Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosphorylation of Threonine 107 by Calcium/Calmodulin dependent Kinase II δ Regulates the Detoxification Efficiency and Proteomic Integrity of Glyoxalase 1

The glyoxalase system is a ubiquitously expressed enzyme system with narrow substrate specificity and is responsible for the detoxification of harmful methylglyoxal (MG), a spontaneous by-product of energy metabolism. Glyoxalase 1 (Glo1) is the first and therefore rate limiting enzyme of this protective system. In this study we were able to show that a phosphorylation of threonine-107 in the Glo1 protein, mediated by Ca2+/Calmodulin-dependent Kinase II delta (CamKIIδ), is associated with elevated catalytic efficiency of Glo1. In fact, Michaelis-Menten kinetics of Glo1 mutants revealed that a permanent phosphorylation of Glo1 was associated with increased Vmax (1.23 µmol/min/mg) and decreased Km (0.19 mM HTA), whereas the non-phosphorylatable Glo1 showed significantly lower Vmax (0.66 µmol/min/mg) and increased Km (0.31 mM HTA). This was also confirmed with human recombinant Glo1 (Vmax (Glo1phos) = 999 µmol/min/mg; Km (Glo1phos) = 0.09 mM HTA vs. Vmax (Glo1red) = 497 µmol/min/mg; Km (Glo1red) = 0.12 mM HTA). Additionally, proteasomal degradation of non-phosphorylated Glo1 via ubiquitination occurred more rapidly as compared to native Glo1. The absence of the responsible kinase CamKIIδ was associated with poor MG detoxification capacity and decreased protein content of Glo1 in a murine CamKIIδ knock-out model. Furthermore, this regulatory mechanism is also related to an altered Glo1 status in cancer, diabetes and during aging. In summary, phosphorylation of threonine-107 in the Glo1 protein by CamKIIδ is a quick and precise mechanism regulating Glo1 activity.
Developing a novel recurrent neural network architecture with fewer parameters and good learning performance

Recurrent neural networks (RNNs) are among the most promising of the many artificial intelligence techniques now under development, showing great potential for memory, interaction, and linguistic understanding. Among the more sophisticated RNNs are long short-term memory (LSTM) and gated recurrent units (GRUs), which emulate animal brain behavior; these methods yield superior memory and learning speed because of the excellent core structure of their architectures. In this study, we attempted to make further improvements in core structure and develop a novel, compact architecture with a high learning speed. We stochastically generated 30000 RNN architectures, evaluated their performance, and selected the one most capable of memorizing long contexts with relatively few parameters. This RNN, YamRNN, had fewer parameters than LSTM and GRU by a factor of two-thirds or better and reduced the time required to achieve the same learning performance on a sequence classification task as LSTM and GRU by 80% at maximum. This novel RNN architecture is expected to be useful for addressing problems such as predictions and analyses on contextual data and also suggests that there is room for the development of better architectures.
Structure dynamics of ApoA-I amyloidogenic variants in small HDL increase their ability to mediate cholesterol efflux

Specific mutations in Apolipoprotein A-I (ApoA-I) of high-density lipoprotein (HDL) are responsible for a late-onset systemic amyloidosis. Carriers do not exhibit increased cardiovascular disease risk despite reduced levels of ApoA-I/ HDL-cholesterol. To explain this paradox, we show that the HDL particle profile of L75P and L174S patients presents a higher relative abundance of the 8.4 nm vs 9.6 nm particles, and that serum from patients, as well as reconstituted 8.4 and 9.6 nm HDL particles (rHDL), possess increased capacity to catalyze cholesterol efflux from macrophages. Synchrotron radiation circular dichroism and hydrogen-deuterium exchange revealed that the variants in 8.4 nm rHDL have altered secondary structure composition and display a more flexible binding to lipids compared to their native counterpart. The reduced HDL-cholesterol levels of patients carrying ApoA-I amyloidogenic variants are thus balanced by higher proportion of small, dense HDL particles and better cholesterol efflux due to altered, region-specific protein structure dynamics.
Selective control of working memory in prefrontal, parietal, and visual cortex

