bluuebunny/crossref_metadata_2025 huggingface dataset:
Long-term responses of life-history strategies to climatic variability in flowering plants
Authors: Boyko James D. , Hagen Eric R. , Beaulieu Jeremy M. , Vasconcelos Thais
Published: October 2022

The evolution of annual or perennial strategies in flowering plants may depend on a broad array of temperature and precipitation variables. Previously documented correlations between life history strategy and climate appear to be clade-specific and fail to consider the coevolution of climatic niches and life history strategies.

Here we combine annual and perennial life history data with geographic distribution for 9,939 flowering plant species and utilize a recently developed method that accounts for the joint evolution of continuous and discrete traits to evaluate two hypotheses: (1) annuals tend to evolve in highly seasonal regions prone to extreme heat and drought, and (2) annuals tend to have faster rates of climatic niche evolution than perennials.

We find temperature, particularly the maximum temperature of the warmest month, is the most consistent climatic factor influencing life history evolution in flowering plants. Unexpectedly, we find that the rates of climatic niche evolution are faster in perennials than in annual lineages.

We propose that annuals are consistently favored in areas prone to extreme heat due to their ability to escape heat stress as seeds, but they tend to be outcompeted by perennials in regions where extreme heat is uncommon or nonexistent.
Neural oscillatory activity and connectivity in children who stutter during a non-speech motor task
Authors: Caruso Valeria C , Wray Amanda Hampton , Lescht Erica , Chang Soo-Eun
Published: October 2022

Neural motor control rests on the dynamic interaction of cortical and subcortical regions, which is reflected in the modulation of oscillatory activity and connectivity in multiple frequency bands. Motor control is thought to be compromised in developmental stuttering, particularly involving circuits in the left hemisphere that support speech, movement initiation and timing control. However, to date evidence comes from adult studies, with limited understanding about motor processes in childhood, closer to the onset of stuttering. In this study, we investigated the neural control of movement initiation in children who stutter and children who do not stutter by evaluating transient changes of EEG oscillatory activity and connectivity during a simple button press motor task. We found reduced modulation of left hemisphere oscillatory power, phase locking to button press and phase connectivity in children who stutter compared to children who do not stutter, consistent with previous findings of dysfunction within the left sensorimotor circuits. Interhemispheric connectivity was also weaker at lower frequencies (delta, theta) and stronger in the beta band in children who stutter than in children who do not stutter. Taken together, these findings indicate weaker engagement of the contralateral left motor network in children who stutter even during low-demand non-speech tasks, and suggest that the right hemisphere might be recruited to support sensorimotor processing in childhood stuttering. Differences in oscillatory dynamics occurred despite comparable task performance between groups, indicating that altered balance of cortical activity might be a core aspect of stuttering, observable during normal motor behavior.
Intrathecal administration of bone marrow stromal cells and TGF-β1 alleviate chemotherapy-induced neuropathic pain in male mice
Authors: Huh Yul , Luo Xin , Liu Di , Jiang Changyu , Ji Ru-Rong
Published: October 2022

Chemotherapy-induced peripheral neuropathy (CIPN) is the de facto clinical side effect that limits the administration of anti-cancer treatments. Recently, we reported that intrathecally injected bone marrow stromal cells (BMSCs) reduced nerve trauma-induced neuropathic pain in male mice via TGF-β1 signaling. In this study, we examined sex-dependent pain relief mediated by intrathecally delivered BMSCs and TGF-β1 in paclitaxel (PTX)-induced CIPN. BMSCs were prepared from primary cultures of male or female mice separately. A single intrathecal injection of BMSCs, prepared from male donors, completely prevented the development of PTX-evoked mechanical allodynia in male mice. However, female mice showed no analgesic response to either male or female BMSCs. Additionally, male mice did not demonstrate an analgesic response to BMSCs from female donors. Intrathecal injection of TGF-β1 neutralizing antibody reversed the analgesic action of BMSCs. Interestingly, spinal administration of TGF-β1 reduced mechanical allodynia in male mice but not in female mice. Ex vivo patch-clamp recordings in spinal cord slices revealed that TGF-β1 inhibited PTX-induced synaptic plasticity, i.e. increase in spontaneous excitatory synaptic currents (sEPsCs), in spinal cord neurons from male mice only. Intrathecal TGF-β1 increased the paw withdrawal threshold in von Frey testing in naïve mice of males but not females, and the antinociceptive effect of TGF-β1 in males was blocked by orchiectomy-induced androgen deficiency. Together, these findings reveal sex dimorphism in BMSC control of mechanical pain through spinal TGF-β1 signaling.
Cultural determinants of the gap between self-estimated navigation ability and wayfinding performance: evidence from 46 countries
Authors: Walkowiak S. , Coutrot A. , Hegarty M. , Velasco P. F. , Wiener J. M. , Dalton R.C. , Hölscher C. , Hornberger M. , Spiers H. J. , Manley E.
Published: October 2022

