J Gen Physiol. 2023 Apr 3;155(4):e202213247. doi: 10.1085/jgp.202213247. Epub 2023 Feb 10.

ABSTRACT

A perennial problem encountered when using small molecules (drugs) to manipulate cell or protein function is to assess whether observed changes in function result from specific interactions with a desired target or from less specific off-target mechanisms. This is important in laboratory research as well as in drug development, where the goal is to identify molecules that are unlikely to be successful therapeutics early in the process, thereby avoiding costly mistakes. We pursued this challenge from the perspective that many bioactive molecules (drugs) are amphiphiles that alter lipid bilayer elastic properties, which may cause indiscriminate changes in membrane protein (and cell) function and, in turn, cytotoxicity. Such drug-induced changes in bilayer properties can be quantified as changes in the monomer↔dimer equilibrium for bilayer-spanning gramicidin channels. Using this approach, we tested whether molecules in the Pathogen Box (a library of 400 drugs and drug-like molecules with confirmed activity against tropical diseases released by Medicines for Malaria Venture to encourage the development of therapies for neglected tropical diseases) are bilayer modifiers. 32% of the molecules in the Pathogen Box were bilayer modifiers, defined as molecules that at 10 µM shifted the monomer↔dimer equilibrium toward the conducting dimers by at least 50%. Correlation analysis of the molecules' reported HepG2 cell cytotoxicity to bilayer-modifying potency, quantified as the shift in the gramicidin monomer↔dimer equilibrium, revealed that molecules producing <25% change in the equilibrium had significantly lower probability of being cytotoxic than molecules producing >50% change. Neither cytotoxicity nor bilayer-modifying potency (quantified as the shift in the gramicidin monomer↔dimer equilibrium) was well predicted by conventional physico-chemical descriptors (hydrophobicity, polar surface area, etc.). We conclude that drug-induced changes in lipid bilayer properties are robust predictors of the likelihood of membrane-mediated off-target effects, including cytotoxicity.

PMID:36763053 | DOI:10.1085/jgp.202213247

Elife. 2023 Feb 10;12:e84245. doi: 10.7554/eLife.84245. Online ahead of print.

ABSTRACT

We analyzed changes in total costs for National Institutes of Health (NIH) awarded Research Project Grants (RPG) issued from fiscal years (FYs) 1998 to 2003. Costs are measured in 'nominal' terms, meaning exactly as stated, or in 'real' terms, meaning after adjustment for inflation. The NIH uses a data-driven price index - the Biomedical Research and Development Price Index (BRDPI) - to account for inflation, enabling assessment of changes in real (that is, BRDPI-adjusted) costs over time. The BRDPI was higher than the general inflation rate from FY1998 until FY2012; since then the BRDPI has been similar to the general inflation rate likely due to caps on senior faculty salary support. Despite increases in nominal costs, recent years have seen increases in the absolute numbers of RPG and R01 awards. Real average and median RPG costs increased during the NIH-doubling (FY1998 to FY2003), decreased after the doubling and have remained relatively stable since. Of note, though, the degree of variation of RPG costs has changed over time, with more marked extremes observed on both higher and lower levels of cost. On both ends of the cost spectrum, the agency is funding a greater proportion of solicited projects, with nearly half of RPG money going towards solicited projects. After adjusting for confounders, we find no independent association of time with BRDPI-adjusted costs; in other words, changes in real costs are largely explained by changes in the composition of the NIH-grant portfolio.

PMID:36762661 | DOI:10.7554/eLife.84245

Nucleic Acids Res. 2023 Feb 10:gkad053. doi: 10.1093/nar/gkad053. Online ahead of print.

ABSTRACT

Inference of global gene regulatory networks from omics data is a long-term goal of systems biology. Most methods developed for inferring transcription factor (TF)-gene interactions either relied on a small dataset or used snapshot data which is not suitable for inferring a process that is inherently temporal. Here, we developed a new computational method that combines neural networks and multi-task learning to predict RNA velocity rather than gene expression values. This allows our method to overcome many of the problems faced by prior methods leading to more accurate and more comprehensive set of identified regulatory interactions. Application of our method to atlas scale single cell data from 6 HuBMAP tissues led to several validated and novel predictions and greatly improved on prior methods proposed for this task.

PMID:36762475 | DOI:10.1093/nar/gkad053

Front Toxicol. 2023 Jan 25;4:1004705. doi: 10.3389/ftox.2022.1004705. eCollection 2022.