Cognitive control guides behavior by controlling what, where, and how information is represented in the brain. Previous work has shown parietal and prefrontal cortex direct attention, which controls the representation of external sensory stimuli1,2. However, the neural mechanisms controlling the selection of representations held ‘in mind’, in working memory, are unknown. To address this, we trained two monkeys to switch between two tasks, requiring them to either select an item from a set of items held in working memory or attend to one stimulus from a set of visual stimuli. Simultaneous neural recordings in prefrontal, parietal, and visual cortex found prefrontal cortex played a primary role in selecting an item from working memory, representing selection before parietal and visual cortex. Surprisingly, a common population representation in prefrontal cortex encoded selection of an item in working memory and attention to an external stimulus, suggesting prefrontal cortex may act as a domain-general controller. Selection acted on memory representations in two ways. First, selection improved the accuracy of memory reports by enhancing the selected item’s representation in prefrontal and parietal cortex. Second, selection transformed memory representations in a task-dependent manner. Before selection, when both items were relevant to the task, the identity of each item was represented in an independent subspace of neural activity. After selection, the representation of only the selected item was transformed into a new subspace that was used to guide the animal’s behavioral report. Together, our results provide insight into how prefrontal cortex controls working memory representations, selectively enhancing and transforming them to support behavior.
A Tractable Drosophila Cell System Enables Rapid Identification of Acinetobacter baumannii Host Factors

Acinetobacter baumannii is an important causative agent of nosocomial infections worldwide. The pathogen also readily acquires resistance to antibiotics, and pan-resistant strains have been reported. A. baumannii is widely regarded as an extracellular bacterial pathogen. However, accumulating evidence demonstrates that the pathogen can invade, survive or persist in infected mammalian cells. Unfortunately, the molecular mechanisms controlling these processes remain poorly understood. Here, we show that Drosophila S2 cells provide several attractive advantages as a model system for investigating the intracellular lifestyle of the pathogen, including susceptibility to bacterial intracellular replication and limited infection-induced host cell death. We also show that the Drosophila system can be used to rapidly identify host factors, including MAP kinase proteins, which confer susceptibility to intracellular parasitism. Finally, analysis of the Drosophila system suggested that host proteins that regulate organelle biogenesis and membrane trafficking contribute to regulating the intracellular lifestyle of the pathogen. Taken together, these findings establish a novel model system for elucidating interactions between A. baumannii and host cells, define new factors that regulate bacterial invasion or intracellular persistence, and identify subcellular compartments in host cells that interact with the pathogen.
JAK1 inhibition blocks lethal sterile immune responses: implications for COVID-19 therapy

Cytokine storms are drivers of pathology and mortality in myriad viral infections affecting the human population. In SARS-CoV-2-infected patients, the strength of the cytokine storm has been associated with increased risk of acute respiratory distress syndrome, myocardial damage, and death. However, the therapeutic value of attenuating the cytokine storm in COVID-19 remains to be defined. Here, we report results obtained using a novel mouse model of lethal sterile anti-viral immune responses. Using a mouse model of Down syndrome (DS) with a segmental duplication of a genomic region encoding four of the six interferon receptor genes (Ifnrs), we demonstrate that these animals overexpress Ifnrs and are hypersensitive to IFN stimulation. When challenged with viral mimetics that activate Toll-like receptor signaling and IFN anti-viral responses, these animals overproduce key cytokines, show exacerbated liver pathology, rapidly lose weight, and die. Importantly, the lethal immune hypersensitivity, accompanying cytokine storm, and liver hyperinflammation are blocked by treatment with a JAK1-specific inhibitor. Therefore, these results point to JAK1 inhibition as a potential strategy for attenuating the cytokine storm and consequent organ failure during overdrive immune responses. Additionally, these results indicate that people with DS, who carry an extra copy of the IFNR gene cluster encoded on chromosome 21, should be considered at high risk during the COVID-19 pandemic. One Sentence Summary Inhibition of the JAK1 kinase prevents pathology and mortality caused by a rampant innate immune response in mice.
Spontaneous liver disease in wild-type C57BL/6JOlaHsd mice fed semisynthetic diet

