Biology subjects

Nguyen, L. T.

Publications and source records attributed to Nguyen, L. T..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

CRISPR-based diagnostics detects invasive insect pests

Rapid identification of organisms is essential across many biological and medical disciplines, from understanding basic ecosystem processes and how organisms respond to environmental change, to disease diagnosis and detection of invasive pests. CRISPR-based diagnostics offers a novel and rapid alternative to other identification methods and can revolutionize our ability to detect organisms with high accuracy. Here we describe a CRISPR-based diagnostic developed with the universal cytochrome-oxidase 1 gene (CO1). The CO1 gene is the most sequenced gene among Animalia, and therefore our approach can be adopted to detect nearly any animal. We tested the approach on three difficult-to-identify moth species (Keiferia lycopersicella, Phthorimaea absoluta, and Scrobipalpa atriplicella) that are major invasive pests globally. We designed an assay that combines recombinase polymerase amplification (RPA) with CRISPR for signal generation. Our approach has a much higher sensitivity than other real time-PCR assays and achieved 100% accuracy for identification of all three species, with a detection limit of up to 120 fM for P. absoluta and 400 fM for the other two species. Our approach does not require a lab setting, reduces the risk of cross-contamination, and can be completed in less than one hour. This work serves as a proof of concept that has the potential to revolutionize animal detection and monitoring.

genetics↗

bioRxiv2023

Sustained Delivery of GLP-1 Receptor Agonists from Injectable Biomimetic Hydrogels Improves Treatment of Diabetes

Glucagon-like peptide-1 (GLP-1) is an incretin hormone and neurotransmitter secreted from intestinal L-cells in response to nutrients to stimulate insulin and block glucagon secretion in a glucose-dependent manner. GLP-1 in itself is rapidly degraded, but long-acting GLP-1 receptor agonists (GLP-1 RAs) have become central in the treatment of T2D because of the beneficial effects extending also beyond glucose control. Currently, these therapeutics must be injected either daily or weekly or taken daily orally, leaving room for technological innovations that enable less frequent administrations, which will reduce patient burden and increase patient compliance. An ideal GLP-1 RA drug product would provide continuous therapy for upwards of four months from a single administration to match the cadence with which T2D patients typically visit their physician. In this work, we leveraged an injectable hydrogel depot technology to develop a long-acting GLP-1 RA drug product. By modulating the hydrogel properties to tune GLP-1 RA retention within the hydrogel depot, we engineered formulations capable of months-long GLP-1 RA delivery. Using a rat model of T2D, we confirmed that a single injection of hydrogel-based therapies exhibits sustained exposure of GLP-1 RA over 42 days, corresponding to a once-every four month therapy in humans. Moreover, these hydrogel therapies maintained optimal management of blood glucose and weight comparable to daily injections of a leading GLP-1 RA drug molecule. The pharmacokinetics and pharmacodynamics of these hydrogel-based long-acting GLP-1 RA treatments are promising for development of novel therapies reducing treatment burden for more effective management of T2D. Progress and PotentialWhile insufficient access to quality healthcare is problematic for consistent management of Type II diabetes (T2D), poor adherence to burdensome treatment regimens is one of the greatest challenges for disease management. Glucagon-like peptide 1 (GLP1) drugs have become central to the treatment of T2D due to their many beneficial effects beyond improving glucose control. Unfortunately, while optimization of GLP1 drugs has reduced treatment frequency from daily to weekly, significant patient burden still leads to poor patience compliance. In this work we developed an injectable hydrogel technology to enable GLP1 drugs only requiring administration once every four months. We showed in a rat model of T2D that one injection of a hydrogel-based therapy improves management of blood glucose and weight when compared with daily injections of the leading drug used clinically. These hydrogel-based GLP1 treatments are promising for reducing treatment burden and more effectively managing T2D. Future ImpactA GLP-1-based drug product providing four months of continuous therapy per administration could be transformational for the management of Type II diabetes (T2D). One of the most challenging aspects of diabetes management with GLP-1 mimics is maintenance of consistent levels of the drugs in the body, which is complicated by poor patient compliance on account of the high frequency of dosing required for current treatments. By leveraging a unique sustained release hydrogel depot technology we develop a months-long GLP-1 drug product candidate that has the potential to reduce patient burden and improving diabetes management. Overall, the hydrogel technology we describe here can dramatically reduce the frequency of therapeutic interventions, significantly increasing patient quality of life and reducing complications of diabetes management. Our next steps will focus on optimization of the drug formulations in a swine model of T2D, which is the most advanced and translationally-relevant animal model for these types of therapeutics. The long-term vision for this work is to translate lead candidate drug products towards clinical evaluation, which will also require comprehensive safety evaluation in multiple species and manufacturing our these materials according to Good Manufacturing Practices. The months-long-acting GLP-1 drug product that will come from this work has the potential to afford thus far unrealized therapeutic impact for the hundreds of millions of people with diabetes worldwide.