Cognitive abilities can vary widely. Some people excel in certain skills, others struggle. However, not all those who describe themselves as gifted are. One possible influence on self-estimates is the surrounding culture. Some cultures may amplify self-assurance and others cultivate humility. Past research has shown that people in different countries can be grouped into a set of consistent cultural clusters with similar values and tendencies, such as attitudes to masculinity or individualism. Here we explored whether such cultural dimensions might relate to the extent to which populations in 46 countries overestimate or underestimate their cognitive abilities in the domain of spatial navigation. Using the Sea Hero Quest navigation test and a large sample (N=383,187) we found cultural clusters of countries tend to be similar in how they self-rate ability relative to their actual performance. Across the world population sampled, higher self-ratings were associated with better performance. However, at the national level, higher self-ratings as a nation were not associated with better performance as a nation. Germanic and Near East countries were found to be most overconfident in their abilities and Nordic countries to be most under-confident in their abilities. Gender stereotypes may play a role in mediating this pattern, with larger national positive attitudes to male stereotyped roles (Hofstede’s masculinity dimension) associated with a greater overconfidence in performance at the national level. We also replicate, with higher precision than prior studies, evidence that older men tend to overestimate their navigation skill more than other groups. These findings give insight into how culture and demographics may impact self-estimates of our abilities.
Nucleotide binding is the critical regulator of ABCG2 conformational transitions
Authors: Gyöngy Zsuzsanna , Mocsár Gábor , Hegedűs Éva , Stockner Thomas , Ritter Zsuzsanna , Homolya László , Schamberger Anita , Orbán Tamás I. , Remenyik Judit , Szakács Gergely , Goda Katalin
Published: October 2022

ABCG2 is an exporter type ABC protein that can expel numerous chemically unrelated xeno- and endobiotics from cells. When expressed in tumor cells or tumor stem cells, ABCG2 confers multidrug resistance, contributing to the failure of chemotherapy.

Molecular details orchestrating substrate translocation and ATP hydrolysis remain elusive. Here we present methods to concomitantly investigate substrate and nucleotide binding by ABCG2 in cells. Using the conformation-sensitive antibody 5D3, we show that the switch from the inward-facing (IF) to the outward-facing (OF) conformation of ABCG2 is induced by nucleotide binding. IF-OF transition is facilitated by substrates, and hindered by the inhibitor Ko143. Direct measurements of 5D3 and substrate binding to ABCG2 indicate that the high-to-low affinity switch of the drug binding site coincides with the transition from the IF to the OF conformation. Low substrate binding persists in the post-hydrolysis state, supporting that dissociation of the ATP hydrolysis products is required to reset the high substrate affinity IF conformation of ABCG2.
Single-cell transcriptomics reveals a mechanosensitive injury signaling pathway in early diabetic nephropathy
Authors: Liu Shuya , Zhao Yu , Lu Shun , Zhang Tianran , Lindenmeyer Maja T. , Nair Viji , Gies Sydney E. , Wu Guochao , Nelson Robert G. , Czogalla Jan , Aypek Hande , Zielinski Stephanie , Liao Zhouning , Schaper Melanie , Fermin Damian , Cohen Clemens D. , Delic Denis , Krebs Christian F. , Grahammer Florian , Wiech Thorsten , Kretzler Matthias , Meyer-Schwesinger Catherine , Bonn Stefan , Huber Tobias B.
Published: October 2022

Diabetic nephropathy (DN) is the leading cause of end-stage renal disease and histopathologic glomerular lesions are among the earliest structural alterations of DN. However, the signaling pathways that initiate these glomerular alterations are incompletely understood. To delineate the cellular and molecular basis for DN initiation, we performed single-cell and bulk RNA sequencing of renal cells from type 2 diabetes mice (BTBRob/ob) at the early stage of DN. Analysis of differentially expressed genes revealed glucose-independent responses in glomerular cell types. The gene regulatory network upstream of glomerular cell programs suggested the activation of mechanosensitive transcriptional pathway MRTF-SRF predominantly taking place in mesangial cells. Importantly, activation of MRTF-SRF transcriptional pathway was also identified in DN glomeruli in independent patient cohort datasets. Furthermore, ex vivo kidney perfusion suggested that the regulation of MRTF-SRF is a common mechanism in response to glomerular hyperfiltration. Overall, our study presents a comprehensive single-cell transcriptomic landscape of early DN, highlighting mechanosensitive signaling pathways as novel targets of diabetic glomerulopathy.
Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells
Authors: Zhao Yixin , Liu Lingjie , Siepel Adam
Published: October 2022

In metazoans, both transcription initiation and the escape of RNA polymerase (RNAP) from promoter-proximal pausing are key rate-limiting steps in gene expression. These processes play out at physically proximal sites on the DNA template and appear to influence one another through steric interactions, leading to a complex dynamic equilibrium in RNAP occupancy of the ~100 bp immediately downstream of the transcription start site. In this article, we examine the dynamics of these processes using a combination of statistical modeling, simulation, and analysis of real nascent RNA sequencing data. We develop a simple probabilistic model that jointly describes the kinetics of transcription initiation, pause-escape, and elongation, and the generation of nascent RNA sequencing read counts under steady-state conditions. We then extend this initial model to allow for variability across cells in promoter-proximal pause site locations and steric hindrance of transcription initiation from paused RNAPs. In an extensive series of simulations over a broad range of parameters, we show that this model enables accurate estimation of initiation and pause-escape rates even in the presence of collisions between RNAPs and variable elongation rates. Furthermore, we show by simulation and analysis of data for human cell lines that pause-escape is often more strongly rate-limiting than conventional “pausing indices” would suggest, that occupancy of the pause site is elevated at many genes, and that steric hindrance of initiation can lead to a pronounced reduction in apparent initiation rates. Our modeling framework is generally applicable for all types of nascent RNA sequencing data and can be applied to a variety of inference problems.
Differential Stability of Task Variable Representations in Retrosplenial Cortex
Authors: Franco Luis M. , Goard Michael J.
Published: October 2022

