Biology subjects

Lopez, M.

Publications and source records attributed to Lopez, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

The transaminase-omega-amidase pathway is a redox switch in glutamine metabolism that generates alpha-ketoglutarate

Oxidative stress is caused by short-lived molecules and metabolic changes belong to the fastest cellular responses. Here we studied how the endothelial cell metabolome reacts to acute oxidative challenges (menadione or H2O2) to identify redox-sensitive metabolic enzymes. H2O2 selectively increased -ketoglutaramate (KGM), a largely uncharacterized metabolite produced by glutamine transamination and a yet unrecognized intermediate of endothelial glutamine catabolism. The enzyme nitrilase-like 2 {omega}-amidase (NIT2) converts KGM to -ketoglutarate (KG). Reversible oxidation of specific cysteine in NIT2 by H2O2 inhibited its catalytic activity. Furthermore, a variant in the NIT2 gene that decreases its expression is associated with high plasma KGM level in humans. Endothelial-specific knockout mice of NIT2 exhibited increased levels of KGM and impaired angiogenesis. Knockout of NIT2 impaired endothelial cell proliferation and sprouting and induced senescence. In conclusion, we show that the glutamine transaminase-{omega}-amidase pathway is a metabolic switch in which NIT2 is the redox-sensitive enzyme. The pathway is modulated in humans and functionally important for endothelial glutamine metabolism.

physiology↗

bioRxiv2024

Genetic diversity within diagnostic sputum samples is mirrored in the culture of Mycobacterium tuberculosis

Culturing Mycobacterium tuberculosis (MTB) from tuberculosis cases is the basis for many research and clinical applications. Paradoxically, it is assumed to impose a diversity bottleneck, which, if true, would entail unexplored consequences. The alternative, culture-free sequencing from diagnostic samples, is a promising but challenging approach both to obtain and analyse the MTB genome from the complex sample. This study obtains high-quality genomes of sputum-culture pairs from two different settings after developing a workflow for sequencing from sputum and a tailored bioinformatics pipeline. Our approach reveals that 88% of variants called in culture-free sequencing analysis are false positives due to supplementary alignments, mostly in enriched-sputa samples. Overall, contrary to the bottleneck dogma, we identify a 97% variant agreement within sputum-culture pairs, with a high correlation also in the variants frequency (0.98). Our findings extrapolate to all publicly available data, thus demonstrating that in most cases culture accurately mirrors clinical samples.

genomics↗

bioRxiv2024

DEFICIENCY OF THE NUTRIENT SENSOR CPT1c IN SF1 NEURONS DISRUPTS THE ENDOCANNABINOID SYSTEM RESULTING IN COMPROMISED SATIETY AND FUEL SELECTION UPON FAT INTAKE

The SF1 neurons of the ventromedial hypothalamus (VMH) are pivotal in governing body weight and adiposity, particularly in response to a high-fat diet (HFD). Previous studies have shown that the activation of SF1 neurons induces satiety, increases energy expenditure, and promotes the preferential use of fats as energy substrate. Furthermore, SF1 neurons are necessary for recovering from insulin-induced hypoglycemia. Here we demonstrate the essential role of the nutritional sensor CPT1c in the activation of SF1 neurons by dietary fats. Mice deficient in CPT1C in SF1 neurons (SF1-CPT1c-KO) are unable to adjust their caloric intake during the initial exposure to a HFD. This is associated with an impaired metabolic transition in the liver, muscle, and adipose tissue, despite a normal response to a glucose or insulin challenge. During chronic HFD exposure, SF1-CPT1c-KO mice are more prone to obesity and glucose intolerance than controls. CPT1c deficiency in SF1 neurons also leads to alterations in hypothalamic endocannabinoid levels and their metabolism. Our findings posit CPT1C in SF1 neurons as a sensor for dietary fats, regulating satiety responses and nutrient partitioning likely through the modulation of the endocannabinoid system.

