bluuebunny/crossref_metadata_2025 huggingface dataset:
csppinet: A Python package for context-specific biological network construction and analysis based on omics data
Authors: de Carvalho L.M.
Published: May 2023

The analysis of large-scale biological data, particularly omics data, has become essential for understanding complex biological systems. In this study, we present a Python package for the construction of context-specific biological networks based on gene expression activity and protein-protein interaction (PPI) data. The package leverages computational tools and the NetworkX library for network analysis. Through a case study focusing on yeast fermentation with glucose and xylose as carbon sources, we demonstrate the package’s capabilities. The context-specific networks derived from these fermentation conditions were compared to highlight the impact of different carbon sources and stages on network dynamics. Hub genes were identified within each network, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to understand their functional implications. The results revealed distinct hub genes and enriched biological processes in each context-specific network. In the glucose-specific network, the exclusively proteins in this network revealed enrichment in terms related tochromosome organization, biological regulation, MAPK signaling pathwayandmismatch repair pathway. Conversely, the exclusively proteins in xylose-specific network revealed enrichment ingeneration of precursor metabolites and energy), mitochondrion organization, response to extracellular stimulus, glutamate metabolic process, cellular response to alcohol, beta-Alanine metabolism, arginine and proline metabolism, glyoxylate and dicarboxylate metabolismandpyruvate metabolism. The developed Python package and context-specific networks provide researchers with a valuable framework to explore complex biological phenomena. By integrating gene expression profiles and PPI data, researchers can gain insights into context-dependent molecular interactions and regulatory mechanisms. These findings contribute to the understanding of cellular behavior and have potential implications in disease mechanisms, biomarker identification, and drug target discovery. The csppinet package is available athttps://github.com/lmigueel/csppinet.
Assessing Fairness of AlphaFold2 Prediction of Protein 3D Structures
Authors: Abbas Usman , Chen Jin , Shao Qing
Published: May 2023

AlphaFold2 is reshaping biomedical research by enabling the prediction of a protein’s 3D structure solely based on its amino acid sequence. This breakthrough reduces reliance on labor-intensive experimental methods traditionally used to obtain protein structures, thereby accelerating the pace of scientific discovery. Despite the bright future, it remains unclear whether AlphaFold2 can uniformly predict the wide spectrum of proteins equally well. Systematic investigation into the fairness and unbiased nature of its predictions is still an area yet to be thoroughly explored. In this paper, we conducted an in-depth analysis of AlphaFold2’s fairness using data comprised of five million reported protein structures from its open-access repository. Specifically, we assessed the variability in the distribution of PLDDT scores, considering factors such as amino acid type, secondary structure, and sequence length. Our findings reveal a systematic discrepancy in AlphaFold2’s predictive reliability, varying across different types of amino acids and secondary structures. Furthermore, we observed that the size of the protein exerts a notable impact on the credibility of the 3D structural prediction. AlphaFold2 demonstrates enhanced prediction power for proteins of medium size compared to those that are either smaller or larger. These systematic biases could potentially stem from inherent biases present in its training data and model architecture. These factors need to be taken into account when expanding the applicability of AlphaFold2.
Proteomic characterization of aging-driven changes in the mouse brain by co-expression network analysis
Authors: Tsumagari Kazuya , Sato Yoshiaki , Aoyagi Hirofumi , Okano Hideyuki , Kuromitsu Junro
Published: May 2023

Brain aging causes a progressive decline in functional capacity and is a strong risk factor for dementias such as Alzheimer’s disease. To characterize age-related proteomic changes in the brain, we used quantitative proteomics to examine brain tissues, cortex and hippocampus, of mice at three age points (3, 15, and 24 months old), and quantified more than 7,000 proteins in total with high reproducibility. We found that many of the proteins upregulated with age were extracellular proteins, such as extracellular matrix proteins and secreted proteins, associated with glial cells. On the other hand, many of the significantly downregulated proteins were associated with synapses, particularly postsynaptic density, specifically in the cortex but not in the hippocampus. Our datasets will be helpful as resources for understanding the molecular basis of brain aging.
Inactive PARP1 causes embryonic lethality and genome instability in a dominant-negative manner
Authors: Shao Zhengping , Lee Brian J. , Zhang Hanwen , Lin Xiaohui , Li Chen , Jiang Wenxia , Chirathivat Napon , Gershik Steven , Shen Michael M. , Baer Richard , Zha Shan
Published: May 2023

PARP1 is recruited and activated by DNA strand breaks, catalyzing the generation of poly-ADP-ribose (PAR) chains from NAD+. PAR relaxes chromatin and recruits other DNA repair factors, including XRCC1 and DNA Ligase 3, to maintain genomic stability. Here we show that, in contrast to the normal development of Parp1-null mice, heterozygous expression of catalytically inactive Parp1 (E988A,Parp1+/A) acts in a dominant-negative manner to disrupt murine embryogenesis. As such, all the surviving F1Parp1+/Amice are chimeras with mixedParp1+/AN(neoR retention) cells that act similarly toParp1+/-. Pure F2Parp1+/Aembryos were found at Mendelian ratios at the E3.5 blastocyst stage but died before E9.5. Compared toParp1-/-cells, genotype and expression-validated pureParp1+/Acells retain significant ADP-ribosylation and PARylation activities but accumulate markedly higher levels of sister chromatin exchange and mitotic bridges. Despite proficiency for homologous recombination and non-homologous end-joining measured by reporter assays and supported by normal lymphocyte and germ cell development,Parp1+/Acells are hypersensitive to base damages, radiation, and Topoisomerase I and II inhibition. The sensitivity ofParp1+/Acells to base damages and Topo inhibitors in particular exceedParp1-/-controls. The findings show that the enzymatically inactive PARP1 protein has a dominant negative role and establishes a clear physiological difference between PARP1 inactivation vs. deletion. As a result, the enzymatically inactive PARP1 has a much more deteriorating impact on normal tissues than previously estimated, providing a mechanism for the on-target side effect of PARP inhibitors used for cancer therapy.