Mouse models are frequently used to study mechanisms of human diseases. Recently, we observed a spontaneous bimodal variation in liver weight in C57BL/6JOlaHsd mice fed a semisynthetic diet. We now characterized the spontaneous variation in liver weight and its relationship with parameters of hepatic lipid and bile acid (BA) metabolism. In male C57BL/6JOlaHsd mice fed AIN-93G from birth to postnatal day (PN)70, we measured plasma BA, lipids, Very low-density lipoprotein (VLDL)-triglyceride (TG) secretion, and hepatic mRNA expression patterns. Mice were sacrificed at PN21, PN42, PN63 and PN70. Liver weight distribution was bimodal at PN70. Mice could be subdivided into two nonoverlapping groups based on liver weight: 0.6 SD 0.1 g (approximately one-third of mice, small liver; SL), and 1.0 SD 0.1 g (normal liver; NL; p<0.05). Liver histology showed a higher steatosis grade, inflammation score, more mitotic figures and more fibrosis in the SL versus the NL group. Plasma BA concentration was 14-fold higher in SL (p<0.001). VLDL-TG secretion rate was lower in SL mice, both absolutely (−66%, p<0.001) and upon correction for liver weight (−44%, p<0.001). Mice that would later have the SL-phenotype showed lower food efficiency ratios during PN21-28, suggesting the cause of the SL phenotype is present at weaning (PN21). Our data show that approximately one-third of C57BL/6JOlaHsd mice fed semisynthetic diet develop spontaneous liver disease with aberrant histology and parameters of hepatic lipid, bile acid and lipoprotein metabolism. Study designs involving this mouse strain on semisynthetic diets need to take the SL phenotype into account. Plasma lipids may serve as markers for the identification of the SL phenotype.
Differential localization patterns of pyruvate kinase isoforms in murine naïve , 1 formative and primed pluripotent states 2 3

11 Mouse embryonic stem cells (mESCs) and mouse epiblast stem cells (mEpiSCs) represent 12 opposite ends of a pluripotency continuum, referred to as naïve and primed pluripotent states, 13 respectively. These divergent pluripotent states differ in several ways including growth factor 14 requirements, transcription factor expression, DNA methylation patterns, and metabolic profiles. 15 Naïve cells employ both glycolysis and oxidative phosphorylation (OXPHOS), whereas primed 16 cells preferentially utilize aerobic glycolysis, a trait shared with cancer cells referred to as the 17 Warburg effect. Until recently, metabolism has been regarded as a by-product of cell fate; however, 18 evidence now supports metabolism as being a driver of stem cell state and fate decisions. Pyruvate 19 kinase muscle isoforms (PKM1 and PKM2) are important for generating and maintaining 20 pluripotent stem cells (PSCs) and mediating the Warburg effect. Both isoforms catalyze the last 21 step of glycolysis generating adenosine triphosphate and pyruvate, however, the precise role(s) of 22 PKM1/2 in naïve and primed pluripotency is not well understood. The primary objective was to 23 characterize the cellular expression and localization patterns of PKM1 and PKM2 in mESCs, 24 chemically transitioned epiblast-like cells (mEpiLCs) representing formative pluripotency, and 25 mEpiSCs using immunoblotting, flow cytometry and confocal microscopy. The results indicate 26 that PKM1 and PKM2 are not only localized to the cytoplasm but also accumulate in differential 27 subnuclear regions of mESC, mEpiLCs and mEpiSCs as determined by a quantitative, confocal 28 was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. The copyright holder for this preprint (which this version posted April 13, 2020. ; https://doi.org/10.1101/2020.04. 12.036251 doi: bioRxiv preprint
Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence

Background COVID-19 is a disease with global public health emergency that have shook the world since its’ first detection in China in December, 2019. Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is the pathogen responsible behind this pandemic. The lethality of different viral strains is found to vary in different geographical locations but the molecular mechanism is yet to be known. Methods Available data of whole genome sequencing of different viral strains published by different countries were retrieved and then analysed using Multiple Sequence Alignment and Pair-wise Sequence Alignment leading to Phylogenetic tree construction. Each location and the corresponding genetic variations were screened in depth. Then the variations are analysed at protein level giving special emphasis on Non Synonymous amino acid substitutions. The fatality rates in different countries were matched against the mutation number, rarity of the nucleotide alterations and functional impact of the Non Synonymous changes at protein level, separately and in combination. Findings All the viral strains have been found to evolve from the viral strain of Taiwan (MT192759) which is 100% identical with the ancestor SARS-CoV-2 sequences of Wuhan (NC 045512.2; submitted on 5th Jan, 2020). Transition from C to T (C>T) is the most frequent mutation in this viral genome and mutations A>T, G>A, T>A are the rarest ones, found in countries with maximum fatality rate i.e Italy, Spain and Sweden. 20 Non Synonymous mutations are located in viral genome spanning Orf1ab polyprotein, Surface glycoprotein, Nucleocapsid protein etc. The functional effect on the structure and function of the protein can favourably or unfavourably interact with the host body. Interpretation The fatality outcome depends on three important factors (a) number of mutation (b) rarity of the allelic variation and (c) functional consequence of the mutation at protein level. The molecular divergence, evolved from the ancestral strain (S) lead to extremely lethal (E), lethal(L) and non lethal (N) strains with the involvement of an Intermediate strain(I).
Origin and Evolution of DNA methyltransferases (DNMT) along the tree of life: A multi-genome survey

Background Cytosine methylation is a common DNA modification found in most eukaryotic organisms including plants, animals, and fungi. (Cytosine-5)-DNA methyltransferases (C5-DNA MTases) belong to the DNMT family of enzymes that catalyze the transfer of a methyl group from S-adenosyl methionine (SAM) to cytosine residues of DNA. In mammals, four members of the DNMT family have been reported: DNMT1, DNMT3a, DNMT3b and DNMT3L, but only DNMT1, DNMT3a and DNMT3b possess methyltransferase activity. There have been many reports about the methylation landscape in different organisms yet there is no systematic report of how the enzyme DNA (C5) methyltransferases have evolved in different organisms. Result DNA methyltransferases are found to be present in all three domains of life. However, significant variability has been observed in length, copy number and sequence identity when compared across kingdoms. Sequence conservation is greatly increased in invertebrates and vertebrates compared to other groups. Similarly, sequence length has been found to be increased while domain lengths remain more or less conserved. Vertebrates are also found to be associated with more conserved DNMT domains. Finally, comparison between single nucleotide polymorphisms (SNPs) prevailing in human populations and evolutionary changes in DNMT vertebrate alignment revealed that most of the SNPs were conserved in vertebrates. Conclusion The sequences (including the catalytic domain and motifs) and structure of the DNMT enzymes have been evolved greatly from bacteria to vertebrates with a steady increase in complexity and specificity. This study provides a systematic report of the evolution of DNA methyltransferase enzyme across different lineages of tree of life.
Designing Feature-Controlled Humanoid Antibody Discovery Libraries Using Generative Adversarial Networks

We demonstrate the use of a Generative Adversarial Network (GAN), trained from a set of over 400,000 light and heavy chain human antibody sequences, to learn the rules of human antibody formation. The resulting model surpasses common in silico techniques by capturing residue diversity throughout the variable region, and is capable of generating extremely large, diverse libraries of novel antibodies that mimic somatically hypermutated human repertoire response. This method permits us to rationally design de novo humanoid antibody libraries with explicit control over various properties of our discovery library. Through transfer learning, we are able to bias the GAN to generate molecules with key properties of interest such as improved stability and developability, lower predicted MHC Class II binding, and specific complementarity-determining region (CDR) characteristics. These approaches also provide a mechanism to better study the complex relationships between antibody sequence and molecular behavior, both in vitro and in vivo. We validate our method by successfully expressing a proof-of-concept library of nearly 100,000 GAN-generated antibodies via phage display. We present the sequences and homology-model structures of example generated antibodies expressed in stable CHO pools and evaluated across multiple biophysical properties. The creation of discovery libraries using our in silico approach allows for the control of pharmaceutical properties such that these therapeutic antibodies can provide a more rapid and cost-effective response to biological threats.
A platform for brain-wide functional ultrasound imaging and analysis of circuit dynamics in behaving mice