neuroscience↗

bioRxiv2024

Indicators to assess interannual variability in marine connectivity processes: a semi-theoretical approach

Oceanographic connectivity in an effective network of protected areas is crucial for restoring and stabilising marine populations. However, temporal variability of connectivity is rarely considered as a criterion in designing and evaluating marine conservation planning. In this study, indicators were defined to characterise occurrence, strength and frequency of the temporal variability in connectivity in a northwestern Mediterranean Sea area. Indicators were tested on semi-theoretically-estimated connections provided by the runs of a passive particle transport model in a climatological year and in three years between 2006 - 2020, showing large deviation from the climatological year. The indicators compared the temporal variability in connectivity of four zones, highlighting differences in connectivity due to their locations and the mesoscale hydrodynamics, and identifying areas that require further investigation. The three indicators also showed that the temporal variability in connectivity was influenced by the duration and depth of particle transport, although no consistent pattern was observed in the indicator variations of the compared zones. Provided that specific objectives will be given when parameterising transport models (i.e., selection of focus species and time period), indicators of temporal variability in connectivity have potential to support, and correctly implement, spatial conservation planning, prioritise the protection of marine resources, and measure the effectiveness of Marine Protected Areas, in line with a long-term vision of ocean management.

ecology↗

bioRxiv2023

Metabolic control of germ layer proportions through regulation of Nodal and Wnt signalling

During embryonic development, cells exit pluripotency to give rise to the three germ layers. Metabolic pathways influence cell fate decisions by modulating the epigenetic, transcriptional, and signalling states of cells. However, the interplay between metabolism and the major signalling pathways that drive the emergence of ectoderm, mesoderm, and endoderm remains poorly understood. Here, we demonstrate an instructive role of glycolytic activity in activating signalling pathways involved in mesoderm and endoderm induction. Using an in vitro model system for mouse gastrulation, we observed that inhibiting glycolysis prevents the upregulation of primitive streak markers, resulting in a significant increase in ectodermal cell fates at the expense of mesodermal and endodermal lineages. We demonstrate that this relationship is dose-dependent, enabling metabolic control of germ layer proportions through exogenous glucose levels. Mechanistically, we found that glycolysis inhibition leads to the downregulation of Wnt, Nodal, and Fgf signalling. Notably, this metabolic phenotype was rescued by Nodal or Wnt signalling agonists in the absence of glycolytic activity, suggesting that glycolytic activity acts upstream of both signalling pathways. Our work underscores the dependence of specific signalling pathways on metabolic conditions and provides mechanistic insight into the nutritional regulation of cell fate decision making.

developmental biology↗

bioRxiv2023

Control of the phage defence mechanisms by Quorum sensing (QS) in clinical isolates of Klebsiella pneumoniae

Multidrug resistant (MDR) bacteria and the shortage of new antibiotics are a serious health problem and have increased the interest in bacteriophages, with great potential as antimicrobial agents but they can induce resistance. The objective of the present study was to reduce the development of phage resistance in K. pneumoniae strains by inhibiting the Quorum Sensing (QS). The QS inhibition by cinnamaldehyde (CAD) was confirmed indirectly by the reduction of biofilm production and directly by a proteomic analysis. Also, the infection assays showed that the phage resistance mechanisms of the bacteria were inhibited when phage-resistant K. pneumoniae strains were treated with a combination of phages with CAD. Finally, these results were confirmed by proteomic analysis as proteins related to the phage defence such as CBASS (bacterial cyclic oligonucleotide-based anti-phage signalling) and R-M systems as well as tail fiber proteins were present under phage treatment but not with the combination. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/570179v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@a97009org.highwire.dtl.DTLVardef@1fa7f02org.highwire.dtl.DTLVardef@a8909corg.highwire.dtl.DTLVardef@ae0284_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2023

Female cichlids attack and avoid-but will still mate with-androgen receptor mutant males that lack male-typical body coloration