ABSTRACT

Background: The whole world has learned about the existence of a highly toxic neuro-paralytic substance called Novichok. A wide range of neuro-paralytic toxins were used during the wars of decades ago, which also had harmful and irreversible effects. Fortunately, the establishment of conventions prohibiting the use of these weapons prevented the adverse clinical consequences of these compounds. What we did in the present study was to evaluate the clinical features of Novichok, how to manage exposure to it, and to evaluate the prognostic aspects associated with this poisoning agent. Methods: The manuscript especial databases including Medline, Web of knowledge, Google scholar, and Scopus were deeply searched by the two blinded investigators for all eligible studies based on the considered keywords. Initially 98 articles were initially collected by database searching that considering eligibility criteria, 83 articles were finally eligible for the final assessment. There is a lack of clinical trials and case-cohort studies on general population about treatment and side effects when it comes to human nerve agents and most of the data in our search is based on animal studies. Results: In evaluating various clinical, auto physiological and prognostic aspects of exposure to these substances, special attention was necessary to the following points. First, Novichok agents are considered more potent than other toxic agents. Pathophysiologically, these agents irreversibly bind acetylcholinesterase and produce a rapid cholinergic toxidrome which is responsible for the clinical manifestations as well as the potential dangerous and life threatening side effects caused by these agents. Uniquely, these agents are thought to also target every neuron in the central and peripheral nervous system. As a managerial and therapeutic approach, early and timely treatment of its related complication along with prevents massive exposure and decontamination in addition to rapid resuscitation can prohibit debilitating neuropathy and death due to facing it. Conclusion: The present review highlights the importance of recognizing the potential acute toxic effects of Novichok agents, diagnostic and therapeutic approaches (life-saving antidotal therapy) to complications and ultimately the application of guidelines to improve the prognosis of exposure to these agents for both victims and medical community.

PMID:36762227 | PMC:PMC9905702 | DOI:10.3389/ftox.2022.1004705

Front Mol Biosci. 2023 Jan 24;10:1133034. doi: 10.3389/fmolb.2023.1133034. eCollection 2023.

NO ABSTRACT

PMID:36762211 | PMC:PMC9904769 | DOI:10.3389/fmolb.2023.1133034

Front Plant Sci. 2023 Jan 24;13:1082752. doi: 10.3389/fpls.2022.1082752. eCollection 2022.

ABSTRACT

The soil is vital for life on Earth and its biodiversity. However, being a non-renewable and threatened resource, preserving soil quality is crucial to maintain a range of ecosystem services critical to ecological balances, food production and human health. In an agricultural context, soil quality is often perceived as the ability to support field production, and thus soil quality and fertility are strictly interconnected. The concept of, as well as the ways to assess, soil fertility has undergone big changes over the years. Crop performance has been historically used as an indicator for soil quality and fertility. Then, analysis of a range of physico-chemical parameters has been used to routinely assess soil quality. Today it is becoming evident that soil quality must be evaluated by combining parameters that refer both to the physico-chemical and the biological levels. However, it can be challenging to find adequate indexes for evaluating soil quality that are both predictive and easy to measure in situ. An ideal soil quality assessment method should be flexible, sensitive enough to detect changes in soil functions, management and climate, and should allow comparability among sites. In this review, we discuss the current status of soil quality indicators and existing databases of harmonized, open-access topsoil data. We also explore the connections between soil biotic and abiotic features and crop performance in an agricultural context. Finally, based on current knowledge and technical advancements, we argue that the use of plant health traits represents a powerful way to assess soil physico-chemical and biological properties. These plant health parameters can serve as proxies for different soil features that characterize soil quality both at the physico-chemical and at the microbiological level, including soil quality, fertility and composition of soil microbial communities.

PMID:36762185 | PMC:PMC9902496 | DOI:10.3389/fpls.2022.1082752

F1000Res. 2022 May 4;11:493. doi: 10.12688/f1000research.110903.1. eCollection 2022.

