Miracle-dz/UniFAR-FTUs huggingface dataset:
Liver inflammation before spinal cord injury worsens neuropathology, hepatic injury, metabolic syndrome and locomotor deficits

Liver inflammation can enhance acute leukocyte recruitment to sites of central nervous system (CNS) injury. The consequences of hepatic inflammation on recovery after injury, however, are unknown. Here, we hypothesize that liver inflammation at the time of spinal cord injury (SCI) will exacerbate spinal cord pathology and impair recovery. Rats receiving SCI with concomitant liver inflammation had worse intraspinal pathology and greater locomotor deficits than rats with baseline liver inflammation. Hepatic inflammation also potentiated SCI-induced non-alcoholic steatohepatitis (NASH), endotoxemia, insulin resistance and adiposity. Circulating and cerebrospinal levels of Fetuin-A were higher in SCI rats with liver inflammation. When microinjected into intact spinal cords, Fetuin-A caused robust macrophage activation, iron accumulation and neuron loss. These studies verify that outcomes from CNS injury are worse if the liver is concomitantly inflamed and implicate Fetuin-A as a potential neuropathological mediator. These novel data suggest hepatic inflammation is a potential clinical target for improving recovery from SCI.
Organoid-derived adult human colonic epithelium responds to co-culture with a probiotic strain of Bifidobacterium longum

In germ-free animals the lack of microbes within the gut results in a propensity to mucosal inflammation among other immune deficits. This suggests microbes are essential for the healthy function of the human gut, but we have lacked a reproducible mechanistic model of interactions between human colonic epithelium and the anaerobic microbes within the gut. To establish the physiological effect of a common anaerobe in the human gut, we co-cultured a probiotic strain of Bifidobacterium longum (35624) with organoid-derived adult human colonic epithelium in asymmetric gas conditions (anoxic apically, 5% oxygen basolaterally) and compared to axenic (‘germ-free’) epithelium. Bacteria proliferated and retained their normal cellular morphology in the presence of the human colonic epithelium. The human colonic mucosa retained trans-epithelial electrical resistance (TEER) consistent with an intact epithelium but lower than in axenic conditions. Changes in TEER corresponded to changes in Claudin-family gene expression. Inflammation was repressed in co-culture as compared to axenic, with reduced expression of executor and pyroptosis caspases; reduced expression of activators and increased expression of inhibitors of NFKB; reduced expression of toll-like-receptors (TLRs) and increased expression of TOLLIP (a negative regulator of TLRs). Consistent with the presence of actively fermenting bacteria that produce lactate and acetate but do not produce butyrate, PPARA expression was increased while PPARG expression was reduced. As in germ-free animal experiments, axenic human colonic mucosa is poised for inflammation. Co-culture with Bifidobacterium longum resolved the pro-inflammatory state while modulating barrier function (via Claudin genes) and cellular energetics (via PPARA and PPARG genes). Importance Experiments in animals demonstrate the importance of microbes with the gut for the health of the gut. Many of the microbes within the healthy gut are strictly anaerobic and cannot grow in the presence of oxygen; human tissues require some oxygen to live. Here we observe the effect of growing an anaerobic bacterium - Bifidobacterium longum - typically found in the human gut with human colonic tissue. We observed that the human tissue responded favorably to being cultivated with the microbe as compared to being alone. This experiment confirms human colonic tissues reduce their inflammation in the presence of a bacteria typically found in the gut.
Ecdysone regulates the Drosophila imaginal disc epithelial barrier, determining the duration of regeneration checkpoint delay