Cortical neurons store information across different timescales, from seconds to years. Although information stability is variable across regions, it can vary within a region as well. Association areas are known to multiplex behaviorally relevant variables, but the stability of their representations is not well understood. Here, we longitudinally recorded the activity of neuronal populations in the retrosplenial cortex (RSC) during the performance of a context-choice association task. We found that the activity of neurons exhibits different levels of stability across days. Using linear classifiers, we quantified the stability of three task-relevant variables. We find that RSC representations of context and trial outcome display higher stability than motor choice, both at the single cell and population levels. Together, our findings show an important characteristic of association areas, where diverse streams of information are stored with varying levels of stability, which may balance representational reliability and flexibility according to behavioral demands.
Spatio-temporal Pattern Formation due to Host-Circuit Interplay in Gene Expression Dynamics
Authors: Chakraborty Priya , Jolly Mohit K. , Roy Ushasi , Ghosh Sayantari
Published: October 2022

Biological systems are majorly dependent on their property of bistability in order to exhibit nongenetic heterogeneity in terms of cellular morphology and physiology. Spatial patterns of phenotypically heterogeneous cells, arising due to underlying bistability, may play significant role in phenomena like biofilm development, adaptation, cell motility etc. While nonlinear positive feedback regulation, like cooperative heterodimer formation are the usual reason behind bistability, similar dynamics can also occur as a consequence of host-circuit interaction. In this paper, we have investigated the pattern formation by a motif with non-cooperative positive feedback, that imposes a metabolic burden on its host due to its expression. In a cellular array set inside diffusible environment, we investigate spatio-temporal diffusion in one dimension as well as in two dimension in the context of various initial conditions respectively. Moreover, the number of cells exhibiting the same steady state, as well as their spatial distribution has been quantified in terms of connected component analysis. The effect of diffusion coefficient variation has been studied in terms of stability of related states and time evolution of patterns.
Taming the data deluge: a novel end-to-end deep learning system for classifying marine biological and environmental images
Authors: Bi Hongsheng , Cheng Yunhao , Cheng Xuemin , Benfield Mark C. , Kimmel David G. , Zheng Haiyong , Groves Sabrina , Ying Kezhen
Published: October 2022

Marine underwater imaging facilitates non-destructive sampling of species at frequencies, durations, and accuracies that are unattainable by conventional sampling methods. These systems necessitate complex automated processes to identify organisms efficiently, however, current frameworks struggle to disentangle ecological foreground components from their dispensable background content. Underwater image processing relies on common architecture: namely image binarization for segmenting potential targets, prior to information extraction and classification by deep learning models. While intuitive, this infrastructure underperforms as it has difficulty in handling: high concentrations of biotic and abiotic particles, rapid changes in dominant taxa, and target sizes that vary by several orders of magnitude. To overcome these issues, a new framework is presented that begins with a scene classifier to capture large within-image variation, such as disparities in particle concentration and dominant taxa. Following scene classification, scene-specific regional convolutional neural network (Mask R-CNN) models were trained to separate target objects into different taxonomic groups. The procedure allows information to be extracted from different image types, while minimizing potential bias for commonly occurring features. Usingin situcoastal PlanktonScope images, we compared the scene-specific models to the Mask R-CNN model including all scene categories without scene classification, defined as the full model, and found that the scene-specific approach outperformed the full model with >20% accuracy in noisy images. The full model missed up to 78% of the dominant taxonomic groups, such asLyngbya, Noctiluca, andPhaeocystiscolonies. This performance improvement is due to the scene classifier, which reduces the variation among images and allows an improved match between the observed taxonomic groups and the taxonomic groups in pre-trained models. We further tested the framework on images from a benthic video camera and an imaging sonar system. Results demonstrate that the procedure is applicable to different types of underwater images and achieves significantly more accurate results than the full model. Given that the unified framework is neither instrument nor ecosystem-specific, the proposed model facilitates deployment throughout the marine biome.
A Platform-Independent Framework for Phenotyping of Multiplex Tissue Imaging Data
Authors: Ahmadian Mansooreh , Rickert Christian , Minic Angela , Wrobel Julia , Bitler Benjamin G , Xing Fuyong , Angelo Michael , Hsieh Elena W , Ghosh Debashis , Jordan Kimberly R
Published: October 2022

