bluuebunny/crossref_metadata_2025 huggingface dataset:
Temporal dynamics of trauma memory persistence
Authors: Bonsall Michael B. , Holmes Emily A.
Published: February 2023

Traumatic events lead to distressing memories, but such memories are made all the worse when they intrude to mind unbidden and recurrently. Intrusive memories are a hallmark of several mental health disorders including posttraumatic stress disorder (PTSD) and can persist for years. Critically, the reduction of intrusive memories provides a treatment target. While cognitive models for psychological trauma exist, these lack formal quantitative structure and robust empirical validation. Here we develop a mechanistically-driven, quantitative framework to extend understanding of the temporal dynamic processes of trauma memory. We show how the marginal gains of interventions for intrusive memories can be enhanced as key properties of the intervention vary. Validating the framework against empirical data highlights that while emerging interventions to reduce occurrence of intrusive memories can be effective, counter-intuitively, maintaining these memories in a sufficiently reactivated state is essential for preventing their persistence.

Author Summary

Intrusive memories and flashbacks after trauma are prominent in several mental disorders. Quantifying these intrusions is the aim of the current study. While many conceptual models for trauma memory exist, none provide a mechanistic framework for validating experimental or clinical evidence. Our approach is to develop a probabilistic description of memory mechanisms to link to the broader goals of trauma treatment. Analysis shows how critical attributes of the framework such as intervention strength and reminder strength determine success in managing intrusive memories. Validation with empirical data shows how the framework can be parameterized and predictions evaluated against observed outcomes. In this way neural mechanisms associated with memory can be combined with broader cognitive processes.
Astrocyte-like subpopulation of NG2 glia in the adult mouse cortex exhibits characteristics of neural progenitor cells and is capable of forming neuron-like cells after ischemic injury
Authors: Janeckova Lucie , Knotek Tomas , Kriska Jan , Hermanova Zuzana , Kirdajova Denisa , Kubovciak Jan , Berkova Linda , Tureckova Jana , Garcia Sara Camacho , Galuskova Katerina , Kolar Michal , Anderova Miroslava , Korinek Vladimir
Published: February 2023

Glia cells expressing neuron-glial antigen 2 (NG2) play a critical role as oligodendrocyte precursor cells (OPCs) in the healthy brain; however, their differentiation potential after ischemic injury remains an unresolved question. Here, we aimed to elucidate the heterogeneity and role of NG2 glia in the ischemic brain. We used transgenic mice to label NG2-expressing cells and their progeny with red fluorescent protein tdTomato in the healthy brains and those after focal cerebral ischemia (FCI). Based on single-cell RNA sequencing, the labeled glial cells were divided into five distinct subpopulations. The identity of these subpopulations was determined based on gene expression patterns. In addition, membrane properties were further analyzed using the patch-clamp technique. Three of the observed subpopulations represented OPCs, whereas the fourth group exhibited characteristics of cells destined for oligodendrocyte fate. The fifth subpopulation of NG2 glia carried astrocytic markers. Importantly, we detected features of neural progenitors in these cells. This subpopulation was present in both healthy and post-ischemic tissue; however, its gene expression changed after ischemia, with genes related to neurogenesis being more abundant. Neurogenic gene expression was monitored over time and complemented by immunohistochemical staining, which showed increased numbers of Purkinje cell protein 4-positive NG2 cells at the edge of the ischemic lesion 12 days after FCI, and NeuN-positive NG2 cells 28 days after injury, indicating the existence of neuron-like cells that develop from NG2 glia in the ischemic tissue. Our results provide further insight into the differentiation plasticity and neurogenic potential of NG2 glia after stroke.

Main Points

Different subpopulations of NG2 glia in the healthy and ischemic adult cortex were identified based on their gene expression and membrane properties.

Astrocyte-like NG2 glia exhibit neurogenic gene expression and are more abundant in post-ischemic tissue.

Progeny of NG2-positive cells carrying neuronal marker NeuN was observed at the edge of the ischemic lesion.
A stochastic analysis of the interplay between antibiotic dose, mode of action, and bacterial competition in the evolution of antibiotic resistance
Authors: Czuppon Peter , Day Troy , Débarre Florence , Blanquart François
Published: February 2023

The use of an antibiotic may lead to the emergence and spread of bacterial strains resistant to this antibiotic. Experimental and theoretical studies have investigated the drug dose that minimizes the risk of resistance evolution over the course of treatment of an individual, showing that the optimal dose will either be the highest or the lowest drug concentration possible to administer; however, no analytical results exist that help decide between these two extremes. To address this gap, we develop a stochastic mathematical model of bacterial dynamics under antibiotic treatment. We explore various scenarios of density regulation (bacterial density affects cell birth or death rates), and antibiotic modes of action (biostatic or biocidal). We derive analytical results for the survival probability of the resistant subpopulation until the end of treatment, the size of the resistant subpopulation at the end of treatment, the carriage time of the resistant subpopulation until it is replaced by a sensitive one after treatment, and we verify these results with stochastic simulations. We find that the scenario of density regulation and the drug mode of action are important determinants of the survival of a resistant subpopulation. Resistant cells survive best when bacterial competition reduces cell birth and under biocidal antibiotics. Compared to an analogous deterministic model, the population size reached by the resistant type is larger and carriage time is slightly reduced by stochastic loss of resistant cells. Moreover, we obtain an analytical prediction of the antibiotic concentration that maximizes the survival of resistant cells, which may help to decide which drug dosage (not) to administer. Our results are amenable to experimental tests and help link the within and between host scales in epidemiological models.
Event-related modulation of alpha rhythm explains the auditory P300 evoked response in EEG
Authors: Studenova A.A. , Forster C. , Engemann D.A. , Hensch T. , Sander C. , Mauche N. , Hegerl U. , Loeffler M. , Villringer A. , Nikulin V.V.
Published: February 2023

