Miracle-dz/UniFAR-FTUs huggingface dataset:
The killing of human gut commensal E. coli ED1a by tetracycline is associated with severe ribosome dysfunction

Ribosomes translate the genetic code into proteins. Recent technical advances have facilitated in situ structural analyses of ribosome functional states inside eukaryotic cells and the minimal bacterium Mycoplasma. However, such analyses of Gram-negative bacteria are lacking, despite their ribosomes being major antimicrobial drug targets. Here we compare two E. coli strains, a lab E. coli K-12 and human gut isolate E. coli ED1a, for which tetracycline exhibits bacteriostatic and bactericidal action, respectively. The in situ ribosome structures upon tetracycline treatment show a virtually identical drug binding-site in both strains, yet the distribution of ribosomal complexes clearly differs. While K-12 retains ribosomes in a translation competent state, tRNAs are lost in the vast majority of ED1a ribosomes. A differential response is also reflected in proteome-wide abundance and thermal stability assessment. Our study underlines the need to include molecular analyses and to consider gut bacteria when addressing antibiotic mode of action. HIGHLIGHTS • Ribosome structures of gram-negative bacteria are analyzed in situ • Tetracyline is bactericidal to gut isolate despite identical ribosome structures • When antibiotic is bacteriostatic, ribosomal translation competent states are retained • When antibiotic is bactericidal, cells rapidly accumulate P-tRNAs-deficient ribosomes GRAPHICAL ABSTRACT
Engineered antigen‐binding fragments for enhanced crystallization of antibody:antigen complexes

The atomic-resolution structural information that X-ray crystallography can provide on the binding interface between a Fab and its cognate antigen is highly valuable for understanding the mechanism of interaction. However, many Fab:antigen complexes are recalcitrant to crystallisation, making the endeavour a significant effort with no guarantee of success. Consequently, there have been significant steps taken to increase the likelihood of Fab:antigen complex crystallisation by altering the Fab framework. In this investigation, we applied the surface entropy reduction strategy coupled with phage-display technology to identify a set of surface substitutions that improve the propensity of a human Fab framework to crystallise. In addition, we showed that combining these surface substitutions with previously reported Crystal Kappa and elbow substitutions results in a striking improvement in Fab and Fab:antigen complex crystallisability, revealing a synergistic relationship between these sets of substitutions. Through comprehensive Fab and Fab:antigen complex crystallisation screenings followed by structure determination and analysis, we defined the roles that each of these substitutions play in facilitating crystallisation and how they complement each other in the process.
Evolution of hierarchy and irreversibility in theoretical cell differentiation model

The process of cell differentiation in multicellular organisms is characterized by hierarchy and irreversibility in many cases. However, the conditions and selection pressures that give rise to these characteristics remain poorly understood. By using a mathematical model, here we show that the network of differentiation potency (differentiation diagram) becomes necessarily hierarchical and irreversible by increasing the number of terminally differentiated states under certain conditions. The mechanisms generating these characteristics are clarified using geometry in the cell state space. The results demonstrate that the appearance of these characteristics can be driven without assuming the adaptive significance. The study also provides a new perspective on the structure of gene regulatory networks that produce hierarchical and irreversible differentiation diagrams. These results indicate some constraints on cell differentiation, which are expected to provide a starting point for theoretical discussion of the implicit limits and directions of evolution in multicellular organisms.
Structural determination of Rickettsia lipid A without chemical extraction confirms shorter acyl chains in later-evolving Spotted Fever Group pathogens

