bluuebunny/crossref_metadata_2025 huggingface dataset:
Following the fate of lytic polysaccharide monooxygenases (LPMOs) under oxidative conditions by NMR spectroscopy
Authors: Christensen Idd A. , Eijsink Vincent G. H. , Stepnov Anton A. , Courtade Gaston , Aachmann Finn L.
Published: February 2023

Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that catalyze oxidative cleavage of polysaccharides, such as cellulose and chitin. LPMO action is key to the efficient varlorization of biomass, but the instability of LPMOs in turnover conditions limits their efficiency. LPMO catalysis requires the presence of a reductant, such as ascorbic acid, and hydrogen peroxide, which can be generatedin situin the presence of molecular oxygen and various electron donors.. While it is known that reduced LPMOs are prone to auto-catalytic oxidative damage due to off-pathway reactions with the oxygen co-substrate, little is known about the structural consequences of such damage. Here, we present atomic-level insight into how the structure of the chitin-activeSmLPMO10A is affected by oxidative damage, using NMR and CD spectroscopy. Incubation with ascorbic acid, led to rearrangements of aromatic residues, followed by more profound structural changes near the copper active site and loss of activity. Longer incubation times induced changes in larger parts of the structure, indicative of progressing oxidative damage. Incubation with ascorbic acid in the presence of chitin led to similar changes in the observable (i.e., not substrate-bound) fraction of the enzyme. Upon subsequent addition of H2O2, which drastically speeds up chitin hydrolysis, NMR signals corresponding to seemingly intactSmLPMO10A reappeared, indicating dissociation of catalytically competent LPMO. Activity assays confirmed thatSmLPMO10A retained catalytic activity when pre-incubated with chitin before being subjected to conditions that induce oxidative damage. Overall, this study provides structural insights into the process of oxidative damage ofSmLPMO10A and demonstrates the protective effect of the substrate. The impact of turnover conditions on aromatic residues in the core of the enzyme suggests a role for these residues in dealing with redox-active species generated in the copper center.
DandD: efficient measurement of sequence growth and similarity
Authors: Bonnie Jessica K. , Ahmed Omar , Langmead Ben
Published: February 2023

Genome assembly databases are growing rapidly. The sequence content in each new assembly can be largely redundant with previous ones, but this is neither conceptually nor algorithmically easy to measure. We propose new methods and a new tool called DandD that addresses the question of how much new sequence is gained when a sequence collection grows. DandD can describe how much human structural variation is being discovered in each new human genome assembly and when discoveries will level off in the future. DandD uses a measure called δ (“delta”), developed initially for data compression. Computing δ directly requires counting k-mers, but DandD can rapidly estimate it using genomic sketches. We also propose δ as an alternative to k-mer-specific cardinalities when computing the Jaccard coefficient, avoiding the pitfalls of a poor choice of k. We demonstrate the utility of DandD’s functions for estimating δ, characterizing the rate of pangenome growth, and computing allpairs similarities using k-independent Jaccard. DandD is open source software available at:https://github.com/jessicabonnie/dandd.
Effective networks mediate right hemispheric dominance of human 40 Hz auditory steady-state response
Authors: Kumar Neeraj , Jaiswal Amit , Roy Dipanjan , Banerjee Arpan
Published: February 2023

Auditory steady-state responses (ASSR) are induced from the brainstem to the neocortex when humans hear periodic amplitude-modulated tonal signals. ASSRs have been argued to be a key marker of auditory temporal processing and pathological reorganization of ASSR – a biomarker of neurodegenerative disorders. However, most of the earlier studies reporting the neural basis of ASSRs were focused on looking at individual brain regions. Here, we seek to characterize the large-scale directed information flow among cortical sources of ASSR entrained by 40 Hz external signals. Entrained brain rhythms with power peaking at 40 Hz were generated using both monaural and binaural tonal stimulation. First, we confirm the presence of ASSRs and their well-known right hemispheric dominance during binaural and both monaural conditions. Thereafter, reconstruction of source activity employing individual anatomy of the participant and subsequent network analysis revealed that while the sources are common among different stimulation conditions, differential levels of source activation and differential patterns of directed information flow using Granger causality among sources underlie processing of binaurally and monaurally presented tones. Particularly, we show bidirectional interactions involving the right superior temporal gyrus and inferior frontal gyrus underlie right hemispheric dominance of 40 Hz ASSR during both monaural and binaural conditions. On the other hand, for monaural conditions, the strength of inter-hemispheric flow from left primary auditory areas to right superior temporal areas followed a pattern that comply with the generally observed contralateral dominance of sensory signal processing.
Meningeal P2X7 signaling mediates migraine-related intracranial mechanical hypersensitivity
Authors: Zhao Jun , Harrison Samantha , Levy Dan
Published: February 2023