Evoked responses and oscillations represent two major electrophysiological phenomena in the human brain yet the link between them remains rather obscure. Here we show how most frequently studied EEG signals: the P300-evoked response and alpha oscillations (8–12 Hz) can be linked with the baseline-shift mechanism. This mechanism states that oscillations generate evoked responses if oscillations have a non-zero mean and their amplitude is modulated by the stimulus. Therefore, the following predictions should hold: 1) the temporal evolution of P300 and alpha amplitude is similar, 2) spatial localisations of the P300 and alpha amplitude modulation overlap, 3) oscillations are non-zero mean, 4) P300 and alpha amplitude correlate with cognitive scores in a similar fashion. To validate these predictions, we analysed the data set of elderly participants (N=2230, 60–82 years old), using a) resting-state EEG recordings to quantify the mean of oscillations, b) the event-related data, to extract parameters of P300 and alpha rhythm amplitude envelope. We showed that P300 is indeed linked to alpha rhythm, according to all four predictions. Our results provide an unifying view on the interdependency of evoked responses and neuronal oscillations and suggest that P300, at least partly, is generated by the modulation of alpha oscillations.
Rainbow trout neomales broodstocks are able to eat and use a high carbohydrate diet during a complete reproductive cycle
Authors: Nathan Favalier , Anne Surget , Vincent Véron , Patrick Maunas , Nicolas Turonnet , Frederic Terrier , Stéphane Panserat , Lucie Marandel
Published: February 2023

The main challenge of the aquaculture relies on the shift from fishmeal to more sustainable ingredients. Interest on carbohydrates has growing rapidly as they are considered as promising resources, providing energy and preserving proteins for growth. However, rainbow trout is considered as a poor user of carbohydrates displaying postprandial hyperglycaemia and impaired growth performances when fed with diets containing more than 20% of carbohydrates. Nonetheless, recent evidence points that broodstocks could be better user of high carbohydrate diet compared to juveniles. However, no study investigates how sex-reversed females – neomales – eat, grow and reproduce under a high carbohydrate diet. Our objective was thus to assess growth and reproductive performances of neomales fed with a high carbohydrate diet during an entire reproductive cycle. Our results demonstrate that neomales display specific metabolic and physiological changes when fed with a high carbohydrate diet compared to both females and males broodstocks as well as compared to juveniles. Altogether, our data demonstrate the critical relevance to formulate specific diets in accordance with specificities of each type of broodstocks (i.e. females, males and neomales).
Molecular Investigation of TSHR gene in Bangladeshi Congenital Hypothyroid patients
Authors: Begum Mst. Noorjahan , Mahtarin Rumana , Islam Md Tarikul , Ahmed Sinthyia , Konika Tasnia Kawsar , Mannoor Kaiissar , Akhteruzzaman Sharif , Qadri Firdausi
Published: February 2023

The disorder of thyroid gland development or thyroid dysgenesis (TH) accounts for 80-85% cases of congenital hypothyroidism (CH). Hence, the understanding of molecular etiology of TH is prerequisite. Mutations in TSHR gene is mostly associated with thyroid dysgenesis, prevent or disrupt normal development of the gland. The current study detects two nonsynonymous mutations (p.Ser508Leu, p.Asp727Glu) in transmembrane (TM)-region (Exon 10) of TSHR gene in 21 patients with dysgenesis by sequencing-based analysis. Later, transmembrane (TM)-region of TSHR protein is modelled by homology modeling. Transmembrane (TM)-region of TSHR protein is targeted by small molecules thyrogenic drugs, MS437 and MS438 to perceive the effect of mutations. The damaging effect in drug-protein complexes of mutants were envisaged by molecular docking and interactions. The binding affinity of wild type protein was much higher than the mutant cases for both of the ligands (MS437 and MS438). Molecular dynamics simulates dynamic behavior of wild type and mutant complexes. MS437-TSHR368-764MT2 and MS438-TSHR368-764MT1 show stable conformations in biological environments. Finally, PCA reveals structural and energy profile discrepancies. TSHR368-764MT1 exhibits much variations than TSHR368-764WT and TSHR368-764MT2, emphasizing more damaging pattern in TSHR368-764MT1. The study might be helpful to understand molecular etiology of thyroid dysgenesis (TH) exploring the mutational impact on TSHR protein to the interaction with agonists.
Gene expression plasticity followed by genetic change during colonization a high-elevation environment
Authors: She Huishang , Hao Yan , Song Gang , Luo Xu , Lei Fumin , Zhai Weiwei , Qu Yanhua
Published: February 2023