Rickettsiae are Gram-negative obligate intracellular parasites of numerous eukaryotes. Human pathogens of the Transitional Group (TRG), Typhus Group (TG), and Spotted Fever Group (SFG) rickettsiae infect blood-feeding arthropods, have dissimilar clinical manifestations, and possess unique genomic and morphological attributes. Lacking glycolysis, rickettsiae pilfer numerous metabolites from host cytosol to synthesize peptidoglycan and lipopolysaccharide (LPS). For LPS, O-antigen immunogenicity varies between SFG and TG pathogens; however, lipid A proinflammatory potential is unknown. We previously demonstrated that R. akari (TRG), R. typhi (TG), and R. montanensis (SFG) produce lipid A with long 2’ secondary acyl chains (C16 or C18) compared to short 2’ secondary acyl chains (C12) in R. rickettsii (SFG) lipid A. To further probe this structural heterogeneity and estimate a time point when shorter 2’ secondary acyl chains originated, we generated lipid A structures for two additional SFG rickettsiae (R. rhipicephali and R. parkeri) utilizing Fast Lipid Analysis Technique adopted for use with tandem mass spectrometry (FLATn). FLATn allowed analysis of lipid A structure directly from host cell-purified bacteria, providing substantial improvement over lipid A chemical extraction. FLATn-derived structures indicate SFG rickettsiae diverging after R. rhipicephali evolved shorter 2’ secondary acyl chains. Bioinformatics analysis of Rickettsia LpxL late acyltransferases revealed discrete active sites and hydrocarbon rulers for long versus short 2’ secondary acyl chain addition. While the significance of different lipid A structures for diverse Rickettsia pathogens is unknown, our success using FLATn will facilitate determining how structural heterogeneity impacts interactions with host lipid A receptors and overall inflammatory potential. IMPORTANCE Deforestation, urbanization, and homelessness lead to spikes in Rickettsioses. Vector-borne human pathogens of Transitional Group (TRG), Typhus Group (TG), and Spotted Fever Group (SFG) rickettsiae differ by clinical manifestations, immunopathology, genome composition, and morphology. We previously showed that lipid A (or endotoxin), the membrane anchor of Gram-negative bacterial lipopolysaccharide (LPS), structurally differs in R. rickettsii (later-evolving SFG) relative to R. montanensis (basal SFG), R. typhi (TG), and R. akari (TRG). As lipid A structure influences recognition potential in vertebrate LPS sensors, further assessment of Rickettsia lipid A structural heterogeneity is needed. Here, we sidestepped the difficulty of ex vivo lipid A chemical extraction by utilizing FLATn, a new procedure for generating lipid A structures directly from host cell-purified bacteria. These data confirm later-evolving SFG pathogens synthesize structurally distinct lipid A. Our findings impact interpreting immune responses to different Rickettsia pathogens and utilizing lipid A adjuvant or anti-inflammatory properties in vaccinology.
Augmented Super-Resolution Radial Fluctuations (aSRRF) Pushing the Limits of Structured Illumination Microscopy

Structured illumination microscopy (SIM) is a versatile super-resolution technique known for its compatibility with a wide range of probes and fast implementation. While 3D SIM is capable of achieving a spatial resolution of ∼120 nm laterally and ∼300 nm axially, attempting to further enhance the resolution through methods such as nonlinear SIM or 4-beam SIM introduces complexities in optical configurations, increased phototoxicity, and reduced temporal resolution. Here, we have developed a novel method that combines SIM with augmented super-resolution radial fluctuations (aSRRF) utilizing a single image through image augmentation. By applying aSRRF reconstruction to SIM images, we can enhance the SIM resolution to ∼50 nm isotopically, without requiring any modifications to the optical system or sample acquisition process. Additionaly, we have incorporated the aSRRF approach into an ImageJ plugin and demonstrated its versatility across various fluorescence microscopy images, showcasing a remarkable two-fold resolution increase.
In vitro reconstitution of the M.tb proteasome core particle reveals conserved aspects of bacterial proteasome assembly