bioengineering↗

bioRxiv2023

Programmable RNA detection with CRISPR-Cas12a

CRISPR is a prominent bioengineering tool and the type V CRISPR-associated protein complex, Cas12a, is widely used in diagnostic platforms due to its innate ability to cleave DNA substrates. Here we demonstrate that Cas12a can also be programmed to directly detect RNA substrates without the need for reverse transcription or strand displacement. We discovered that while the PAM-proximal "seed" region of the crRNA exclusively recognizes DNA for initiating trans-cleavage, the PAM-distal region or 3-end of the crRNA can tolerate both RNA and DNA substrates. Utilizing this property, we developed a method named Split Activators for Highly Accessible RNA Analysis or SAHARA to detect RNA sequences at the PAM-distal region of the crRNA by merely supplying a short ssDNA or a PAM containing dsDNA to the seed region. Notably, SAHARA is Mg2+ concentration- and pH-dependent, and it was observed to work robustly at room temperature with multiple orthologs of Cas12a. SAHARA also displayed a significant improvement in the specificity for target recognition as compared to the wild-type CRISPR-Cas12a, at certain positions along the crRNA. By employing SAHARA we achieved amplification-free detection of picomolar concentrations of miRNA-155 and hepatitis C virus RNA. Finally, SAHARA can use a PAM-proximal DNA as a switch to control the trans-cleavage activity of Cas12a for the detection of both DNA and RNA targets. With this, multicomplex arrays can be made to detect distinct DNA and RNA targets with pooled crRNA/Cas12a complexes. In conclusion, SAHARA is a simple, yet powerful nucleic acid detection platform based on Cas12a that can be applied in a multiplexed fashion and potentially be expanded to other CRISPR-Cas enzymes. O_FIG O_LINKSMALLFIG WIDTH=125 HEIGHT=200 SRC="FIGDIR/small/525716v1_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@5edb2dorg.highwire.dtl.DTLVardef@187678borg.highwire.dtl.DTLVardef@9f0184org.highwire.dtl.DTLVardef@11cb1a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2022

Formulation excipients and their role in insulin stability and association state in formulation

While excipients are often overlooked as the "inactive" ingredients in pharmaceutical formulations, they often play a critical role in protein stability and absorption kinetics. Recent work has identified an ultrafast absorbing insulin formulation that is the result of excipient modifications. Specifically, the insulin monomer can be isolated by replacing zinc and the phenolic preservative metacresol with phenoxyethanol as an antimicrobial agent and an amphiphilic acrylamide copolymer excipient for stability. A greater understanding is needed of the interplay between excipients, insulin association state, and stability in order to optimize this formulation. Here, we formulated insulin with different preservatives and stabilizing excipient concentrations using both insulin lispro and regular human insulin and assessed the insulin association states using analytical ultracentrifugation as well as formulation stability. We determined that phenoxyethanol is required to eliminate hexamers and promote a high monomer content even in a zinc-free lispro formulation. There is also a concentration dependent relationship between the concentration of polyacrylamide-based copolymer excipient and insulin stability, where a concentration greater than 0.1 g/mL copolymer is required for a mostly monomeric zinc-free lispro formulation to achieve stability exceeding that of Humalog in a stressed aging assay. Further, we determined that under the formulation conditions tested zinc-free regular human insulin remains primarily hexameric and is not at this time a promising candidate for rapid-acting formulations.

bioengineering↗

bioRxiv2022

An RNA binding protein, RNP1A, works with Contractility Kit proteins to facilitate macropinocytosis