ABSTRACT

Synthetic lethal interactions (SLIs), genetic interactions in which the simultaneous inactivation of two genes leads to a lethal phenotype, are promising targets for therapeutic intervention in cancer, as exemplified by the recent success of PARP inhibitors in treating BRCA1/2-deficient tumors. We present SL-Cloud, a new component of the Institute for Systems Biology Cancer Gateway in the Cloud (ISB-CGC), that provides an integrated framework of cloud-hosted data resources and curated workflows to enable facile prediction of SLIs. This resource addresses two main challenges related to SLI inference: the need to wrangle and preprocess large multi-omic datasets and the availability of multiple comparable prediction approaches. SL-Cloud enables customizable computational inference of SLIs and testing of prediction approaches across multiple datasets. We anticipate that cancer researchers will find utility in this tool for discovery of SLIs to support further investigation into potential drug targets for anticancer therapies.

PMID:36761837 | PMC:PMC9880341 | DOI:10.12688/f1000research.110903.1

Biodivers Data J. 2022 Aug 19;10:e87261. doi: 10.3897/BDJ.10.e87261. eCollection 2022.

ABSTRACT

BACKGROUND: The genus Troglohyphantes Joseph, 1882 (Araneae, Linyphiidae) includes 131 species, mainly distributed across the main European mountain ranges. The Alps and the north-western Dinarides account for 66 species, most of them showing narrow or even point-like distributions. The majority of Troglohyphantes spiders dwell in subterranean habitats including caves, mines, soil litter, rocky debris and other moist and shaded retreats. Despite being intensively studied from taxonomic, ecological and biogeographic standpoints, knowledge on the status of conservation and on the potential risk of extinction of these spiders is lagging. To date, only three species have been included in the global IUCN Red List, but their status has not been updated ever since their last assessment in 1996. The aim of this contribution is to assess the Alpine and north-western Dinaric species of the genus Troglohyphantes and to re-assess the species previously evaluated, according to the last version of the IUCN Red List Categories and Criteria.

NEW INFORMATION: Amongst the 66 species here considered, 62 had sufficient data to allow the quantification of their Extent Of Occurrence (EOO) and Area Of Occupancy (AOO). Most of the species have a narrow distribution range, with an estimated EOO < 20,000 km2 and AOO < 2,000 km2, meeting the thresholds for the inclusion in the threatened categories. Five species have a more widespread distribution (EOO > 20,000 km2), extending across multiple countries. The quality of the data on distribution of four species was not sufficient to provide a reliable estimation of the distribution range.A continuing decline in EOO, AOO and habitat quality was inferred for 30 species. The majority of them were subterranean specialised species, with a reduced thermal tolerance and a low dispersal ability. Accordingly, changes in subterranean microclimatic conditions due to climate change represent a major threat for these species. Land-use change and habitat alteration were identified as additional relevant threats for several species.A considerable proportion of the species here assessed was found in protected areas and in sites of the Natura 2000 network. In addition, 14 species are formally protected by national and sub-national legislation. At present, 25 species are listed in the regional Red Lists.Long-term monitoring programmes, management plans for both the species and their habitats, expansion of the extant protected areas and designation of new ones, should be considered as the most effective approaches to species conservation.

PMID:36761670 | PMC:PMC9848466 | DOI:10.3897/BDJ.10.e87261

Front Oncol. 2023 Jan 23;12:1110168. doi: 10.3389/fonc.2022.1110168. eCollection 2022.

ABSTRACT

[This corrects the article DOI: 10.3389/fonc.2022.679115.].

PMID:36761432 | PMC:PMC9904199 | DOI:10.3389/fonc.2022.1110168

Front Immunol. 2023 Jan 24;13:1061290. doi: 10.3389/fimmu.2022.1061290. eCollection 2022.

ABSTRACT

The systemic bio-organization of humans and other mammals is essentially "preprogrammed", and the basic interacting units, the cells, can be crudely mapped into discrete sets of developmental lineages and maturation states. Over several decades, however, and focusing on the immune system, we and others invoked evidence - now overwhelming - suggesting dynamic acquisition of cellular properties and functions, through tuning, re-networking, chromatin remodeling, and adaptive differentiation. The genetically encoded "algorithms" that govern the integration of signals and the computation of new states are not fully understood but are believed to be "smart", designed to enable the cells and the system to discriminate meaningful perturbations from each other and from "noise". Cellular sensory and response properties are shaped in part by recurring temporal patterns, or features, of the signaling environment. We compared this phenomenon to associative brain learning. We proposed that interactive cell learning is subject to selective pressures geared to performance, allowing the response of immune cells to injury or infection to be progressively coordinated with that of other cell types across tissues and organs. This in turn is comparable to supervised brain learning. Guided by feedback from both the tissue itself and the neural system, resident or recruited antigen-specific and innate immune cells can eradicate a pathogen while simultaneously sustaining functional homeostasis. As informative memories of immune responses are imprinted both systemically and within the targeted tissues, it is desirable to enhance tissue preparedness by incorporating attenuated-pathogen vaccines and informed choice of tissue-centered immunomodulators in vaccination schemes. Fortunately, much of the "training" that a living system requires to survive and function in the face of disturbances from outside or within is already incorporated into its design, so it does not need to deep-learn how to face a new challenge each time from scratch. Instead, the system learns from experience how to efficiently select a built-in strategy, or a combination of those, and can then use tuning to refine its organization and responses. Efforts to identify and therapeutically augment such strategies can take advantage of existing integrative modeling approaches. One recently explored strategy is boosting the flux of uninfected cells into and throughout an infected tissue to rinse and replace the infected cells.