Cortical spreading depolarization (CSD) is a key pathophysiological event that underlies visual and sensory auras in migraine. CSD is also thought to drive the headache phase in migraine by promoting the activation and mechanical sensitization of trigeminal primary afferent nociceptive neurons that innervate the cranial meninges. The factors underlying meningeal nociception in the wake of CSD remain poorly understood but potentially involve the parenchymal release of algesic mediators and damage-associated molecular patterns, particularly ATP. Here, we explored the role of ATP-P2X purinergic receptor signaling in mediating CSD-evoked meningeal afferent activation and mechanical sensitization. Male rats were subjected to a single CSD episode. In vivo, extracellular single-unit recording was used to measure meningeal afferent ongoing activity changes. Quantitative mechanical stimuli using a servomotor force-controlled stimulator assessed changes in the afferent’s mechanosensitivity. Manipulation of meningeal P2X receptors was achieved via local administration of pharmacological agents. Broad-spectrum P2X receptor inhibition, selective blockade of the P2X7 receptor, and its related pannexin 1 channel suppressed CSD-evoked afferent mechanical sensitization but did not affect the accompanying afferent activation response. Surprisingly, inhibition of the pronociceptive P2X2/3 receptor did not affect the activation or sensitization of meningeal afferents post-CSD. P2X7 signaling underlying afferent mechanosensitization was localized to the meninges and did not affect CSD susceptibility. We propose that meningeal P2X7 and Pannexin 1 signaling, potentially in meningeal macrophages or neutrophils, mediates the mechanical sensitization of meningeal afferents, which contributes to migraine pain by exacerbating the headache during normally innocuous physical activities.

Significance Statement

Activation and sensitization of meningeal afferents play a key role in migraine headache, but the underlying mechanisms remain unclear. Here, using a rat model of migraine with aura involving cortical spreading depolarization (CSD), we demonstrate that meningeal purinergic P2X7 signaling and its related Pannexin 1 pore, but not nociceptive P2X2/3 receptors, mediate prolonged meningeal afferent sensitization. Additionally, we show that meningeal P2X signaling does not contribute to the increased afferent ongoing activity in the wake of CSD. Our finding points to meningeal P2X7 signaling as a critical mechanism underlying meningeal nociception in migraine, the presence of distinct mechanisms underlying the activation and sensitization of meningeal afferents in migraine, and highlight the need to target both processes for effective migraine therapy.
Sex and interferon gamma signaling regulate microglia migration in adult mouse cortexin vivo
Authors: Boghozian Roobina , Sharma Sorabh , Cheema Manjinder , Brown Craig E.
Published: February 2023

Although microglia possess the unique ability to migrate, whether mobility is evident in all microglia, is sex dependent, and what molecular mechanisms drive this, is poorly understood in the adult brain. Using longitudinalin vivoimaging of sparsely labelled microglia, we find a relatively small population of microglia are mobile under normal conditions. Following injury (microbleed), the population of mobile microglia increased in a sex-dependent manner, with male microglia migrating significantly greater distances towards the microbleed relative to their female counterparts. To understand the signaling pathways involved, we interrogated the role of interferon gamma (IFNγ). Our data show that in male mice, stimulating microglia with IFNγ or inducible microglial specific knockdown of IFNγ receptor 1 stimulates or inhibits migration, respectively, whereas female microglia were generally unaffected. These findings highlight the diversity of microglia migratory responses to injury, its dependence on sex and the signaling mechanisms that modulate this behavior.
Discovery of A Polymorphic Gene Fusion via Bottom-Up Chimeric RNA Prediction
Authors: Elfman Justin , Goins Lynette , Heller Tessa , Singh Sandeep , Wang Yuh-Hwa , Li Hui
Published: February 2023

Gene fusions and their chimeric products are typically considered hallmarks of cancer. However, recent studies have found chimeric transcripts in non-cancer tissues and cell lines. In addition, efforts to annotate structural variation at large scale have found examples of gene fusions with potential to produce chimeric transcripts in normal tissues. In this report, we provide a means for targeting population-specific chimeric RNAs to enrich for those generated by gene fusion events. We identify 57 such chimeric RNAs from the GTEx cohort, includingSUZ12P1-CRLF3 and TFG-ADGRG7, whose distribution we assessed across the populations of the 1000 Genomes Project. We reveal thatSUZ12P1-CRLF3results from a common complex structural variant in populations with African heritage, and identify its likely mechanism for formation. Additionally, we utilize a large cohort of clinical samples to characterize theSUZ12P1-CRLF3chimeric RNA, and find an association between the variant and indications of Neurofibramatosis Type I. We present this gene fusion as a case study for identifying hard-to-find and potentially functional structural variants by selecting for those which produce population-specific fusion transcripts.

KEY POINTS

- Discovery of 57 polymorphic chimeric RNAs

- Characterization of SUZ12P1-CRLF3 polymorphic chimeric RNA and corresponding rearrangement

- Novel bottom-up approach to identify structural variants which produce transcribed gene fusions
RTCpredictor: Identification of Read-Through Chimeric RNAs from RNA Sequencing Data
Authors: Singh Sandeep , Shi Xinrui , Ahmad Syed Basil , Manley Tommy , Piczak Claire , Phung Christopher , Sun Yunan , Lynch Sarah , Sharma Aadi , Li Hui
Published: February 2023