Phenotypic plasticity facilitates organismal invasion of novel environments, and the resultant phenotypic change may later be modified by genetic change, so called “plasticity first”. Herein we quantify gene expression plasticity and regulatory adaptation in a wild bird (Eurasian Tree Sparrow) from its original lowland (ancestral stage), experimentally implemented hypoxia acclimation (plastic stage) and colonized highland (colonized stage). Using a group of co-expressed genes from the cardiac and flight muscle, respectively, we demonstrate that gene expression plasticity to hypoxia tolerance is more often reversed than reinforced at the colonized stage. By correlating gene expression change with muscle phenotypes, we show that colonized tree sparrows reduce maladaptive plasticity that largely associates with decrease hypoxia tolerance. Conversely, adaptive plasticity that is congruent with increase hypoxia tolerance is often reinforced in the colonized tree sparrows. Genes displaying large levels of reinforcement or reversion plasticity (i.e., 200% of original level) show greater genetic divergence between ancestral and colonized populations. Overall, our work demonstrates that gene expression plasticity at the initial stage of high-elevation colonization can be reversed or reinforced through selection-driven adaptive modification.
Variability of the innate immune response is globally constrained by transcriptional bursting
Authors: Alachkar Nissrin , Norton Dale , Wolkensdorfer Zsofia , Muldoon Mark , Paszek Pawel
Published: February 2023

Transcription of almost all mammalian genes occurs in stochastic bursts, however the fundamental control mechanisms that allow appropriate single-cell responses remain unresolved. Here we utilise single cell genomics data and stochastic models of transcription to perform global analysis of the toll-like receptor (TLR)-induced gene expression variability. Based on analysis of more than 2000 TLR-response genes across multiple experimental conditions we demonstrate that the single-cell, gene-by-gene expression variability can be empirically described by a linear function of the population mean. We show that response heterogeneity of individual genes can be characterised by the slope of the mean-variance line, which captures how cells respond to stimulus and provides insight into evolutionary differences between species. We further demonstrate that linear relationships theoretically determine the underlying transcriptional bursting kinetics, revealing different regulatory modes of TLR response heterogeneity. Stochastic modelling of temporal scRNA-seq count distributions demonstrates that increased response variability is associated with larger and more frequent transcriptional bursts, which emerge via increased complexity of transcriptional regulatory networks between genes and different species. Overall, we provide a methodology relying on inference of empirical mean-variance relationships from single cell data and new insights into control of innate immune response variability.
A Mechanistic Insight into Sources of Error of Visual Working Memory in Multiple Sclerosis
Authors: Motahharynia Ali , Pourmohammadi Ahmad , Adibi Armin , Shaygannejad Vahid , Ashtari Fereshteh , Adibi Iman , Sanayei Mehdi
Published: February 2023

Working memory (WM) is one of the most affected cognitive domains in multiple sclerosis (MS), which is mainly studied by the previously established binary model for information storage (slot model). However, recent observations based on the continuous reproduction paradigms have shown that assuming dynamic allocation of WM resources (resource model) instead of the binary hypothesis will give more accurate predictions in WM assessment. Moreover, continuous reproduction paradigms allow for assessing the distribution of error in recalling information, providing new insights into the organization of the WM system. Hence, by utilizing two continuous reproduction paradigms, memory-guided localization (MGL) and analog recall task with sequential presentation, we investigated WM dysfunction in MS. Our results demonstrated an overall increase in recall error and decreased recall precision in MS. Furthermore, computational modeling of the results from the sequential paradigm determined that imprecision in decoding information and swap error (mistakenly reporting the feature of other presented items) were responsible for WM dysfunction in MS. Overall, this study offered a sensitive measure for assessing WM deficit and provided new insight into the organization of the WM system in MS population.
Towards estimating the number of strains that make up a natural bacterial population
Authors: Viver Tomeu , Conrad Roth E. , Rodriguez-R Luis M. , Ramírez Ana S. , Venter Stephanus N. , Rocha-Cárdenas Jairo , Llabrés Mercè , Amann Rudolf , Konstantinidis Konstantinos T. , Rossello-Mora Ramon
Published: February 2023

What a strain is and how many strains make up a natural bacterial population remain elusive concepts despite their apparent importance for assessing the role of intra-population diversity in disease emergence or response to environmental perturbations. To advance these concepts, we sequenced 138 randomly selectedSalinibacter ruberisolates from two solar salterns and assessed these genomes against companion short-read metagenomes from the same samples. The distribution of genome-aggregate average nucleotide identity (ANI) values among these isolates revealed a bimodal distribution, with significantly lower occurrence of values between 99.2% and 99.8% relative to ANI >99.8% or <99.2%, revealing a natural “gap” in the sequence space within species. Accordingly, we used this ANI gap to define genomovars and a higher ANI value of >99.99% and shared gene-content >99.0% to define strains. Using these thresholds and extrapolating from how many metagenomic reads each genomovar uniquely recruited, we estimated that –although our 138 isolates represented about 80% of theSal. ruberpopulation– the total population in one pond is composed of 5,500 to 11,000 genomovars, the great majority of which appear to be rarein situ. These data also revealed that the most frequently recovered isolate in lab media was often not the most abundant genomovarin situ, suggesting that cultivation biases are significant, even in cases that cultivation procedures are thought to be robust. Preliminary analyses of available genomes revealed that the thresholds used for defining strains and distinct intra-species units (genomovars) may be broadly applicable to additional bacterial species.