Significance Statement

PARP1 is the primary target of PARP enzymatic inhibitors. The use of PARP inhibitors for cancer therapy is based not only on the extreme sensitivity of BRCA1/2-deficient cancer cells to PARP1 inhibition but also on the nonessential role of PARP1 in normal tissues. Here we show that in contrast to the normal development of Parp1-null mice, the mouse model expressing the catalytically inactive Parp1 on only one allele (E988A,Parp1+/A) dies embryonically with high levels of genomic instability. The results reveal the severe dominant-negative impact of catalytically inactive PARP1, indicating the presence of enzymatically inactive PARP1 is much more damaging to normal tissues than previously anticipated. These findings provide a mechanism for clinical PARP inhibitors’ unexpected normal tissue toxicity.
Study protocol for a systems evaluation of an infant mental health service: integration of ‘Little Minds Matter’ into the early years system
Authors: Masefield Sarah , Ellwood Alison , Blower Sarah , Dickerson Josie , Moss Rachael H. , Ahern Sara
Published: May 2023

Infant Mental Health relates to how well a child develops socially and emotionally from birth to age three. There is a well-established link between parent-infant relationship quality, Infant Mental Health, and longer-term social and emotional development, however, there is a lack of evidence-based interventions that support the parent-infant relationship and/or protect against poor Infant Mental Health. Little Minds Matter is a specialist Infant Mental Health service developed in Bradford (UK) to support parent-infant relationships by providing training and consultation for professionals and direct clinical work to families. The efficacy of this intervention will depend upon how well it becomes embedded within the early years system. This study aims to apply a systems approach to evaluate this service and provide a perspective on the challenges to embedding a complex service within a healthcare system. Multiple methods will be used to investigate embeddedness within the wider early years system. Routine collected quantitative data about the service will be used to develop a system map showing interaction with related services. Qualitative data will be collected through interviews with individuals involved in the design and provision of the Little Minds Matter service, and professionals working within the early years system. Framework analysis will be used to analyse the data inductively and deductively within a systems approach. The findings from this study will provide evidence for the ongoing implementation of the Little Minds Matter Service for providers and commissioning bodies. Exploring this methodological approach to evaluation will have application more broadly for researchers evaluating complex interventions and services within a wider system.
Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores
Authors: Datler Julia , Hansen Jesse M , Thader Andreas , Schlögl Alois , Hodirnau Victor-Valentin , Schur Florian KM
Published: May 2023

Poxviruses are among the largest double-stranded DNA viruses with members such as Variola virus, Monkeypox virus and the famous vaccination strain Vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core, found in all infectious poxvirus forms, has remained sparse. While major core proteins have been annotatedviaindirect experimental evidence, their structures have remained elusive and they could not be assigned to the individual architectural features of the core. Hence, which proteins constitute which layers of the core, such as the so-called palisade layer and the inner core wall has remained enigmatic.

Here, we have performed a multi-modal cryo-electron microscopy (cryo-EM) approach to elucidate the structural determinants of the VACV core. In combination with molecular modeling using AlphaFold, we unambiguously identify trimers formed by the cleavage product of A10 as the key component of the palisade layer. This allows us to place previously-obtained descriptions of protein interactions within the core wall into perspective and to provide a substantially revised model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely identical amongPoxviridae, implying that our structural observations should be generalizable over most, if not all members of this important virus family.

One sentence summary

Single-particle cryo-EM, cryo-electron tomography, and AlphaFold modeling reveal the structural architecture of the poxvirus core and identify trimers of protein A10 as the key component of the palisade layer.
Neuromuscular fatigue reduces responsiveness when controlling leg external forces
Authors: Kudzia Pawel , Wakeling James M. , Robinovitch Stephen N. , Donelan J. Maxwell
Published: May 2023

In legged movement, our legs push against the ground, generating external force vectors that enable agile movements. Neuromuscular fatigue can reduce agility by causing physiological changes, such as slowing muscle reaction time, altering proprioception, and delaying neuromuscular control. Fatigue may deteriorate the nervous system’s control of leg external forces, contributing to reductions in agility. In this study, we investigated the effect of fatigue on the performance of the nervous system in controlling the vertical component of leg external force ground reaction forces. We hypothesized that increased leg fatigue would lead to declines in both the responsiveness (speed) and accuracy of leg force control. To test this hypothesis, we used an apparatus that allowed participants to exert controlled vertical forces with one leg against a force plate while immobilizing the rest of their bodies. Participants adjusted their leg external force to match step targets displayed on a screen. We induced fatigue by having participants maintain submaximal leg forces, and we measured leg force control performance between fatigue trials. Results showed a significant 26% reduction in mean maximum force production, leading to a substantial decline in leg force control responsiveness, as evidenced by a 23% increase in rise time and a 25% narrowing of bandwidth. However, fatigue did not significantly reduce leg force control accuracy. Understanding the effects of fatigue on leg force control can inform the development of strategies and technologies to sustain agile performance, even in the presence of fatigue.

