Virus type A

A communal respiratory syncytial virus (RSV) causes mild to severe illness, predominantly in older adults, or people with certain chronic medical conditions, and in particular, in young children. Symptoms may include runny nose, cough, fever, and difficulty breathing. In most cases, the infection is mild and resolves on its own, but in some cases, it can lead to more serious illness such as bronchiolitis or pneumonia. The RSV genome codes for ten proteins, NS1, NS2, N, P, M, SH, G, F, M2 and L. We aimed to identify the RSV geographical distribution and transmission pattern using site parsimonious frequencies, and investigate hotspot regions across the complete RSV genomes. These results indicated that RSV strains circulating in South and North America are not mixed to the European samples, however, genomes reported from Australia are the direct decedents of European samples. Samples reported from the United Kingdom were found diverse. Further, this report provides a comprehensive mutational analysis of all the individual RSV genes and in particular the 32 hotspot substituting regions circulating across the globe in RSV type A samples. This is the first comprehensive analysis of RSV type A that features mutational frequencies across the whole genome providing more clues for epidemiological control and drug development.

evolutionary biology↗

bioRxiv2023

SERS nanowire chip and machine learning enabled instant identification and classification of clinically relevant wild-type and antibiotic resistant bacteria at species and strain level

The world health organization considers antimicrobial resistance (AMR) to be a critical global public health problem. Conventional culture-based methods that are used to detect and identify bacterial infection are slow. Thus, there is a growing need for the development of robust, cost-effective, and fast diagnostic solutions for the identification of pathogens. Surface-enhanced Raman spectroscopy (SERS) can be used to identify target analytes with sensitivity down to the single-molecule level. Here, we developed a SERS chip by optimizing the entire fabrication pipeline of the metal-assisted chemical etching (MACE) method. The MACE approach offers a large-scale, densely packed silver (Ag) nanostructure on top of silicon nanowires (Si-NWs) with a large aspect ratio that significantly enhances the Raman signal due to localised surface plasmonic enhancement. The optimised SERS chips exhibited sensitivity down to 10-12 M concentration of R6G molecule and detected reproducible Raman spectra of bacteria down to a concentration of 100 colony forming units (CFU)/ml, which is a thousand times lower than the clinical threshold of bacterial infections like UTI (105 CFU/ml). A Siamese neural network model was used to classify SERS Raman spectra from bacteria specimens. The trained model identified 12 different bacterial species, including those which are causative agents for tuberculosis and urinary tract infection (UTI). Next, the SERS chips and another Siamese neural network model were used to differentiate antibiotic-resistant strains from susceptible strains of E. coli. The enhancement offered by SERS chip enabled acquisitions of Raman spectra of bacteria directly in the synthetic urine by spiking the sample with only 103 CFU/ml E. coli. Thus, the present study lays the ground for the identification and quantification of bacteria on SERS chips, thereby offering a potential future use for rapid, reproducible, label-free, and low limit detection of clinical pathogens.

biophysics↗

bioRxiv2023

Different Coexisting Mpox Lineages Were Continuously Circulating in Humans Prior to 2022

The origin and hazardous potential of human mpox is obscured by a lack of genomic data between the 2018, when exportations from Nigeria were recorded, and 2022 when the global outbreak started. Here, 18 genomes from patients across southern Nigeria in 2019/20 reveal multiple lineages of Monkeypox virus have achieved sustained human-to-human transmission, co-existing in humans for several years and accumulating mutations consistent with APOBEC3 activity suggesting the virus in humans is now segregated from its natural reservoir. Remarkably, three genomes have disruptions in the A46R gene, which contributes to innate immune modulation. The data demonstrates that the A.2 lineage, multiply exported to North America since 2021 independently of the global outbreak, has persisted in Nigeria for more than two years prior to its latest exportation. One-Sentence SummaryMpox is now a human diseae evolving in humans with multiple variants taking separate paths towards adaptation, some analogous to those of Variola

microbiology↗

bioRxiv2022

Simple Models For Neuroscience Research Discoveries: How Often Are These Models Used In Africa