Cell shape regulation is important for many biological processes. Some cell shape regulating proteins harbor mechanoresponsive properties that enable them to sense and respond to mechanical cues, allowing for cell adaptation. In Dictyostelium discoideum, mechanoresponsive network proteins include Cortexillin I and IQGAP1, which assemble in the cytoplasm into macromolecular complexes, which we term Contractility Kits. In vivo fluorescence cross-correlation spectroscopy revealed that Cortexillin I also interacts with an RNA-binding protein, RNP1A. The rnp1A knockdown cells have reduced cell growth rate, reduced adhesion, defective cytokinesis, and a gene expression profile that indicates rnp1A knockdown cells shift away from the vegetative growth state. RNP1A binds to transcripts encoding proteins involved in macropinocytosis. One of these, DlpA, facilitates macropinosome maturation, similar to RNP1A. Loss of different CK proteins leads to macropinocytotic defects characterized by reduced macropinocytotic crown size. RNP1A interacts with IQGAP1 in vivo and has cross-talk with IQGAP1 during macropinocytosis. Overall, RNP1A contributes to macropinocytosis, in part through interacting with transcripts encoding macropinocytotic proteins like dlpA, and does so in coordination with the Contractility Kit proteins.

cell biology↗

bioRxiv2022

Amplification of Olfactory Signals by Anoctamin 9 is Essential for Mammalian Olfaction: a Risk Factor for the Covid-19-associated Anosmia

Sensing smells of foods, prey, or predators determines animal survival. Olfactory sensory neurons in the olfactory epithelium (OE) detect odorants, where cAMP and Ca2+ play a significant role in transducing odorant inputs to electrical activity. Here we show Anoctamin 9, a cation channel activated by cAMP/PKA pathway, is expressed in the OE and amplifies olfactory signals. Ano9- deficient mice had reduced olfactory behavioral sensitivity, electro-olfactogram signals, and neural activity in the olfactory bulb. In line with the difference in olfaction between birds and other vertebrates, chick ANO9 failed to respond to odorants, whereas chick CNGA2, a major transduction channel, showed greater responses to cAMP. Importantly, single-cell transcriptome data from Covid-19 patients revealed that Ano9 transcripts were markedly suppressed among genes in the olfactory signal pathway. The signal amplification by ANO9 is essential for mammalian olfactory transduction, whose downregulation may be a risk factor for the olfactory dysfunction in Covid-19 patients.

cell biology↗

bioRxiv2022

The genome of tropically adapted Brahman cattle (Bos taurus indicus) reveals novel genome variation in production animals

Recent advances in sequencing technology have revolutionised access to large scale genomic data that can be assembled into a platinum quality genome. Here we present a high quality genome assembly with less than 300 gaps of a Brahman cow (B. taurus indicus). The assembly was generated using 195GB of PacBio and 169GB of Oxford Nanopore Technologies sequence data. The high quality genome assembly allows us to identify substantial GC content variation that is positively associated with gene rich islands, and negatively associated with genetic variation in the form of structural variants. In addition, 92371 structural variants that are segregating in the brahman population were identified. Gene ontology analysis revealed that genes with varying copy numbers were enriched for gene ontology terms related to immune function. This analysis has revealed the complex structure of the mammalian genome of an outbred species, and identifies the ability of long read data from diploid species can be used to not only assemble a high quality genome, but also discover novel genetic variation within that genome.

genomics↗

bioRxiv2021

Image recognition based on deep learning in Haemonchus contortus motility assays

Poor efficacy of some anthelmintics and rising concerns about the widespread drug resistance have highlighted the need for new drug discovery. The parasitic nematode Haemonchus contortus is an important model organism widely used for studies of drug resistance and drug screening with the current gold standard being the motility assay. We applied a deep learning approach Mask R-CNN for analysing motility videos containing varying rates of motile worms and compared it to other commonly used algorithms with different levels of complexity, namely the Wiggle Index and the Wide Field-of-View Nematode Tracking Platform. Mask R-CNN consistently outperformed the other algorithms in terms of the detection of worms as well as the precision of motility forecasts, having a mean absolute percentage error of 7.6% and a mean absolute error of 5.6% for the detection and motility forecasts, respectively. Using Mask R-CNN for motility assays confirmed the common problem with algorithms that use non-maximum suppression in detecting overlapping objects, which negatively impacts the overall precision. The use of intersect over union as a measure of the classification of motile / non-motile instances had an overall accuracy of 89%, indicating that it is a viable alternative to previously used methods based on movement characteristics, such as body bends. In comparison to the existing methods evaluated here, Mask R-CNN performed better and we anticipate that this method will broaden the number of possible approaches to video analysis of worm motility.