According to the WHO, one in three people in the world has a latent tuberculosis infection. Tuberculosis is caused by the bacterium Mycobacterium tuberculosis (M.tb). The development of multi-drug resistant (MDR) tuberculosis indicates a need for novel treatments. Hence, it is important to find a second line of treatment for patients infected with MDR tuberculosis. The proteasome is known to be necessary for survival under stress and pathogenicity in M.tb. However, our ability to use the proteasome as drug target has been limited by our abilities to screen for inhibitor compounds in vitro. The proteasome is a protease complex that degrades proteins and is crucial for the maintenance of protein homeostasis within cells. Like many protein complexes, the proteasome must assemble into a specific quaternary structure in order to be active. Specifically, the proteolytically-active proteasome Core Particle (CP) consists of 28 subunits (14 α and 14 β) that must assemble into a barrel-like structure in order to become catalytically active. Hence, understanding the assembly process in not only important from a basic cell biological perspective, but may also serve as the basis for the discovery of novel assembly inhibitors. In this study, we have established for the first time a protocol to express and purify the M.tb α and β subunits separately in vitro. The subunits are soluble monomers on purification and only assemble into active CPs upon reconstitution. Our assembly experiments revealed that M.tb CP assembly pathway is almost certainly identical to that seen in previous experiments on the CP from the bacterium Rhodococcus erythropolis (R.e), but assembly in M.tb is much slower. Interestingly, we found that subunits from M.tb and R.e spontaneously self-assembled into active hybrid proteasomes on reconstitution with each other, despite having only 65% sequence similarity. Our work thus strongly suggests that the CP assembly pathway is conserved across bacteria, and the ability to perform in vitro assembly experiments on the M.tb proteasome opens up the possibility of performing critical experiments, including screening for potential molecules that could inhibit assembly, directly in this clinically-relevant organism.
Conversational production and comprehension: fMRI-evidence reminiscent of the classic Broca-Wernicke model

A key question in neurolinguistics is whether language production and comprehension share neural infrastructure, but this question has not been addressed in the context of actual conversation. We utilized a public fMRI dataset where participants (N=24) engaged in unscripted conversations with a confederate outside the scanner via an audio-video link. We provide evidence indicating that production and comprehension, in a conversational setting, diverge with respect to how they modulate the recruitment of regions in the left-lateralized perisylvian language network. Activity in the left inferior frontal gyrus was stronger in production than in comprehension. Compared to production, comprehension showed stronger recruitment of the left anterior middle temporal gyrus and superior temporal sulcus, but this was not the case for the posterior aspect of these loci. Although our results are reminiscent of the classic Broca-Wernicke model, the anterior temporal activation is a notable difference from that model. This is one of the findings which may be a consequence of the conversational setting, another being that conversational production activated what we interpret as higher-level socio-pragmatic processes. In conclusion, we present evidence supporting that the above-mentioned frontal vs temporal regions in the language network are functionally segregated during conversation.
A novel tamanavirus (Flaviviridae) of the European common frog (Rana temporaria) encodes a divergent class 1b XRN1-resistant RNA element

Flavivirids are small, enveloped, positive-sense RNA viruses from the Flaviviridae family with genomes between ∼9-13kb. Metatranscriptomic analyses of metazoan organisms have revealed a diversity of flavivirus-like or flavivirid viral sequences in fish and marine invertebrate groups. To date, however, no flavivirus-like or flavivirid has been identified in amphibians. To remedy this, we investigated the virome of the European common frog (Rana temporaria) in the United Kingdom, utilising high-throughput sequencing at six catch locations. De novo assembly revealed a coding-complete virus contig of a novel flavivirid ∼11.2kb in length. The virus encodes a single open reading frame of 3456 amino acids and 5’ and 3’ untranslated regions (UTRs) of 227 and 666nt, respectively. We named this virus Rana tamanavirus (RaTV), as BLASTp analysis of the polyprotein showed the closest relationships to Tamana bat virus (TABV) and Cyclopterus lumpus virus from Pteronotus parnellii and Cyclopterus lumpus, respectively. Phylogenetic analysis of the RaTV polyprotein compared to Flavivirus and Flavivirus-like members indicated that RaTV was sufficiently divergent and basal to the vertebrate Tamanavirus clade. In addition to the Mitcham strain, partial but divergent RaTV, 95.64-97.39% pairwise nucleotide identity, were also obtained from the Poole and Deal samples, indicating that RaTV is widespread in UK frog samples. Bioinformatic analyses of putative secondary structures in the 3′-UTR of RaTV indicated a potential exoribonuclease-resistant RNA (xrRNA) structure identified in flaviviruses and TABV. To examine this biochemically, we conducted an in vitro XRN1 digestion assay showing that RaTV likely forms a divergent but functionally homologous XRN1-resistant xrRNA.
Identification of SNP markers for canine mammary gland tumours in females based on a genome-wide association study – preliminary results