New and Noteworthy

We developed a method to probe the influence of neuromuscular fatigue on the control of leg external forces. Our findings demonstrate that while fatigue significantly diminishes responsiveness (speed), it does not compromise the accuracy of control. These insights enhance our understanding of legged agility and could guide the development of strategies for optimizing leg force control performance. This study paves the way for future research aimed at identifying and employing effective strategies to maintain agility in the face of fatigue.
Genome wide characterization and expression analysis of CrRLK1L gene family in wheat unravels their roles in development and stress-specific responses
Authors: Gawande Nilesh D. , Sankaranarayanan Subramanian
Published: May 2023

Catharanthus roseusreceptor-like kinase 1-like (CrRLK1L) genes encode a subfamily of receptor-like kinases (RLK) that regulate diverse processes during plant growth, development and stress responses. This study aims to provide a comprehensive genome-wide functional characterization of CrRLK1L family in bread wheat (Triticum aestivum). The genome ofT. aestivumencodes 15CrRLK1Lfamily genes that has 43 paralogous copies with three homeologs each, except for-2-Dand-7-A, which were found to be absent. In addition, a frame shift deletion was identified in the Paralog-2-B. Chromosomal localization analysis revealed a markedly uneven distribution ofTa-CrRLK1Lgenes across seven different chromosomes, with chromosome 4 housing the highest number of genes while chromosome 6 lacked any CrRLK1L genes. Tissue-specific gene expression analysis revealed distinct expression patterns among the members of the gene family, with certain members exhibiting heightened expression in reproductive tissues. Gene expression analysis under various abiotic and biotic stress conditions unveiled differential regulation of different gene family members. An examination of cis-acting elements in the promoter regions, identified specific elements crucial for plant growth and developmental processes. This comprehensive genome wide analysis and expression study provide valuable insights into the essential functions of CrRLK1L members in wheat.
THE STRIATAL HETERODIMERS A2AR-D2Rs ARE LINKED TO ERGOGENIC EFFECTS OF CAFFEINE
Authors: Alves Ana Cristina de Bem , Santos Naiara de Souza , Tavares Ana Paula , Panatta Gabriela , Aguiar Aderbal S
Published: May 2023

Adenosine 2A receptors (A2ARs) are abundant in the striatum, and they are found co-localized with dopamine D2 receptors (D2R) and in the heterodimer form A2AR-D2R. Previous we demonstrated that caffeine delays central fatigue through adenosine 2A receptors (A2ARs) antagonism, striatal neuroplasticity and mitochondrial metabolism enhancement. In this study we demonstrate the participation of striatal A2AR-D2R in the ergogenic outcomes. Two-hundred swiss adult mice were treated systemically (i.p.) and centrally (striatum-st.) with caffeine, SCH58261 (A2AR antagonist), DPCPX (A1R antagonist) and haloperidol (D2R antagonist), and performed the open field test, treadmill incremental exercise and grip strength meter test We observed that A2AR-D2R antagonic effects are linked to motor control (p< 0.05) and enhancement of power (p< 0.05). However, the role of A2AR-D2R in the mechanism of strength generation seems to differ from motor control.
Mutation Patterns Predict Drug Sensitivity in Acute Myeloid Leukemia
Authors: Qin Guangrong , Dai Jin , Chien Sylvia , Martins Timothy J. , Loera Brenda , Nguyen Quy , Oakes Melanie L. , Tercan Bahar , Aguilar Boris , Hagen Lauren , McCune Jeannine , Gelinas Richard , Monnat Raymond J. , Shmulevich Ilya , Becker Pamela S.
Published: May 2023

Acute myeloid leukemia (AML) is an aggressive malignancy of myeloid progenitor cells characterized by successive acquisition of genetic alterations. This inherent heterogeneity poses challenges in the development of precise and effective therapies. To gain insights into the genetic influence on drug response and optimize treatment selection, we performed targeted sequencing,ex vivodrug screening, and single-cell genomic profiling on leukemia cell samples derived from AML patients. We detected genetic signatures associated with sensitivity or resistance to specific agents. By integrating large public datasets, we discovered statistical patterns of co-occurring and mutually exclusive mutations in AML. The application of single-cell genomic sequencing unveiled the co-occurrence of variants at the individual cell level, highlighting the presence of distinct sub- clones within AML patients. Machine learning models were built to predictex vivodrug sensitivity using the genetic variants. Notably, these models demonstrated high accuracy in predicting sensitivity to some drugs, such as MEK inhibitors. Our study provides valuable resources for characterizing AML patients and predicting drug sensitivity, emphasizing the significance of considering subclonal distribution in drug response prediction. These findings provide a foundation for advancing precision medicine in AML. By tailoring treatment based on individual genetic profiles and functional testing, as well as accounting for the presence of subclones, we envision a future of improved therapeutic strategies for AML patients.