Read-through chimeric RNAs are gaining attention in cancer and other research fields, yet current tools often fail in predicting them. We have thus developed the first read-through chimeric RNA specific prediction method, RTCpredictor, utilizing a fast ripgrep algorithm to search for all possible exon-exon combinations of parental gene pairs. Compared with other ten popular tools, RTCpredictor achieved top performance on both simulated and real datasets. We randomly selected up to 30 candidate read-through chimeras predicted from each software method and experimentally validated a total of 109 read-throughs and on this set, RTCpredictor outperformed all the other methods. In addition, RTCpredictor (https://github.com/sandybioteck/RTCpredictor) has less memory requirements and faster execution time.
TheDrosophila melanogasterY-linked gene,WDY, is required for sperm to swim in the female reproductive tract
Authors: Hafezi Yassi , Omurzakov Arsen , Carlisle Jolie A. , Caldas Ian V. , Wolfner Mariana F. , Clark Andrew G.
Published: February 2023

Unique patterns of inheritance and selection on Y chromosomes lead to the evolution of specialized gene functions. Yet characterizing the function of genes on Y chromosomes is notoriously difficult. We report CRISPR mutants in Drosophila of the Y-linked gene,WDY, which is required for male fertility.WDYmutants produce mature sperm with beating tails that can be transferred to females but fail to enter the female sperm storage organs. We demonstrate that the sperm tails ofWDYmutants beat approximately half as fast as wild-type sperm’s and that the mutant sperm do not propel themselves within the male ejaculatory duct or female reproductive tract (RT). These specific motility defects likely cause the sperm storage defect and sterility of the mutants. Regional and genotype-dependent differences in sperm motility suggest that sperm tail beating and propulsion do not always correlate. Furthermore, we find significant differences in the hydrophobicity of key residues of a putative calcium-binding domain between orthologs ofWDYthat are Y-linked and those that are autosomal. Given thatWDYappears to be evolving under positive selection, our results suggest thatWDY’s functional evolution coincides with its transition from autosomal to Y-linked inDrosophila melanogasterand its most closely related species. Finally, we show that mutants for another Y-linked gene,PRY, also show a sperm storage defect that may explain their subfertility. In contrast toWDY, PRYmutants do swim in the female RT, suggesting they are defective in yet another mode of motility, navigation, or a necessary interaction with the female RT. Overall, we provide direct evidence for the long-held presumption that protein-coding genes on the Drosophila Y regulate sperm motility.
Experience-Dependent Plasticity in Nucleus Laminaris of the Barn Owl
Authors: Carr Catherine E. , Wang Tiffany , Kraemer Ira , Capshaw Grace , Ashida Go , Köppl Christine , Kempter Richard , Kuokkanen Paula T.
Published: February 2023

Barn owls experience increasing interaural time differences (ITDs) during development, because their head width more than doubles in the month after hatching. We therefore hypothesized that their ITD detection circuit might be modified by experience. To test this, we raised owls with unilateral ear inserts that delayed and attenuated the acoustic signal, then measured the ITD representation in the brainstem nucleus laminaris (NL) when they were adult. The ITD circuit is composed of delay line inputs to coincidence detectors, and we predicted that plastic changes would lead to shorter delays in the axons from the manipulated ear, and complementary shifts in ITD representation on the two sides. In owls that received ear inserts starting around P14, the maps of ITD shifted in the predicted direction, but only on the ipsilateral side, and only in those tonotopic regions that hadnotexperienced auditory stimulation prior to insertion. The contralateral map did not change. Experience-dependent plasticity of the ITD circuit occurs in NL, and our data suggest that ipsilateral and contralateral delays are independently regulated. Thus, altered auditory input during development leads to long-lasting changes in the representation of ITD.

Significance Statement

The early life of barn owls is marked by increasing sensitivity to sound, and by increasing ITDs. Their prolonged post-hatch development allowed us to examine the role of altered auditory experience on the development of ITD detection circuits. We raised owls with a unilateral ear insert and found that their maps of ITD were altered by experience, but only in those tonotopic regions that hadnotexperienced auditory stimulation prior to insertion. Thus experience-induced plasticity allows the sound localization circuits to be customized to individual characteristics, such as the size of the head, and potentially to compensate for natural conductive hearing losses.
Predicting the Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins
Authors: Qin Sanbo , Zhou Huan-Xiang
Published: February 2023

How the sequences of intrinsically disordered proteins (IDPs) code for functions is still an enigma. Dynamics, in particular residue-specific dynamics, holds crucial clues. Enormous efforts have been spent to characterize residue-specific dynamics of IDPs, mainly through NMR spin relaxation experiments. Here we present a sequence-based method, SeqDYN, for predicting residue-specific backbone dynamics of IDPs. SeqDYN employs a mathematical model with 21 parameters: one is a correlation length and 20 are the contributions of the amino acids to slow dynamics. Training on a set of 45 IDPs reveals aromatic, Arg, and long-branched aliphatic amino acids as the most active in slow dynamics whereas Gly and short polar amino acids as the least active. SeqDYN predictions not only provide an accurate and insightful characterization of sequence-dependent IDP dynamics but may also serve as indicators in a host of biophysical processes, including the propensities of IDP sequences to undergo phase separation.
PhylteR: efficient identification of outlier sequences in phylogenomic datasets
Authors: Comte Aurore , Tricou Théo , Tannier Eric , Joseph Julien , Siberchicot Aurélie , Penel Simon , Allio Rémi , Delsuc Frédéric , Dray Stéphane , de Vienne Damien M.
Published: February 2023

In phylogenomics, incongruences between gene trees, resulting from both artifactual and biological reasons, can decrease the signal-to-noise ratio and complicate species tree inference. The amount of data handled today in classical phylogenomic analyses precludes manual error detection and removal. However, a simple and efficient way to automate the identification of outliers from a collection of gene trees is still missing.