PMID:36761169 | PMC:PMC9904014 | DOI:10.3389/fimmu.2022.1061290

Oncol Lett. 2023 Jan 17;25(2):86. doi: 10.3892/ol.2023.13672. eCollection 2023 Feb.

ABSTRACT

Bacteriophages effectively counteract diverse bacterial infections, and their ability to treat most types of cancer has been explored using phage engineering or phage-virus hybrid platforms. In the present study, it was demonstrated that the bacteriophage MS2 can affect the expression of genes associated with the proliferation and survival of LNCaP prostate epithelial cells. LNCaP cells were exposed to bacteriophage MS2 at a concentration of 1×107 plaque forming units/ml for 24-48 h. After exposure, various cellular parameters, including cell viability, morphology, and changes in gene expression, were examined. MS2 affected cell viability adversely, reducing viability by 25% in the first 4 h of treatment; however, cell viability recovered within 24-48 h. Similarly, the AKT, androgen receptor, integrin α5, integrin β1, MAPK1, MAPK3, STAT3, and peroxisome proliferator-activated receptor-γ coactivator 1α genes, which are involved in various normal cellular processes and tumor progression, were significantly upregulated, whereas the expression levels of HSP90, ITGB5, ITGB3, HSP27, ITGAV, and PI3K genes were unchanged. Therefore, based on viability and gene expression changes, bacteriophage MS2 severely impaired LNCaP cells by reducing anchorage-dependent survival and androgen signaling. A caveolin-mediated endocytosis mechanism for MS2-mediated signaling in prostate cancer cells was proposed based on reports involving bacteriophages T4, M13, and MS2, and their interactions with LNCaP and PC3 cell lines.

PMID:36760518 | PMC:PMC9878357 | DOI:10.3892/ol.2023.13672

Front Cell Dev Biol. 2023 Jan 25;11:1086823. doi: 10.3389/fcell.2023.1086823. eCollection 2023.

ABSTRACT

Kidney tubuloids are cell models that are derived from human or mouse renal epithelial cells and show high similarities with their in vivo counterparts. Tubuloids grow polarized in 3D, allow for long-term expansion, and represent multiple segments of the nephron, as shown by their gene expression pattern. In addition, human tubuloids form tight, functional barriers and have been succesfully used for drug testing. Our knowledge of mouse tubuloids, on the other hand, is only minimal. In this study, we further characterized mouse tubuloids and differentiated them towards the collecting duct, which led to a significant upregulation of collecting duct-specific mRNAs of genes and protein expression, including the water channel AQP2 and the sodium channel ENaC. Differentiation resulted in polarized expression of collecting duct water channels AQP2 and AQP3. Also, a physiological response to desmopressin and forskolin stimulation by translocation of AQP2 to the apical membrane was demonstrated. Furthermore, amiloride-sensitive ENaC-mediated sodium uptake was shown in differentiated tubuloids using radioactive tracer sodium. This study demonstrates that mouse tubuloids can be differentiated towards the collecting duct and exhibit collecting duct-specific function. This illustrates the potential use of mouse kidney tubuloids as novel in vitro models to study (patho)physiology of kidney diseases.

PMID:36760360 | PMC:PMC9905633 | DOI:10.3389/fcell.2023.1086823

Bioinformatics. 2023 Feb 9:btad080. doi: 10.1093/bioinformatics/btad080. Online ahead of print.

ABSTRACT

MOTIVATION: Knowledge graphs (KG) are being adopted in industry, commerce, and academia. Biomedical KG present a challenge due to the complexity, size, and heterogeneity of the underlying information.