Simple animal model systems such as Drosophila, Zebrafish, and C. Elegans have enabled numerous breakthroughs in understanding human health and disease. Their conserved biological processes, ever-expanding established procedures for handling, and amenability for molecular and genetic manipulation, in addition to the minimal ethical concerns, have made these models preferred choices in several life science disciplines globally. Owing to their cheap maintenance cost, adopting these model systems will help bridge the research gap between Africa and the Global North and contribute to advancing scientific knowledge in African universities through practical sessions. However, the extent to which these models are used across Africa is unknown. Here, we analysed the use of Drosophila, Zebrafish, and C. elegans model systems in scientific publications from African laboratories from the year 2000 to 2021. Of 1851 PubMed-indexed publications in which at least one simple animal model was mentioned, 168 used at least one of these models for the actual investigation. With an average of 21 articles per country, South Africa, Nigeria, Kenya, Egypt, Morocco, and Tunisia contributed 75% of these studies. The remaining 25% were contributed by seven other countries at 2-7 articles per country. From here, we extracted and analysed information on funding and international collaboration. This revealed that 24.4 % of the studies were exclusively funded locally, 28.57 % exclusively funded internationally, 15.5% received both local and international funding, and the rest (31.5%) were unfunded, revealing that there is satisfactory access to funds for simple animal model studies, especially from external funders. By analysing the pattern of collaborations, we show that most of these studies had international collaborations, while very few collaborated within Africa. Our work provides data on the current state of research using simple model systems in African laboratories and argues that incorporating these models will advance biomedical science research in Africa.

neuroscience↗

bioRxiv2022

MultiGML: Multimodal Graph Machine Learning for Prediction of Adverse Drug Events

Adverse drug events constitute a major challenge for the success of clinical trials. Several computational strategies have been suggested to estimate the risk of adverse drug events in preclinical drug development. While these approaches have demonstrated high utility in practice, they are at the same time limited to specific information sources and thus neglect a wealth of information that is uncovered by fusion of different data sources, including biological protein function, gene expression, chemical compound structure, cell-based imaging, etc. In this work we propose an integrative and explainable Graph Machine Learning approach (MultiGML), which fuses knowledge graphs with multiple further data modalities to predict drug related adverse events. MultiGML demonstrates excellent prediction performance compared to alternative algorithms, including various knowledge graph embedding techniques. MultiGML distinguishes itself from alternative techniques by providing in-depth explanations of model predictions, which point towards biological mechanisms associated with predictions of an adverse drug event. MotivationAdverse drug events are a major risk for failure of late-stage clinical trials. Attempts to prevent adverse drug events in preclinical drug development include experimental procedures for measuring liver-toxicity, cardio-toxicity, etc. Yet these procedures are costly and cannot fully guarantee success in later clinical studies, specifically in situations without a reliable animal model. Computational approaches developed for adverse event prediction have shown to be valuable, but are mostly limited to single data sources. Our approach successfully integrates various data sources on protein functions, gene expression, chemical compound structures and more, into the prediction of adverse events. A main distinguishing characteristic is the explainability of our model predictions which allow further insight into biological mechanisms.

bioinformatics↗

bioRxiv2022

Mutated cells mediate distinct inflammatory responses in clonal hematopoiesis

Clonal hematopoiesis (CH) is an age-associated phenomenon that increases risk for hematologic malignancy and cardiovascular disease. CH is thought to enhance disease risk through inflammation in the peripheral blood1. Here, we profile peripheral blood gene expression in 66,968 single cells from a cohort of 17 CH patients and 7 controls. Using a novel mitochondrial DNA barcoding approach, we were able to identify and separately compare mutant TET2 and DNMT3A cells to non-mutant counterparts. We discovered the vast majority of mutated cells were in the myeloid compartment. Additionally, patients harboring DNMT3A and TET2 CH mutations possessed a pro-inflammatory profile in CD14+ monocytes through previously unrecognized pathways such as galectin and macrophage Inhibitory Factor (MIF). We also found that T cells from CH patients, though mostly un-mutated, had decreased expression of GTPase of the immunity associated protein (GIMAP) genes, which are critical to T cell development, suggesting that CH may impair T cell function. Key points- CD14+ monocytes from clonal hematopoiesis patients stimulate inflammation through increased cytokine expression. - T cells from clonal hematopoiesis are deficient in GIMAP expression, suggesting CH may impair T cell differentiation.