Significance Statement

Strains are the smallest distinguishable units within a microbial species. Strains that carry unique gene content often underly the emergence of disease outbreaks and the response of the species to environmental perturbations. Therefore, a major challenge in microbiome research across environmental and clinical settings is to evaluate how many strains of the same species coexist in nature and how dominant strains emerge from this diversity. Unfortunately, the available theoretical concept of strain is not directly applicable to culture-independent surveys. Here, we provide such a practical definition for strain and use it to show that that the number of strains making up a natural bacterial population may be large, in the order of a few thousands, but not infinite.
MYC-driven increases in mitochondrial DNA copy number occur early and persist throughout prostatic cancer progression
Authors: Chen Jiayu , Zheng Qizhi , Hicks Jessica L. , Trabzonlu Levent , Ozbek Busra , Jones Tracy , Vaghasia Ajay , Larman Tatianna C. , Wang Rulin , Markowski Mark C. , Denmeade Sam R. , Pienta Kenneth J. , Hruban Ralph H. , Antonarakis Emmanuel S. , Gupta Anuj , Dang Chi V , Yegnasubramanian Srinivasan , De Marzo Angelo M.
Published: February 2023

Increased mitochondrial function may render some cancers vulnerable to mitochondrial inhibitors. Since mitochondrial function is regulated partly by mitochondrial DNA copy number (mtDNAcn), accurate measurements of mtDNAcn could help reveal which cancers are driven by increased mitochondrial function and may be candidates for mitochondrial inhibition. However, prior studies have employed bulk macrodissections that fail to account for cell type-specific or tumor cell heterogeneity in mtDNAcn. These studies have often produced unclear results, particularly in prostate cancer. Herein, we developed a multiplexin situmethod to spatially quantify cell type specific mtDNAcn. We show that mtDNAcn is increased in luminal cells of high-grade prostatic intraepithelial neoplasia (HGPIN), is increased in prostatic adenocarcinomas (PCa), and is further elevated in metastatic castration-resistant prostate cancer. Increased PCa mtDNAcn was validated by two orthogonal methods and is accompanied by increases in mtRNAs and enzymatic activity. Mechanistically, MYC inhibition in prostate cancer cells decreases mtDNA replication and expression of several mtDNA replication genes, and MYC activation in the mouse prostate leads to increased mtDNA levels in the neoplastic prostate cells. Ourin situapproach also revealed elevated mtDNAcn in precancerous lesions of the pancreas and colon/rectum, demonstrating generalization across cancer types using clinical tissue samples.
A tRNA modification inMycobacterium tuberculosisfacilitates optimal intracellular growth
Authors: Tomasi Francesca G. , Kimura Satoshi , Rubin Eric J. , Waldor Matthew K.
Published: February 2023

Diverse chemical modifications fine-tune the function and metabolism of tRNA. Although tRNA modification is universal in all kingdoms of life, profiles of modifications, their functions, and physiological roles have not been elucidated in most organisms including the human pathogen,Mycobacterium tuberculosis(Mtb), the causative agent of tuberculosis. To identify physiologically important modifications, we surveyed the tRNA ofMtb, using tRNA sequencing (tRNA-seq) and genome-mining. Homology searches identified 23 candidate tRNA modifying enzymes that are predicted to create 16 tRNA modifications across all tRNA species. Reverse transcription-derived error signatures in tRNA-seq predicted the sites and presence of 9 modifications. Several chemical treatments prior to tRNA-seq expanded the number of predictable modifications. Deletion ofMtbgenes encoding two modifying enzymes, TruB and MnmA, eliminated their respective tRNA modifications, validating the presence of modified sites in tRNA species. Furthermore, the absence ofmnmAattenuatedMtbgrowth in macrophages, suggesting that MnmA-dependent tRNA uridine sulfation contributes toMtbintracellular growth. Our results lay the foundation for unveiling the roles of tRNA modifications inMtbpathogenesis and developing new therapeutics against tuberculosis.
Non-decision time: the Higg’s boson of decision
Authors: Bompas A. , Sumner P. , Hedge C.
Published: February 2023

Generative models of decision now permeate all subfields of psychology, cognitive and clinical neuroscience. To successfully represent decision mechanisms, it is necessary to also assume the presence of delays for sensory and motor information to travel through the brain; but like the Higg’s boson in particle physics, directly observing this “non-decision time” from behaviour long appeared beyond reach. Here, we describe and apply a set of methods to empirically measure and characterise the properties of non-decision time in fast visually guided decisions (without requiring modelling assumptions). We gather 11 datasets from humans and monkeys from multiple labs and validate the method by showing that visual properties (brightness, colour, size) consistently affect empirically measured non-decision time, as predicted by neurophysiology. We then show that endogenous factors (pro-active slowing, attention) consistently do not affect non-decision time, in contrast to widespread reports based on model fits. Last, contrasting empirically observed non-decision time with estimates from the EZ, DDM and LBA models, we conclude that models cannot be generally trusted to provide valid estimates, either at a group level or for individual differences, and propose a hybrid approach that combines our empirical method with standard modelling.
It’s all about location: reliance on spatial rather than visual context when trying to remember
Authors: Taub Keren , Yuval-Greenberg Shlomit
Published: February 2023

