Miracle-dz/UniFAR-FTUs huggingface dataset:
WormPaths: Caenorhabditis elegans metabolic pathway annotation and visualization

Abstract In our group, we aim to understand metabolism in the nematode Caenorhabditis elegans and its relationships with gene expression, physiology, and the response to therapeutic drugs. Visualization of the metabolic pathways that comprise the metabolic network is extremely useful for interpreting a wide variety of experiments. Detailed annotated metabolic pathway maps for C. elegans are mostly limited to pan-organismal maps, many with incomplete or inaccurate pathway and enzyme annotations. Here, we present WormPaths, which is composed of two parts: (1) the careful manual annotation of metabolic genes into pathways, categories, and levels, and (2) 62 pathway maps that include metabolites, metabolite structures, genes, reactions, and pathway connections between maps. These maps are available on the WormFlux website. We show that WormPaths provides easy-to-navigate maps and that the different levels in WormPaths can be used for metabolic pathway enrichment analysis of transcriptomic data. In the future, we envision further developing these maps to be more interactive, analogous to road maps that are available on mobile devices.
An Open Source Platform for Presenting Dynamic Visual Stimuli

Abstract Operant behavior procedures often rely on visual stimuli to cue the initiation or secession of a response, and to provide a means for discriminating between two or more simultaneously available responses. While primate and human studies typically use Liquid-Crystal Display (LCD) or Organic Light-Emitting Diode (OLED) monitors and touch screens, rodent studies use a variety of methods to present visual cues ranging from traditional incandescent light bulbs, single LEDs, and, more recently, touch screen monitors. Commercially available systems for visual stimulus presentation are costly, challenging to customize, and are typically closed source. We developed an open-source, highly-modifiable visual stimulus presentation platform that can be combined with a 3D-printed operant response device. The device uses an 8 × 8 matrix of LEDs, and can be expanded to control much larger LED matrices. Implementing the platform is low-cost (<$70 USD per device in the year 2020). Using the platform, we trained rats to make nosepoke responses and discriminate between two distinct visual cues in a location-independent manner. This visual stimulus presentation platform is a cost-effective way to implement complex visually-guided operant behavior, including the use of moving or dynamically changing visual stimuli.
Species-specific sensitivity to TGFβ signaling and changes to the Mmp13 promoter underlie avian jaw development and evolution

Developmental control of jaw length is critical for survival. The jaw skeleton arises from neural crest mesenchyme and previously we demonstrated that these progenitors upregulate bone-resorbing enzymes including Matrix metalloproteinase 13 (Mmp13) when generating short quail beaks versus long duck bills. Inhibiting bone resorption or Mmp13 increases jaw length. Here, we uncover mechanisms establishing species-specific levels of Mmp13 and bone resorption. Quail show greater activation of, and sensitivity to Transforming Growth Factor-Beta (TGFβ) signaling than duck; where mediators like SMADs and targets like Runx2, which bind Mmp13, become elevated. Inhibiting TGFβ signaling decreases bone resorption. We discover a SMAD binding element in the quail Mmp13 promoter not found in duck and single nucleotide polymorphisms (SNPs) near a RUNX2 binding element that affect expression. Switching the SNPs and SMAD site abolishes TGFβ-sensitivity in the quail Mmp13 promoter but makes duck responsive. Thus, differential regulation of TGFβ signaling and Mmp13 promoter structure underlie avian jaw development and evolution.
SHMT1-RNA interaction dynamically regulates serine and glycine concentration in cells

Michele Monti∗†,1, 2 Giulia Guiducci∗,3, 4 Alessio Paone, Serena Rinaldo, Giorgio Giardina, Francesca Cutruzzola†,3 and Gian Gaetano Tartaglia†1, 5, 3 Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona RNA System Biology Lab, Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163, Genoa, Italy La Sapienza University, Rome Piazzale Aldo Moro 5 Barts Cancer Institute, Centre for Cancer Cell and Molecular Biology, John Vane Science Centre, Charterhouse Square, Queen Mary University of London, London EC1M 6BQ, UK. RNA System Biology Lab, Department of Neuroscience and Brain Technologies (IIT), Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
Endothelial SOCS3 maintains homeostasis and promotes survival in endotoxemic mice

