Miracle-dz/UniFAR-FTUs huggingface dataset:
New insights into biocathode material as a key determinant of electro-methanogenic activity and significance of extracellular polymeric substances

Carbon-based electrodes have been mostly used as a biocathode material in microbial electrolysis cell assisted anaerobic digestion (MEC-AD) due to their excellent biocompatibility and higher surface area over metal-based electrodes. Here, we report a multifaceted approach combining characterization of microbial communities, extracellular polymeric substances (EPS), redox oxygen species (ROS), and expression of genes associated with extracellular electron transfer (EET) to shed light on mechanisms governing electro-methanogenic activity in different biocathode materials. Carbon fiber and stainless-steel mesh biocathode were tested in MEC-AD systems fed with synthetic glucose medium. Despite the higher specific surface area provided by carbon fiber biocathode, methanogenesis performance was much inferior (100.3 mL CH4) than that obtained from a stainless steel biocathode (179.5 mL CH4). Interestingly, biofilms did not entirely cover the surfaces of carbon fibers, while stainless steel biocathode showed evenly denser biofilms with higher biovolume (30.2±4.2 vs. 13.5±2.8 μm3/μm2). Analyses of microbial communities indicated that the key mechanism for electro-methanogenesis in both reactors was hydrogenotrophic methanogenesis by Methanobacterium species. The redox activity of EPS derived from biocathode, as well as expressions of EET genes, suggested that electro-methanogenesis via direct electron transfer might have occurred to some extent in both biocathodes. Higher abundance of strictly hydrogenotrophic Methanobacterium sp. and homoacetogenic Acetobacterium appeared to play a major role in higher methanogenesis performance from stainless steel biocathode. It was possibly attributed to effective catalysis of hydrogen evolution reaction (HER) on stainless steel biocathode. The most considerable secretion of EPS accompanied by the lowest ROS level in stainless steel biocathode indicated that higher EPS possibly protected cells from harsh metabolic conditions (e.g., unfavorable local pH) induced by faster HER. The results of this study have important significance in the development of effective biocathode for MEC-AD systems. Highlights Stainless-steel mesh outperformed carbon fibers for methanogenic biocathode. Multifaceted characterization of biofilms unveiled underlying mechanisms. The results confirmed H2-utilizing methanogenesis is the dominant pathway. Homoacetogenesis only played a crucial role in the stainless-steel biocathode. Biocathode EPS might be responsible for superior methanogenesis. Graphical Abstract
Protein turnover dynamics suggest a diffusion to capture mechanism for peri-basal body recruitment and retention of intraflagellar transport proteins

Intraflagellar transport (IFT) is essential for construction and maintenance of cilia. IFT proteins concentrate at the basal body, where they are thought to assemble into trains and bind cargoes for transport. To study the mechanisms of IFT recruitment to this peri-basal body pool, we quantified protein dynamics of eight IFT proteins, as well as five other basal body localizing proteins, using fluorescence recovery after photobleaching in vertebrate multiciliated cells. We found that members of the IFT-A and IFT-B protein complexes show distinct turnover kinetics from other basal body components. Additionally, known IFT sub-complexes displayed shared dynamics, and these dynamics were not altered during cilia regeneration as compared to homeostasis. Finally, we evaluated the mechanisms of basal body recruitment by depolymerizing cytosolic MTs, which suggested that IFT proteins are recruited to basal bodies through a diffusion-to-capture mechanism. Our survey of IFT protein dynamics provides new insights into IFT recruitment to basal bodies, a crucial step in ciliogenesis.
Micromanipulation of amyloplasts with optical tweezers in Arabidopsis stems