One Sentence Summary:

Integrative computational and experimental analysis of mutation patterns and drug responses provide biologic insight and therapeutic guidance for patients with adult AML.
PKCδ regulates chromatin remodeling and DNA repair through SIRT6
Authors: Affandi Trisiani , Haas Ami , Ohm Angela M. , Wright Gregory M. , Black Joshua C. , Reyland Mary E.
Published: May 2023

Protein kinase C delta (PKCδ) is a ubiquitous kinase whose function is defined in part by localization to specific cellular compartments. Nuclear PKCδ is both necessary and sufficient for IR-induced apoptosis, while inhibition of PKCδ activity provides radioprotectionin vivo.How nuclear PKCδ regulates DNA-damage induced cell death is poorly understood. Here we show that PKCδ regulates histone modification, chromatin accessibility, and double stranded break (DSB) repair through a mechanism that requires SIRT6. Overexpression of PKCδ promotes genomic instability and increases DNA damage and apoptosis. Conversely, depletion of PKCδ increases DNA repair via non-homologous end joining (NHEJ) and homologous recombination (HR) as evidenced by more rapid formation of NHEJ (DNA-PK) and HR (Rad51) DNA damage foci, increased expression of repair proteins, and increased repair of NHEJ and HR fluorescent reporter constructs. Nuclease sensitivity indicates that PKCδ depletion is associated with more open chromatin, while overexpression of PKCδ reduces chromatin accessibility. Epiproteome analysis revealed that PKCδ depletion increases chromatin associated H3K36me2, and reduces ribosylation of KDM2A and chromatin bound KDM2A. We identify SIRT6 as a downstream mediator of PKCδ. PKCδ-depleted cells have increased expression of SIRT6, and depletion of SIRT6 reverses the changes in chromatin accessibility, histone modification and NHEJ and HR DNA repair seen with PKCδ-depletion. Furthermore, depletion of SIRT6 reverses radioprotection in PKCδ-depleted cells. Our studies describe a novel pathway whereby PKCδ orchestrates SIRT6- dependent changes in chromatin accessibility to increase DNA repair, and define a mechanism for regulation of radiation-induced apoptosis by PKCδ.

One Sentence Summary

Protein kinase C delta modifies chromatin structure via SIRT6 to regulate DNA repair.
THE PALISADE LAYER OF THE POXVIRUS CORE IS COMPOSED OF FLEXIBLE A10-TRIMERS
Authors: Liu Jiasui , Corroyer-Dulmont Simon , Pražák Vojtěch , Khusainov Iskander , Bahrami Karola , Welsch Sonja , Vasishtan Daven , Obarska-Kosińska Agnieszka , Thorkelsson Sigurdur R. , Grunewald Kay , Quemin Emmanuelle R. J. , Turoňová Beata , Locker Jacomina Krijnse
Published: May 2023

Although vaccinia virus (VACV) is the best studied poxvirus, the structure of the mature virus (MV) remains poorly understood. Its asymmetric shape, size and compactness poses a major challenge for electron microscopy (EM) analysis, including cryoEM. Sub-viral particles, in particular membrane-free viral cores, may overcome these limitations. We compare cores obtained by detergent-stripping MVs with cores in the cellular cytoplasm, early in infection. By combining cryo-electron tomography (cryoET), subtomogram averaging (STA) and AlphaFold2 (AF2), abundant core-structures are analyzed, focusing on the prominent palisade layer on the core surface. On detergent-stripped cores, the palisade is composed of densely packed trimers of the major core protein A10. On the core surface they display a random order and their classification indicate structural flexibility. On cytoplasmic cores A10 is organized in a similar manner, indicating that the structures obtainedin vitroare physiologically relevant. CryoET and STA also uncover unexpected details of the layers beneath the palisade both onin vitroandin situcores, that are compared to AF2 structure predictions of known VACV core-associated proteins. Altogether, our data identify for the first time the structure and molecular composition of the palisade units. The results are discussed in the context of the VACV replicative cycle, the assembly and disassembly of the infectious MV.
scGHOST: Identifying single-cell 3D genome subcompartments
Authors: Xiong Kyle , Zhang Ruochi , Ma Jian
Published: May 2023

New single-cell Hi-C (scHi-C) technologies enable probing of the genome-wide cell-to-cell variability in 3D genome organization from individual cells. Several computational methods have been developed to reveal single-cell 3D genome features based on scHi-C data, including A/B compartments, topologically-associating domains, and chromatin loops. However, no scHi-C analysis method currently exists for annotating single-cell subcompartments, which are crucial for providing a more refined view of large-scale chromosome spatial localization in single cells. Here, we present SCGHOST, a single-cell subcompartment annotation method based on graph embedding with constrained random walk sampling. Applications of SCGHOST to scHi-C data and single-cell 3D genome imaging data demonstrate the reliable identification of single-cell subcompartments and offer new insights into cell-to-cell variability of nuclear subcompartments. Using scHi-C data from the human prefrontal cortex, SCGHOST identifies cell type-specific subcompartments that are strongly connected to cell type-specific gene expression, suggesting the functional implications of single-cell subcompartments. Overall, SCGHOST is an effective new method for single-cell 3D genome subcompartment annotation based on scHi-C data for a broad range of biological contexts.
Influence of visual information on sniffing behavior in a routinely trichromatic primate
Authors: Weiß Brigitte M. , Widdig Anja
Published: May 2023