Regeneration of Drosophila imaginal discs, larval precursors to adult tissues, produces a systemic response, a regeneration checkpoint that coordinates regenerative growth with developmental progression. This regeneration checkpoint is coordinated by the release of the relaxin-family peptide Dilp8 from regenerating tissues. Secreted Dilp8 protein can be detected within the imaginal disc lumen. The disc epithelium separates from the lumen from the larval hemolymph and the targets for Dilp8 activity in the brain and prothoracic gland. Here we demonstrate that the imaginal disc epithelial barrier limits Dilp8 signaling and checkpoint delay. We also observe that the wing imaginal disc barrier becomes more restrictive during development, becoming impermeable only at end of the final larval instar. This change in barrier permeability is driven by the steroid hormone ecdysone and correlates with changes in localization of Coracle, a component of the septate junctions that is required for the late, impermeable epithelial barrier. Based on these observations, we propose that the imaginal disc epithelial barrier regulates the duration of the regenerative checkpoint, providing a mechanism by which tissue function can signal the completion of regeneration. Summary Statement Ecdysone signaling directs the Drosophila third instar imaginal disc epithelial barrier to mature, becoming more restrictive. This mature barrier limits Dilp8 signaling and determines the duration of the regeneration checkpoint.
Gene regulation of the avian malaria parasite Plasmodium relictum, during the different stages within the mosquito vector

The malaria parasite Plasmodium relictum is one of the most widespread species of avian malaria. As is the case in its human counterparts, bird Plasmodium undergoes a complex life cycle infecting two hosts: the arthropod vector and the vertebrate host. In this study, we examine the transcriptome of P. relictum (SGS1) during crucial timepoints within its natural vector, Culex pipiens quinquefasciatus. Differential gene-expression analyses identified genes linked to the parasites life-stages at: i) a few minutes after the blood meal is ingested, ii) during peak oocyst production phase, iii) during peak sporozoite phase and iv) during the late-stages of the infection. A large amount of genes coding for functions linked to host-immune invasion and multifunctional genes was active throughout the infection cycle. One gene associated with a conserved Plasmodium membrane protein with unknown function was upregulated throughout the parasite development in the vector, suggesting an important role in the successful completion of the sporogonic cycle. Transcript annotation further revealed novel genes, which were significantly differentially expressed during the infection in the vector as well as upregulation of reticulocyte-binding proteins, which raises the possibility of the multifunctionality of these RBPs. We establish the existence of highly stage-specific pathways being overexpressed during the infection. This first study of gene-expression of a non-human Plasmodium species in its natural vector provides a comprehensive insight into the molecular mechanisms of the common avian malaria parasite P. relictum and provides essential information on the evolutionary diversity in gene regulation of the Plasmodium’s vector stages.
The left dorsal stream causally mediates the tone labeling in absolute pitch

Background Absolute pitch (AP) refers to the ability of effortlessly identifying given pitches without the reliance on any reference pitch. Correlative evidence suggests that the left posterior dorsolateral prefrontal cortex (DLPFC) is responsible for the process underlying pitch labeling in AP. Objective Here, we aimed at investigating the causal relationship between the DLPFC and the pitch-labeling process underlying AP. Methods To address this, we measured sight-reading performance of right-handed AP possessors and matched control musicians (N =18 per sample) under cathodal and sham transcranial direct current stimulation of the left DLPFC. The participants were instructed to report visually presenting notations as accurately and fast as possible by playing with their right hand on a piano. The notations were simultaneously presented with distracting auditory stimuli that either matched or mismatched them in different semitone degrees. Results Unlike the control participants, the AP possessors revealed an interference effect in that they responded slower in mismatching conditions than in the matching one. Under cathodal stimulation, half of the time discrepancies between matching and mismatching conditions vanished; specifically, the ones with small up to moderate deviations. Conclusions These findings confirm that the pitch-labeling process underlying AP occurs automatically and is largely non-suppressible when triggered by tone exposure. The improvement of the AP possessors’ sight-reading performance in response to the suppression of the left DLPFC using cathodal stimulation confirms a causal relationship between this brain structure and pitch labeling.
Spelling Changes and Fluorescent Tagging With Prime Editing Vectors for Plants