Abstract Introduction The development of genetic research over recent decades has enabled the discovery of new genetic markers, such as single nucleotide polymorphisms (SNPs). This, as well as the full sequencing of the dog genome, has enabled genome-wide association studies (GWAS) to be used in the search for genetic causes of canine mammary tumours (CMTs). Material and Methods Genotypic data containing 175,000 SNPs, which had been obtained using the Illumina CanineHD BeadChip microarray technique, were available for analysis in this study. The data concerned 118 bitches, including 36 animals with CMT, representing various breeds and age groups. Statistical analysis was performed in two steps: quality control of genotyping data and genome-wide association analysis based on dominant, recessive, overdominant, codominant, and log-additive models with the single SNP effects. Results A total of 40 different SNPs significantly associated with CMT appearance were detected. Moreover, twelve SNPs showed statistical significance in more than one model. Of all the significant SNPs, two, namely BICF2G630136001 in the overdominant model and TIGRP2P107898_rs9044787 in the log-additive model, reached the 5−8 significance level. The other SNPs were significant to a 1−5 level. Conclusion In the group of SNPs indicated as significant in the GWAS analysis, several transpired to be localised within genes that may play an important role in CMT.
Individual Variability in the Structural Connectivity Architecture of the Human Brain

The human brain shows higher variability in functional connectivity in the heteromodal association cortex but lower variability in the unimodal cortex. As the anatomical substrate of functional connectivity, the temporal-spatial pattern of individual variability in structural connectivity remains largely unknown. In the present study, we depicted the temporal-spatial pattern of individual variability in structural connectivity, which is highest in the limbic regions and lowest in the unimodal sensorimotor regions. With increasing age, the variability in structural connectivity increased. Our results demonstrated that this specific spatial distribution relates to the plasticity of synapses and white matter. We proposed a modified ridge regression model to predict cognition individually and generate idiographic brain mapping. Individual variability in structural connectivity is significantly correlated with idiographic brain mapping. Overall, our study has potential implications for understanding biological and genetic mechanisms of variability in structural connectivity, guiding interventions to promote successful cognitive ageing and interpreting statistical maps in the human connectome.
Impact of combinatorial histone modifications on acetyllysine recognition by the ATAD2 and ATAD2B bromodomains

The ATPase family AAA+ domain containing 2 (ATAD2) protein, and its paralog ATAD2B, have a C-terminal bromodomain that functions as a ‘reader’ of acetylated lysine residues on histone proteins. Using a structure-function approach, we investigated the ability of the ATAD2 and ATAD2B bromodomains to select acetylated lysine among multiple histone post-translational modifications. Isothermal titration calorimetry experiments revealed that the ATAD2 and ATAD2B bromodomains selectively recognize distinct patterns of acetylated lysine residues on the N-terminal tails of histone proteins. Adjacent methylation or phosphorylation marks were found to either enhance or weaken the recognition of acetylated lysine by the ATAD2/B bromodomains. Complementary structural studies provide mechanistic insights into how residues within the bromodomain binding pocket coordinate the acetyllysine group in the context of adjacent post- translational modifications. Furthermore, we investigated how sequence changes in amino acids of the histone ligands, either as ‘onco’ mutations or as histone variants, impact the recognition of an adjacent acetylated lysine residue. In summary, our study highlights how the interplay between multiple combinations of histone modifications influences the ‘reader’ activity of the ATAD2 and ATAD2B bromodomains, resulting in distinct binding modes of the two bromodomains. KEY POINTS Multiple independent ATAD2 gene duplication events are evident during metazoan evolution, indicating expansion of functionality in the ATAD2 gene family and suggesting distinct functions for ATAD2 and ATAD2B. High-resolution structures of the ATAD2 and ATAD2B bromodomains in complex with their histone ligands demonstrate how multiple post-translational modifications are coordinated. Recognition of different subsets acetylated histone ligands by the ATAD2 and ATAD2B bromodomains is driven by unique features within the binding pockets of these paralogous proteins. Onco-histone mutations and histone variants that change the amino acid sequence of the histone tails modulate the ATAD2 and ATAD2B bromodomain activity. This study demonstrates how the combinatorial activity of multiple post- translational modifications forms a histone code and influences the recognition of acetylated lysine by bromodomain-containing proteins.
OBSTRUCTIVE SLEEP APNEA: PART I. DIAGNOSIS AND EVALUATION.