RESULTS: In this work we present the Scalable Precision Medicine Open Knowledge Engine (SPOKE), a biomedical KG connecting millions of concepts via semantically meaningful relationships. SPOKE contains 27 million nodes of 21 different types and 53 million edges of 55 types downloaded from 41 databases. The graph is built on the framework of 11 ontologies that maintain its structure, enable mappings, and facilitate navigation. SPOKE is built weekly by python scripts which download each resource, check for integrity and completeness, and then create a "parent table" of nodes and edges. Graph queries are translated by a REST API and users can submit searches directly via an API or a graphical user interface. Conclusions/Significance: SPOKE enables the integration of seemingly disparate information to support precision medicine efforts.

AVAILABILITY: The SPOKE neighborhood explorer is available at https://spoke.rbvi.ucsf.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

PMID:36759942 | DOI:10.1093/bioinformatics/btad080

Genome Med. 2023 Feb 9;15(1):8. doi: 10.1186/s13073-023-01154-x.

ABSTRACT

BACKGROUND: Efficient presentation of mutant peptide fragments by the human leukocyte antigen class I (HLA-I) genes is necessary for immune-mediated killing of cancer cells. According to recent reports, patient HLA-I genotypes can impact the efficacy of cancer immunotherapy, and the somatic loss of HLA-I heterozygosity has been established as a factor in immune evasion. While global deregulated expression of HLA-I has also been reported in different tumor types, the role of HLA-I allele-specific expression loss - that is, the preferential RNA expression loss of specific HLA-I alleles - has not been fully characterized in cancer.

METHODS: Here, we use RNA and whole-exome sequencing data to quantify HLA-I allele-specific expression (ASE) in cancer using our novel method arcasHLA-quant.

RESULTS: We show that HLA-I ASE loss in at least one of the three HLA-I genes is a pervasive phenomenon across TCGA tumor types. In pancreatic adenocarcinoma, tumor-specific HLA-I ASE loss is associated with decreased overall survival specifically in the basal-like subtype, a finding that we validated in an independent cohort through laser-capture microdissection. Additionally, we show that HLA-I ASE loss is associated with poor immunotherapy outcomes in metastatic melanoma through retrospective analyses.

CONCLUSIONS: Together, our results highlight the prevalence of HLA-I ASE loss and provide initial evidence of its clinical significance in cancer prognosis and immunotherapy treatment.

PMID:36759885 | DOI:10.1186/s13073-023-01154-x

BMC Cancer. 2023 Feb 9;23(1):134. doi: 10.1186/s12885-023-10614-x.

ABSTRACT

OBJECTIVE(S): Breast tumors show heterogeneity containing cancer stem cells as a small subpopulation of a tumor mass. CD44 as a cancer stem cells antigen is abnormally expressed by carcinomas of epithelial origin. Also, overexpression of CD44 variable isoforms (CD44v) is associated with malignancy in breast cancer. In the present research, our objective was to evaluate the immunogenicity of prepared nanoparticles containing a novel recombinant CD44v (rCD44v) protein in the mouse model.

MATERIALS AND METHODS: CD44 gene was expressed in E. coli BL21 DE3 using the pET28a-CD44 vector. The expressed rCD44v protein was purified, encapsulated into the chitosan nanoparticles, and administered to BALB/c mice. ELISA was used to evaluate the immunoglobulin levels of immunized animals. For challenge experiment, 2 × 106 4T1-CD44 tumor cells were injected subcutaneously in mice, and tumor size, necrosis, and metastases were measured. Finally, cell proliferation assay, cytokines assay, and neutralization assay of the mouse anti-rCD44v on the human breast cancer cell line were examined.

RESULTS: The measured size of chitosan-rCD44v nanoparticles was 146.5 nm. Recombinant CD44v encapsulated by chitosan nanoparticles increases immunological responses via the adjuvant nature of chitosan nanoparticles. In the immunized mice, IgG and IgA titers were significantly increased. Tumor growth in injection and nano-injection test groups compared with the mice control groups displayed a significant reduction (P < 0.05). A high amount of splenocytes secreting IFNγ and IL-17 was seen in immunized mice with rCD44v (P < 0.05). Furthermore, a smaller size of lung metastases compared to the control mice groups was detected.

CONCLUSION: The encapsulated rCD44v within the chitosan nanoparticles induced a significant immune response in mice and can establish significant protection against breast cancer. Therefore, it can be considered a vaccine candidate for breast cancer therapeutic modalities.