bioinformatics↗

bioRxiv2021

Prowler: A novel trimming algorithm for Oxford Nanopore sequence data

MotivationQuality control (QC) tools are critical in DNA sequencing analysis because they increase the accuracy of sequence alignments and thus the reliability of results. Oxford Nanopore Technologies (ONT) QC is currently rudimentary, generally based on whole read average quality. This results in discarding reads that contain regions of high quality sequence. Here we propose Prowler, a multi-window approach inspired by algorithms used to QC short read data. Importantly, we retain the phase and read length information by optionally replacing trimmed sections with Ns. ResultsProwler was applied to mammalian and bacterial datasets, to assess effects on alignment and assembly respectively. Compared to Nanofilt, alignments of data QCed with Prowler had lower error rates and more mapped reads. Assemblies of Prowler QCed data had a lower error rate than Nanofilt QCed data however this came at some cost to assembly contiguity. Availability and implementationProwler is implemented in Python and is available at: https://github.com/ProwlerForNanopore/ProwlerTrimmer Contacte.ross@uq.edu.au Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2021

Ultra-fast insulin-pramlintide co-formulation for improved glucose management in diabetic rats

Dual-hormone replacement therapy with insulin and amylin in patients with type 1 diabetes has the potential to improve glucose management. Unfortunately, currently available formulations require burdensome separate injections at mealtimes and have disparate pharmacokinetics that do not mimic endogenous co-secretion. Here, we use amphiphilic acrylamide copolymers to create a stable co-formulation of monomeric insulin and amylin analogues (lispro and pramlintide) with synchronous pharmacokinetics and ultra-rapid action. The co-formulation is stable for over 16 hours under stressed aging conditions, whereas commercial insulin lispro (Humalog) aggregates in 8 hours. The faster pharmacokinetics of monomeric insulin in this co-formulation resulted in increased insulin-pramlintide overlap of 75 {+/-} 6% compared to only 47 {+/-} 7% for separate injections. The co-formulation resulted in similar delay in gastric emptying compared to pramlintide delivered separately. In a glucose challenge, in rats the co-formulation reduced deviation from baseline glucose compared to insulin only, or separate insulin and pramlintide administrations. Further, comparison of interspecies pharmacokinetics of monomeric pramlintide suggests that pharmacokinetics observed for the co-formulation will be well preserved in future translation to humans. Together these results suggest that the co-formulation has the potential to improve mealtime glucose management and reduce patient burden in the treatment of diabetes.

bioengineering↗

bioRxiv2021

Parental-fetal interplay of immune genes leads to intrauterine growth restriction

Intrauterine growth restriction (IUGR) of fetuses affects 5-10% of pregnancies and is associated with perinatal morbidity, mortality and long-term health issues. Understanding genetic predisposition to IUGR is challenging, owing to extensive gene polymorphisms, linkage disequilibrium, and maternal and paternal influence. Here, we demonstrate that the inhibitory receptor, KIR2DL1, expressed on maternal uterine natural killer (uNK) cells, in interaction with the paternally-inherited HLA-C*05, an HLA-C group 2 allotype, expressed on fetal trophoblast cells, causes IUGR in a humanised mouse model. Micro-CT imaging of the uteroplacental vasculature revealed reduced uterine spiral artery diameter and increased segment length, increasing fetal blood flow resistance. Single cell RNA-Seq from the maternal-fetal interface highlighted expression programs activated by KIR2DL1-induced IUGR in several placental cell types, including degradation of extracellular matrix components, angiogenesis, and uNK cell communication, suggesting a complex response underlying IUGR. As current IUGR treatments are insufficient, our findings provide important insight for drug development.

immunology↗

bioRxiv2021

Multicellular immune hubs and their organization in MMRd and MMRp colorectal cancer

Immune responses to cancer are highly variable, with mismatch repair-deficient (MMRd) tumors exhibiting more anti-tumor immunity than mismatch repair-proficient (MMRp) tumors. To understand the rules governing these varied responses, we transcriptionally profiled 371,223 cells from colorectal tumors and adjacent normal tissues of 28 MMRp and 34 MMRd patients. Analysis of 88 cell subsets and their 204 associated gene expression programs revealed extensive transcriptional and spatial remodeling across tumors. To discover hubs of interacting malignant and immune cells, we identified expression programs in different cell types that co-varied across patient tumors and used spatial profiling to localize coordinated programs. We discovered a myeloid cell-attracting hub at the tumor-luminal interface associated with tissue damage, and an MMRd-enriched immune hub within the tumor, with activated T cells together with malignant and myeloid cells expressing T-cell-attracting chemokines. By identifying interacting cellular programs, we thus reveal the logic underlying spatially organized immune-malignant cell networks.

cancer biology↗

bioRxiv2020

Natural Oil Blend Formulation (NOBF) as an anti- African Swine Fever Virus (ASFV) agent in Primary Porcine Alveolar Macrophases (PAM) cells of Swine

