bluuebunny/crossref_metadata_2025 huggingface dataset:
Neural circuit models for evidence accumulation through choice-selective sequences
Authors: Brown Lindsey S. , Cho Jounhong Ryan , Bolkan Scott S. , Nieh Edward H. , Schottdorf Manuel , Tank David W. , Brody Carlos D. , Witten Ilana B. , Goldman Mark S.
Published: September 2023

Decision making is traditionally thought to be mediated by populations of neurons whose firing rates persistently accumulate evidence across time. However, recent decision-making experiments in rodents have observed neurons across the brain that fire sequentially as a function of spatial position or time, rather than persistently, with the subset of neurons in the sequence depending on the animal’s choice. We develop two new candidate circuit models, in which evidence is encoded either in the relative firing rates of two competing chains of neurons or in the network location of a stereotyped pattern (“bump”) of neural activity. Encoded evidence is then faithfully transferred between neuronal populations representing different positions or times. Neural recordings from four different brain regions during a decision-making task showed that, during the evidence accumulation period, different brain regions displayed tuning curves consistent with different candidate models for evidence accumulation. This work provides mechanistic models and potential neural substrates for how graded-value information may be precisely accumulated within and transferred between neural populations, a set of computations fundamental to many cognitive operations.
Permanent Neonatal diabetes-causing Insulin mutations have dominant negative effects on beta cell identity
Authors: Zhang Yuwei , Sui Lina , Du Qian , Haataja Leena , Yin Yishu , Viola Ryan , Xu Shuangyi , Nielsson Christian Ulrik , Leibel Rudolph L. , Barbetti Fabrizio , Arvan Peter , Egli Dieter
Published: September 2023

Heterozygous coding sequence mutations of theINSgene are a cause of permanent neonatal diabetes (PNDM) that results from beta cell failure. We explored the causes of beta cell failure in two PNDM patients with two distinctINSmutations. Using b and mutated hESCs, we detected accumulation of misfolded proinsulin and impaired proinsulin processingin vitro, and a dominant-negative effect of these mutations on the in vivo performance of patient-derived SC-beta cells after transplantation into NSG mice. These insulin mutations derange endoplasmic reticulum (ER) homeostasis, and result in the loss of beta-cell mass and function. In addition to anticipated apoptosis, we found evidence of beta-cell dedifferentiation, characterized by an increase of cells expressing both Nkx6.1 and ALDH1A3, but negative for insulin and glucagon. These results highlight both known and novel mechanisms contributing to the loss and functional failure of human beta cells with specific insulin gene mutations.
WITHDRAWN: Demographic and ecological drivers of infectome diversity in companion cats
Authors: Sun Yankuo , Xing Jiabao , Xu Sijia , Li Yue , Gao Han , Cheng Song , Kuang Qiyuan , Dong Jun , Zhang Tianyou , Lu Gang , Baele Guy , Zhang Guihong
Published: September 2023

Withdrawal Statement

The authors have withdrawn their manuscript owing to data ambiguity. Therefore, the authors do not wish this work to be cited as a reference for the project. If you have any questions, please contact the corresponding author.
Visual cortical area contributions to the transient, multifocal and steady-state VEP: A forward model-informed analysis
Authors: Mohr Kieran S , Geuzebroek Anna C , Kelly Simon P
Published: September 2023

Central to our understanding of how visual evoked potentials (VEPs) contribute to visual processing is the question of where their anatomical sources are. Three well-established measures of low-level visual cortical activity are widely used: the first component (“C1”) of the transient and multifocal VEP, and the steady-state VEP (SSVEP). Although primary visual cortex (V1) activity has often been implicated in the generation of all three signals, their dominant sources remain uncertain due to the limited resolution and methodological heterogeneity of source modelling. Here, we provide the first characterisation of all three signals in one analytic framework centred on the ‘cruciform model’, which describes how scalp topographies of V1 activity vary with stimulus location due to the retinotopy and unique folding pattern of V1. We measured the transient C1, multifocal C1, and SSVEPs driven by an 18.75Hz and 7.5Hz flicker, and regressed them against forward-models of areas V1, V2 and V3 generated from the Benson-2014 retinotopy atlas. The topographic variations of all four VEP signals across the visual field were better captured by V1 models, explaining between 2-6 times more variance than V2/V3. Models with all three visual areas improved fit further, but complementary analyses of temporal dynamics across all three signals indicated that the bulk of extrastriate contributions occur considerably later than V1. Overall, our data support the use of peak C1 amplitude and SSVEPs to probe V1 activity, although the SSVEP contains stronger extrastriate contributions. Moreover, we provide elaborated heuristics to distinguish visual areas in VEP data based on signal lateralization as well as polarity inversion.
Glioblastoma is spatially organized by neurodevelopmental programs and a glial-like wound healing response
Authors: Mossi Albiach Alejandro , Janusauskas Jokubas , Kapustová Ivana , Kvedaraite Egle , Codeluppi Simone , Munting Johannes B. , Borm Lars E. , Kjaer Jacobsen Jesper , Shamikh Alia , Persson Oscar , Linnarsson Sten
Published: September 2023