PMID:36759786 | DOI:10.1186/s12885-023-10614-x

Nat Microbiol. 2023 Feb 9. doi: 10.1038/s41564-023-01320-2. Online ahead of print.

ABSTRACT

Functional metagenomics is a powerful experimental tool to identify antibiotic resistance genes (ARGs) in the environment, but the range of suitable host bacterial species is limited. This limitation affects both the scope of the identified ARGs and the interpretation of their clinical relevance. Here we present a functional metagenomics pipeline called Reprogrammed Bacteriophage Particle Assisted Multi-species Functional Metagenomics (DEEPMINE). This approach combines and improves the use of T7 bacteriophage with exchanged tail fibres and targeted mutagenesis to expand phage host-specificity and efficiency for functional metagenomics. These modified phage particles were used to introduce large metagenomic plasmid libraries into clinically relevant bacterial pathogens. By screening for ARGs in soil and gut microbiomes and clinical genomes against 13 antibiotics, we demonstrate that this approach substantially expands the list of identified ARGs. Many ARGs have species-specific effects on resistance; they provide a high level of resistance in one bacterial species but yield very limited resistance in a related species. Finally, we identified mobile ARGs against antibiotics that are currently under clinical development or have recently been approved. Overall, DEEPMINE expands the functional metagenomics toolbox for studying microbial communities.

PMID:36759752 | DOI:10.1038/s41564-023-01320-2

Nat Chem Biol. 2023 Feb 9. doi: 10.1038/s41589-023-01265-x. Online ahead of print.

ABSTRACT

Bioluminescence imaging (BLI) allows non-invasive visualization of cells and biochemical events in vivo and thus has become an indispensable technique in biomedical research. However, BLI in the central nervous system remains challenging because luciferases show relatively poor performance in the brain with existing substrates. Here, we report the discovery of a NanoLuc substrate with improved brain performance, cephalofurimazine (CFz). CFz paired with Antares luciferase produces greater than 20-fold more signal from the brain than the standard combination of D-luciferin with firefly luciferase. At standard doses, Antares-CFz matches AkaLuc-AkaLumine/TokeOni in brightness, while occasional higher dosing of CFz can be performed to obtain threefold more signal. CFz should allow the growing number of NanoLuc-based indicators to be applied to the brain with high sensitivity. Using CFz, we achieve video-rate non-invasive imaging of Antares in brains of freely moving mice and demonstrate non-invasive calcium imaging of sensory-evoked activity in genetically defined neurons.

PMID:36759751 | DOI:10.1038/s41589-023-01265-x

ISME J. 2023 Feb 9. doi: 10.1038/s41396-023-01373-5. Online ahead of print.

ABSTRACT

Antimicrobial resistance (AMR) is a significant threat to public health. Plasmids are principal vectors of AMR genes, significantly contributing to their spread and mobility across hosts. Nevertheless, little is known about the dynamics of plasmid genetic exchange across animal hosts. Here, we use theory and methodology from network and disease ecology to investigate the potential of gene transmission between plasmids using a data set of 21 plasmidomes from a single dairy cow population. We constructed a multilayer network based on pairwise plasmid genetic similarity. Genetic similarity is a signature of past genetic exchange that can aid in identifying potential routes and mechanisms of gene transmission within and between cows. Links between cows dominated the transmission network, and plasmids containing mobility genes were more connected. Modularity analysis revealed a network cluster where all plasmids contained a mobM gene, and one where all plasmids contained a beta-lactamase gene. Cows that contain both clusters also share transmission pathways with many other cows, making them candidates for super-spreading. In support, we found signatures of gene super-spreading in which a few plasmids and cows are responsible for most gene exchange. An agent-based transmission model showed that a new gene invading the cow population will likely reach all cows. Finally, we showed that edge weights contain a non-random signature for the mechanisms of gene transmission, allowing us to differentiate between dispersal and genetic exchange. These results provide insights into how genes, including those providing AMR, spread across animal hosts.

PMID:36759552 | DOI:10.1038/s41396-023-01373-5

Diabetologia. 2023 Feb 10. doi: 10.1007/s00125-023-05878-8. Online ahead of print.