genetics↗

bioRxiv2022

Falcon gut microbiome is shaped by diet and enriched in Salmonella

The gut microbiome is increasingly being appreciated as a master regulator of animal health. However, most avian gut microbiome studies have focused on birds of economic importance while the gut microbiomes of raptors remain underexplored. Here we examine the gut microbiota of 29 samples from four Falco species including hybrid birds-- raptors of historic importance --in the context of avian evolution by sequencing the 16S rDNA V4 region. Our results reveal that evolutionary histories and diet are significantly associated with avian gut microbiota in general, whereas diet plays a major role in shaping the falcon gut microbiota. Multiple analyses revealed that gut microbial diversity, composition, and abundance of key diet-discriminating bacterial genera in the falcon gut closely resemble those of carnivorous raptors rather than those of their closest phylogenetic relatives. Furthermore, the falcon microbiota is dominated by Firmicutes and consists of Salmonella at appreciable levels. Salmonella presence may potentially alter the functional capacity of the falcon gut microbiota as its abundance is associated with depletion of multiple predicted metabolic pathways involved in protein mass buildup, muscle maintenance, and enrichment of antimicrobial compound degradation, thus increasing the pathogenic potential of the falcon gut and presents a potential risk to human health. Author Summary in Arabic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/517295v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1440126org.highwire.dtl.DTLVardef@1a76b91org.highwire.dtl.DTLVardef@870bccorg.highwire.dtl.DTLVardef@17ac82_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2022

Low-cost and highly efficient: A method for high-quality nucleic acid isolation from cotton fibres

Gene expression analyses to study the development of cotton fibers require high-quality nucleic acid. The conventional methods of nucleic acid extraction results in sub-quality nucleic acids with low yields. Young fibers are rich in polyphenols and sugars that react with nucleic acid to form phenols and insoluble substances. Furthermore, mature fibers contain more than 95% cellulose, hindering the nucleic acid isolation. Cytoplasm collapse and cellulose deposition also result in a very low yield of nucleic acid. Three different methods of RNA isolation from different cotton tissues were compared in this study to determine the best and most efficient one. The integrity and quality of RNA were analyzed using UV spectrum, agarose gel electrophoresis, RIN values, PCR, and Northern blot hybridization. RNA of functional quality was observed when using the high ion and pH method, with an A260/A280 ratio up to 1.87 and an average yield of 0.68 mg g-1 from fiber cells. From leaves, we found an A260/A280 ratio of 2.02 and an average yield of 6.35 mg g-1, which is suitable for molecular biology experiments. The extraction buffer with a high ion density and pH value include Tris-HCl, LiCl, EDTA, SDS, sodium deoxycholate, Nonident P-40, mercaptoethanol, and PVP. The addition of sodium deoxycholate and Nonider-40 (NP-40) enhances the density of other salt compounds and elevates the pH value. The results depicted that the high ion and pH method is a simple and effective way to extract a copious amount of high-quality RNA from polysaccharide-rich tissues. This method is also suitable for the extraction of cotton genomic DNA with high purity. Genomic DNA extracted from cotton using this method showed an A260/A230 ratio up to 2.09 and a yield of 1.44 mg g-1. This method is useful for isolating DNA and RNA from cotton fibers and produces high yields and quality at a comparatively low cost.

genomics↗

bioRxiv2022

Empagliflozin reduces renal lipotoxicity in experimental Alport syndrome

Sodium-glucose cotransporter-2 inhibitors (SGLT2i) are anti-hyperglycemic agents that prevent glucose reabsorption in proximal tubular cells. SGLT2i improves renal outcomes in both diabetic and non-diabetic patients, indicating it may have beneficial effects beyond glycemic control. Here, we demonstrate that SGLT2i affects energy metabolism and renal lipotoxicity in experimental Alport syndrome (AS). In vitro, we found that SGLT2 protein expression levels in human and mouse podocytes were similar to tubular cells. Newly established immortalized podocytes from Col4a3 knockout mice (AS podocytes) accumulate lipid droplets along with increased apoptosis when compared to wildtype podocytes. Treatment with SGLT2i empagliflozin reduces lipid droplet accumulation and apoptosis in AS podocytes. Empagliflozin inhibits the utilization of glucose/pyruvate as a metabolic substrate in AS podocytes. In vivo, we demonstrate that empagliflozin reduces albuminuria and prolongs the survival of AS mice. Empagliflozin-treated AS mice show decreased serum blood urea nitrogen and creatinine levels in association with reduced triglyceride and cholesterol ester content in kidney cortices when compared to AS mice. Lipid accumulation in kidney cortices correlates with the decline in renal function. In summary, empagliflozin reduces renal lipotoxicity and improves kidney function in experimental AS in association with the energy substrates switch from glucose to fatty acids in podocytes.