Here, we present PhylteR, a method that allows a rapid and accurate detection of outlier sequences in phylogenomic datasets, i.e. species from individual gene trees that do not follow the general trend. PhylteR relies on DISTATIS, an extension of multidimensional scaling to 3 dimensions to compare multiple distance matrices at once. In PhylteR, these distance matrices extracted from individual gene phylogenies represent evolutionary distances between species according to each gene.

On simulated datasets, we show that PhylteR identifies outliers with more sensitivity and precision than a comparable existing method. We also show that PhylteR is not sensitive to ILS-induced incongruences, which is a desirable feature. On a biological dataset of 14,463 genes for 53 species previously assembled for Carnivora phylogenomics, we show (i) that PhylteR identifies as outliers sequences that can be considered as such by other means, and (ii) that the removal of these sequences improves the concordance between the gene trees and the species tree. Thanks to the generation of numerous graphical outputs, PhylteR also allows for the rapid and easy visual characterisation of the dataset at hand, thus aiding in the precise identification of errors. PhylteR is distributed as an R package on CRAN and as containerized versions (docker and singularity).
The Design of Brainstem Interfaces: Characterisation of Physiological Artefacts and Implications for Closed-loop Algorithms
Authors: Deli Alceste , Toth Robert , Zamora Mayela , Divanbeighi Zand Amir P. , Green Alexander L. , Denison Timothy
Published: February 2023

Surgical neuromodulation through implantable devices allows for stimulation delivery to subcortical regions, crucial for symptom control in many debilitating neurological conditions. Novel closed-loop algorithms deliver therapy tailor-made to endogenous physiological activity, however rely on precise sensing of signals such as subcortical oscillations. The frequency of such intrinsic activity can vary depending on subcortical target nucleus, while factors such as regional anatomy may also contribute to variability in sensing signals. While artefact parameters have been explored in more ‘standard’ and commonly used targets (such as the basal ganglia, which are implanted in movement disorders), characterisation in novel candidate nuclei is still under investigation. One such important area is the brainstem, which contains nuclei crucial for arousal and autonomic regulation. The brainstem provides additional implantation targets for treatment indications in disorders of consciousness and sleep, yet poses distinct anatomical challenges compared to central subcortical targets. Here we investigate the region-specific artefacts encountered during activity and rest while streaming data from brainstem implants with a cranially-mounted device in two patients. Such artefacts result from this complex anatomical environment and its interactions with physiological parameters such as head movement and cardiac functions. The implications of the micromotion-induced artefacts, and potential mitigation, are then considered for future closed-loop stimulation methods.
LimoRhyde2: genomic analysis of biological rhythms based on effect sizes
Authors: Obodo Dora , Outland Elliot H. , Hughey Jacob J.
Published: February 2023

Genome-scale data have revealed daily rhythms in various species and tissues. However, current methods to assess rhythmicity largely restrict their focus to quantifying statistical significance, which may not reflect biological relevance. To address this limitation, we developed a method called LimoRhyde2 (the successor to our method LimoRhyde), which focuses instead on rhythm-related effect sizes and their uncertainty. For each genomic feature, LimoRhyde2 fits a curve using a series of linear models based on periodic splines, moderates the fits using an Empirical Bayes approach called multivariate adaptive shrinkage (Mash), then uses the moderated fits to calculate rhythm statistics such as peak-to-trough amplitude. The periodic splines capture non-sinusoidal rhythmicity, while Mash uses patterns in the data to account for different fits having different levels of noise. To demonstrate LimoRhyde2’s utility, we applied it to multiple circadian transcriptome datasets. Overall, LimoRhyde2 prioritized genes having high-amplitude rhythms in expression, whereas a prior method (BooteJTK) prioritized “statistically significant” genes whose amplitudes could be relatively small. Thus, quantifying effect sizes using approaches such as LimoRhyde2 has the potential to transform interpretation of genomic data related to biological rhythms.
PCP4 immunoreactivity suggests the presence of hippocampal region CA2 in solitary, social and eusocial mole-rat species
Authors: Stöber Tristan M. , Oosthuizen Maria K.
Published: February 2023

Because African mole-rats express diverse social behaviors, they are prime candidates to study the effect of sociability on the evolution of brain circuits. This study compared the expression of Purkinje Cell Protein 4 (PCP4) in hippocampal slices of solitary Cape mole-rats, social Highveld mole-rats, and eusocial Damaraland and naked mole-rats. PCP4 is an established marker for pyramidal cells of hippocampal region CA2, a key structure for social memory and aggression. We observed prominent PCP4 immunoreactivity in the central part of thecornu Ammonisfor all mole-rat species. While further verification is required, these findings suggest the extend of CA2 does not drastically differ despite varying social behaviors. Future studies may use this work as a starting point to explore the relationship between environmental requirements and the functional role of CA2.
Consensus tissue domain detection in spatial multi-omics data using MILWRM
Authors: Kaur Harsimran , Heiser Cody N. , McKinley Eliot T. , Ventura-Antunes Lissa , Harris Coleman R. , Roland Joseph T. , Shrubsole Martha J. , Coffey Robert J. , Lau Ken S. , Vandekar Simon
Published: February 2023