When people try to remember visual information, they often move their eyes similarly to encoding. The mechanism underlying this behavior has not yet been fully understood. Specifically, it is unclear whether the purpose of this behavior is to recreate the visual input produced during encoding, or the motor and spatial elements of encoding. In this experiment, participants (N=40) encoded pairs of greyscale objects, overlaying colored squares. During test, participants were asked about objects’ orientation, while presented with squares of the same colors, either at the same location (controlled trials) or switched in their locations (test trials) relative to encoding. Results show that during test trials, participants tended to gaze at the square appearing at the location where the remembered object was previously presented, rather than on the square of the same color. This indicates a superiority of motor and spatial elements of eye movements rather than near-peripheral visual cues.
Validation of the association between MRI and gene signatures in facioscapulohumeral dystrophy muscle: implications for clinical trial design
Authors: Wong Chao-Jen , Friedman Seth D. , Snider Lauren , Bennett Sean R. , Jones Takako I. , Jones Peter L. , Shaw Dennis W.W. , Blemker Silvia S. , Riem Lara , DuCharme Olivia , Lemmers Richard J.F.L. , van der Maarel Silvère M. , Wang Leo H. , Tawil Rabi , Statland Jeffrey M. , Tapscott Stephen J.
Published: February 2023

Identifying the aberrant expression of DUX4 in skeletal muscle as the cause of facioscapulohumeral dystrophy (FSHD) has led to rational therapeutic development and clinical trials. Several studies support the use of MRI characteristics and the expression of DUX4-regulated genes in muscle biopsies as biomarkers of FSHD disease activity and progression, but reproducibility across studies needs further validation. We performed lower-extremity MRI and muscle biopsies in the mid-portion of the tibialis anterior (TA) muscles bilaterally in FSHD subjects and validated our prior reports of the strong association between MRI characteristics and expression of genes regulated by DUX4 and other gene categories associated with FSHD disease activity. We further show that measurements of normalized fat content in the entire TA muscle strongly predict molecular signatures in the mid-portion of the TA. Together with moderate-to-strong correlations of gene signatures and MRI characteristics between the TA muscles bilaterally, these results suggest a whole muscle model of disease progression and provide a strong basis for inclusion of MRI and molecular biomarkers in clinical trial design.
Interrogation and validation of the interactome of neuronal Munc18-interacting Mint proteins with AlphaFold2
Authors: Weeratunga Saroja , Gormal Rachel S. , Liu Meihan , Eldershaw Denaye , Livingstone Emma K. , Malapaka Anusha , Wallis Tristan P. , Bademosi Adekunle T. , Jiang Anmin , Healy Michael D. , Meunier Frederic A. , Collins Brett M.
Published: February 2023

Munc18-interacting proteins (Mints) are multi-domain adaptors that regulate neuronal membrane trafficking, signalling and neurotransmission. Mint1 and Mint2 are highly expressed in the brain with overlapping roles in the regulation of synaptic vesicle fusion required for neurotransmitter release by interacting with the essential synaptic protein Munc18-1. Here, we have used AlphaFold2 to identify and then validate the mechanisms that underpin both the specific interactions of neuronal Mint proteins with Munc18-1 as well as their wider interactome. We find a short acidic α-helical motif (AHM) within Mint1 and Mint2 is necessary and sufficient for specific binding to Munc18-1 and binds a conserved surface on Munc18-1 domain3b. In Munc18-1/2 double knockout neurosecretory cells mutation of the Mint-binding site reduces the ability of Munc18-1 to rescue exocytosis, and although Munc18-1 can interact with Mint and Sx1a proteins simultaneouslyin vitrowe find they have mutually reduced affinities, suggesting an allosteric coupling between the proteins. Using AlphaFold2 to then examine the entire cellular network of putative Mint interactors provides a structural model for their assembly with a variety of known and novel regulatory and cargo proteins including ARF3/ARF4 small GTPases, and the AP3 clathrin adaptor complex. Validation of Mint1 interaction with a new predicted binder TJAP1 provides experimental support that AlphaFold2 can correctly predict interactions across such large-scale datasets. Overall, our data provides insights into the diversity of interactions mediated by the Mint family and shows that Mints may help facilitate a key trigger point in SNARE complex assembly and vesicle fusion.
Transition to the structurally vulnerable nuclear state is an integral part of mouse embryonic development
Authors: Masahito Tanaka , Sakanoue Rin , Takasu Atsushi , Watanabe Naoko , Shimamoto Yuta , Miyamoto Kei
Published: February 2023

Upon fertilization, germ cells are reprogrammed to acquire the ability to develop into an entire organism. Whereas extensive studies have focused on epigenetic reprogramming of chromatin states during development, changes of the nucleus that surrounds chromatin are ill-defined. Here, we show that nuclei become structurally and mechanically vulnerable at the 2-cell stage during mouse embryonic development. The 2-cell stage nuclei are extraordinarily plastic and deformable in contrast to those of 1-cell and 4-cell stages. The mechanically vulnerable nuclear state is attained by autophagy-mediated loss of lamin B1 from the nuclear membrane. This developmentally programmed lamin B1 dynamics is required for chromatin organization and major zygotic genome activation. We thus demonstrate that structural reprogramming of nuclei is a major determinant of embryonic gene expression and acquisition of totipotency.
ALL-tRNAseq enables robust tRNA profiling in tissue samples
Authors: Scheepbouwer Chantal , Aparicio-Puerta Ernesto , Gomez-Martin Cristina , Verschueren Heleen , van Eijndhoven Monique , Wedekind Laurine E. , Giannoukakos Stavros , Hijmering Nathalie , Gasparotto Lisa , van der Galien Hilde T. , van Rijn Roos S. , Aronica Eleonora , Kibbelaar Robby , Heine Vivi M. , Wesseling Pieter , Noske David P. , Vandertop W. Peter , de Jong Daphne , Pegtel D. Michiel , Hackenberg Michael , Wurdinger Tom , Gerber Alan , Koppers-Lalic Danijela
Published: February 2023