Imaging of large-scale circuit dynamics is crucial to gain a better understanding of brain function, but most techniques have a limited depth of field. Here we describe vfUSI, a platform for brain-wide volumetric functional ultrasound imaging of hemodynamic activity in awake head-fixed mice. We combined high-frequency 1024-channel 2D-array transducer with advanced multiplexing and high-performance computing for real-time 3D Power Doppler imaging at high spatiotemporal resolution (220×280×175-μm3 voxel size, up to 6 Hz). In addition, we developed a standardized software pipeline for registration and segmentation based on the Allen Mouse Common Coordinate Framework, allowing for temporal analysis in 268 individual brain regions. We demonstrate the high sensitivity of vfUSI in multiple experimental situations where stimulus-evoked activity can be recorded using a minimal number of trials. We also mapped neural circuits in vivo across the whole brain during optogenetic activation of specific cell-types. Moreover, we revealed the sequential activation of sensory-motor regions during a grasping water droplet task. vfUSI will become a key neuroimaging technology because it combines ease of use, reliability, and affordability.
Structural basis for the inhibition of SARS-CoV-2 main protease by antineoplastic drug Carmofur

The antineoplastic drug Carmofur was shown to inhibit SARS-CoV-2 main protease (Mpro). Here the X-ray crystal structure of Mpro in complex with Carmofur reveals that the carbonyl reactive group of Carmofur is covalently bound to catalytic Cys145, whereas its fatty acid tail occupies the hydrophobic S2 subsite. Carmofur inhibits viral replication in cells (EC50 = 24.30 μM) and it is a promising lead compound to develop new antiviral treatment for COVID-19.
Increased capillary stalling is associated with endothelial glycocalyx loss in subcortical vascular dementia

Proper regulation and patency of cerebral microcirculation are crucial for maintaining a healthy brain. Capillary stalling, i.e., the brief interruption of microcirculation has been observed in the normal brain and several diseases related to microcirculation. We hypothesized that endothelial glycocalyx, which is located on the luminal side of the vascular endothelium and involved in cell-to-cell interaction regulation in peripheral organs, is also related to cerebral capillary stalling. We measured capillary stalling and the cerebral endothelial glycocalyx (cEG) in male mice using in vivo optical coherence tomography angiography (OCT-A) and two-photon microscopy. Our findings revealed that some capillary segments were prone to capillary stalling and had less cEG. In addition, we demonstrated that the enzymatic degradation of the cEG increased the capillary stalling, mainly by leukocyte plugging. Further, we noted decreased cEG along with increased capillary stalling in a mouse model of subcortical vascular dementia (SVaD) with impaired cortical microcirculation. Moreover, gene expression related to cEG production or degradation changed in the SVaD model. These results indicate that cEG mediates capillary stalling and impacts cerebral blood flow and is involved in the pathogenesis of SVaD.
Mathematical modeling of genetic pest management through female‐specific lethality: Is one locus better than two?

Many novel genetic approaches are under development to combat insect pests. One genetic strategy aims to suppress or locally eliminate a species through large, repeated releases of genetically engineered strains that render female offspring unviable under field conditions. Strains with this female-killing (FK) characteristic have been developed either with all of the molecular components in a single construct or with the components in two constructs inserted at independently assorting loci. Strains with two constructs are typically considered to be only of value as research tools and for producing solely male offspring in rearing factories which are subsequently sterilized by radiation before release. A concern with the two-construct strains is that once released, the two constructs would become separated and therefore non-functional. The only FK strains that have been released in the field without sterilization are single-construct strains. Here, we use a population genetics model with density dependence to evaluate the relative effectiveness of female killing approaches based on single- and two-construct arrangements. We find that, in general, the single-construct arrangement results in slightly faster population suppression, but the two-construct arrangement can eventually cause stronger suppression and cause local elimination with a smaller release size. Based on our results, there is no a priori reason that males carrying two independently segregating constructs need to be sterilized prior to release. In some cases, a fertile release would be more efficient for population suppression.