Prime editing (PE) is a recent adaptation of the CRISPR-Cas system that uses a Cas9(H840A)-reverse transcriptase (RT) fusion and a guide RNA (pegRNA) amended with template and primer binding site (PBS) sequences to achieve RNA-templated conversion of the target DNA, allowing specified substitutions, insertions, and deletions. In the first report of PE in plants, a variety of edits in rice and wheat were described, including insertions up to 15 bp. Several studies in rice quickly followed, but none reported a larger insertion. Here, we report easy-to-use vectors for PE in dicots and monocots, their validation in Nicotiana benthamiana, rice and Arabidopsis, and an insertion of 66 bp that enabled split-GFP fluorescent tagging.
TMEM180 contributes to colorectal cancer proliferation through intracellular metabolic pathways

TMEM180, a novel colon cancer–specific membrane protein with a 12-transmembrane topology, is upregulated at low oxygen. Previously, we established a humanized monoclonal antibody against TMEM180 aimed at clinical trials. Prior to such trials, it is necessary to clarify the function of this molecule in cancer. To compare SW480 human colon cancer cells and their TMEM180-knockdown derivatives, we analyzed proliferation and oxygen consumption, and also performed phosphorylation proteomics, metabolomics, and next-generation sequencing. The results revealed that TMEM180 promoted the growth of colon cancer but had almost no effect on oxygen consumption or expression of phosphorylated proteins. By contrast, glycolysis differed dramatically between SW480 and TMEM180-knockdown cells. TMEM180 promotes nitric oxide synthesis, suggesting that it promotes glucose metabolism and glutamine metabolism, thereby contributing to cancer growth. Overall, the results of this study support the clinical development of an anti-TMEM180 antibody.
Evaluating brain structure traits as endophenotypes using polygenicity and discoverability

Human brain structure traits have been hypothesized to be broad endophenotypes for neuropsychiatric disorders, implying that brain structure traits are comparatively ‘closer to the underlying biology’. Genome-wide association studies from large sample sizes allow for the comparison of common variant genetic architectures between traits to test the evidence supporting this claim. Endophenotypes, compared to neuropsychiatric disorders, are hypothesized to have less polygenicity, with greater effect size of each susceptible SNP, requiring smaller sample sizes to discover them. Here, we compare polygenicity and discoverability of brain structure traits, neuropsychiatric disorders, and other traits (89 in total) to directly test this hypothesis. We found reduced polygenicity (FDR = 0.01) and increased discoverability of cortical brain structure traits, as compared to neuropsychiatric disorders (FDR = 3.68×10−9). We predict that ~8M samples will be required to explain the full heritability of cortical surface area by genome-wide significant SNPs, whereas sample sizes over 20M will be required to explain the full heritability of major depressive disorder. In conclusion, we find reduced polygenicity and increased discoverability of cortical structure compared to neuropsychiatric disorders, which is consistent with brain structure satisfying the higher power criterion of endophenotypes.
Global transcriptional regulators fine-tune the translational and metabolic machinery in Escherichia coli under anaerobic fermentation

Complex regulatory interactions between genetic and metabolic networks together confer robustness against external and internal perturbations in an organism such as Escherichia coli. In balanced exponential growth, this robustness is attributed to cost-effective metabolism by means of efficient resource allocation coordinated by the interplay of global transcriptional regulators with growth-rate dependent machinery. Here, we reappraise the role of global transcriptional regulators FNR, ArcA and IHF, integral to sustaining proteome-efficiency in anaerobic fermentative conditions, fundamental for optimal growth of E. coli. We reveal at the transcriptome and metabolome level, that absence of these global regulators ensued a disruption of nitrogen homeostasis, overexpression of otherwise unnecessary or hedging genes and impairment in core bottleneck steps and amino acid metabolism. Notably, our findings emphasize their importance in optimizing the metabolic proteome resources essential for rapid exponential growth. Consequentially, the perturbations in the metabolic proteome as a result of deletion of global regulators unbalances the ribosomal proteome share imposing a high translation program, though at the expense of lowered efficiency. We illustrate that disruption of this inherent trade-off between metabolic and ribosomal proteomic investment eventually culminate to lowered growth rates. Despite no changes in gene expression related to glucose import, our findings elucidate that the accumulations of intracellular metabolites directly modulated by growth rate, negatively impacts the glucose uptake. Our results employing the proteome allocation theory and quantitative experimental measurements, suffices to explain the physiological consequences of altered translational and metabolic efficiency in the cell, driven by the loss of these global regulators.
A Correspondence Between Normalization Strategies in Artificial and Biological Neural Networks