SOCS3 is the main inhibitor of the JAK/STAT3 pathway. This pathway is activated by interleukin 6 (IL-6), a major mediator of the cytokine storm during shock. To determine its role in the vascular response to shock, we challenged mice lacking SOCS3 in the adult endothelium (SOCS3iEKo) with a non-lethal dose of lipopolysaccharide (LPS). SOCS3iEKo mice died 16-24 hours post-injection after severe kidney failure. Loss of SOCS3 led to an LPS-induced type I interferon-like program, and high expression of pro-thrombotic and pro-adhesive genes. Consistently, we observed intraluminal leukocyte adhesion and NETosis, as well as retinal venular leukoembolization. Notably, heterozygous mice displayed an intermediate phenotype, suggesting a gene dose effect. In vitro studies were performed to study the role of SOCS3 protein levels in the regulation of the inflammatory response. In HUVEC, pulse-chase experiments showed that SOCS3 protein has a half-life below 20 minutes. Inhibition of SOCS3 ubiquitination and proteasomal degradation leads to protein accumulation and a stronger inhibition of IL-6 signaling and barrier function loss. Together, our data demonstrates that the regulation of SOCS3 protein levels is critical to inhibit IL-6-mediated endotheliopathy during shock and provides a promising new therapeutic avenue to prevent MODS though stabilization of endothelial SOCS3. Graphical abstract
Standardization of inducer-activated broad host range expression modules: debugging and refactoring an alkane-responsive AlkS/PalkB device

Although inducible heterologous expression systems have been available since the birth of recombinant DNA technology, the diversity of devices and genetic architectures of the corresponding vectors have often resulted in a lack of reproducibility and interoperability. In an effort to increase predictability of expression of genes of interest in a variety of possible bacterial hosts we propose a composition standard for debugging and reassembling all regulatory parts that participate in the performance of such devices. As a case study we address the n-octane and dicyclopropyl ketone (DCPK)-inducible PalkB promoter of the alkane biodegradation pOCT plasmid of Pseudomonas putida. The standardized expression module consisted of an edited alkS regulatory gene that is divergently expressed and separated of PalkB by a synthetic DNA buffer sequence. The native DNA sequence of the structural alkS gene was modified to alleviate the catabolite repression exerted by some carbon and nitrogen sources through the Crc/Hfq complex of some hosts. The PalkB promoter along with the alkS variants were then formatted as SEVA (Standard European Vector Architecture) cargoes and their activity parameters in P. putida determined with GFP and luminiscent reporters. The thereby refactored system showed improvements in various features desirable in conditional expression modules: inducibility, capacity, noise reduction and on/off ratio. When applied to other promoter/regulator pairs, the compositional standard thereby implemented in the AlkS/PalkB module will enable more complex genetic programming in non-model bacteria.
Periscope Proteins are variable-length regulators of bacterial cell surface interactions

Significance The structure of single and tandem SHIRT domains from the streptococcal surface protein Sgo_0707 were determined. In conjunction with biophysics and molecular dynamics simulations, the results show that the observed gene length variation would result in differential projection of the host ligand binding domain on the bacterial cell surface. An analysis of long-read DNA sequence data reveals many other repetitive bacterial surface proteins that appear to undergo gene length variation. We propose that these variable-length “Periscope Proteins” represent an important mechanism of bacterial cell surface modification with potential roles in infection and immune evasion. Changes at the cell surface enable bacteria to survive in dynamic environments, such as diverse niches of the human host. Here, we reveal “Periscope Proteins” as a widespread mechanism of bacterial surface alteration mediated through protein length variation. Tandem arrays of highly similar folded domains can form an elongated rod-like structure; thus, variation in the number of domains determines how far an N-terminal host ligand binding domain projects from the cell surface. Supported by newly available long-read genome sequencing data, we propose that this class could contain over 50 distinct proteins, including those implicated in host colonization and biofilm formation by human pathogens. In large multidomain proteins, sequence divergence between adjacent domains appears to reduce interdomain misfolding. Periscope Proteins break this “rule,” suggesting that their length variability plays an important role in regulating bacterial interactions with host surfaces, other bacteria, and the immune system.
Branching of sporogenic aerial hyphae in sflA and sflB mutants of Streptomyces coelicolor correlates to ectopic localization of DivIVA and FtsZ in time and space

Bacterial cytokinesis starts with the polymerization of the tubulin-like FtsZ, which forms the cell division scaffold. SepF aligns FtsZ polymers and also acts as a membrane anchor for the Z-ring. While in most bacteria cell division takes place at midcell, during sporulation of Streptomyces many septa are laid down almost simultaneously in multinucleoid aerial hyphae. The genomes of streptomycetes encode two additional SepF paralogs, SflA and SflB, which can interact with SepF. Here we show that the sporogenic aerial hyphae of sflA and sflB mutants of Streptomyces coelicolor frequently branch, a phenomenon never seen in the wild-type strain. The branching coincided with ectopic localization of DivIVA along the lateral wall of sporulating aerial hyphae. Constitutive expression of SflA and SflB largely inhibited hyphal growth, further correlating SflAB activity to that of DivIVA. SflAB localized in foci prior to and after the time of sporulation-specific cell division, while SepF co-localized with active septum synthesis. Foci of FtsZ and DivIVA frequently persisted between adjacent spores in spore chains of sflA and sflB mutants, at sites occupied by SflAB in wild-type cells. This may be caused by the persistance of SepF multimers in the absence of SflAB. Taken together, our data show that SflA and SflB play an important role in the control of growth and cell division during Streptomyces development.
Plasmodiophora brassicae chitin-binding effectors guard and mask spores during infection