Glioblastoma is the deadliest brain cancer, characterized by great cellular diversity and unique histology. To understand the spatial organization of transcriptional cell states, we mapped the expression of 888 genes in centimeter-scaletissuesectionsfromalargepatientcohort.Wefoundahierarchyofcellularstatesakintonormal brain development, including proliferating and differentiated cells interacting with the stroma. We discovered that mesenchymal-like glioblastoma cells comprised a major glial-like wound-response component and a distinct gliosarcoma-specific malignant fibroblast type. Our analysis highlighted hypoxia, tissue damage, and woundhealingasmajorfactorsinglioblastomaspatialorganization.Tumormicroenvironment variedalongthe hypoxia gradient, inducing the recruitment of monocytes and pro-tumorigenic macrophages, and propagating wound response program activation in malignant glial cells. Our study reveals the dynamic progression of glioblastoma organization independent of its mutational profile, in response to tumor-induced injury.
A kidney-hypothalamus axis promotes compensatory glucose production in response to glycosuria
Authors: Faniyan Tumininu S. , Zhang Xinyi , Morgan Donald A. , Robles Jorge , Bathina Siresha , Brookes Paul S. , Rahmouni Kamal , Perry Rachel J. , Chhabra Kavaljit H.
Published: September 2023

The kidneys facilitate energy conservation through reabsorption of nutrients including glucose. Almost all the filtered blood glucose is reabsorbed by the kidneys. Loss of glucose in urine (glycosuria) is offset by an increase in endogenous glucose production to maintain normal energy supply in the body. How the body senses this glucose loss and consequently enhances glucose production is unclear. Using renalGlut2knockout mice, we demonstrate that elevated glycosuria activates the hypothalamic-pituitary-adrenal axis, which in turn drives endogenous glucose production. This phenotype was attenuated by selective afferent renal denervation, indicating the involvement of the afferent nerves in promoting the compensatory increase in glucose production. In addition, through plasma proteomics analyses we observed that acute phase proteins - which are usually involved in body’s defense mechanisms against a threat – were the top candidates which were either upregulated or downregulated in renalGlut2KO mice. Overall, afferent renal nerves contribute to promoting endogenous glucose production in response to elevated glycosuria and loss of glucose in urine is sensed as a biological threat in mice. These findings may be useful in improving efficiency of drugs like SGLT2 inhibitors that are intended to treat hyperglycemia by enhancing glycosuria but are met with a compensatory increase in endogenous glucose production.
CD4+T cell-derived IL21 regulates stem cell fate in acute myeloid leukemia by activation of p38-MAPK signaling
Authors: Rubino Viviana , Hüppi Michelle , Höpner Sabine , Tortola Luigi , Taylor Lea , Keller Irene , Bruggman Remy , Kronig Marie-Noëlle , Bacher Ulrike , Kopf Manfred , Ochsenbein Adrian F. , Riether Carsten
Published: September 2023

Self-renewal programs in leukemia stem cells (LSCs) predict poor prognosis in acute myeloid leukemia (AML) patients. We identified CD4+T cell-derived interleukin (IL) 21 as an important negative regulator of self-renewal of murine and human LSCs, but not hematopoietic stem cells. IL21/IL21R signaling favored asymmetric cell division and differentiation in LSCs through accumulation of reactive oxygen species (ROS) and activation of p38-MAPK signaling, resulting in reduced LSCs number and significantly prolonged survival in murine AML models. In human AML, serum IL21 at diagnosis was identified as an independent positive prognostic biomarker for outcome and correlated with better survival and higher complete remission rate in patients that underwent high-dose chemotherapy. IL21 inhibited primary AML LSCs function in vitro by activating ROS and p38-MAPK signaling and this effect was enhanced by cytarabine treatment. Consequently, promoting IL21/IL21R signaling on LSCs may be a novel approach to decrease stemness and increase differentiation in AML.
Prot-SCL: State of the art Prediction of Protein Subcellular Localization from Primary Sequence Using Contrastive Learning
Authors: Giannakoulias Sam , Ferrie John J. , Apicello Andrew , Mitchell Carter
Published: September 2023