Spatially resolved molecular assays provide high dimensional genetic, transcriptomic, proteomic, and epigenetic information in situ and at various resolutions. Pairing these data across modalities with histological features enables powerful studies of tissue pathology in the context of an intact microenvironment and tissue structure. Increasing dimensions across molecular analytes and samples require new data science approaches to functionally annotate spatially resolved molecular data. A specific challenge is data-driven cross-sample domain detection that allows for analysis within and between consensus tissue compartments across high volumes of multiplex datasets stemming from tissue atlasing efforts. Here, we present MILWRM – multiplex image labeling with regional morphology – a Python package for rapid, multi-scale tissue domain detection and annotation. We demonstrate MILWRM’s utility in identifying histologically distinct compartments in human colonic polyps and mouse brain slices through spatially-informed clustering in two different spatial data modalities. Additionally, we used tissue domains detected in human colonic polyps to elucidate molecular distinction between polyp subtypes. We also explored the ability of MILWRM to identify anatomical regions of mouse brain and their respective distinct molecular profiles.
Auditory memory of complex sounds in sparsely distributed, highly correlated neurons in the auditory cortex
Authors: Kang HiJee , Kanold Patrick O.
Published: February 2023

Listening in complex sound environments requires rapid segregation of different sound sources e.g., speakers from each other, speakers from other sounds, or different instruments in an orchestra, and also adjust auditory processing on the prevailing sound conditions. Thus, fast encoding of inputs and identifying and adapting to reoccurring sounds are necessary for efficient and agile sound perception. This adaptation process represents an early phase of developing implicit learning of sound statistics and thus represents a form of auditory memory. The auditory cortex (ACtx) is known to play a key role in this encoding process but the underlying circuits and if hierarchical processing exists are not known. To identify ACtx regions and cells involved in this process, we simultaneously imaged population of neurons in different ACtx subfields using in vivo 2-photon imaging in awake mice. We used an experimental stimulus paradigm adapted from human studies that triggers rapid and robust implicit learning to passively present complex sounds and imaged A1 Layer 4 (L4), A1 L2/3, and A2 L2/3. In this paradigm, a frozen spectro-temporally complex ‘Target’ sound would be randomly re-occurring within a stream of random other complex sounds. We find distinct groups of cells that are specifically responsive to complex acoustic sequences across all subregions indicating that even the initial thalamocortical input layers (A1 L4) respond to complex sounds. Cells in all imaged regions showed decreased response amplitude for reoccurring Target sounds indicating that a memory signature is present even in the thalamocortical input layers. On the population level we find increased synchronized activity across cells to the Target sound and that this synchronized activity was more consistent across cells regardless of the duration of frozen token within Target sounds in A2, compared to A1. These findings suggest that ACtx and its input layers play a role in auditory memory for complex sounds and suggest a hierarchical structure of processes for auditory memory.
Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation
Authors: Sharon Itai , Schmeing T. Martin
Published: February 2023

Cyanophycin is a bacterial biopolymer used for storage of fixed nitrogen. It is composed of a backbone of L-aspartate residues with L-arginines attached to each of their side chains. Cyanophycin is produced by cyanophycin synthetase 1 (CphA1) using Arg, Asp and ATP, and is degraded in two steps. First, cyanophycinase breaks down the backbone peptide bonds, releasing β-Asp-Arg dipeptides. Then, these dipeptides are broken down into free Asp and Arg by enzymes with isoaspartyl dipeptidase activity. Two bacterial enzymes are known to possess promiscuous isoaspartyl dipeptidase activity: isoaspartyl dipeptidase (IadA) and isoaspartyl aminopeptidase (IaaA). We performed a bioinformatic analysis to investigate whether genes for cyanophycin metabolism enzymes cluster together or are spread around the microbial genomes. Many genomes showed incomplete contingents of known cyanophycin metabolizing genes. Cyanophycin synthetase and cyanophycinase are usually clustered together when recognizable genes for each are found within a genome. Cyanophycinase and isoaspartyl dipeptidase genes typically cluster within genomes lackingcphA1. About one-third of genomes with genes for CphA1, cyanophycinase and IaaA show these genes clustered together, while the proportion is around one-sixth for CphA1, cyanophycinase and IadA. We used X-ray crystallography and biochemical studies to characterize an IadA and an IaaA from two such clusters. The enzymes retained their promiscuous nature, showing that being associated with cyanophycin-related genes did not make them specific for β-Asp-Arg dipeptides derived from cyanophycin degradation.
Plant diversity in the diet of Costa Rican primates in contrasting habitats: a meta-analysis
Authors: Chaves Óscar M. , Morales-Cerdas Vanessa , Calderón-Quirós Jazmín , Azofeifa-Rojas Inés , Riba-Hernández Pablo , Solano-Rojas Daniela , Chaves-Cordero Catalina , Chacón-Madrigal Eduardo , Melin Amanda D.
Published: February 2023