Intracellular sedimentation of highly dense, starch-filled amyloplasts toward the gravity vector is likely a key initial step for gravity sensing in plants. However, recent live-cell imaging technology revealed that most amyloplasts continuously exhibit dynamic, saltatory movements in the endodermal cells of Arabidopsis stems. These complicated movements led to questions about what type of amyloplast movement triggers gravity sensing. Here we show that a confocal microscope equipped with optical tweezers can be a powerful tool to trap and manipulate amyloplasts noninvasively, while simultaneously observing cellular responses such as vacuolar dynamics in living cells. A near-infrared (λ = 1064 nm) laser that was focused into the endodermal cells at 1 mW of laser power attracted and captured amyloplasts at the laser focus. The optical force exerted on the amyloplasts was theoretically estimated to be up to 1 pN. Interestingly, endosomes and trans-Golgi networks were trapped at 30 mW but not at 1 mW, which is probably due to lower refractive indices of these organelles than that of the amyloplasts. Because amyloplasts are in close proximity to vacuolar membranes in endodermal cells, their physical interaction could be visualized in real time. The vacuolar membranes drastically stretched and deformed in response to the manipulated movements of amyloplasts by optical tweezers. Our new method provides deep insights into the biophysical properties of plant organelles in vivo and opens a new avenue for studying gravity-sensing mechanisms in plants.
Interpreting Coronary Artery Disease Risk Through Gene–Environment Interactions in Gene Regulation

Cardiovascular disease (CVD) is the leading cause of morbidity and mortality worldwide. Epidemiological and genome-wide association studies have identified environmental and genetic risk factors for CVD. Using human vascular endothelial cells treated with dexamethasone, retinoic acid, caffeine, and selenium. GWAS and eQTL studies identified thousands of genetic variants associated with complex traits and gene expression. Despite the important role of environmental exposures in complex traits, only a limited number of environmental factors were measured in these studies. Measuring molecular phenotypes in tightly controlled cellular environments provides a more tractable setting to study gene–environment interactions in the absence of other confounding variables. We performed RNA-seq and ATAC-seq in endothelial cells exposed to retinoic acid, dexamethasone, caffeine, and selenium to model genetic and environmental effects on gene regulation in the vascular endothelium—a common site of pathology in cardiovascular disease. We found that genes near regions of differentially accessible chromatin were more likely to be differentially expressed [OR = (3.41, 6.52), p<10−16]. Furthermore, we confirmed that environment-specific changes in transcription factor binding are a key mechanism for cellular response to environmental stimuli. Single nucleotide polymorphisms (SNPs) in these transcription response factor footprints for dexamethasone, caffeine, and retinoic acid were enriched in GTEx eQTLs from artery tissues, indicating that these environmental conditions are latently present in GTEx samples. Additionally, SNPs in footprints for response factors in caffeine are enriched in colocalized eQTLs for coronary artery disease (CAD), suggesting a role for caffeine in CAD risk. By combining GWAS, eQTLs, and response genes, we annotated environmental components that can increase or decrease disease risk through changes in gene expression in 43 genes. Interestingly, each treatment may amplify or buffer genetic risk for CAD, depending on the particular SNP or gene considered.
Identifying and prioritizing potential human-infecting viruses from their genome sequences

Rapid assessment of which animal viruses may be capable of infecting humans is currently intractable, but would allow their prioritization for further investigation and pandemic preparedness. We developed machine learning algorithms that identify candidate zoonoses using evolutionary signals of host range encoded in viral genomes. This reduces lists of hundreds of viruses with uncertain human infectivity to tractable numbers for prioritized research, generalizes to virus families excluded from model training, can distinguish high risk viruses within families that contain a minority of zoonotic species, and could have identified the exceptional risk of SARS-CoV-2 prior to its emergence. Genome-based risk assessment allows identification of high-risk viruses immediately upon discovery, increasing both the feasibility and likelihood of downstream virological and ecological characterization and allowing for evidence-driven virus surveillance.
New Insights and Enhanced Human Norovirus Cultivation in Human Intestinal Enteroids