A key challenge in animal behavior is disentangling the social stimuli that drive conspecific behaviors. For behaviors like birdsong, insights can be made through the experimental isolation of relevant cues that affect behavior. However, for some species like teleost fish, putative sexual signaling cues are inextricably linked to others, making it difficult to parse the precise roles distinct signals play in driving conspecific behaviors. In the African cichlid Astatotilapia burtoni, males are dominant or subordinate, wherein bright coloration and territorial and courtship behavior inextricably correlate positively with rank. Here, we leveraged androgen receptor (AR) mutant male A. burtoni that lack dominance-typical coloration but not behavior to isolate the role of male coloration in driving female mating behaviors in this species. We found in independent behavioral assays that females behave aggressively towards AR mutant but not WT males but still mated with both types of males. Females showed enhanced activation of esr2b+ cells in the hypothalamus when housed with either mutant or WT males and this activation scaled with spawning activities. Therefore, there is not a simple relationship between male coloration and female mating behaviors in A. burtoni, suggesting independent sensory mechanisms converge on hypothalamic esr2b+ cells to coordinate behavioral output.

animal behavior and cognition↗

bioRxiv2023

A Foundational Large Language Model for Edible Plant Genomes

Significant progress has been made in the field of plant genomics, as demonstrated by the increased use of high-throughput methodologies that enable the characterization of multiple genome-wide molecular phenotypes. These findings have provided valuable insights into plant traits and their underlying genetic mechanisms, particularly in model plant species. Nonetheless, effectively leveraging them to make accurate predictions represents a critical step in crop genomic improvement. We present AO_SCPLOWGROC_SCPLOWNT, a foundational large language model trained on genomes from 48 plant species with a predominant focus on crop species. We show that AO_SCPLOWGROC_SCPLOWNT can obtain state-of-the-art predictions for regulatory annotations, promoter/terminator strength, tissue-specific gene expression, and prioritize functional variants. We conduct a large-scale in silico saturation mutagenesis analysis on cassava to evaluate the regulatory impact of over 10 million mutations and provide their predicted effects as a resource for variant characterization. Finally, we propose the use of the diverse datasets compiled here as the Plants Genomic Benchmark (PGB), providing a comprehensive bench-mark for deep learning-based methods in plant genomic research. The pre-trained AO_SCPLOWGROC_SCPLOWNT model is publicly available on HuggingFace at https://huggingface.co/InstaDeepAI/agro-nucleotide-transformer-1b for future research purposes.

genomics↗

bioRxiv2023

Androgen receptor alpha regulates aromatase expression in the ventromedial hypothalamus of male cichlids

Social behaviors are regulated by sex steroid hormones such as androgens and estrogens. However, the specific molecular and neural processes modulated by steroid hormones to generate social behaviors remain to be elucidated. We investigated whether some actions of androgen signaling in the control of social behavior may occur through the regulation of estradiol synthesis in the highly social cichlid fish Astatotilapia burtoni. Specifically, we examined the expression of cyp19a1, a brain-specific aromatase, in the brains of male A. burtoni lacking a functional AR gene, which was recently found to be necessary for aggression in this species. We found that cyp19a1 expression is higher in wild-type males compared to AR mutant males in the homolog of the mammalian ventromedial hypothalamus (VMH), a brain region that governs aggression across taxa. Using in situ hybridization chain reaction (HCR), we determined that AR+ and cyp19a1+ cells are commonly nearby, but very infrequently was co-expression observed, including in the fish VMH. We speculate that AR may modulate cyp19a1 expression in the fish VMH to govern aggression through an indirect, potentially transsynaptic, mechanism. These studies provide novel insights into the hormonal mechanisms of social behavior and lay a foundation for future functional studies.

neuroscience↗

bioRxiv2023

Molecular Studies of Phages-Klebsiella pneumoniae in a Mucoid Environment: Innovative use of mucolytic agents prior to the administration of lytic phages