cell biology↗

bioRxiv2022

Highly sensitive quantitative phase microscopy and deep learning complement whole genome sequencing for rapid detection of infection and antimicrobial resistance

The current state-of-the-art infection and antimicrobial resistance diagnostics (AMR) is based mainly on culture-based methods with a detection time of 48-96 hours. Slow diagnoses lead to adverse patient outcomes that directly correlate with the time taken to administer optimal antimicrobials. Mortality risk doubles with a 24-hour delay in providing appropriate antibiotics in cases of bacteremia. Therefore, it is essential to develop novel methods that can promptly and accurately diagnose microbial infections at both species and strain levels in clinical settings. Here, we demonstrate that the complimentary use of label-free optical assay with whole-genome sequencing (WGS) can enable high-speed culture-free diagnosis of infection and AMR. Our assay is based on microscopy methods exploiting label-free, highly sensitive quantitative phase microscopy (QPM) followed by deep convolutional neural networks (DCNNs) based classification. We benchmarked our proposed workflow on 21 clinical isolates from four WHO priority pathogens (Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, and Acinetobacter baumannii) that were antibiotic susceptibility testing (AST) phenotyped, and their antimicrobial resistance (AMR) profile was determined by WGS. The proposed optical assay was in good agreement with the WGS characterization. Highly accurate classification based on the gram staining (100% for gram-negative and 83.4% for gram-positive), species (98.6%), and resistant/susceptible type (96.4%), as well as at the individual strain level (100% accurate in predicting 19 out of the 21 strains). These results demonstrate the potential of the QPM assay as a rapid and first-stage tool for species, presence, and absence of AMR, and strain-level classification, which WGS can follow up for confirmation of the pathogen ID and the characterization of the AMR profile and susceptibility antibiotic. Taken together, all this information is of high clinical importance. Such a workflow could potentially facilitate efficient antimicrobial stewardship and prevent the spread of AMR.

microbiology↗

bioRxiv2021

Accelerating manufacturing to start large-scale supply of a new adenovirus-vectored vaccine within 100 days

The Coalition for Epidemic Preparedness Innovations 100-day moonshot aspires to launch a new vaccine within 100 days of pathogen identification. Here, we describe work to optimize adenovirus vector manufacturing for rapid response, by minimizing time to clinical trial and first large-scale supply, and maximizing the output from the available manufacturing footprint. We describe a rapid viral seed expansion workflow that allows vaccine release to clinical trials within 60 days of antigen sequence identification, followed by vaccine release from globally distributed sites within a further 40 days. We also describe a new perfusion-based upstream production process, designed to maximize output while retaining simplicity and suitability for existing manufacturing facilities. This improves upstream volumetric productivity of ChAdOx1 nCoV-19 by around four-fold and remains compatible with the existing downstream process, yielding drug substance sufficient for 10000 doses from each liter of bioreactor capacity. Transition to a new production process across a large manufacturing network is a major task. In the short term, the rapid seed generation workflow could be used with the existing production process. We also use techno-economic modelling to show that, if linear scale-up were achieved, a single cleanroom containing two 2000 L bioreactors running our new perfusion-based process could supply bulk drug substance for around 120 million doses each month, costing <0.20 EUR/dose. We estimate that a manufacturing network with 32000 L of bioreactor capacity could release around 1 billion doses of a new vaccine within 130 days of genomic sequencing of a new pathogen, in a hypothetical surge campaign with suitable prior preparation and resources, including adequate fill-and-finish capacity. This accelerated manufacturing process, along with other advantages such as thermal stability, supports the ongoing value of adenovirus-vectored vaccines as a rapidly adaptable and deployable platform for emergency response.

bioengineering↗