Transfer RNAs (tRNAs) are small adaptor RNAs essential for mRNA translation. Alterations in the cellular tRNA population can directly affect mRNA decoding rates and translational efficiency during cancer development and progression. To evaluate changes in the composition of the tRNA pool, multiple sequencing approaches have been developed to overcome reverse transcription blocks caused by the stable structures of these molecules and their numerous base modifications. However, it remains unclear whether current sequencing protocols faithfully capture tRNAs existing in cells or tissues. This is specifically challenging for clinical tissue samples that often present variable RNA qualities. For this reason, we developed ALL-tRNAseq, which combines the highly processive MarathonRT and RNA demethylation for the robust assessment of tRNA expression, together with a randomized adapter ligation strategy prior to reverse transcription to assess tRNA fragmentation levels in both cell lines and tissues. Incorporation of tRNA fragments not only informed on sample integrity but also significantly improved tRNA profiling of tissue samples. Our data showed that our profiling strategy effectively improves classification of oncogenic signatures in glioblastoma and diffuse large B-cell lymphoma tissues, particularly for samples presenting higher levels of RNA fragmentation, further highlighting the utility of ALL-tRNAseq for translational research.
Synthesis, analysis of molecular and crystal structures, estimation of intermolecular interactions and biological properties of 1-benzyl-6-fluoro-3-[5-(4-methylcyclohexyl)-1,2,4-oxadiazol-3-yl]-7-(piperidin-1-yl)quinolin-4-one
Authors: Vaksler Yevhenii , Hryhoriv Halyna V. , Ivanov Vladimir V. , Kovalenko Sergiy M. , Georgiyants Victoriya A. , Langer Thierry
Published: February 2023

The title compound, C30H33N4O2F, can be obtained via a two-step synthetic scheme involving 1-benzyl-6-fluoro-4-oxo-7-(piperidin-1-yl)-1,4-dihydroquinoline-3-carbonitrile as a starting compound that undergoes substitution with hydroxylamine and subsequent cyclization with 4-methylcyclohexane-1-carboxylic acid. It crystallizes from 2-propanol in the triclinic space group P\overline{1} with a molecule of the title compound and one of 2-propanol in the asymmetric unit. After the molecular structure was clarified using NMR and LC/MS, the molecular and crystalline arrangements were defined with SC-XRD. A Hirshfeld surface analysis was performed for a better understanding of the intermolecular interactions. One strong (O—H...O) and three weak [C—H...F (intramolecular) and two C—H...O] hydrogen bonds were found. The contributions of short contacts to the Hirshfeld surface were estimated using two-dimensional fingerprint plots showing that O...H/H...O, C...H/H...C and C...C contacts are the most significant for the title compound and O...H for the 2-propanol. The crystal structure appears to have isotropically packed tetramers containing two molecules of the title compound and two molecules of 2-propanol as the building unit according to analysis of the distribution of pairwise interaction energies. A molecular docking study was carried out to evaluate the interactions of the title compound with the active centers of macromolecules corresponding to viral targets, namely, anti-hepatitis B activity [HBV, capsid Y132A mutant (VCID 8772) PDB ID: 5E0I] and anti-COVID-19 main protease activity (PDB ID: 6LU7). The data obtained revealed a noticeable affinity towards them that exceeded that of the reference ligands.
Crystal structures of di-μ-chlorido-bis({(E)-5-(ethylamino)-4-methyl-2-[(pyridin-2-yl)diazenyl]phenolato}copper(II)) and chloridobis(1,10-phenanthroline)copper(II) chloride tetrahydrate
Authors: Meier Alex , Mian Mohammad Rasel , Ou Siyu , Lovell Scott , Mure Minae
Published: February 2023

The dark-red title complex crystallized from an equimolar methanol solution of (E)-5-(ethylamino)-4-methyl-2-[(pyridin-2-yl)diazenyl]phenol and CuCl2(phen) (phen = 1,10-phenanthroline) as a centrosymmetric dimer, [CuCl(C14H15N4O)]2. The Cu atoms are bridged by two Cl ligands and have a slightly distorted square-pyramidal coordination, where two N atoms from the azo and the pyridine moieties, a phenolic O and a Cl atom comprise the base and the other Cl occupies the apex position. The apical Cu—Cl bond, 2.6192 (4) Å, is longer than the basal one, 2.2985 (3) Å, due to Jahn–Teller distortion. The dimers are associated via weak intermolecular hydrogen bonds and π–π stacking interactions between phenyl and pyridine rings. A monomeric by-product of the same reaction, [CuCl(phen)2]Cl·4H2O, has a trigonal–bipyramidal coordination of Cu with equatorial Cl ligand, and extensive outer-sphere disorder. In the structure of 4, the packing of cations leaves continuous channels containing disordered Cl− anions and solvent molecules. The identity of the solvent (water or a water/methanol mixture) was not certain. The disordered anion/solvent regions comprise 28% of the unit-cell volume. The disorder was approximated by five partly occupied positions of the Cl− anion and ten positions of O atoms with a total occupancy of 3, giving a total of 48 electrons per asymmetric unit, in agreement with the integral electron density of 47.8 electrons in the disordered region, as was estimated using the BYPASS-type solvent-masking program [van der Sluis & Spek (1990). Acta Cryst. A46, 194–201].
Halogen-bonded co-crystal containing 1,3-diiodoperchlorobenzene and the photoproduct rtct-tetrakis(pyridin-4-yl)cyclobutane resulting in a zigzag topology
Authors: Bosch Eric , Unruh Daniel K. , Santana Carlos L. , Groeneman Ryan H.
Published: February 2023