Human noroviruses (HuNoVs) are highly contagious and cause acute and sporadic diarrheal illness in all age groups. In addition, chronic infections occur in immunocompromised cancer and transplant patients. ABSTRACT Human noroviruses (HuNoVs) are the leading cause of epidemic and sporadic acute gastroenteritis worldwide. We previously demonstrated human intestinal stem cell-derived enteroids (HIEs) support cultivation of several HuNoV strains. However, HIEs did not support virus replication from every HuNoV-positive stool sample, which led us to test and optimize new medium conditions, identify characteristics of stool samples that allow replication, and evaluate consistency of replication over time. Optimization of our HIE-HuNoV culture system has shown the following: (i) a new HIE culture medium made with conditioned medium from a single cell line and commercial media promotes robust replication of HuNoV strains that replicated poorly in HIEs grown in our original culture medium made with conditioned media from 3 separate cell lines; (ii) GI.1, 11 GII genotypes (GII.1, GII.2, GII.3, GII.4, GII.6, GII.7, GII.8, GII.12, GII.13, GII.14, and GII.17), and six GII.4 variants can be cultivated in HIEs; (iii) successful replication is more likely with virus in stools with higher virus titers; (iv) GII.4_Sydney_2012 virus replication was reproducible over 3 years; and (v) HuNoV infection is restricted to the small intestine, based on replication of two viral strains in duodenal and ileal HIEs, but not colonoids, from two susceptible donors. These results improve the HIE culture system for HuNoV replication. Use of HIEs by several laboratories worldwide to study the molecular mechanisms that regulate HuNoV replication confirms the usefulness of this culture system, and our optimized methods for virus replication will advance the development of effective therapies and methods for virus control. IMPORTANCE Human noroviruses (HuNoVs) are highly contagious and cause acute and sporadic diarrheal illness in all age groups. In addition, chronic infections occur in immunocompromised cancer and transplant patients. These viruses are antigenically and genetically diverse, and there are strain-specific differences in binding to cellular attachment factors. In addition, new discoveries are being made on strain-specific differences in virus entry and replication and the epithelial cell response to infection in human intestinal enteroids. Human intestinal enteroids are a biologically relevant model to study HuNoVs; however, not all strains can be cultivated at this time. A complete understanding of HuNoV biology thus requires cultivation conditions that will allow the replication of multiple strains. We report optimization of HuNoV cultivation in human intestinal enteroid cultures to increase the numbers of cultivatable strains and the magnitude of replication, which is critical for testing antivirals, neutralizing antibodies, and methods of virus inactivation.
Comparative analysis of histone H3K4me3 modifications between early embryos and somatic tissues in cattle

Epigenetic changes induced in the early developmental stages by the surrounding environment can have not only short-term but also long-term consequences throughout life. This concept constitutes the “Developmental Origins of Health and Disease” (DOHaD) hypothesis and encompasses the possibility of controlling livestock health and diseases by epigenetic regulation during early development. As a preliminary step for examining changes of epigenetic modifications in early embryos and their long-lasting effects in fully differentiated somatic tissues, we aimed to obtain high-throughput genome-wide histone H3 lysine 4 trimethylation (H3K4me3) profiles of bovine early embryos and to compare these data with those from adult somatic tissues in order to extract common and typical features between these tissues in terms of H3K4me3 modifications. Bovine blastocysts were produced in vitro and subjected to chromatin immunoprecipitation-sequencing analysis of H3K4me3. Comparative analysis of the blastocyst-derived H3K4me3 profile with publicly available data from adult liver and muscle tissues revealed that the blastocyst profile could be used as a “sieve” to extract somatic tissue-specific modifications in genes closely related to tissue-specific functions. Furthermore, principal component analysis of the level of common modifications between blastocysts and somatic tissues in meat production-related and imprinted genes well characterized inter- and intra-tissue differences. The results of this study produced a referential genome-wide H3K4me3 profile of bovine early embryos and revealed its common and typical features in relation to the profiles of adult tissues. Supplementary information Supplementary data are submitted along with the main manuscript. The ChIP-seq datasets for bovine blastocysts have been deposited in the Gene Expression Omnibus of NCBI with accession number GSE161221.
Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution

We perform an extensive genomic analysis of freshwater adaption in threespine stickleback to predict evolution in other species. Similar forms often evolve repeatedly in nature, raising long-standing questions about the underlying mechanisms. Here, we use repeated evolution in stickleback to identify a large set of genomic loci that change recurrently during colonization of freshwater habitats by marine fish. The same loci used repeatedly in extant populations also show rapid allele frequency changes when new freshwater populations are experimentally established from marine ancestors. Marked genotypic and phenotypic changes arise within 5 years, facilitated by standing genetic variation and linkage between adaptive regions. Both the speed and location of changes can be predicted using empirical observations of recurrence in natural populations or fundamental genomic features like allelic age, recombination rates, density of divergent loci, and overlap with mapped traits. A composite model trained on these stickleback features can also predict the location of key evolutionary loci in Darwin’s finches, suggesting that similar features are important for evolution across diverse taxa.
GSAP Regulates Amyloid Beta Production through Modulation of Amyloid Precursor Protein Trafficking

In addition to participating in γ-secretase activity, presenilin 1 (PS1) regulates trafficking and subcellular localization of β-amyloid precursor protein (APP). We previously showed that gamma-secretase activating protein (GSAP) selectively modulates γ-secretase activity by inducing conformational change in PS1. However, little is known whether and how GSAP might influence APP trafficking and consequent generation of β-amyloid (Aβ) peptides. Here, to explore whether GSAP has any role in regulating APP trafficking, and to systematically investigate the intracellular trafficking routes of APP, we paired total internal reflection fluorescence microscopy, high-speed line scanning microscopy, and 4D microscopy with comprehensive imaging analysis methodologies to depict the elusive modes of APP trafficking at a single-vesicle level. Mobility and diffusivity changes reveal the existence of two kinetically distinct pathways, classified into mobile and immobile pools, for vesicular APP trafficking, suggesting high association between immobile vesicle pool and amyloidogenic processing. GSAP knockdown significantly lowers immobile pool without overturning APP vesicle diffusivity, suggesting that GSAP affects vesicular APP trafficking by retaining APP in membrane microdomains known to favor amyloidogenic processing. Our study reveals a novel role of GSAP in the regulation of Aβ-peptide formation that modulates switching of APP vesicles between immobile and mobile pools, which may help identifying new therapeutic strategies to treat Alzheimer’s disease.
Experience-related alterations in white matter structure and gene expression in adult rats

White matter (WM) plasticity during adulthood is a recently described phenomenon by which experience can shape brain structure. It has been observed in humans using diffusion tensor imaging (DTI). However, it remains unclear which mechanisms drive or underlie WM plasticity in adulthood. Here, we combined DTI and mRNA expression analysis and examined the effects of somatosensory experience in adult rats. Somatosensory experience resulted in differences in WM and grey matter structure. C-FOS mRNA expression, a marker of cortical activity, in the barrel cortex correlated with the structural WM measures, suggesting that WM plasticity is activity-dependent. Analysis of myelin-related genes revealed higher myelin basic protein expression in WM, while genome-wide RNA sequencing analysis identified 134 differentially-expressed genes regulating proteins involved in functions related to cell proliferation and differentiation, neuronal activity modulation and regulation of myelination. In conclusion, the macroscale measures of WM differences identified in response to somatosensory experience are supported by molecular evidence, which strongly suggest myelination as, at least, one of the underlying mechanisms.
Characterization of plasma membrane proteins from maize roots (Zea mays L.) under multiple abiotic stresses using LC-MS/MS technique