Most catarrhine primates are considered to be strongly visually oriented, obtaining information about conspecifics and their environment from a diversity of visual cues. Other sensory modalities may provide information that is redundant and/or complimentary to visual cues. When cues from multiple sensory modalities are available, these may reinforce or suppress each other, as shown in several taxa ranging from insects to humans. Here, we tested how the presence and ambiguity of visual information affects the use of olfactory cues when exploring food and non-food items in semi-free ranging Barbary macaques at Affenberg Salem, Germany. We presented monkeys with pipes containing food (peanuts, popcorn), non-food (stones, feces) or no items in transparent or opaque containers, and assessed whether animals looked, sniffed and/or grabbed into the pipes depending on visibility of the contents (experiment 1). Visual information had no robust effect on sniffing probability, but it did affect sniffing behavior with respect to the timing of olfactory inspections (i.e. whether sniffing occurred first). Both visual and olfactory information affected, whether or not monkeys attempted to retrieve the items from the pipes. Furthermore, we manipulated the visual appearance of familiar food items (popcorn) with food colorant (experiment 2), which resulted in substantially increased olfactory inspections compared to unmanipulated popcorn. Taken together, reliance on the olfactory sense was modulated by the available visual information, emphasizing the interplay between different sensory modalities for obtaining information about the environment.
PEP444c encoded within theMIR444cgene regulates microRNA444c accumulation in barley
Authors: Chojnacka A , Smoczynska A , Bielewicz D , Pacak A , Hensel G , Kumlehn J , Karlowski WM , Grabsztunowicz M , Sobieszczuk-Nowicka E , Jarmolowski A , Szweykowska-Kulinska Z
Published: May 2023

MicroRNAs are small, non-coding RNA molecules that regulate expression of their target genes. TheMIR444gene family is present exclusively in monocotyledons, and microRNAs444 from this family have been shown to target certain MADS-box transcription factors in rice and barley. We identified three barleyMIR444(MIR444a/b/c) genes and comprehensively characterized their structure and the processing pattern of the primary transcripts (pri-miRNAs444). Pri-microRNAs444 undergo extensive alternative splicing, by which functional and non-functional pri-miRNA444 isoforms are generated. We show that barley pri-miRNAs444 contain numerous open reading frames (ORFs) whose transcripts associate with ribosomes. Using specific antibodies, we provide evidence that selected ORFs encoding PEP444a withinMIR444aand PEP444c withinMIR444care expressed in barley plants. Moreover, we demonstrate that CRISPR-associated endonuclease 9 (Cas9)-mediated mutagenesis of the PEP444c encoding sequence results in a decreased level ofPEP444transcript in barley shoots and roots, and a 5-fold reduced level of mature microRNA444c in roots. Taken together, our observations suggest that PEP444c encoded by theMIR444cgene is involved in microRNA444c biogenesis in barley.
Understanding the molecular basis for enhanced glutenase activity of actinidin
Authors: Puja Shivangi , Seth Shreya , Hora Rachna , Kaur Satinder , Mishra Prakash Chandra
Published: May 2023

Management of gluten intolerance is currently possible only by consumption of gluten free diet(GFD) for a lifetime. The scientific community has been searching for alternatives to GFD, like inclusion of natural proteases with meals or pre-treatment of gluten containing foods with glutenases. Actinidin from kiwifruit has shown considerable promise in digesting immunogenic gliadin peptides as compared to other plant derived cysteine proteases. Through this article, we have attempted to understand the structural basis for elevated protease action of actinidin against gliadin peptides by using anin silicoapproach. Docking experiments reveal key differences between the binding of gliadin peptide to actinidin and papain, which may be responsible for their differential digestive action. Sequence comparison of different plant cysteine proteases highlights amino acid residues surrounding the active site pocket of actinidin that are unique to this molecule and hence likely to contribute to its digestive properties.

Graphical summary
Computational insights on the destabilizing mutations in the binding site of 3CL-protease SARS-CoV-2 Omicron (VOC)
Authors: Ullah Samee , Amir Afreenish , Ikram Aamer , Vicidomini Caterina , Palumbo Rosanna , Roviello Giovanni N.
Published: May 2023

The COVID-19 (Corona Virus Disease 19) pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is causing enormous difficulties in the world’s economies and there is uncertainty as to whether the current prophylactic measures will offer adequate protection globally after the appearance of virus variants that like that indicated as Omicron emerged in the presence of global vaccine-based immunization. While several studies are available describing the main differences in the spike protein of Omicron compared to the other variants previously emerged, there was no structural insights into the 3CL-protease (3CLpro) associated to the new variant. Herein, we performed a computational study based on genomic data and amino acid sequences available in the most updated COVID-19-related databases that allowed us to build upin silicothe 3D structure of Omicron 3CLpro. Moreover, by molecular dynamics simulation we demonstrated that currently available drugs acting as inhibitors of the SARS-CoV-2 main protease could be less effective in the case of Omicron variant due to the different chemical interactions in the binding site occurred after the recent amino acid mutations. Ultimately, our study highlights the need of exploitingin silicoand in vitro methods to discover novel 3CLproinhibitors starting from the computationally based structure we presented herein, and more in general to direct the major efforts to targeting the most conserved 3CLproregions that appeared unchanged in the context of the Omicron variant.
Water will find its way: transport through narrow tunnels in hydrolases
Authors: Sequeiros-Borja Carlos , Thirunavukarasu Aravind Selvaram , Dongmo Foumthuim Cedrix J. , Brezovsky Jan
Published: May 2023