In human-modified tropical landscapes, the survival of arboreal vertebrates, particularly primates, depends on their plant dietary diversity. Here, we assessed diversity of plants included in the diet of Costa Rican non-human primates, CR-NHP (i.e.Alouatta palliata palliata,Ateles geoffroyi,Cebus imitator, andSaimiri oerstedii) inhabiting different habitat types across the country. Specifically, we assessed by analyzing 37 published and unpublished datasets: (i) richness and dietary α-plant diversity, (ii) the β-diversity of dietary plant species and the relative importance of plant species turnover and nestedness contributing to these patterns, and (iii) the main ecological drivers of the observed patterns in dietary plant . Diet data were available for 34Alouatta, 16Cebus, 8Ateles, and 5Saimirigroups. Overall dietary plant species richness was higher inAlouatta(476 spp.), followed byAteles(329 spp.),Cebus(236 spp.), andSaimiri(183 spp.). However, rarefaction curves showed that α-diversity of plant species was higher inAtelesthan in the other three primate species. The γ-diversity of plants was 868 species (95% C.I.=829-907 species). The three most frequently reported food species for all CR-NHP wereSpondias mombin,Bursera simaruba, andSamanea saman. In general, plant species turnover, rather than nestedness, explained the dissimilarity in plant diet diversity (βsim> 0.60) of CR_NHP. Finally, primate species, habitat type (life zone and disturbance level) and, to a lesser degree, sampling effort were the best predictors of the dietary plant assemblages. Our findings suggest that CR-NHP diets were diverse, even in severely-disturbed habitats.
Structure Primed Embedding on the Transcription Factor Manifold Enables Transparent Model Architectures for Gene Regulatory Network and Latent Activity Inference
Authors: Tjärnberg Andreas , Beheler-Amass Maggie , Jackson Christopher A , Christiaen Lionel A , Gresham David , Bonneau Richard
Published: February 2023

The modeling of gene regulatory networks (GRNs) is limited due to a lack of direct measurements of regulatory features in genome-wide screens. Most GRN inference methods are therefore forced to model relationships between regulatory genes and their targets with expression as a proxy for the upstream independent features, complicating validation and predictions produced by modeling frameworks. Separating covariance and regulatory influence requires aggregation of independent and complementary sets of evidence, such as transcription factor (TF) binding and target gene expression. However, the complete regulatory state of the system,e.g. TF activity (TFA) is unknown due to a lack of experimental feasibility, making regulatory relations difficult to infer. Some methods attempt to account for this by modeling TFA as a latent feature, but these models often use linear frameworks that are unable to account for non-linearities such as saturation, TF-TF interactions, and other higher order features. Deep learning frameworks may offer a solution, as they are capable of modeling complex interactions and capturing higher-order latent features. However, these methods often discard central concepts in biological systems modeling, such as sparsity and latent feature interpretability, in favor of increased model complexity. We propose a novel deep learning autoencoder-based framework,StrUcture Primed Inference of Regulation using latent Factor ACTivity(SupirFactor), that scales to single cell genomic data and maintains interpretability to perform GRN inference and estimate TFA as a latent feature. We demonstrate that SupirFactor outperforms current leading GRN inference methods, predicts biologically relevant TFA and elucidates functional regulatory pathways through aggregation of TFs.
A hybrid method for discovering interferon-gamma inducing peptides in human and mouse
Authors: Dhall Anjali , Patiyal Sumeet , Raghava Gajendra P. S.
Published: February 2023

A host-specific technique has been developed for annotating interferon-gamma (IFN-γ) inducing peptides, it is an updated version of IFNepitope. In this study, dataset used for developing prediction method contain experimentally validated 25492 and 7983 IFN-γ inducing peptides in human and mouse host, respectively. In initial phase, machine learning techniques have been exploited to develop classification model using wide range of peptide features. In most of the case, models based on extra tree perform better than other machine learning techniques. In case of peptide features, compositional feature particularly dipeptide composition performs better than one-hot encoding or binary profile. Our best machine learning based models achieved AUROC 0.89 and 0.83 for human and mouse host, respectively. In order to improve machine learning based models or alignment free models, we explore potential of similarity-based technique BLAST. Finally, a hybrid model has been developed that combine best machine learning based model with BLAST and achieved AUROC 0.90 and 0.85 for human and mouse host, respectively. All models have been evaluated on an independent/validation dataset not used for training or testing these models. Newly developed method performs better than existing method on independent dataset. The major objective of this study is to predict, design and scan IFN-γ inducing peptides, thus server/software have been developed (https://webs.iiitd.edu.in/raghava/ifnepitope2/).

Highlights

An updated method for predicting interferon-gamma (IFN-γ) inducing peptides.

A wide range of features have been generated using Pfeature tool.

Models were trained and tested on experimentally validated datasets.

Hybrid models developed by combining machine-learning and BLAST.

IFNepitope2 server is available to design subunit or peptide-based vaccines.
Mapping evidence on cryptococcal antigen infection among HIV-infected persons in sub-Saharan Africa- A Scoping Review Protocol
Authors: Dlamini Khululiwe , Moetlhoa Boitumelo , Turner Astrid , Maluleke Kuhlula , Mashamba-Thompson Tivani
Published: February 2023

Introduction

Infections of the central nervous system are a considerable basis of mortality in people living with Human immunodeficiency virus (HIV), with progression to cryptococcal meningitis documented at around 15% of HIV-associated mortality globally, with nearly three-quarters occurring in the sub-Saharan Africa. Discoveries from previous studies preluded that mortality amid cryptococcal antigen (CrAg) positive persisted to be elevated than in CrAg negative persons. One feasible interpretation of this could be due to undiagnosed cryptococcus. Laboratory investigations towards prompt identification of cryptococcal disease prior to cryptococcal meningitis has progressed to point-of-care testing with high sensitivity and specificity as seen with the CrAg lateral flow assay screening to expedite treatment. The aim of the study is to map and translate evidence on CrAg infection among HIV-infected persons in sub-Saharan Africa (SSA).