The formation and crystal structure of a zigzag network held together by I...N halogen bonds is reported. In particular, the halogen-bond donor is 1,3-diiodoperchlorobenzene (C6I2Cl4
) while the acceptor is the photoproduct rtct-tetrakis(pyridin-4-yl)cyclobutane (TPCB). Curiously, within the resulting co-crystal (C6I2Cl4
)·(TPCB), the photoproduct accepts only two halogen bonds between neighbouring 4-pyridyl rings and as a result behaves as a bent two-connected node rather than the expected four-connected centre. In addition, the photoproduct, TPCB, is also found to engage in C—H...N hydrogen bonds, forming an extended zigzag chain.
Crystal structure and Hirshfeld surface analysis of isopropyl 4-[2-fluoro-5-(trifluoromethyl)phenyl]-2,6,6-trimethyl-5-oxo-1,4,5,6,7,8-hexahydroquinoline-3-carboxylate
Authors: Yıldırım Sema Öztürk , Akkurt Mehmet , Çetin Gökalp , Şimşek Rahime , Butcher Ray J. , Bhattarai Ajaya
Published: February 2023

In the title compound, C23H25F4NO3, the 1,4-dihydropyridine ring adopts a distorted boat conformation, while the cyclohexene ring is almost showing a half-chair conformation. In the crystal, intermolecular N—H...O hydrogen bonds connect the molecules into chains with graph-set motif C(6) parallel to the a-axis. These chains are linked together by C—H...O and C—H...F interactions, forming a three-dimensional network. In addition, C—H...π interactions link the molecules into layers parallel to the (100) plane. A Hirshfeld surface analysis was performed to further investigate the intermolecular interactions.
20 years of crystal hits: progress and promise in ultrahigh-throughput crystallization screening
Authors: Lynch Miranda L. , Snell M. Elizabeth , Potter Stephen A. , Snell Edward H. , Bowman Sarah E. J.
Published: February 2023

Diffraction-based structural methods contribute a large fraction of the biomolecular structural models available, providing a critical understanding of macromolecular architecture. These methods require crystallization of the target molecule, which remains a primary bottleneck in crystal-based structure determination. The National High-Throughput Crystallization Center at Hauptman–Woodward Medical Research Institute has focused on overcoming obstacles to crystallization through a combination of robotics-enabled high-throughput screening and advanced imaging to increase the success of finding crystallization conditions. This paper will describe the lessons learned from over 20 years of operation of our high-throughput crystallization services. The current experimental pipelines, instrumentation, imaging capabilities and software for image viewing and crystal scoring are detailed. New developments in the field and opportunities for further improvements in biomolecular crystallization are reflected on.
Thioredoxin‐1 regulates the autophagy induced by oxidative stress through LC3‐II in human lens epithelial cells
Authors: Hu Jianghua , Liu Jinxia , Chen Silong , Zhang Chengshou , Shen Lifang , Yao Ke , Yu Yibo
Published: February 2023

Oxidative stress plays a major role in age‐related cataract development. The cellular antioxidant protein thioredoxin‐1 (Trx‐1) and its negative regulator, thioredoxin binding protein‐2 (TBP‐2), are pivotal in the cellular redox balance during oxidative stress. The aim of this study is to investigate the effect of Trx‐1 and TBP‐2 on LC3 I/LC3 II in oxidative stress‐induced autophagy in human lens epithelial cells (LECs). In our study, LECs were treated with 50 μM H2O2 for different durations, and the expression of Trx‐1 and TBP‐2 were measured by RT‐PCR and Western blot. Trx‐1 activity was evaluated by the thioredoxin activity fluorescent assay. The subcellular localization of Trx‐1 and TBP‐2 was evaluated by cellular immunofluorescence. The interaction between Trx‐1 and TBP‐2 was examined by co‐immunoprecipitation. The cell viability was detected using CCK‐8, and the expression of LC3‐II/LC3‐I was detected to evaluate the autophagy. The results showed that the mRNA levels of the Trx‐1 and TBP‐2 were kinetically changed after treatment with H2O2 for different durations. Exposure to H2O2 increased the expression of TBP‐2 but not Trx‐1, while the exposure inhibited Trx‐1 activity. TBP‐2 was co‐localized with Trx‐1, and exposure to H2O2 increased the interaction between TBP‐2 and Trx‐1. Trx‐1 overexpression enhanced the autophagic response under normal circumstances and it might regulate autophagy in the initial phase. This study demonstrates the differential role of Trx‐1 in cellular oxidative stress response, oxidative stress increased Trx‐1 interaction with TBP‐2, and Trx‐1/TBP‐2 regulated the autophagic response in the initial phase through LC3‐II.
The Knightly Brothers of Bernard of Clairvaux and the Twelfth‐Century Cistercian Lay Monk*
Authors: Millan‐Cole Joseph
Published: February 2023

Abbot Bernard of Clairvaux (r. 1115–1153) was a prominent twelfth‐century religious leader whose knightly family collectively converted to monastic life with him in adulthood around 1113. Following Clairvaux's foundation in 1115, Bernard's brothers held roles of significant estate seniority despite their own professional limitations as newly converted and apparently illiterate knights. This study discusses their professional backgrounds and contexts as “lay monks” or monachi laici, converts who possessed no prior church grade or formally recognised Latin competence. The careers of Bernard's brothers and other Benedictines across the eleventh to early thirteenth centuries illuminate a number of the ways in which secular converts could contribute to their abbeys as culturally mixed and prosperous religious estate communities.
Demystifying the ‘gold standard’ of arms export controls: US arms exports to conflict zones
Authors: Erickson Jennifer L.
Published: February 2023