A fundamental challenge at the interface of machine learning and neuroscience is to uncover computational principles that are shared between artificial and biological neural networks. In deep learning, normalization methods, such as batch normalization, weight normalization, and their many variants, help to stabilize hidden unit activity and accelerate network training, and these methods have been called one of the most important recent innovations for optimizing deep networks. In the brain, homeostatic plasticity represents a set of mechanisms that also stabilize and normalize network activity to lie within certain ranges, and these mechanisms are critical for maintaining normal brain function. In this survey, we discuss parallels between artificial and biological normalization methods at four spatial scales: normalization of a single neuron’s activity, normalization of synaptic weights of a neuron, normalization of a layer of neurons, and normalization of a network of neurons. We argue that both types of methods are functionally equivalent — i.e., they both push activation patterns of hidden units towards a homeostatic state, where all neurons are equally used — and that such representations can increase coding capacity, discrimination, and regularization. As a proof of concept, we develop a neural normalization algorithm, inspired by a phenomena called synaptic scaling, and show that this algorithm performs competitively against existing normalization methods on several datasets. Overall, we hope this connection will inspire machine learners in three ways: to uncover new normalization algorithms based on established neurobiological principles; to help quantify the trade-offs of different homeostatic plasticity mechanisms used in the brain; and to offer insights about how stability may not hinder, but may actually promote, plasticity.
Selected reaction monitoring for the quantification of Escherichia coli ribosomal proteins

Ribosomes are the sophisticated machinery that is responsible for protein synthesis in a cell. Recently, quantitative mass spectrometry (qMS) based on data-dependent acquisition (DDA) have been widely used to understand the biogenesis and function of ribosomes. However, DDA-based qMS sometimes does not provide the reproducible and quantitatively reliable analysis that is needed for high-throughput hypothesis testing. To overcome this problem, we developed a highly sensitive, specific, and accurate method to quantify all ribosomal proteins (r-proteins) by combining selected reaction monitoring (SRM) and isotope labeling. We optimized the SRM methods using purified ribosomes and Escherichia coli lysates, and verified this approach as a high-throughput analytical tool by detecting 41 of the 54 r-proteins separately synthesized in E. coli S30 extracts. The SRM methods will enable us to utilize qMS as a high-throughput hypothesis testing tool in the research of E. coli ribosomes, and they have potential to accelerate the understanding of ribosome biogenesis, function, and the development of engineered ribosomes with additional functions.
DEVELOPMENT OF A CULTURE-INDEPENDENT POLYMERASE CHAIN REACTION-BASED ASSAY FOR THE DETECTION OF LACTOBACILLI IN STRETCHED CHEESE

The purpose of this research was to develop a culture-independent assay based on polymerase chain reaction (PCR) for the specific detection of lactobacilli present in very low amounts in natural microflora during the processing of traditional pasta filata cheese. The utility of casein micelle solubilization with Triton X-100 was also evaluated before proceeding to DNA extraction and PCR detection. By using primers related to cell envelope proteinase and gassericin B genes, proteolytic lactobacilli were successfully detected in samples from which they had not previously been isolated by plate counting. The sensitivity of the method is estimated to be 1000 cfu/mL. The speed of the DNA extraction protocol and the sensitivity and reliability of the PCR assay even make it feasible to detect nondominant populations of Lactobacillus species in cheese.
Incorporating genome-based phylogeny and trait similarity into diversity assessments helps to resolve a global collection of human gut metagenomes