Methodology

The proposed scoping review will be conducted using guidelines proposed by Arksey and O’Malley methodological framework and Levac et al advanced method. It will be guided by the Preferred Reporting Items for Systematic Reviews and Meta-Analysis for Scoping Reviews. A comprehensive literature search of studies published from the first relevant publication to 2022 will be conducted on multiple electronic databases. Additional sources (grey literature) will also be searched. The search strategy will be generated and implemented by the principal investigator with assistance from a subject specialist, and an information specialist. Two reviewers will screen eligible studies. The screening will be guided by an inclusion and exclusion criteria. The mixed method appraisal tool (MMAT) version 2018 will be used to appraise the quality of the empirical studies.

Discussion

The proposed scoping review will map and translate evidence on CrAg infection among HIV-infected persons in sub-Saharan Africa. Synthesising and sharing recent evidence in this area has potential to help guide future research and interventions aimed at improving the management of CrAg infection among HIV-infected persons in sub-Saharan Africa and other high HIV-burdened settings.
Accuracy and reliability of self-administered visual acuity tests: Systematic review of pragmatic trials
Authors: Thirunavukarasu Arun James , Hassan Refaat , Limonard Aaron , Savant Shalom Vitreous
Published: February 2023

Background

Remote self-administered visual acuity (VA) tests have the potential to allow patients and non-specialists to assess vision without eye health professional input. Validation in pragmatic trials is necessary to demonstrate the accuracy and reliability of tests in relevant settings to justify deployment.

Methods

A systematic review was undertaken in accordance with a preregistered protocol (CRD42022385045). The Cochrane Library, Embase, MEDLINE, and Scopus were searched. Screening was conducted according to the following criteria: (1) English languge; (2) primary research article; (3) visual acuity test conducted remotely; (4) no clinical administration of remote test; (5) accuracy or reliability of remote test analysed. There were no restrictions on trial participants. Quality assessment was conducted with QUADAS-2.

Results

Of 1227 identified reports, 10 studies were ultimately included. One study was at high risk of bias and two studies exhibited concerning features of bias; all studies were applicable. Three trials—of DigiVis, iSight Professional, and Peek Acuity—from two studies suggested that accuracy of the remote tests was comparable to clinical assessment. All other trials exhibited inferior accuracy, including conflicting results from a pooled study of iSight Professional and Peek Acuity. Two studies evaluated test-retest agreement—one trial provided evidence that DigiVis is as reliable as clinical assessment. The three most accurate tests required access to digital devices. Reporting was inconsistent and often incomplete, particularly with regards to describing methods and conducting statistical analysis.

Conclusions

Remote self-administered VA tests appear promising, but further pragmatic trials are indicated to justify deployment at scale to facilitate patient or non-specialist led assessment which could augment teleophthalmology, non-specialist eye assessment, pre-consultation triage, and autonomous long-term monitoring of vision.
Prognostic impact of dynamic evolution in renal function among patients undergoing elective percutaneous coronary intervention
Authors: Xiang Yifei , Lin Xueqin , Cai Xiaoling , Zhang Liwei , Luo Manqing , Zeng Jilang , Guo Yansong , Lin Kai-Yang
Published: February 2023

Background

Previous studies have shown that chronic kidney disease(CKD) affected the long-term prognosis of patients underwent the elective percutaneous coronary intervention(EPCI). However, the prognostic impact in patients with the development of the contrast-associated acute kidney injury(CA-AKI) and recovery or progression of CA-AKI were controversial. For the moment, little attention has been paid to the relationship between the dynamic evolution of renal function and its prognosis.

Methods

We used three stages to characterize the dynamic evolution of renal function, namely the occurrence of CKD at baseline, the occurrence of CA-AKI in the postoperative period and the occurrence of post kindey injury(PKI) at 3 - 6 months postoperatively. Cardiac death and all-cause mortality were used as the endpoint of the study. PKI(+) was defined as CA-AKI not recovered or an increase in absolute serum creatinine (SCr) ≤0.3 mg/dl or a SCr relative increase in creatinine ≤ 50% after 3 - 6 months. PKI(-) was defined as CA-AKI recovered or SCr elevation not meeting the PKI(+) requirement.