This article examines why US‐made and US‐supplied weapons consistently appear in conflicts around the world, despite the United States having what is commonly lauded as the ‘gold standard’ of national arms export control systems. On paper, US law and policy discourage arms transfers to areas engaged in or at risk of conflict. US arms export controls also informed the creation of the UN Arms Trade Treaty (ATT), which provides legally binding conventional arms export criteria. Yet in the recent Yemen, Syria and Libya conflicts, among many others, the United States has directly supplied or indirectly facilitated the supply of weapons to conflict parties. This article highlights two factors that help to account for this apparent policy failure: the flexible design of US law and policy and the inherent challenges of ensuring that weapons in conflict zones—especially small arms—go to and stay with their intended recipients. These findings have important implications for US foreign policy, ATT implementation and the human costs of conflict around the world.
Delivery of miR‐3529‐3p using MnO2‐SiO2‐APTES nanoparticles combined with phototherapy suppresses lung adenocarcinoma progression by targeting HIGD1A
Authors: Zhang Ying , Wang Ran‐Ran , Liu Rui , Xie Shu‐Yang , Jiao Fei , Li You‐Jie , Xin Jiaxuan , Zhang Han , Wang Zhenbo , Yan Yun‐Fei
Published: February 2023

Background

The present study aimed to investigate the function of miR‐3529‐3p in lung adenocarcinoma and MnO2‐SiO2‐APTES (MSA) as a promising multifunctional delivery agent for lung adenocarcinoma therapy.

Methods

Expression levels of miR‐3529‐3p were evaluated in lung carcinoma cells and tissues by qRT‐PCR. The effects of miR‐3529‐3p on apoptosis, proliferation, metastasis and neovascularization were assessed by CCK‐8, FACS, transwell and wound healing assays, tube formation and xenografts experiments. Luciferase reporter assays, western blot, qRT‐PCR and mitochondrial complex assay were used to determine the targeting relationship between miR‐3529‐3p and hypoxia‐inducible gene domain family member 1A (HIGD1A). MSA was fabricated using MnO2 nanoflowers, and its heating curves, temperature curves, IC50, and delivery efficiency were examined. The hypoxia and reactive oxygen species (ROS) production was investigated by nitro reductase probing, DCFH‐DA staining and FACS.

Results

MiR‐3529‐3p expression was reduced in lung carcinoma tissues and cells. Transfection of miR‐3529‐3p could promote apoptosis and suppress cell proliferation, migration and angiogenesis. As a target of miR‐3529‐3p, HIGD1A expression was downregulated, through which miR‐3529‐3p could disrupt the activities of complexes III and IV of the respiratory chain. The multifunctional nanoparticle MSA could not only efficiently deliver miR‐3529‐3p into cells, but also enhance the antitumor function of miR‐3529‐3p. The underlying mechanism may be that MSA alleviates hypoxia and has synergistic effects in cellular ROS promotion with miR‐3529‐3p.

Conclusions

Our results establish the antioncogenic role of miR‐3529‐3p, and demonstrate that miR‐3529‐3p delivered by MSA has enhanced tumor suppressive effects, probably through elevating ROS production and thermogenesis.
Functional and structural brain abnormalities in substance use disorder: A multimodal meta‐analysis of neuroimaging studies
Authors: Yan Hong , Xiao Shu , Fu Siying , Gong Jiaying , Qi Zhangzhang , Chen Guanmao , Chen Pan , Tang Guixian , Su Ting , Yang Zibin , Wang Ying
Published: February 2023

Introduction

Numerous neuroimaging studies of resting‐state functional imaging and voxel‐based morphometry (VBM) have revealed that patients with substance use disorder (SUD) may present brain abnormalities, but their results were inconsistent. This multimodal neuroimaging meta‐analysis aimed to estimate common and specific alterations in SUD patients by combining information from all available studies of spontaneous functional activity and gray matter volume (GMV).

Methods

A whole‐brain meta‐analysis on resting‐state functional imaging and VBM studies was conducted using the Seed‐based d Mapping with Permutation of Subject Images (SDM‐PSI) software, followed by multimodal overlapping to comprehensively investigate function and structure of the brain in SUD.

Results

In this meta‐analysis, 39 independent studies with 47 datasets related to resting‐state functional brain activity (1444 SUD patients; 1446 healthy controls [HCs]) were included, as well as 77 studies with 89 datasets for GMV (3457 SUD patients; 3774 HCs). Patients with SUD showed the decreased resting‐state functional brain activity in the bilateral anterior cingulate cortex/medial prefrontal cortex (ACC/mPFC). For the VBM meta‐analysis, patients with SUD showed the reduced GMV in the bilateral ACC/mPFC, insula, thalamus extending to striatum, and left sensorimotor cortex.

Conclusions

This multimodal meta‐analysis exhibited that SUD shows common impairment in both function and structure in the ACC/mPFC, suggesting that the deficits in functional and structural domains could be correlated together. In addition, a few regions exhibited only structural impairment in SUD, including the insula, thalamus, striatum, and sensorimotor areas.