Multiplex imaging is a powerful tool to analyze the structural and functional states of cells in their morphological and pathological contexts. However, hypothesis testing with multiplex imaging data is a challenging task due to the extent and complexity of the information obtained. Various computational pipelines have been developed and validated to extract knowledge from specific imaging platforms. A common problem with customized pipelines is their reduced applicability across different imaging platforms: Every multiplex imaging technique exhibits platform-specific characteristics in terms of signal-to-noise ratio and acquisition artifacts that need to be accounted for to yield reliable and reproducible results. We propose a pixel classifier-based image preprocessing step that aims to minimize platform-dependency for all multiplex image analysis pipelines. Signal detection and noise reduction as well as artifact removal can be posed as a pixel classification problem in which all pixels in multiplex images can be assigned to two general classes of either I) signal of interest or II) artifacts and noise. The resulting feature representation maps contain pixel-accurate representations of the input data, but exhibit signifi-cantly increased signal-to-noise ratios with normalized pixel values as output data. We demonstrate the validity of our proposed image preprocessing approach by comparing the results of two well-accepted and widely-used image analysis pipelines.
Repurposing of Drugs Against Mutated Strain of Eurasian Avian Like H1N1 (EA H1N1) Swine Flu Virus, Genotype 4(G4) Virus
Authors: Ghimire Sangita , Sahukhal Sandhya , Shrestha Ayush , Adhikari Sarmila , Subedi Samiran , Budha Keshab Raj , Aryal Pramod
Published: October 2022

Mutation, reassortment and recombination have led to the evolution and the emergence of more pathogenic and new subtypes of influenza virus. The surge of highly mutated viruses has prompted the need of coherent solution for the so called “medical holocaust” viral outbreaks. The genotype 4 of EAH1N1 strain has been circulating in the swine population as a dominant genotype, exhibiting even human to human transmission. This has risen the possibility of causing another global health threat as a lethal viral outbreak in the future. The Computer Aided Drug Discovery (CADD) could be a prudent mechanism to develop new drug candidates against such disease for its mitigation. In this regard, the computationalin silicomethods had been envisaged in this research for the prediction of lead compounds against the selected proteins of EA H1N1 G4 strain, namely Haemagglutinin (HA) and Polymerase acidic protein(PA). The research focused on the selection of the target viral protein and molecular docking for the identification of putative ligands. It was followed by the identification of the probable mutations and assessment of effectiveness of identified drugs against their respective targets. Total of 3 compounds Enalapril, Enalaprilat and Ivabradine have been identified as a potential inhibitor of HA and PA protein that were prioritized on the basis of preference index parameter and binding energy of compound with the respective target. Besides, the probable mutations in each target protein in future were predicted and all these 3 top hits were found to be effective against mutated variant of these proteins. Thus, Enalapril, Enalaprilat and Ivabradine could be the lead compounds to explore further as multi target inhibiting drugs against wild and mutant variant of target proteins.
Chronic restraint stress decreases resistance to punishment during cocaine self-administration via a dopamine D1-like receptor-mediated mechanism in prelimbic medial prefrontal cortex
Authors: Ball Kevin T. , Edson Hunter
Published: October 2022

We recently reported that male rats displayed greater resistance to punishment during cocaine self-administration compared to females. Moreover, daily restraint stress decreased this resistance in males, while having no effect in females. The purpose of the present study was to extend these findings by determining whether chronic stress-induced dopamine release in prelimbic medial prefrontal cortex mediates the effect of stress on punished cocaine self-administration. Thus, male rats were trained to press a lever for i.v. cocaine infusions (0.50 mg/kg/infusion) paired with a discrete tone + light cue in daily 3-hr sessions. Subsequently, 50% of the lever presses were punished by a mild footshock that gradually increased in intensity over 7 days. During the punishment phase, rats were exposed to a chronic restraint stress procedure (3 h/day) or control procedure (unstressed). Rats also received bilateral microinjections of the D1-like receptor antagonist SCH-23390 (0.25 μg/0.5 μl/side) or vehicle (0.5 μl/side) delivered to prelimbic cortex prior to daily treatments. Relapse tests were conducted 1 and 8 days after the last punishment session. Chronically stressed rats displayed reduced cocaine self-administration during punishment relative to unstressed rats, an effect prevented by co-administration of SCH-23390 to prelimbic cortex with daily restraint. Neither stress nor SCH-23390 treatment had significant effects on subsequent relapse-like behavior. These results establish a specific role for prelimbic D1-like receptors in chronic stress-induced suppression of punished cocaine self-administration in male rats. As such, these findings may inform novel methods to facilitate self-imposed abstinence in cocaine-dependent men.
A reversible SRC-relayed COX2-inflammatory program drives therapeutic resistance in BRAFV600Ecolorectal tumors
Authors: Ruiz-Saenz Ana , Atreya Chloe E. , Wang Changjun , Pan Bo , Dreyer Courtney A. , Brunen Diede , Prahallad Anirudh , Muñoz Denise P. , Ramms Dana J. , Burghi Valeria , Spassov Danislav S. , Fewings Eleanor , Hwang Yeonjoo C. , Cowdrey Cynthia , Moelders Christina , Schwarzer Cecilia , Wolf Denise M. , Hann Byron , VandenBerg Scott R. , Shokat Kevan , Moasser Mark M. , Bernards René , Gutkind J. Silvio , van ‘t Veer Laura J. , Coppé Jean-Philippe
Published: October 2022