ABSTRACT

AIMS/HYPOTHESIS: Non-alcoholic fatty liver disease (NAFLD) associated with type 2 diabetes may more easily progress towards severe forms of non-alcoholic steatohepatitis (NASH) and cirrhosis. Although the Wnt effector transcription factor 7-like 2 (TCF7L2) is closely associated with type 2 diabetes risk, the role of TCF7L2 in NAFLD development remains unclear. Here, we investigated how changes in TCF7L2 expression in the liver affects hepatic lipid metabolism based on the major risk factors of NAFLD development.

METHODS: Tcf7l2 was selectively ablated in the liver of C57BL/6N mice by inducing the albumin (Alb) promoter to recombine Tcf7l2 alleles floxed at exon 5 (liver-specific Tcf7l2-knockout [KO] mice: Alb-Cre;Tcf7l2f/f). Alb-Cre;Tcf7l2f/f and their wild-type (Tcf7l2f/f) littermates were fed a high-fat diet (HFD) or a high-carbohydrate diet (HCD) for 22 weeks to reproduce NAFLD/NASH. Mice were refed a standard chow diet or an HCD to stimulate de novo lipogenesis (DNL) or fed an HFD to provide exogenous fatty acids. We analysed glucose and insulin sensitivity, metabolic respiration, mRNA expression profiles, hepatic triglyceride (TG), hepatic DNL, selected hepatic metabolites, selected plasma metabolites and liver histology.

RESULTS: Alb-Cre;Tcf7l2f/f essentially exhibited increased lipogenic genes, but there were no changes in hepatic lipid content in mice fed a normal chow diet. However, following 22 weeks of diet-induced NAFLD/NASH conditions, liver steatosis was exacerbated owing to preferential metabolism of carbohydrate over fat. Indeed, hepatic Tcf7l2 deficiency enhanced liver lipid content in a manner that was dependent on the duration and amount of exposure to carbohydrates, owing to cell-autonomous increases in hepatic DNL. Mechanistically, TCF7L2 regulated the transcriptional activity of Mlxipl (also known as ChREBP) by modulating O-GlcNAcylation and protein content of carbohydrate response element binding protein (ChREBP), and targeted Srebf1 (also called SREBP1) via miRNA (miR)-33-5p in hepatocytes. Eventually, restoring TCF7L2 expression at the physiological level in the liver of Alb-Cre;Tcf7l2f/f mice alleviated liver steatosis without altering body composition under both acute and chronic HCD conditions.

CONCLUSIONS/INTERPRETATION: In mice, loss of hepatic Tcf7l2 contributes to liver steatosis by inducing preferential metabolism of carbohydrates via DNL activation. Therefore, TCF7L2 could be a promising regulator of the NAFLD associated with high-carbohydrate diets and diabetes since TCF7L2 deficiency may lead to development of NAFLD by promoting utilisation of excess glucose pools through activating DNL.

DATA AVAILABILITY: RNA-sequencing data have been deposited into the NCBI GEO under the accession number GSE162449 ( www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE162449 ).

PMID:36759348 | DOI:10.1007/s00125-023-05878-8

Physiol Behav. 2023 Feb 7:114106. doi: 10.1016/j.physbeh.2023.114106. Online ahead of print.

ABSTRACT

The zebrafish is an important biomedical research organism. In most research, zebrafish are removed from their home tank and subsequently their phenotype is measured. The method of handling the fish, however, may significantly affect a variety of phenotypes. This is particularly problematic for studies of brain function that measure behavioral or neuronal responses. Nevertheless, the potential effects of handling have not been analyzed, and in fact are usually ignored. Here, we explore the effects of two usual and two rarely or never-before employed handling methods on the behavior of adult zebrafish. We exposed each fish to one of four handling methods, a between subject experimental design: (1) net chasing followed by air-suspension, (2) gentle net catching (without chasing) followed by air-suspension, (3) gentle net catching followed by being placed in a beaker (no chasing and very short air-suspension), (4) transportation in home tank and pouring the fish directly into the test tank (no chasing, netting or air-suspension). With these handling methods, the fish were placed in a test tank and their swim path was videorecorded and analyzed. Handling significantly affected swim path parameters, duration and frequency of immobility, absolute turn angle and its temporal variance and velocity, but not the distance to bottom. The behavioral effects confirmed that chasing and netting induce robust behavioral changes, and that pouring the fish from its home to its test tank is least aversive for zebrafish. We recommend using this latter method to reduce experimental error variation and increase reproducibility of results.

PMID:36758848 | DOI:10.1016/j.physbeh.2023.114106