Mucins are important glycoproteins that form a protective layer throughout the gastrointestinal and respiratory tracts. There is scientific evidence of increase in phage-resistance in the presence of mucin for some bacterial pathogens. Manipulation in mucin composition may ultimately influence the effectiveness of phage therapy. In this work, two clinical strains of K. pneumoniae (K3574 and K3325), were exposed to the lytic bacteriophage vB_KpnS-VAC35 in the presence and absence of mucin on a long-term co-evolution assay, in an attempt to mimic in vitro the exposure to mucins that bacteria and their phages face in vivo. Enumerations of the bacterial and phage counts at regular time intervals were conducted, and extraction of the genomic DNA of co- evolved bacteria to the phage, the mucin and both was performed. We determined the frequency of phage-resistant mutants in the presence and absence of mucin and including a mucolytic agent (N-acetyl L-cysteine, NAC), and sequenced these conditions using Nanopore. We phenotypically demonstrated that the presence of mucin induces the emergence of bacterial resistance against lytic phages, effectively decreased in the presence of NAC. In addition, the genomic analysis revealed some of the genes relevant to the development of phage resistance in long-term co- evolution, with a special focus on the mucoid environment. Genes involved in the metabolism of carbohydrates were mutated in the presence of mucin. In conclusion, the use of mucolytic agents prior to the administration of lytic phages could be an interesting therapeutic option when addressing K. pneumoniae infections in environments where mucin is overproduced.

microbiology↗

bioRxiv2023

Epigenetic variation causes heritable variation in complex traits in the mollusk Biomphalaria glabrata, vector of the human parasite Schistosoma mansoni

DNA methylation variation may play a role in phenotypic variation as it can be directly affected by the environment and be inherited. DNA methylation variations were introduced into the parasite vector snail Biomphalaria glabrata with low genetic diversity by chemical treatment in F0 and followed over 3 generations using epigenetic recombinant inbred lines (epiRILs). We observed phenotypic variation in complex traits such as fecundity and susceptibility to infestation by Schistosoma mansoni and DNA methylation differences in F3. Both, increase and decrease of infestation success (up to 100% and down to 20% prevalence in epiRILs and from 86% to 94% in control RILs) indicated variation in complex resistance/compatibility trait. Average prevalence in control RILs was 84{+/-}5% but only 68{+/-}21 % in epiRILs. Fecundity also changed and was in average 47{+/-}7% in control RILs and 59{+/-}18% in epiRILs, being 12% higher in epiRILs. We found that the heritability h2 of the fecundity in the epiRILs was between 0.5 and 0.6 depending on the method used to estimate it. We developed a model for introducing epimutant offspring snails into resident susceptible populations. If genetic assimilation of the resistant phenotype occured in a small fraction of the introduced epimutant snails, we predict that the susceptible phenotype is replaced by the resistant phenotype after 50-70 generations.

ecology↗

bioRxiv2023

Immunomodulatory Leptin Receptor+ Sympathetic Perineurial Cells Protect Against Obesity by Facilitating Neuroendocrine-Mediated Brown Adipose Tissue Thermogenesis

Adipose tissues (ATs) are innervated by sympathetic nerves, which drive reduction of fat mass via lipolysis and thermogenesis. Here, we report a population of immunomodulatory leptin receptor (LepR)-expressing barrier cells which ensheath sympathetic axon bundles in adipose tissues. These LepR-expressing Sympathetic Perineurial Cells (SPCs) produce IL33, a factor for maintenance and recruitment of regulatory T cell (Treg) and eosinophils in AT. Brown adipose tissues (BAT) of mice lacking IL33 in SPCs (SPCIL33cKO) have fewer Treg and eosinophils, resulting in increased BAT inflammation. SPCIL33cKO mice are more susceptible to diet-induced obesity, independently of food intake. Furthermore, SPCIL33cKO mice have impaired adaptive thermogenesis, and are unresponsive to leptin-induced rescue of metabolic adaptation. We, therefore, identify LepR-expressing SPCs as a source of IL33 which orchestrate an anti-inflammatory environment in BAT, preserving sympathetic-mediated thermogenesis and body weight homeostasis. LepR+ IL33+ SPCs provide a cellular link between leptin and immune regulation of body weight, unifying neuroendocrinology and immunometabolism as previously disconnected fields of obesity research. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/539963v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@195fa69org.highwire.dtl.DTLVardef@16b2e5eorg.highwire.dtl.DTLVardef@1b12b62org.highwire.dtl.DTLVardef@973c1b_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- Sympathetic Perineurial Cells (SPCs) co-express LepR+ and IL33 - SPC-derived IL33 prevents BAT inflammation via Treg and eosinophil recruitment - Obesity is worsened in high fat diet-fed SPCIL33cKO mice, despite normal food intake - Adaptive thermogenesis is impaired in SPCIL33cKO mice - Rescue of metabolic adaptation to fasting by leptin is impaired in SPCIL33cKO mice - SPCs link leptin to immunometabolic regulation of body weight homeostasis