BRAFV600Emutation confers a poor prognosis in metastatic colorectal cancer (CRC) despite combinatorial targeted therapies based on the latest understanding of signaling circuitry. To identify parallel resistance mechanisms induced by BRAF/MEK/EGFR co-targeting, we used a high throughput kinase activity mapping platform. We found that SRC kinases are systematically activated in BRAFV600ECRC following targeted inhibition of BRAF ± EGFR, and that coordinated targeting of SRC with BRAF ± EGFR increases efficacyin vitroandin vivo. SRC drives resistance to BRAF ± anti-EGFR therapy independently of ERK signaling by inducing transcriptional reprogramming via beta-catenin (CTNNB1). The EGFR-independent compensatory activation of SRC kinases is mediated by an autocrine prostaglandin E2-loop that can be blocked with cyclooxygenase-2 (COX2) inhibitors. Co-targeting of COX2 with BRAF+EGFR promotes durable suppression of tumor growth in patient-derived tumor xenograft (PDX) models. COX2 inhibition represents a novel drug-repurposing strategy to overcome therapeutic resistance in BRAFV600ECRC.
Physiological Changes Associated with Copper Sulfate-Induced Emesis in Felines
Authors: Murphey Charles P. , Shulgach Jonathan A. , Amin Pooja R. , Douglas Nerone K. , Bielanin John P. , Sampson Jacob T. , Horn Charles C. , Yates Bill J.
Published: October 2022

Nausea is a common disease symptom, yet there is no consensus regarding its physiological markers. In contrast, the process of vomiting is well documented as sequential muscular contractions of the diaphragm and abdominal muscles and esophageal shortening. Nausea, like other self-reported perceptions, is difficult to distinguish in preclinical models, but based on human experience emesis is usually preceded by nausea. Here we focused on measuring gastrointestinal and cardiorespiratory changes prior to emesis to provide additional insights into markers for nausea. Felines were instrumented to chronically record heart rate, respiration, and electromyographic (EMG) activity from the stomach and duodenum before and after intragastric delivery of saline or copper sulfate (CuSO4, from 83 to 322 mg). CuSO4is a prototypical emetic test agent that triggers vomiting primarily by action on GI vagal afferent fibers when administered intragastrically. CuSO4infusion elicited a significant increase in heart rate, decrease in respiratory rate, and a disruption of gastric and intestinal EMG activity several minutes prior to emesis. The change in EMG activity was most consistent in the duodenum. Administration of saline did not induce these effects. Increasing the dose of CuSO4did not alter the physiologic changes induced by the treatment. It is postulated that the intestinal EMG activity was related to a retrograde movement of chyme from the intestine to the stomach. These findings suggest that monitoring of intestinal EMG activity, perhaps in combination with heart rate, may provide the best indicator of the onset of nausea following treatments and in disease conditions, including GI disease, associated with emesis.
Thermococci-to-ClostridiaPathway for the Evolution of the Bacteria Domain
Authors: Wong Tze-Fei , Chan Chung-Kwon , Xue Hong
Published: October 2022

With the identification of an archaeal Last Universal Common Ancestor phylogenetically related toMethanopyrus, the origin of Bacteria becomes a choice between independent emergence versus descent from Archaea. Recently, use of the similarity between paralogous valyl-tRNA synthetase (VARS) and isoleucyl-tRNA synthetase (IARS) as a measure of the ages of bacteria indicated that an Ancestral Bacterial Cluster centred at clostridialMahella australiensis(Mau) were the oldest bacteria. ClostridialThermincola potens(Tpo) also displayed an elevated similarity VARS-IARS bitscore. Overall, the high-bitscore bacteria dominated byClostridiacomprised a number of hydrogen producers. A search for archaea capable of hydrogen production that might be ancestral to the Bacteria domain yielded candidates led byThermococciwhich, likeClostridia, form hydrogen through dark fermentation. A two-domain VARS tree based onMahella,Thermincola, a broad spectrum of archaea together with both well known and newly reported species ofThermococciallocated these twoClostridiato a minor-Thermococcal division on the tree. The kinship betweenThermoccociandClostridiasuggested by this allocation was substantiated by conserved oligopeptide segments on their VARS sequences. It was therefore suggested that aThermococci-to-Clostridiaevolutionary pathway brought about the emergence of the Bacteria domain.
The PENGUIN approach to reconstruct protein interactions at enhancer-promoter regions and its application to prostate cancer
Authors: Armaos Alexandros , Serra François , Núñez-Carpintero Iker , Seo Ji-Heui , Baca Sylvan C. , Gustincich Stefano , Valencia Alfonso , Freedman Matthew L. , Cirillo Davide , Giambartolomei Claudia , Tartaglia Gian Gaetano
Published: October 2022

Here we introduce Promoter-ENhancer-GUided Interaction Networks (PENGUIN), a method to uncover protein-protein interaction (PPI) networks at enhancer-promoter contacts. By integrating H3K27ac-HiChIP data and tissue-specific PPI information, PENGUIN enables cluster enhancers-promoter PPI networks (EPINs) and pinpoint actionable factors.

Validating PENGUIN in cancer (LNCaP) and benign (LHSAR) prostate cell lines, we observed distinct CTCF-enriched clusters, which identifies diverse chromatin conformations. In LNCaP, we found an EPIN cluster enriched with oncogenes and prostate cancer-associated SNPs. We uncovered a total of 208 SNPs in LNCaP EPINs and used CRISPR/Cas9 knockout and RNAi screens to confirm their relevance.