Bobby Joseph Babu, Mahesh CM, Rameshkumar PC, Vinay P Reddy, Chandrashekar BS and Harish Koushik. Manuscript Info Abstract: Obstructive sleep apnea (OSA) is a common disorder that is characterized by repetitive partial or complete cessation of airflow, associated with oxyhemoglobin desaturation and increased effort to breath. Patients with undiagnosed sleep apnea represent a major public health problem. Dental professionals have a unique doctor patient relationship that can help them in recognizing the sleep disorder and co-managing the patients along with a physician or a sleep-specialist. This article discusses the etiology and pathogenesis, clinical features and risk factors, consequences, diagnosis and evaluation of Obstructive sleep apnea.
Understanding US Inflation during the COVID-19 Era

ABSTRACT:This paper analyzes the dramatic rise in US inflation since 2020, which we decompose into a rise in core inflation as measured by the weighted median inflation rate and deviations of headline inflation from core. We explain the rise in core inflation with two factors: the tightening of the labor market as captured by the ratio of job vacancies to unemployment, and the pass-through into core inflation from past shocks to headline inflation. The headline shocks themselves are explained largely by increases in energy prices and by supply chain problems as captured by backlogs of orders for goods and services. Looking forward, we simulate the future path of inflation for alternative paths of the unemployment rate, focusing on the projections of Federal Reserve policymakers in which unemployment rises only modestly to 4.4 percent. We find that this unemployment path returns inflation to near the Federal Reserve's target only under optimistic assumptions about both inflation expectations and the Beveridge curve relating the unemployment and vacancy rates. Under less benign assumptions about these factors, the inflation rate remains well above target unless unemployment rises by more than the Federal Reserve projects.
Characteristics of Size Change of Tropical Cyclones Traversing the Philippines

This study investigates the size changes of tropical cyclones (TCs) traversing the Philippines based on a 37-yr statistical analysis. TC size is defined by the radius of 30-kt (≈15.4 m s−1) wind speed (R30) from the best track data of the Japan Meteorological Agency. A total of 71 TCs passed the Philippines during 1979–2015. The numbers of size increase (SI; 36) and size decrease (SD; 34) cases are very similar; however, the last 15 years have seen more SI cases (17) than SD cases (11). SI and SD cases mostly occur along northerly and southerly paths, respectively, after TCs pass the Philippines. Before landfall, SI cases have small initial sizes and weak intensities, but SD cases have larger initial sizes and stronger intensities. After landfall, most SI cases are intensifying storms, and most SD cases are nonintensifying storms. Composite analyses of vertical wind shear, absolute angular momentum flux, relative humidity, and sea surface temperature between SI and SD cases are compared. All of these values are larger in SI cases than in SD cases. Furthermore, the interdecadal difference in the ratio of the numbers of SI to SD cases reveals an unusually high number of SI cases during 2001–15. The synoptic patterns between 1979–2000 and 2001–15 are analyzed. The high SI ratio in the latter period is related to strong southwesterly wind in the south of the South China Sea that raised relative humidity, warmed the sea surface, and increased import of angular momentum flux.
FB15k-CVT: A Challenging Dataset for Knowledge Graph Embedding Models

Knowledge Graphs (KGs) are an essential component of neuro-symbolic AI. KG Embedding Models (KGEMs) are used to represent elements of a KG (its entities and relations) in a vector space, to enable efficient processing and reasoning over knowledge. Most KGEMs are evaluated against datasets derived from the Freebase KG: FB15k and FB15k-237. In this paper, we identify limitations in these datasets with respect to Compound Value Types (CVTs), which are nodes introduced in Freebase as a substitute for 𝑛 -ary relations. In FB15k and FB51k-237, CVTs have been removed, thereby eliminating valuable information. To evaluate whether KGEMs can learn semantically accurate representations of entities and relations in Freebase, we introduce here a new dataset named FB15k-CVT, which reintroduces the deleted CVT nodes. In a preliminary evaluation, we assess the limitations of baseline KGEMs (TransE, DistMult) in the presence of CVTs. The evaluation suggests that KGEMs based on tensor decomposition are more promising than translational models but, most of all, it calls for further experiments with KGEMs that can answer conjunctive queries or that preserve logical entailment.