An aqueous environment is vital for life as we know it, and water is essential for nearly all biochemical processes at a molecular level. Proteins utilize water molecules in various ways. Consequently, proteins must transport water molecules across their internal network of tunnels to reach the desired action sites, either within them or functioning as molecular pipes to control cellular osmotic pressure. Despite water playing a crucial role in enzymatic activity and stability, its transport has been largely overlooked, with studies primarily focusing on water transport across membrane proteins. The transport of molecules through a protein’s tunnel network is challenging to study experimentally, making molecular dynamics simulations the most popular approach for investigating such events. In this study, we focused on the transport of water molecules across three different α/β-hydrolases: haloalkane dehalogenase, epoxide hydrolase, and lipase. Using a 5 μs adaptive simulation per system, we observed that only a few tunnels were responsible for the majority of water transport in dehalogenase, in contrast to a higher diversity of tunnels in other enzymes. Interestingly, water molecules could traverse narrow tunnels with sub-angstrom bottlenecks, which is surprising given the commonly accepted water molecule radius of 1.4 Å. Our analysis of the transport events in such narrow tunnels revealed a markedly increased number of hydrogen bonds formed between the water molecules and the protein, likely compensating for the steric penalty of the process. Overall, these commonly disregarded narrow tunnels accounted for ∼20% of the total water transport observed, emphasizing the need to surpass the standard geometrical limits on the functional tunnels to properly account for relevant transport processes. Finally, we demonstrated how the obtained insights could be applied to explain the differences in a mutant of the human soluble epoxide hydrolase associated with a higher incidence of ischemic stroke.
Sex-biased regulatory changes in the placenta of native highlanders contribute to adaptive fetal development
Authors: Yue Tian , Guo Yongbo , Qi Xuebin , Zheng Wangshan , Zhang Hui , Wang Bin , Liu Kai , Zhou Bin , Zeng Xuerui , Ouzhuluobu  , He Yaoxi , Su Bing
Published: May 2023

Compared with lowlander migrants, native Tibetans have a higher reproductive success at high altitude though the underlying mechanism remains unclear. Here, we compared the transcriptome and histology of full-term placentas between native Tibetans and Han migrants. We found that the placental trophoblast shows the largest expression divergence between Tibetans and Han, and Tibetans show decreased immune response and endoplasmic reticulum stress. Remarkably, we detected a sex-biased expression divergence, where the male-infant placentas show a greater between-population difference than the female-infant placentas. The umbilical cord plays a key role in the sex-biased expression divergence, which is associated with the higher birth weight of the male newborns of Tibetans. We also identified adaptive histological changes in the male-infant placentas of Tibetans, including larger umbilical artery wall and umbilical artery intima and media, and fewer syncytial knots. These findings provide valuable insights into the sex-biased adaptation of human populations, with significant implications for medical and genetic studies of human reproduction.
Harmonization of CSF and imaging biomarkers for Alzheimer’s disease biomarkers: need and practical applications for genetics studies and preclinical classification
Authors: Timsina Jigyasha , Ali Muhammad , Do Anh , Wang Lihua , Sung Yun Ju , Cruchaga Carlos
Published: May 2023

INTRODUCTION

In Alzheimer’s disease (AD) research, cerebrospinal fluid (CSF) Amyloid beta (Aβ), Tau and pTau are the most accepted and well validated biomarkers. Several methods and platforms exist to measure those biomarkers which leads to challenges in combining data across studies. Thus, there is a need to identify methods that harmonize and standardize these values.

METHODS

We used a Z-score based approach to harmonize CSF and amyloid imaging data from multiple cohorts and compared GWAS result using this method with currently accepted methods. We also used a generalized mixture modelling to calculate the threshold for biomarker-positivity.

RESULTS

Z-scores method performed as well as meta-analysis and did not lead to any spurious results. Cutoffs calculated with this approach were found to be very similar to those reported previously.

DISCUSSION

This approach can be applied to heterogeneous platforms and provides biomarker cut-offs consistent with the classical approaches without requiring any additional data.
Antibiotic prophylaxis and hospitalization of horses subjected to median laparotomy: gut microbiota trajectories and abundance increase ofEscherichia
Authors: Kauter Anne , Brombach Julian , Lübke-Becker Antina , Kannapin Dania , Bang Corinna , Franzenburg Sören , Stoeckle Sabita D. , Mellmann Alexander , Effelsberg Natalie , Köck Robin , Guenther Sebastian , Wieler Lothar H. , Gehlen Heidrun , Semmler Torsten , Wolf Silver A. , Walther Birgit
Published: May 2023

Horse clinics are hotspots for the accumulation and spread of clinically relevant and zoonotic multidrug-resistant bacteria, including extended-spectrum β-lactamase producing (ESBL) Enterobacterales. Although median laparotomy in cases of acute equine colic is a frequently performed surgical intervention, knowledge about the effects of peri-operative antibiotic prophylaxis (PAP) based on a combination of penicillin and gentamicin on the gut microbiota is limited. Therefore, we collected fecal samples of horses from a non-hospitalized control group (CG) and from horses receiving either a pre-surgical single-shot (SSG) or a peri-operative 5-day (5DG) course of PAP. To assess differences between the two PAP regimens and the CG, all samples obtained at hospital admission (t0), on days three (t1) and ten (t2) after surgery, were screened for ESBL-producing Enterobacterales and subjected to 16S rRNA V1– V2 gene sequencing.