PENGUIN’s application in prostate cancer demonstrates its potential for studying human diseases. The approach allows exploration in different cell types and combinations of GWAS data, offering promising avenues for future investigations. In conclusion, PENGUIN provides valuable insights into the interplay between enhancer-promoter interactions and PPI networks, facilitating the identification of relevant genes and potential intervention targets.
Anticancer and antibacterial activities of secondary bioactive compounds from endosymbiotic bacteria of aphid and their surrounding organisms (Predator and protector)
Authors: Alsufyani Taghreed A. , Al-Otaibi Najwa , Alotaibi Noura J. , M’sakni Nour H , Alghamdi Eman M.
Published: October 2022

Secondary metabolites of bacterial origin are a valuable source of diverse molecules with antibacterial and anticancer activities. In the current study, 10 endosymbiotic bacteria were isolated from aphids, aphid predators and ants. Bacterial strains were identified based on the 16S rRNA gene. Crude extracts were prepared from each isolated bacteria and tested for their antibacterial activities using the disk diffusion method. The extracts of three bacterial species;Planococcussp,Klebsiella aerogenes, Enterococcus aviumfromAphis punicae, Chrysoperia carneaandTapinoma magnum, respectively were found to have strong antibacterial activities against one or more of the five pathogenic bacteria tested. The inhibition zones ranged from 10.00± 0.13 to 20.00± 1.11mm with minimum inhibitory concentration (MIC) values ranged from 0.156 mg/mL to 1.25 mg/mL. The notable antibacterial activity was for the crude extract ofK. aerogenesagainstKlebsiella pneumoniaandEscherichia coliat MIC value of 0.156 mg/mL. The cytotoxic activity of the crude extracts varied according to the tested cell line. The most cytotoxic effect was for the extracts ofK. aerogenesandE. aviumat a concentration of 0.16 mg/mL against lung carcinoma epithelial cells (A549) with cell reduction of 79.4% and 67.2%, respectively. Crude extracts ofK. aerogenesandPantoea agglomeransat a concentration of 0.16 mg/mL showed 69.4% and 67.8% cell reduction against human colon cancer (Hct116), respectively. Gas chromatography–mass spectrometry (GC-MS) analysis of three crude extracts revealed the presence of several bioactive secondary metabolites that have been reported previously to possess antibacterial and anticancer properties. To the best of our knowledge, this is the first study to report the biological activities of endosymbiotic bacteria from aphids, aphid predators and ants. The promising data presented in this study opens a new avenue for alternative drugs to overcome the continuous emergence of multidrug-resistant bacteria and to find alternative drugs for traditional cancer therapies.
Efficient transfection of Atlantic salmon primary hepatocyte cells for functional assays and gene editing
Authors: Datsomor Alex K , Wilberg Ragnhild , Torgersen Jacob S , Sandve Simen R , Harvey Thomas N
Published: October 2022

The expansion of genomic resources for Atlantic salmon over the past half decade has enabled efficient interrogation of genetic traits by large-scale correlation of genotype to phenotype. Moving from correlation to causation will require genotype-phenotype relationships to be tested experimentally in a cost-efficient and cell context relevant manner. To enable such future experiments, we have developed a method for the isolation and genetic manipulation of primary hepatocytes from Atlantic salmon for use in heterologous expression, reporter assay, and gene editing experiments. We chose the liver as the tissue of interest because it is the metabolic hub and many current Atlantic salmon research projects focus on understanding metabolic processes to improve traits such as growth rate, total fat content, and omega-3 content. We find that isolated primary hepatocytes are optimally transfected with both plasmid and ribonucleoprotein using a Neon electroporator at 1400 V, 10 ms, and 2 pulses. Transfection efficiency with plasmid and cutting efficiency with ribonucleoprotein was optimally 46% and 60%, respectively. We also demonstrate a 26-fold increase in luciferase expression under the promoter of the key liver metabolic gene, elovl5b, compared to empty vector, in line with expected liver-specific expression. Taken together, this work provides a valuable resource enabling transfection and gene editing experiments in a context relevant and cost-effective system.
Understanding Vascular Endothelial Cell Behavior Using a Mechanical Strain Gradient Generated by an Electromagnetic Stretching Device
Authors: Yang Michelle L. , Zuo Catalina , Liu Jiafeng , Man Kun , Zuo Zhenyu , Yang Yong
Published: October 2022

Cardiovascular diseases cause an estimated 17.9 million deaths globally each year (World Health Organization). Endothelial cells that line the vasculature and the endocardium are subjected to cyclic mechanical stretch. Deviation from physiological stretch can alter the endothelial function, having the risk of atherosclerosis and myocardial infarction. To understand the mechanical stretch effects, cell culture platforms that provide mechanical stretch have been developed. However, most of them have fixed strain and frequency, sometime not in the pathophysiological range. We thus developed a novel, electromagnetically driven, uniaxial stretching device, where cells were grown on a flexible polydimethylsiloxane (PDMS) membrane mounted onto a 3-D printed track. The strain of the membrane was readily controlled by tailoring the track design and the frequency was determined by electromagnetic actuation. Furthermore, the mechanical strain gradient was generated on a PDMS membrane with a tapered thickness. This strain gradient, ranging from 1.5% to 40%, covered both physiological and pathological vascular stretch ranges. When human vascular endothelial cells were subjected to the cyclic stretch, the cells exhibited strain-dependent cell and nuclear orientation and elongation perpendicular to the stretching direction, compared to the random cell and nuclear orientation under the static condition. However, the overstretching led to deviation from the aforementioned orientation and elongation, and impaired the tight junctions, leading to a leaky endothelium. This novel, versatile, cost-effective, pathophysiologically relevant stretching device provides a useful platform for advancement of vascular disease research and treatment.
MDM2 inhibitors, nutlin-3a and navtemadelin, retain efficacy in human and mouse cancer cells cultured in hypoxia
Authors: Clavero Ada Lerma , Boqvist Paula Lafqvist , Ingelshed Katrine , Bosdotter Cecilia , Sedimbi Saikiran , Jiang Long , Wermeling Fredrik , Vojtesek Borivoj , Lane David P. , Kannan Pavitra
Published: October 2022