Results

We prospectively enrolled 2951 patients who underwent EPCI from 2012 to 2018. They were divided into three groups according to baseline CKD and CA-AKI: STAGE I[Unimpaired renal function group, CKD(-)/CA-AKI(-) (n=1247)], STAGE II[Partially impaired renal function group, IIa: CKD(-)/CA-AKI(+) (n=91) and IIb: CKD(+)/CA-AKI(-) (n=1472)] and STAGE III[severely impaired renal function group, CKD(+)/CA-AKI(+) (n=141)]. Subsequently, based on the occurrence of PKI, they were divided into six groups: STAGE I/PKI(-) (n=1212), STAGE I/PKI(+) (n=35), STAGE II/PKI(-) (n=1508), STAGE II/PKI(+) (n=55), STAGE III/PKI(-) (n=108), STAGE III/PKI(+) (n=33). In a mean follow-up period of 3.33± 1.39 years, we found that from STAGE I, STAGE II to STAGE III at baseline groups, the incidence of the primary outcome significantly increased. Meanwhile, from the baseline groups to the follow-up groups, the dynamic changes in renal function were observed. At the follow-uo groups, the occurrence of PKI did not affect the prognosis of patients in the STAGE I group(hazard ratio [HR] = 0.94, 95%CI: 0.15–8.11, p = 0.949) and the STAGE III group(hazard ratio [HR] = 1.19, 95%CI: 0.50–2.83 p = 0.689). However, for the STAGE II group (hazard ratio [HR] = 2.65, 95%CI: 1.42–4.94, p = 0.002), the development of PKI would lead to a poor prognosis for patients.

Conclusion

In patients undergoing EPCI, the occurrence of CKD and CA-AKI affected the long-term prognosis of patients. The prognostic impact of the occurrence of PKI depended on the renal function of patients. In patients with unimpaired renal function or severely impaired renal function, the prognostic impact of PKI was negligible. However, in patients with partially impaired renal function, avoidance of PKI could beneficial for their long-term prognosis.
FDX1 regulates cellular protein lipoylation through direct binding to LIAS
Authors: Dreishpoon Margaret B. , Bick Nolan R. , Petrova Boryana , Warui Douglas M. , Cameron Alison , Booker Squire J. , Kanarek Naama , Golub Todd R. , Tsvetkov Peter
Published: February 2023

Ferredoxins are a family of iron-sulfur (Fe-S) cluster proteins that serve as essential electron donors in numerous cellular processes that are conserved through evolution. The promiscuous nature of ferredoxins as electron donors enables them to participate in many metabolic processes including steroid, heme, vitamin D and Fe-S cluster biosynthesis in different organisms. However, the unique natural function(s) of each of the two human ferredoxins (FDX1 and FDX2) are still poorly characterized. We recently reported that FDX1 is both a crucial regulator of copper ionophore induced cell death and serves as an upstream regulator of cellular protein lipoylation, a mitochondrial lipid-based post translational modification naturally occurring on four mitochondrial enzymes that are crucial for TCA cycle function. Here we show that FDX1 regulates protein lipoylation by directly binding to the lipoyl synthase (LIAS) enzyme and not through indirect regulation of cellular Fe-S cluster biosynthesis. Metabolite profiling revealed that the predominant cellular metabolic outcome of FDX1 loss-of-function is manifested through the regulation of the four lipoylation-dependent enzymes ultimately resulting in loss of cellular respiration and sensitivity to mild glucose starvation. Transcriptional profiling of cells growing in either normal or low glucose conditions established that FDX1 loss-of-function results in the induction of both compensatory metabolism related genes and the integrated stress response, consistent with our findings that FDX1 loss-of-functions is conditionally lethal. Together, our findings establish that FDX1 directly engages with LIAS, promoting cellular protein lipoylation, a process essential in maintaining cell viability under low glucose conditions.
Cardiac Troponin I Directly Binds and Inhibits Mitochondrial ATP Synthase: a Noncanonical Role in the Post-Ischemic Heart
Authors: Elezaby Aly , Lin Amanda J , Vijayan Vijith , Pokhrel Suman , Bechara Luiz RG , Ostberg Nicolai P , Queliconi Bruno B , Campos Juliane C , Ferreira Julio CB , Haileselassie Bereketeab , Mochly-Rosen Daria
Published: February 2023

Cardiac troponin I (cTnI) is a sarcomeric protein critical to myocyte contraction. Unexpectedly, we found that some cTnI localized to the mitochondrial matrix in the heart, inhibited mitochondrial functions when stably expressed in non-cardiac cells and increased opening of the mitochondrial permeability transition pore under oxidative stress. Direct, specific, and saturable binding of cTnI to ATP synthase was demonstratedin vitro, using immune-captured ATP synthase, and in cells using proximity ligation assay. cTnI binding doubled F1F0ATPase activity, whereas skeletal troponin I and several human mutant cTnI variants associated with familial hypertrophic cardiomyopathy did not. A rationally-designed ten amino acid peptide, P888, inhibited cTnI binding to ATP synthase, inhibited cTnI-induced increase in ATPase activityin vitro, and reduced cardiac injury following transient ischemiain vivo. We therefore suggest that mitochondria-associated cTnI may inhibit cardiac ATP synthase under basal conditions; pharmacological agents that release this inactivating effect of cTnI and thus preventing ATP hydrolysis during cardiac ischemia may increase the reservoir of functional mitochondria to reduce cardiac injury.

Significance Statement

Cardiac troponin I (cTnI) is a key sarcomeric protein involved in the regulation of myocardial contractility. We found that some cTnI is present in the mitochondrial matrix where it binds to ATP synthase, disrupting mitochondrial function; inhibition of the cTnI-ATP synthase interaction with a selective peptide inhibitor reduces cardiac dysfunction following ischemia and reperfusion injury. Several pathogenic cTnI mutations associated with hypertrophic cardiomyopathy do not affect ATP synthase activity, suggesting a potential mechanism that contributes to the diverse pathologies associated with these mutations.