We included 48 samples in the SSG (n=16 horses), 45 in the 5DG (n=15) and 20 in the CG (n=10). Two samples (6.5%) were positive for ESBL-producing Enterobacterales at t0while this rate increased to 67% at t1and decreased only slightly at t2(61%). Shannon diversity index (SDI) was used to evaluate alpha-diversity changes, revealing that horses suffering from acute colic seemed to have a compromised fecal microbiota composition (5DG, SDImeanof 5.90; SSG, SDImeanof 6.17) when compared to the CG (SDImeanof 6.53) at t0, although the difference lacked significance. Alpha-diversity decreased significantly in both PAP groups at t1, while at t2the onset of microbiome recovery was noticed. Although we did not identify a significant SDImeandifference with respect to PAP duration, the community structure (beta-diversity) was considerably restricted in samples of the 5DG at t1, most likely due to the ongoing administration of antibiotics. An increased abundance ofEnterobacteriaceae,especiallyEscherichia, was noted for both study groups at t1. Further studies are needed to reveal important factors promoting the increase and residency of ESBL-producing Enterobacterales among hospitalized horses.
The tumor microbiome as a predictor of outcomes in patients with metastatic melanoma treated with immune checkpoint inhibitors
Authors: Wheeler Caroline E. , Coleman Samuel S. , Hoyd Rebecca , Denko Louis , Chan Carlos H.F. , Churchman Michelle L. , Denko Nicholas , Dodd Rebecca D. , Eljilany Islam , Hardikar Sheetal , Husain Marium , Ikeguchi Alexandra P. , Jin Ning , Ma Qin , McCarter Martin D. , Osman Afaf E.G. , Robinson Lary A. , Singer Eric A. , Tinoco Gabriel , Ulrich Cornelia M. , Zakharia Yousef , Spakowicz Daniel , Tarhini Ahmad A. , Tan Aik Choon
Published: May 2023

Emerging evidence supports the important role of the tumor microbiome in oncogenesis, cancer immune phenotype, cancer progression, and treatment outcomes in many malignancies. In this study, we investigated the metastatic melanoma tumor microbiome and potential roles in association with clinical outcomes, such as survival, in patients with metastatic disease treated with immune checkpoint inhibitors (ICIs). Baseline tumor samples were collected from 71 patients with metastatic melanoma before treatment with ICIs. Bulk RNA-seq was conducted on the formalin-fixed paraffin-embedded (FFPE) tumor samples. Durable clinical benefit (primary clinical endpoint) following ICIs was defined as overall survival ≥24 months and no change to the primary drug regimen (responders). We processed RNA-seq reads to carefully identify exogenous sequences using the {exotic}tool. The 71 patients with metastatic melanoma ranged in age from 24 to 83 years, 59% were male, and 55% survived >24 months following the initiation of ICI treatment. Exogenous taxa were identified in the tumor RNA-seq, including bacteria, fungi, and viruses. We found differences in gene expression and microbe abundances in immunotherapy responsive versus non-responsive tumors. Responders showed significant enrichment of several microbes includingFusobacterium nucleatum, and non-responders showed enrichment of fungi, as well as several bacteria. These microbes correlated with immune-related gene expression signatures. Finally, we found that models for predicting prolonged survival with immunotherapy using both microbe abundances and gene expression outperformed models using either dataset alone. Our findings warrant further investigation and potentially support therapeutic strategies to modify the tumor microbiome in order to improve treatment outcomes with ICIs.

Significance

We analyzed the tumor microbiome and interactions with genes and pathways in metastatic melanoma treated with immunotherapy, and identified several microbes associated with immunotherapy response and immune-related gene expression signatures. Machine learning models that combined microbe abundances and gene expression outperformed models using either dataset alone in predicting immunotherapy responses.
A pancreatic cancer mouse model with human immunity
Authors: Miyamura Norio , Suzuki Kodai , Friedman Richard A. , Floratos Aristidis , Kunisada Yuki , Masuda Kazuya , Lowy Andrew M. , Tsuji Moriya , Sugahara Kazuki N.
Published: May 2023

Pancreatic ductal adenocarcinoma (PDAC) is characterized by a tumor immune microenvironment (TIME) that promotes resistance to immunotherapy. A preclinical model system that facilitates studies of the TIME and its impact on the responsiveness of human PDAC to immunotherapies remains an unmet need. We report a novel mouse model, which develops metastatic human PDAC that becomes infiltrated by human immune cells recapitulating the TIME of human PDAC. The model may serve as a versatile platform to study the nature of human PDAC TIME and its response to various treatments.
Inferring chromosomal instability from copy number aberrations as a measure of chromosomal instability across human cancers
Authors: Taluri Sasha , Oza Vishal H. , Soelter Tabea M. , Fisher Jennifer L. , Lasseigne Brittany N.
Published: May 2023

Background

Cancer is a complex disease that is the second leading cause of death in the United States. Despite research efforts, the ability to manage cancer and select optimal therapeutic responses for each patient remains elusive. Chromosomal instability (CIN) is primarily a product of segregation errors wherein one or many chromosomes, in part or whole, vary in number. CIN is an enabling characteristic of cancer, contributes to tumor-cell heterogeneity, and plays a crucial role in the multistep tumorigenesis process, especially in tumor growth and initiation and in response to treatment.