Activation of p53 by small molecule MDM2 inhibitors can induce cell cycle arrest or death in p53 wildtype cancer cells. However, cancer cells exposed to hypoxia can develop resistance to other small molecules, such as chemotherapies, that activate p53. Here, we evaluated whether hypoxia could render cancer cells insensitive to two MDM2 inhibitors with different potencies, nutlin-3a and navtemadlin. Inhibitor efficacy and potency were evaluated under short-term hypoxic conditions in human and mouse cancer cells expressing different p53 genotypes (wild-type, mutant, or null). Treatment of wild-type p53 cancer cells with MDM2 inhibitors reduced cell growth by >75% in hypoxia through activation of the p53-p21 signaling pathway; no inhibitor-induced growth reduction was observed in hypoxic mutant or null p53 cells except at very high concentrations. The concentration of inhibitors needed to induce the maximal p53 response was not significantly different in hypoxia compared to normoxia. However, inhibitor efficacy varied by species and by cell line, with stronger effects at lower concentrations observed in human cell lines than in mouse cell lines grown as 2D and 3D cultures. Together, these results indicate that MDM2 inhibitors retain efficacy in hypoxia, suggesting they could be useful for targeting acutely hypoxic cancer cells.
Quantitative analysis of calcium oxalate monohydrate and dihydrate for elucidating the formation mechanism of calcium oxalate kidney stones
Authors: Maruyama Mihoko , Sawada Koichi P. , Tanaka Yutaro , Okada Atsushi , Momma Koichi , Nakamura Masanori , Mori Ryota , Furukawa Yoshihiro , Sugiura Yuki , Tajiri Rie , Taguchi Kazumi , Hamamoto Shuzo , Ando Ryosuke , Tsukamoto Katsuo , Takano Kazufumi , Imanishi Masayuki , Yoshimura Masashi , Yasui Takahiro , Mori Yusuke
Published: October 2022

We aimed to identify and quantitatively analyze calcium oxalate (CaOx) kidney stones on the order of micrometers, with a focus on the quantitative identification of calcium oxalate monohydrate (COM) and dihydrate (COD). Fourier Transform Infrared (FTIR) spectroscopy, powder X-ray diffraction (PXRD), and microfocus X-ray CT measurements (micro-CT) were performed, and the results were compared. The extended analysis method of the FTIR spectrum, focusing on the 780 cm−1peak, made it possible to achieve a reliable analysis of the COM/COD ratio. We succeeded in the quantitative analysis of COM/COD in the region of 50 × 50 μm by microscopic FTIR for thin sections of kidney stones, and by the micro-CT for bulk samples. The extended analysis method of the FTIR spectrum focusing on the 780 cm−1peak was introduced to analyze the COM/COD ratio. The analysis results based on PXRD measurement with micro sampling, microscopic FTIR analysis of a thin section, and micro-CT observation of a bulk sample of a kidney stone showed roughly consistent results, indicating that all methods can be used complementarily. This quantitative analysis method evaluates the detailed CaOx composition on the preserved stone surface and provides information on the stone formation processes and interactions with organic molecules.
Multigenerational effect of heat stress on theDrosophila melanogastersperm proteome
Authors: Khan Shagufta , Mishra Rakesh K
Published: October 2022

The notion that genes are the sole units of heredity and that a barrier exists between soma and germline has been a major hurdle in elucidating the heritability of traits that were observed to follow a non-Mendelian inheritance pattern. It was only after the conception of epigenetics by Conrad Waddington that the effect of parental environment on subsequent generations via non-DNA sequence-based mechanisms, such as DNA methylation, chromatin modifications, non-coding RNAs and proteins, could be established, now referred to as multigenerational epigenetic inheritance. Despite growing evidence, the male gamete-derived epigenetic factors that mediate the transmission of such phenotypes are seldom explored, particularly in the model organismDrosophila melanogaster. Using the heat stress-induced multigenerational epigenetic inheritance paradigm in a widely used position-effect variegation line ofDrosophila, namedwhite-mottled, we have dissected the effect of heat stress on the sperm proteome in the current study. We demonstrate that multiple successive generations of heat stress at the early embryonic stage results in a significant downregulation of proteins associated with a diverse set of functions, such as translation, chromatin organization, microtubule-based processes, and generation of metabolites and energy, in the sperms. Based on our findings, we propose chromatin-based epigenetic mechanisms, a well-established mechanism for multigenerational effects, as a plausible way of transmitting heat stress memory via the male germline in this case. Moreover, we show that despite these heat stress-induced changes, the life-history traits, such as reproductive fitness and stress tolerance of the subsequent generations, are unaffected, probing the evolutionary relevance of multigenerational epigenetic effects.
Parsing brain-behavior heterogeneity in very preterm born children using integrated similarity networks
Authors: Hadaya Laila , Dimitrakopoulou Konstantina , Vanes Lucy , Kanel Dana , Fenn-Moltu Sunniva , Gale-Grant Oliver , Counsell Serena J , Edwards A David , Saqi Mansoor , Batalle Dafnis , Nosarti Chiara
Published: October 2022