physiology↗

bioRxiv2023

Elastin-like polypeptide delivery of anti-inflammatory peptides to the brain following ischemic stroke

Inflammatory processes are activated following ischemic strokes and lead to increased tissue damage for weeks following the ischemic insult, but there are no approved therapies that target this inflammation-induced secondary injury. Here, we report that SynB1-ELP-p50i, a novel protein inhibitor of the nuclear factor kappa B (NF-{kappa}B) inflammatory cascade bound to drug carrier elastin-like polypeptide (ELP), is able to enter both neurons and microglia, cross the blood-brain barrier, localize exclusively in the ischemic core and penumbra in Wistar-Kyoto and spontaneously hypertensive rats (SHRs), and reduce infarct volume in male SHRs. Additionally, in male SHRs, SynB1-ELP-p50i treatment improves survival for 14 days following stroke with no effects of toxicity or peripheral organ dysfunction. These results show high potential for ELP-delivered biologics for therapy of ischemic stroke and other central nervous system disorders and further support targeting inflammation in ischemic stroke.

neuroscience↗

bioRxiv2023

Long COVID manifests with T cell dysregulation, inflammation, and an uncoordinated adaptive immune response to SARS-CoV-2

Long COVID (LC), a type of post-acute sequelae of SARS-CoV-2 infection (PASC), occurs after at least 10% of SARS-CoV-2 infections, yet its etiology remains poorly understood. Here, we used multiple "omics" assays (CyTOF, RNAseq/scRNAseq, Olink) and serology to deeply characterize both global and SARS-CoV-2-specific immunity from blood of individuals with clear LC and non-LC clinical trajectories, 8 months following infection and prior to receipt of any SARS-CoV-2 vaccine. Our analysis focused on deep phenotyping of T cells, which play important roles in immunity against SARS-CoV-2 yet may also contribute to COVID-19 pathogenesis. Our findings demonstrate that individuals with LC exhibit systemic inflammation and immune dysregulation. This is evidenced by global differences in T cell subset distribution in ways that imply ongoing immune responses, as well as by sex-specific perturbations in cytolytic subsets. Individuals with LC harbored increased frequencies of CD4+ T cells poised to migrate to inflamed tissues, and exhausted SARS-CoV-2-specific CD8+ T cells. They also harbored significantly higher levels of SARS-CoV-2 antibodies, and in contrast to non-LC individuals, exhibited a mis-coordination between their SARS-CoV-2-specific T and B cell responses. RNAseq/scRNAseq and Olink analyses similarly revealed immune dysregulatory mechanisms, along with non-immune associated perturbations, in individuals with LC. Collectively, our data suggest that proper crosstalk between the humoral and cellular arms of adaptive immunity has broken down in LC, and that this, perhaps in the context of persistent virus, leads to the immune dysregulation, inflammation, and clinical symptoms associated with this debilitating condition.