Aims

Multiple studies have reported different metrics for analyzing copy number aberrations as surrogates of CIN from DNA copy number variation data. However, these metrics differ in how they are calculated with respect to the type of variation, the magnitude of change, and the inclusion of breakpoints. Here we compared metrics capturing CIN as either numerical aberrations, structural aberrations, or a combination of the two across 33 cancer data sets from The Cancer Genome Atlas (TCGA).

Methods and results

Using CIN inferred by methods in the CINmetrics R package, we evaluated how six copy number CIN surrogates compared across TCGA cohorts by assessing each across tumor types, as well as how they associate with tumor stage, metastasis, and nodal involvement, and with respect to patient sex.

Conclusions

We found that the tumor type impacts how well any two given CIN metrics correlate. While we also identified overlap between metrics regarding their association with clinical characteristics and patient sex, there was not complete agreement between metrics. We identified several cases where only one CIN metric was significantly associated with a clinical characteristic or patient sex for a given tumor type. Therefore, caution should be used when describing CIN based on a given metric or comparing it to other studies.
In vivofunctional phenotypes from a computational epistatic model of evolution
Authors: Alvarez Sophia , Nartey Charisse M. , Mercado Nicholas , de la Paz Alberto , Huseinbegovic Tea , Morcos Faruck
Published: May 2023

Computational models of evolution are valuable for understanding the dynamics of sequence variation, to infer phylogenetic relationships or potential evolutionary pathways and for biomedical and industrial applications. Despite these benefits, few have validated their propensities to generate outputs within vivofunctionality, which would enhance their value as accurate and interpretable evolutionary algorithms. We demonstrate the power of epistasis inferred from natural protein families to evolve sequence variants in an algorithm we developed called Sequence Evolution with Epistatic Contributions. Utilizing the Hamiltonian of the joint probability of sequences in the family as fitness metric, we sampled and experimentally tested forin vivo β-lactamase activity inE. coliTEM-1 variants. These evolved proteins can have dozens of mutations dispersed across the structure while preserving sites essential for both catalysis and interactions. Remarkably, these variants retain family-like functionality while being more active than their WT predecessor. We found that depending on the inference method used to generate the epistatic constraints, different parameters simulate diverse selection strengths. Under weaker selection, local Hamiltonian fluctuations reliably predict relative changes to variant fitness, recapitulating neutral evolution. SEEC has the potential to explore the dynamics of neofunctionalization, characterize viral fitness landscapes and facilitate vaccine development.
Inhibitors of cannabinoid receptor 1 suppress the cellular entry of Lujo virus
Authors: Kimura Miyuki , Matsuoka Risa , Taniguchi Satoshi , Maruyama Junki , Paessler Slobodan , Oka Saori , Yamashita Atsushi , Fukuhara Takasuke , Matsuura Yoshiharu , Tani Hideki
Published: May 2023

Lujo virus (LUJV), which belongs to Mammarenavirus, familyarenaviridae, has emerged as pathogen causing severe hemorrhage fever with high mortality. Currently, there are no effective treatments for arenaviruses, including LUJV. Here, we screened chemical compound libraries of Food and Drug Administration (FDA)-approved drug and G protein-coupled receptor-associated drugs to identify effective antivirals against LUJV targeting cell entry using a vesicular stomatitis virus-based pseudotyped virus bearing the LUJV envelope glycoprotein (GP). Cannabinoid receptor 1 (CB1) antagonists, such as rimonabant, AM251 and AM281, have been identified as robust inhibitors of LUJV entry. The IC50of rimonabant was 0.26 and 0.53 μM in Vero and Huh7 cells, respectively. Analysis of the cell fusion activity of the LUJV GP in the presence of CB1 inhibitors revealed that these inhibitors suppressed the fusion activity of the LUJV GP. Moreover, rimonabant, AM251 and AM281 reduced the infectivity of authentic LUJVin vitro,suggesting that the antiviral activity of CB1 antagonists against LUJV is mediated, at least in part, by inhibition of the viral entry, especially, membrane fusion. These findings suggest promising candidates for developing new therapies against LUJV infections.

Importance

To investigate antiviral drugs against Lujo virus (LUJV), we screened chemical compound libraries to identify effective antivirals against LUJV entry. CB1 antagonists were identified as robust inhibitors of LUJV entry. The cell fusion activity of LUJV GP was suppressed by CB1 inhibitors. Furthermore, CB1 antagonists reduced the infectivity of authentic LUJV. These findings suggest promising candidates for developing new therapies against LUJV infections.