African swine fever is one of the severe pathogens of swine. It has a significant impact on production and on economics. So far, there are no known remedies, such as vaccines or drugs, reported. The natural oil blend formulation (NOBF) successfully tested against the African swine fever virus (ASFV) in in vitro conditions. The natural oil blend formulation (NOBF) combines Eucalyptus globulus, Pinus sylvestris, and Lavandula latifolia. We used a two-fold serial dilution to test the NOBF formulation dose. The in vitro trial results demonstrated that NOBF up to dilution 13 or 0.000625 ml deactivates the lethal dose 105HAD50 of ASFV. There was no hemadsorption (Rosetta formation) up to dilution 12 or 0.00125 ml of NOBF. The Ct value of the NOBF group at 96 hours post-infection was the same as the initial value or lower (25), whereas the Ct value of positive controls increased several folds (17.84). The in vitro trial demonstrated that NOBF can deactivate the African swine fever virus. HIGHLIGHTSO_LIThe natural oil blend formulation (NOBF) was formulated using three natural oils, i.e., Eucalyptus globulus, Pinus sylvestris, and Lavandula latifolia. C_LIO_LIThe in vitro trial was conducted using porcine alveolar macrophages (PAMs) and further passaged in the PAMs; the stock used in the present study was that obtained after the 15th passage. C_LIO_LIThe natural oil blend formulation (NOBF) showed protection against ASF virus up to a dilution of 13 or 0.000625 of a dilution of 16 or 0.000078 ml that was tried. C_LIO_LIThe real-time PCR analysis showed that the virus did not replicate in the NOBF group, which implies that either ASFV growth was inhibited in the presence of NOBF or that it was inactivated. C_LIO_LIThe in vitro trial outcome showed that NOBF has anti-ASFV properties. C_LI

pathology↗

bioRxiv2020

Optogenetic activation of heterotrimeric Gi proteins by LOV2GIVe - a rationally engineered modular protein

Heterotrimeric G-proteins are signal transducers that mediate the action of many natural extracellular stimuli as well as of many therapeutic agents. Non-invasive approaches to manipulate the activity of G-proteins with high precision are crucial to understand their regulation in space and time. Here, we engineered LOV2GIVe, a modular protein that allows the activation of Gi proteins with blue light. This optogenetic construct relies on a versatile design that differs from tools previously developed for similar purposes, i.e. metazoan opsins, which are light-activated GPCRs. To make LOV2GIVe, we fused a peptide derived from a non-GPCR protein that activates Gi (but not Gs, Gq, or G12) to a small plant protein domain, such that light uncages the G-protein activating module. Targeting LOV2GIVe to cell membranes allowed for light-dependent activation of Gi proteins in different experimental systems. In summary, LOV2GIVe expands the armamentarium and versatility of tools available to manipulate heterotrimeric G-protein activity. GRAPHICAL SUMMARY O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/253781v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@1870610org.highwire.dtl.DTLVardef@19f2b2dorg.highwire.dtl.DTLVardef@cb9e57org.highwire.dtl.DTLVardef@88924_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2020

Immunomagnetic Sequential Ultrafiltration (iSUF) Platform for Enrichment and Purification of Extracellular Vesicles from Biofluids

Extracellular vesicles (EVs) derived from tumor cells have the potential to provide a much-needed source of non-invasive molecular biomarkers for liquid biopsies. However, current methods for EV isolation have limited specificity towards tumor-derived EVs that limit their clinical use. Here, we present an approach called immunomagnetic sequential ultrafiltration (iSUF) that consists of sequential stages of purification and enrichment of EVs (nonspecifically and specifically) in approximately 2 h. In iSUF, EVs present in different volumes of biofluids (0.5 mL to 100 mL) can be significantly enriched (up to 1000 times), with up to 99 % removal of contaminating proteins (e.g., albumin). The EV recovery rate by iSUF for cell culture media (CCM), serum, and urine corresponded to 98.0% {+/-} 3.6%, 96.0% {+/-} 2.0% and 94.0% {+/-} 1.9%, respectively (p > 0.05). The final step of iSUF enables the separation of tumor-specific EVs by incorporating immunomagnetic beads specific to a target subpopulation of EVs. Serum from a small cohort of clinical samples from metastatic breast cancer (BC) patients and healthy donors were processed by the iSUF platform and the isolated EVs from patients showed significantly higher expression levels of BC biomarkers (i.e., HER2, CD24, and miR21).