The aim of this study was to understand the response of maize inbred plants showing tolerance when exposed to various abiotic stresses (drought x low-N and waterlogging x low-N stress) simultaneously. The plants under stress expressed higher photosynthetic efficiency, increase in plant height, leaf area, and were able to maintain relatively high leaf relative water content and less decrease in morphological parameters. Therefore, to understand the processes controlling the tolerance to various stresses we analyzed maize roots plasma membranes proteome of treated plants only using LC-MS/MS techniques. The large number of proteins (295) were identified which were mainly trans membrane proteins, low abundance proteins, and root specific proteins. Further, a few proteins were selected like high-affinity Nitrate transporter, NR enzyme, PEP carboxylase, and Glutamine synthetase proteins their induction were validated by qRT-PCR approach in control and treated plants. The qRT-PCR results indicated the gene of all four proteins were expressed in treated and control plants. We concluded the high-affinity nitrate transporter proteins might represent the executive part of the protective response that plays a significant role in low-N stress tolerance. The presence of other major proteins like kinases, stress-responsive TFs, calmodulin, aquaporins, stress-related proteins, and many more proteins and their interaction with nitrate transporter proteins and their role can be validated only after comparing it with control samples.
Molecular and Spectroscopic Characterization of Green and Red Cyanine Fluorophores from the Alexa Fluor and AF Series

The use of fluorescence techniques has had an enormous impact on various research fields including imaging, biochemical assays, DNA-sequencing and medical technologies. This has been facilitated by the availability of numerous commercial dyes, but often information about the chemical structures of dyes (and their linkers) are a well-kept secret. This can lead to problems for applications where a knowledge of the dye structure is necessary to predict (unwanted) dye-target interactions, or to establish structural models of the dye-target complex. Using a combination of spectroscopy, mass spectrometry and molecular dynamics simulations, we here investigate the molecular structures and spectroscopic properties of dyes from the Alexa Fluor (Alexa Fluor 555 and 647) and AF series (AF555, AF647, AFD647). Based on available data and published structures of the AF and Cy dyes, we present two possible structures for Alexa Fluor 555. We also resolve conflicting reports on the linker composition of Alexa Fluor 647. A comprehensive comparison between Alexa Fluor and AF dyes by continuous-wave absorption and emission spectroscopy, quantum yield determination, fluorescence lifetime and anisotropy spectroscopy of free and protein-attached dyes, supports the suggestion that the Alexa Fluor and AF dyes have a high degree of structural similarity. In addition, we compared Alexa Fluor 555 and Alexa Fluor 647 to their structural homologs AF555 and AF(D)647 in single-molecule FRET applications. Both pairs showed excellent performance in solution-based smFRET experiments using alternating laser excitation demonstrating that the AF-fluorophores are an attractive alternative to Alexa- and Cy-dyes for smFRET studies, and suggesting their usefulness for other fluorescence applications.
Long-read RNA sequencing reveals widespread sex-specific alternative splicing in threespine stickleback fish

Alternate isoforms contribute immensely to phenotypic diversity across eukaryotes. While short read RNA-sequencing has increased our understanding of isoform diversity, it is challenging to accurately detect full-length transcripts, preventing the identification of many alternate isoforms. Long-read sequencing technologies have made it possible to sequence full length alternative transcripts, accurately characterizing alternative splicing events, alternate transcription start and end sites, and differences in UTR regions. Here, we utilize PacBio long read RNA-sequencing (Iso-Seq) to examine the transcriptomes of five tissues in threespine stickleback fish (Gasterosteus aculeatus), a widely used genetic model species. The threespine stickleback fish has a refined genome assembly with gene annotations that are based on short-read RNA sequencing and predictions from coding sequence of other species. This suggests some of the existing annotations may be inaccurate or alternative transcripts may not be fully characterized. Using Iso-Seq we detected thousands of novel isoforms, indicating many isoforms are absent in the current Ensembl gene annotations. In addition, we refined many of the existing annotations within the genome. We noted many improperly positioned transcription start sites that were refined with long-read sequencing. The Iso-Seq predicted transcription start sites were more accurate, verified through ATAC-seq. We were also able to detect many alternative splicing events between sexes and across tissues. We found a substantial number of genes in both somatic and gonad tissue that had sex-specific isoforms. Our study highlights the power of long-read sequencing to study the complexity of transcriptomes, greatly improving genomic resources for the threespine stickleback fish.