immunology↗

bioRxiv2023

The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

Closing the gap between measurable genetic information and observable traits is a longstanding challenge in genomics. Yet, the prediction of molecular phenotypes from DNA sequences alone remains limited and inaccurate, often driven by the scarcity of annotated data and the inability to transfer learning between prediction tasks. Here, we present an extensive study of foundation models pre-trained on DNA sequences, named the Nucleotide Transformer, ranging from 50M up to 2.5B parameters and integrating information from 3,202 diverse human genomes, as well as 850 genomes selected across diverse phyla, including both model and non-model organisms. These transformer models yield transferable, context-specific representations of nucleotide sequences, which allow for accurate molecular phenotype prediction even in low-data settings. We show that the developed models can be fine-tuned at low cost and despite low available data regime to solve a variety of genomics applications. Despite no supervision, the transformer models learned to focus attention on key genomic elements, including those that regulate gene expression, such as enhancers. Lastly, we demonstrate that utilizing model representations can improve the prioritization of functional genetic variants. The training and application of foundational models in genomics explored in this study provide a widely applicable stepping stone to bridge the gap of accurate molecular phenotype prediction from DNA sequence. Code and weights available on GitHub in Jax and HuggingFace in Pytorch. Example notebooks to apply these models to any downstream task are available on HuggingFace.

genomics↗

bioRxiv2022

Genomic accordions may hold the key to Monkeypox Clade IIb's increased transmissibility

The currently expanding monkeypox epidemic is caused by a subclade IIb descendant of a monkeypox virus (MPXV) lineage traced back to Nigeria in 1971. In contrast to monkeypox cases caused by clade I and subclade IIa MPXV, the prognosis of current cases is generally favorable, but person-to-person transmission is much more efficient. MPXV evolution is driven by selective pressure from hosts and loss of virus-host interacting genes. However, there is no satisfactory genetic explanation using single-nucleotide polymorphisms (SNPs) for the observed increased MPXV transmissibility. We hypothesized that key genomic changes may occur in the genomes low-complexity regions (LCRs), which are highly challenging to sequence and have been dismissed as uninformative. Using a combination of highly sensitive techniques, we determined a first high-quality MPXV genome sequence of a representative of the current epidemic with LCRs resolved at unprecedented accuracy. This effort revealed significant variation in short-tandem repeats within LCRs. We demonstrate that LCR entropy in the MPXV genome is significantly higher than that of SNPs and that LCRs are not randomly distributed. In silico analyses indicate that expression, translation, stability, or function of MPXV orthologous poxvirus genes (OPGs) 153, 204, and 208 could be affected in a manner consistent with the established "genomic accordion" evolutionary strategies of orthopoxviruses. Consequently, we posit that genomic studies focusing on phenotypic MPXV clade-/subclade-/lineage-/strain differences should change their focus to the study of LCR variability instead of SNP variability.

genomics↗

bioRxiv2022

Molecular analysis of the interactions between phages and the bacterial host Klebsiella pneumoniae