bioengineering↗

bioRxiv2020

Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection

The CRISPR/Cas12a RNA-guided complexes have a tremendous potential for nucleic acid detection due to its ability to indiscriminately cleave ssDNA once bound to a target DNA. However, the current CRISPR/Cas12a systems are limited to detecting DNA in a picomolar detection limit without an amplification step. Here, we developed a platform with engineered crRNAs and optimized conditions that enabled us to detect DNA, DNA/RNA heteroduplex and methylated DNA with higher sensitivity, achieving a limit of detection of in femtomolar range without any target pre-amplification step. By extending the 3- or 5-ends of the crRNA with different lengths of ssDNA, ssRNA, and phosphorothioate ssDNA, we discovered a new self-catalytic behavior and an augmented rate of LbCas12a-mediated collateral cleavage activity as high as 3.5-fold compared to the wild-type crRNA. We applied this sensitive system to detect as low as 25 fM dsDNA from the PCA3 gene, an overexpressed biomarker in prostate cancer patients, in simulated urine over 6 hours. The same platform was used to detect as low as ~700 fM cDNA from HIV, 290 fM RNA from HCV, and 370 fM cDNA from SARS-CoV-2, all within 30 minutes without a need for target amplification. With isothermal amplification of SARS-CoV-2 RNA using RT-LAMP, the modified crRNAs were incorporated in a paper-based lateral flow assay that could detect the target with up to 23-fold higher sensitivity within 40-60 minutes.

bioengineering↗

bioRxiv2020

Helicobacter small RNA regulates host adaptation and carcinogenesis

Type-1 carcinogenic Helicobacter pylori that is known to evolve during long-term infection, enters the stomach orally and causes gastric cancer using the carcinogenic protein CagA1. However, little is known about the adaptation mechanisms of H. pylori when the environment changes from the outside to the inside of the living body. Here we show that small non-coding RNA HPnc4160 is a crucial novel RNA molecule of H. pylori that negatively regulates bacterial-host adaptation and gastric cancer. H. pylori isolated from gerbils stomachs eight weeks post-infection acquired mutations in the increased number of T-repeats within the upstream region of the HPnc4160 coding region, which leads to reduced HPnc4160 expression levels that also seen in cancer patients-derived H. pylori. By comparing RNA-seq and iTRAQ analysis between wild-type and hpnc4160 deficient mutant strains, we identified eight targets of HPnc4160 including cagA and unknown factors. Mice infection experiment revealed that the hpnc4160 deficient mutant had a higher number of colonized bacteria in the mice stomach than the wild-type strain, indicating that reduced expression levels of HPnc4160 was important for bacterial host adaptation. The expression level of HPnc4160 was lower in the clinical isolates derived from gastric cancer patients compared with non-cancer-derived strains, while the mRNA expression levels of target factors were higher. Our findings highlight the first discovery that HPnc4160 is an important small RNA for bacteria to adapt to the host environment leading to gastric carcinogenesis.

microbiology↗

bioRxiv2020

Genome-wide co-expression distributions as a metric to prioritize genes of functional importance

Genome-wide gene expression is routinely used as a tool to gain a systems-level understanding of complex, biological processes. Numerical approaches that have been used to highlight influential genes include abundance, differential expression, differential variation, network connectivity and differential connectivity. Network connectivity tends to be built on a small subset of extremely high co-expression signals that are deemed significant, but this overlooks the vast majority of pairwise signals. Here, we aimed to assess a complementary strategy, namely whether the entire shape of the distribution of genome-wide co-expression values contains a meaningful biological signal that has hitherto remained hidden from view. We have developed a computational pipeline to assign one of 8 distributions (including normal, skewed, bimodal, kurtotic, inverted) to every gene. We then used a hypergeometric enrichment process to determine if particular genes (regulators versus non-regulators) and properties (differentially expressed or not) tend to be associated with particular distributions greater than would be expected by chance. Examination of several distinct data sets spanning 4 species indicates that there is indeed an additional biological signal present in the genome-wide distribution of co-expression values which would be overlooked by currently adopted approaches. Author summaryHigh-throughput technologies, such as RNA-Seq, enables access to a vast amount of data. Here, we describe a new approach to interrogate these data and extract further information to help researchers to understand complex phenotypes. Our method is based on gene-level co-expression distributions which were compared to eight possible template shapes to group genes with similar behaviours. The method was tested using five different datasets and the consistency of the results indicate it can be used as a complementary strategy to analyse transcriptomic data.

bioinformatics↗