Plants have a sophisticated and multilayered immune system. However, plant pathogens, helped by effector proteins, have found several strategies to evade plant immunity. For instance, the clubroot pathogen, Plasmodiophora brassicae, is able to turn the roots of the susceptible hosts into nutrient-sink galls surpassing patterns-triggered immunity (PTI) and effector-triggered immunity (ETI). Chitin, the main component of P. brassicae spores cell walls and a well-known pathogens-associated molecular pattern (PAMP), can elicit PTI but is also the target of plant chitinases and chitin deacetylases. The fact that P. brassicae does not trigger PTI during the infection of the susceptible hosts motivated a genome-wide search of genes coding for secreted chitin-related proteins. We found that P. brassicae genome encodes a large repertoire of candidate-secreted effectors containing the chitin-binding domain carbohydrate-binding module family 18 (CBM18), along with chitinases and chitin deacetylases domains. The role of such proteins in the pathogenicity of the clubroot pathogen is unknown. Here, we characterized the function of two effectors, PbChiB2 and PbChiB4, which are transcriptionally activated during the spores transition to uninucleate primary plasmodium and during the spore formation. Through co-precipitation, we found that recombinant PbChiB2 and PbChiB4 bind to the spores and to chitin oligomers in vitro. We also showed that both proteins suppress chitin-triggered activation of the immune MPK3 and MPK6 in the host Brassica napus. These findings suggest a dual role for the P. brassicae CBM18 proteins as effectors for protecting zoospores and resting spores formation and for suppressing chitin-triggered immunity during the infection.
An efficient lentiviral CRISPRi approach to silence genes in primary human monocytes

Human primary monocytes are critical in controlling immune responses and tissue homeostasis. However, to identify and study molecular components that underlie the function of these cells, there remains a need to develop methods to perturb genes in these cells. Here we report lentiviral-based delivery of dCas9-KRAB and guide RNAs to efficiently silent target genes, such as CD45 and CD209. We further show that sgRNAs against TICAM1 dampen proinflammatory cytokine and interferon expression in response to lipopolysaccharide. When delivered by lentivirus, sgRNAs are incorporated into the genome, thus enabling pooled screening to perturb and identify coding and non-coding elements that contribute to the functions of primary human monocytes.
Functional MRI based simulations of ECoG grid configurations for optimal measurement of spatially distributed hand-gesture information

Objective. In electrocorticography (ECoG), the physical characteristics of the electrode grid determine which aspect of the neurophysiology is measured. For particular cases, the ECoG grid may be tailored to capture specific features, such as in the development and use of brain–computer interfaces (BCI). Neural representations of hand movement are increasingly used to control ECoG based BCIs. However, it remains unclear which grid configurations are the most optimal to capture the dynamics of hand gesture information. Here, we investigate how the design and surgical placement of grids would affect the usability of ECoG measurements. Approach. High resolution 7T functional MRI was used as a proxy for neural activity in ten healthy participants to simulate various grid configurations, and evaluated the performance of each configuration for decoding hand gestures. The grid configurations varied in number of electrodes, electrode distance and electrode size. Main results. Optimal decoding of hand gestures occurred in grid configurations with a higher number of densely-packed, large-size, electrodes up to a grid of ~5 × 5 electrodes. When restricting the grid placement to a highly informative region of primary sensorimotor cortex, optimal parameters converged to about 3 × 3 electrodes, an inter-electrode distance of 8 mm, and an electrode size of 3 mm radius (performing at ~70% three-class classification accuracy). Significance. Our approach might be used to identify the most informative region, find the optimal grid configuration and assist in positioning of the grid to achieve high BCI performance for the decoding of hand-gestures prior to surgical implantation.
Novel multicellular prokaryote discovered next to an underground stream

The emergence of multicellularity is a key event in the evolution of life and is an attractive challenge among researchers, including those investigating the artificial design of cellular behavior1. Multicellular organisms are widely distributed on Earth, and retracing the specific conditions conducive for the initial transition from unicellularity to multicellularity is difficult. However, by examining organisms that inhabit unique (e.g., isolated) environmental niches, we may be able to get a glimpse into primitive multicellularity in the context of a given environment. Here we report the discovery of a new bacterium that displayed multicellular-like characteristics and behavior. The bacterium, which was isolated adjacent to an underground stream in a limestone cave, is to be named Jeongeupia sacculi sp. nov. HS-3. On a solid surface, HS-3 self-organizes its filamentous cells to form an appearance similar to the nematic phase of a liquid crystal2. Mature colonies produce and accommodate clusters of coccobacillus progeny, and release them upon contact with water. HS-3 demonstrated novel, spatiotemporally regulated multicellularity that can resolve the so-called ‘competition-dispersal trade-off’ problem3. This study illustrates a hypothetical missing link on the emergence of multicellularity.
Intergroup lethal gang attacks do not require fission-fusion dynamics to evolve