Tree-based diversity measures incorporate phylogenetic or phenotypic relatedness into comparisons of microbial communities. This improves the identification of explanatory factors compared to tree-agnostic diversity measures. However, applying tree-based diversity measures to metagenome data is more challenging than for single-locus sequencing (e.g., 16S rRNA gene). The Genome Taxonomy Database (GTDB) provides a genome-based reference database that can be used for species-level metagenome profiling, and a multi-locus phylogeny of all genomes that can be employed for diversity calculations. Moreover, traits can be inferred from the genomic content of each representative, allowing for trait-based diversity measures. Still, it is unclear how metagenome-based assessments of microbiome diversity benefit from incorporating phylogeny or phenotype into measures of diversity. We assessed this by measuring phylogeny-based, trait-based, and tree-agnostic diversity measures from a large, global collection of human gut metagenomes composed of 33 studies and 3348 samples. We found phylogeny- and trait-based alpha diversity to better differentiate samples by westernization, age, and gender. PCoA ordinations of phylogeny- or trait-based weighted UniFrac explained more variance than tree-agnostic measures, which was largely a result of these measures emphasizing inter-phylum differences between Bacteroidaceae (Bacteroidota) and Enterobacteriaceae (Proteobacteria) versus just differences within Bacteroidaceae (Bacteroidota). The disease state of samples was better explained by tree-based weighted UniFrac, especially the presence of Shiga toxin-producing E. coli (STEC) and hypertension. Our findings show that metagenome diversity estimation benefits from incorporating a genome-derived phylogeny or traits. Importance Estimations of microbiome diversity are fundamental to understanding spatiotemporal changes of microbial communities and identifying which factors mediate such changes. Tree-based measures of diversity are widespread for amplicon-based microbiome studies due to their utility relative to tree-agnostic measures; however, tree-based measures are seldomly applied to shotgun metagenomics data. We evaluated the utility of phylogeny-, trait-, and tree-agnostic diversity measures on a large scale human gut metagenome dataset to help guide researchers with the complex task of evaluating microbiome diversity via metagenomics.
Biological and molecular characterization of six Shiga toxin-producing Escherichia coli (STEC) strains encoding the stx2 gene in Colombia

Shiga toxin-producing Escherichia coli (STEC) is a bacterial pathogen that cause diarrhea and severe human diseases. Its principal virulence factor are the Shiga toxins Stx1 and Stx2 which have been identified diverse subtypes considered to be responsible for severe complications of STEC infection. These toxins are encoded in temperate bacteriophages and their expression is linked to phage lithic cycle, which is regulated by late genes and the Q anti-terminator protein. The aim of this study was to characterize biologically and molecularly STEC strains encoding stx2 gene isolated from cattle feces in Colombia. We selected six STEC strains, which were evaluated its Stx production, the Stx2 subtypes, induction of the lithic cycle of bacteriophages and its late region. The results evidenced two highlighted strains with high levels of Stx production and induction of the lithic cycle, compared with the others. Likewise, the strains evaluated showed three Stx2 subtypes: Stx2a, Stx2c, and Stx2d. Regarding the late region, most of the strains carried the qO111 allele and only one strain showed differences in the ninG gene. Although the sample was limited, variability was observed in the Stx production assay, induction of the lithic cycle, Stx2 subtypes and late region of the phages, which could indicate the diversity of the phages carrying STEC strains in Colombia.
Temporally integrated single cell RNA sequencing analysis of controlled and natural primary human DENV-1 infections

Controlled dengue human infection studies present an opportunity to address many longstanding questions in the field of flavivirus biology. However, limited data are available on how the immunological and transcriptional response elicited by an attenuated challenge virus compares to that associated with a wild-type DENV infection. To bridge this knowledge gap, we utilized scRNAseq to analyze PBMC from individuals enrolled in a DENV-1 controlled human challenge study and from individuals experiencing a natural primary DENV-1 infection. While both controlled and natural DENV infection resulted in overlapping patterns of inflammatory gene upregulation, natural DENV infection was accompanied with a more pronounced suppression in gene products associated with protein translation and mitochondrial function, principally in monocytes. This suggests that the immune response elicited by controlled and natural primary DENV infection are similar, but that natural DENV infection has a more pronounced impact on basic cellular processes to induce a multi-layered anti-viral state