Very preterm birth (VPT; ≤ 32 weeks’ gestation) is associated with altered brain development and cognitive and behavioral difficulties across the lifespan. However, heterogeneity in outcomes among individuals born VPT makes it challenging to identify those most vulnerable to neurodevelopmental sequelae. Here, we aimed to stratify VPT children into distinct behavioral subgroups and explore between-subgroup differences in neonatal brain structure and function. 198 VPT children (98 females) previously enrolled in the Evaluation of Preterm Imaging study (EudraCT 2009-011602-42) underwent Magnetic Resonance Imaging at term-equivalent age and neuropsychological assessments at 4-7 years. Using an integrative clustering approach, we combined neonatal socio-demographic, clinical factors and childhood socio-emotional and executive function outcomes, to identify distinct subgroups of children based on their similarity profiles in a multidimensional space. We characterized resultant subgroups using domain-specific outcomes (temperament, psychopathology, IQ and cognitively stimulating home environment) and explored between-subgroup differences in neonatal brain volumes (voxel-wise Tensor-Based-Morphometry), functional connectivity (voxel-wise degree centrality) and structural connectivity (Tract-Based-Spatial-Statistics). Results showed two-and three-cluster data-driven solutions. The two-cluster solution comprised a ‘resilient’ subgroup (lower psychopathology and higher IQ, executive function and socio-emotional outcomes) and an ‘at-risk’ subgroup (poorer behavioral and cognitive outcomes). The three-cluster solution showed an additional third ‘intermediate’ subgroup displaying behavioral and cognitive outcomes intermediate between the resilient and at-risk subgroups. The resilient subgroup had the most cognitively stimulating home environment and the at-risk subgroup showed the highest neonatal clinical risk, while the intermediate subgroup showed the lowest clinical but the highest socio-demographic risk. Compared to the intermediate subgroup, the resilient subgroup displayed larger neonatal insular and orbitofrontal volumes and stronger orbitofrontal functional connectivity, while the at-risk group showed widespread white matter microstructural alterations. These findings suggest that risk stratification following VPT birth is feasible and could be used translationally to guide personalized interventions aimed at promoting children’s resilience.
Posteromedial thalamic nucleus activity significantly contributes to perceptual discrimination
Authors: Qi Jia , Ye Changquan , Naskar Shovan , Inácio Ana R. , Lee Soohyun
Published: October 2022

Higher-order sensory thalamic nuclei are densely connected with multiple cortical and subcortical areas, yet the role of these nuclei remains elusive. The posteromedial (POm) thalamic nucleus, the higher-order thalamic nucleus in the rodent somatosensory system, is an anatomical hub broadly connected with multiple sensory and motor brain areas, yet weakly responds to passive sensory stimulation and whisker movements. To understand the role of POm in sensory perception, we developed a self-initiated, two-alternative forced-choice task in freely moving mice during active sensing. Using optogenetic and chemogenetic manipulation, we show that POm thalamic nucleus plays a significant role in sensory perception and the projection from the primary somatosensory cortex to POm is critical for the contribution of POm in sensory perception during active sensing.
A Synthetic Dynamic Polyvinyl Alcohol Photoresin for Fast Volumetric Bioprinting of Functional Ultrasoft Hydrogel Constructs
Authors: Qiu Wanwan , Gehlen Jenny , Bernero Margherita , Gehre Christian , Schädli Gian Nutal , Müller Ralph , Qin Xiao-Hua
Published: October 2022

Tomographic volumetric bioprinting (VBP) enables fast photofabrication of cell-laden hydrogel constructs in one step, addressing the limitations of conventional layer-by-layer additive manufacturing. However, existing biomaterials that fulfill the physicochemical requirements of VBP are limited to gelatin-based photoresins of high polymer concentrations. The printed microenvironments are predominantly static and stiff, lacking sufficient capacity to support 3D cell growth. We here report a dynamic resin based on thiol-ene photo-clickable polyvinyl alcohol (PVA) and thermo-sensitive sacrificial gelatin for fast VBP of functional ultrasoft cell-laden hydrogel constructs within 7-15 seconds. Using gelatin allows VBP of permissive hydrogels with low PVA contents of 1.5%, providing a stress-relaxing environment for fast cell spreading, 3D osteogenic differentiation of embedded human mesenchymal stem cells and matrix mineralization. Additionally, site-specific immobilization of molecules-of-interest inside a PVA hydrogel is achieved by 4D tomographic thiol-ene photopatterning. This technique may enable spatiotemporal control of cell-material interactions and guidedin vitrotissue formation using programmed cell-friendly light. Altogether, this study introduces a synthetic dynamic photoresin enabling fast VBP of functional ultrasoft hydrogel constructs with well-defined physicochemical properties and high efficiency.