Lethal gang attacks, in which multiple aggressors attack a single victim, are among the most widespread forms of violence between human groups. Chimpanzees (Pan troglodytes), as well as wolves (Canis lupus), spotted hyaenas (Crocuta crocuta), and lions (Panthera leo), perform gang attacks during raids. In raids, a few individuals of a group enter another group’s territory and attack its members if found in numerical disadvantage. Current theory predicts that raids and gang attacks are linked to fission-fusion dynamics, i.e., the capacity of a group to split into smaller subgroups of variable size and composition. However, over the last decade, research on social mammals without fission-fusion societies nor raiding have shown that they may also be involved in intergroup lethal gang attacks. Thus, neither fission-fusion dynamics nor raiding are required for gang attacks to evolve. Based on our first-ever reports of intergroup gang attacks in the crested macaque (Macaca nigra), combined with the synthesis of earlier observations of such attacks in several species living in stable groups, we develop a new hypothesis about the proximate causes leading to lethal intergroup aggression. We propose that the ability to estimate numerical odds, form coalitionary bonds, and show hostility towards outgroup individuals may suffice to trigger intergroup gang attacks when the conditions favour an imbalance of power between victims and attackers.
Criticality Creates a Functional Platform for Network Transitions Between Internal and External Processing Modes in the Human Brain

Continuous switching between internal and external modes in the brain is a key process of constructing inner models of the outside world. However, how the brain continuously switches between two modes remains elusive. Here, we propose that a large synchronization fluctuation of the brain network emerging only near criticality (i.e., a balanced state between order and disorder) spontaneously creates temporal windows with distinct preferences for integrating internal information of the network and external stimuli. Using a computational model and empirical data analysis during alterations of consciousness in human, we present that synchronized and incoherent networks respectively bias toward internal and external information with specific network configurations. The network preferences are the most prominent in conscious states; however, they disrupt in altered states of consciousness. We suggest that criticality produces a functional platform of the brain’s capability for continuous switching between two modes, which is crucial for the emergence of consciousness.
SARS-CoV-2 mutations among minks show reduced lethality and infectivity to humans

SARS-CoV-2 infection in minks has become a serious problem, as the virus may mutate and reinfect humans; some countries have decided to cull minks. Here, the virus sequencing data in minks were analysed and compared to those of human-virus. Although the mink-virus maintained the characteristics of human-virus, some variants rapidly mutated, adapting to minks. Some mink-derived variants infected humans, which accounted for 40% of the total SARS-CoV-2 cases in the Netherlands. These variants appear to be less lethal and infective compared to those in humans. Variants that have mutated further among minks were not found in humans. Such mink-viruses might be suitable for vaccination for humans, such as in the case of the smallpox virus, which is less infective and toxic to humans.
Functional Characterization of a Lassa Virus Fusion Inhibitors Adaptive Mutant

Lassa virus (LASV) glycoprotein complex (GPC) contains retained stable-signal peptide (SSP), GP1, and GP2. SSP interacts with GP2 and provides an interface targeted by numerous fusion inhibitors. Serially passaging of LASV with inhibitors allowed some adaptive mutants to be obtained of which most had mutations located in the transmembrane (TM) domain of GP2. In the current study, we focused on the F446L mutant, which is reported to confer resistance to ST-series inhibitors. We found that F446L conferred cross-resistance to structurally distinct inhibitors. Furthermore, F446L increased the fusion activities of LASV and Mopeia virus GPC, elevating the pH threshold for fusion of LASV and promoting fusion of MOPV at neutral pH. F446L exerted little effect on the pseudotype viral growth profile or thermostability. By introducing other residues to the conserved F446 locus, it was found that this site was less compatible with a similar tyrosine residue and was intolerable to charged residues. These results help characterize the fusion inhibitor target located in the TM domain of GP2, which should be useful for drug and vaccine design. IMPORTANCE The LASV SSP-GP2 interface provides an Achilles heel that is targeted by numerous inhibitors. However, the emergence of resistant viruses is a major concern for direct antiviral drugs. In this study, we investigated the F446L mutant located in the GPC TM domain to determine the relationship between drug resistance, membrane fusion activity, viral growth kinetics, and thermostability. These results will be helpful in monitoring drug-resistant variants, as well as the advancement of drug and vaccine design.