Lytic phages are currently considered among the best options for treating infections caused by multi-drug resistant pathogens. Phages have some advantages over conventional antibiotics. For example, phages acquire modifications in accordance with their environment, and thus with the bacteria present, which has led to the co-evolution of both types of organism. Therefore, both phages and bacteria have acquired resistance mechanisms for protection. In this context, the aims of the present study were to analyze the proteins isolated from twenty-one novel lytic phages of Klebsiella pneumoniae in search of defence mechanisms against bacteria and also to determine the infective capacity of the phages. A proteomic study was also conducted to investigate the defence mechanisms of two clinical isolates of Klebsiella pneumoniae infected by phages. For this purpose, the twenty-one lytic phages were sequenced and de novo assembled using the Illumina-Miseq system and Spades V.3.15.2 respectively. Gene annotation was performed with Patric, Blast, Hhmer and Hhpred tools. The evolutionary relationships between phages were determined by RaxML. The host-range was determined in a collection of forty-seven clinical isolates of K. pneumoniae, revealing the variable infectivity capacity of the phages. Genome sequencing showed that all of the phages were lytic phages belonging to the family Caudovirales. The size and GC content of the phages ranged from 39,371 to 178,532 bp and from 41.72 % to 53.76 %, respectively. Phage sequence analysis revealed that the proteins were organized in functional modules within the genome. Although most of the proteins have unknown functions, multiple proteins were associated with defence mechanisms against bacteria, including the restriction-modification (RM) system, the toxin-antitoxin (TA) system, evasion of DNA degradation, blocking of host RM, the orphan CRISPR-Cas system and the anti-CRISPR system. Proteomic study of the phage-host interactions (i.e. between isolates K3574 and K3320, which have intact CRISPR-Cas systems, and phages vB_KpnS-VAC35 and vB_KpnM-VAC36, respectively) revealed the presence of several defence mechanisms against phage infection (prophage, plasmid, defence/virulence/resistance and oxidative stress proteins) in the bacteria, and of the Acr candidate (anti-CRISPR protein) in the phages. IMPORTANCEPhages, viral parasites of bacteria, have long protected the Earths biosphere against bacterial overgrowth and could now help in the fight against antimicrobial resistance. However, researchers, including microbiologists and infectious disease specialists, require more knowledge about the interactions between phages and their bacterial hosts and about the defence mechanisms in both viruses and bacteria. In this study, we analyzed the molecular mechanisms of viral and bacterial defence in phages infecting clinical isolates of Klebsiella pneumoniae. Viral defence mechanisms included RM system evasion, the Toxin-Antitoxin system, DNA degradation evasion, blocking of host RM and resistance to the abortive infection system (Abi), anti-CRISPR and CRISPR-Cas systems. Regarding bacterial defence mechanisms, proteomic analysis revealed overexpression of proteins involved in the prophage (FtsH protease modulator), plasmid (cupin phosphomannose isomerase protein), defence/virulence/resistance (porins, efflux pumps, LPS, pili elements, quorum network proteins, TA systems and methyltransferases), oxidative stress mechanisms and Acr candidates (anti-CRISPR protein). The findings reveal some important molecular mechanisms involved in the phage-host bacterial interactions; however, further study in this field is required to improve the efficacy of phage therapy.

microbiology↗

bioRxiv2022

Alcohol dependence modifies brain networks activated during abstinence and reaccess: a c-fos-based analysis in mice

High-level alcohol consumption causes neuroplastic changes in the brain that lead to negative affective and somatic symptoms when alcohol is withdrawn, promoting relapse drinking. We have some understanding of these plastic changes in defined brain circuits and cell types, but unbiased approaches are needed to explore broader patterns of adaptations. Here, we employed whole-brain c-fos mapping and network analysis to assess how brain-wide patterns of neuronal activity are altered during acute alcohol abstinence and reaccess in a well-characterized model of alcohol dependence. Mice underwent four cycles of chronic intermittent ethanol vapor exposure (CIE) with alternating weeks of voluntary alcohol drinking, and a subset of mice underwent forced swim stress (FSS) prior to drinking sessions to further escalate alcohol consumption. After four CIE cycles, brains were collected from mice in each group either 24 hours (abstinence) or immediately following a one-hour period of alcohol reaccess. Brains from CIE mice during acute abstinence displayed widespread neuronal activation relative to those from AIR mice, independent of FSS, and this increase in c-fos was reversed by reaccess drinking. For network analysis, mice were then classified as high or low drinkers (HD or LD). We computed Pearson correlations for all pairs of brain regions and used graph theoretical methods to identify changes in network properties associated with high-drinking behavior. Network modularity, a measure of network segregation into communities, was increased in HD mice after alcohol reaccess relative to abstinence. Within-community strength and diversity measures were computed for each region and condition, and highly coactive regions were identified. One high-diversity region, the cortical amygdala (COA), was further interrogated using a chemogenetic approach. COA silencing in CIE mice reduced voluntary drinking, validating our network analysis and indicating that this region may play an important but underappreciated role in alcohol dependence.

neuroscience↗