Protein subcellular localization is a critically important parameter to consider when designing expression constructs and production strategies for industry scale protein production. In this study, we present Prot-SCL an innovative self-supervised machine learning approach to predict protein subcellular localization exclusively from primary sequence. The models herein were learned from a dataset of subcellular localizations derived by exhaustively analyzing the Uniprot database. The set of localization data was rigorously curated for machine learning by employing group sampling following clustering of the protein sequences. The novel component of this approach lies in the development of a triplet neural network architecture capable of generating meaningful embeddings for classification of protein subcellular localization. We observed a robust predictive power for our classical gradient boosted machine learning models trained on these triplet embeddings in both cross validation and in generalization to the testing set. Importantly, we have made this extensive dataset of protein subcellular localizations publicly accessible, facilitating future, need-based, localization studies. Finally, we provide the relevant codebase to encourage a wider adoption and expansion of this methodology.

GRAPHICAL ABSTRACT
Inflammation-Induced Claudin-2 Upregulation Limits Pancreatitis Progression by Enhancing Tight Junction-Controlled Pancreatic Ductal Transport
Authors: Kesaraju Sneha , Li Yueying , Xing Junjie , Tracy Melissa , Wannemo Kristin , Holder Aysha , Zhao Piao , Khan Mohammed Azizuddin , Kainov Joseph , Rana Niyati , Sidahmed Mohammed , Hyoju Sanjiv , Smith Lexi , Matthews Jonathan , Tay Savas , Khalili-Araghi Fatemeh , Rana Maunak , Oakes Scott A. , Shen Le , Weber Christopher R.
Published: September 2023

Pancreatitis is an inflammatory disease of the pancreas that can arise due to various factors, including environmental risks such as diet, alcohol, and smoking, as well as genetic predispositions. In some cases, pancreatitis may progress and become chronic, leading to irreversible damage and impaired pancreatic function. Genome-wide association studies (GWAS) have identified polymorphisms at the X-linkedCLDN2locus as risk factors for both sporadic and alcohol-related chronic pancreatitis.CLDN2encodes claudin-2 (CLDN2), a paracellular cation-selective channel localized at tight junctions and expressed in the pancreas and other secretory organs. However, whether and how CLDN2 may modify pancreatitis susceptibility remains poorly understood. We aimed to clarify the potential role of CLDN2 in the onset and progression of pancreatitis.

We employed multiple methodologies to examine the role of CLDN2 in human pancreatic tissue, caerulein-induced experimental pancreatitis mouse model, and pancreatic ductal epithelial organoids. In both human chronic pancreatitis tissues and caerulein-induced experimental pancreatitis, CLDN2 protein was significantly upregulated in pancreatic ductal epithelial cells. Our studies using pancreatic ductal epithelial organoids and mice demonstrated the inflammatory cytokine IFNγ upregulates claudin-2 expression at both RNA and protein levels. Following caerulein treatment,IfngKO mice had diminished upregulation of CLDN2 relative to WT mice, indicating that caerulein-induced claudin-2 expression is partially driven by IFNγ. Functionally,Cldn2knockout mice developed more severe caerulein-induced experimental pancreatitis, indicating CLDN2 plays a protective role in pancreatitis development. Pancreatic ductal epithelial organoid-based studies demonstrated that CLDN2 is critical for sodium-dependent water transport and necessary for cAMP-driven, CFTR-dependent fluid secretion. These findings suggest that functional crosstalk between CLDN2 and CFTR is essential for fluid transport in pancreatic ductal epithelium, which may protect against pancreatitis by adjusting pancreatic ductal secretion to prevent worsening autodigestion and inflammation.

In conclusion, our studies suggest CLDN2 upregulation during pancreatitis may play a protective role in limiting disease development, and decreased CLDN2 function may increase pancreatitis severity. These results point to the possibility of modulating pancreatic ductal CLDN2 function as an approach for therapeutic intervention of pancreatitis.
Understanding the biosynthesis of human IgMs through a combinatorial expression of mutant subunits that affect different assembly steps
Authors: Hasegawa Haruki , Wang Songyu , Kast Eddie , Chou Hui-Ting , Kaur Mehma , Janlaor Tanakorn , Mostafavi Mina , Wang Yi-Ling , Li Peng
Published: September 2023

Polymeric IgMs are secreted from plasma cells abundantly despite their structural complexity and intricate multimerization steps. To gain new insights into IgM’s assembly mechanics that underwrite the high-level secretion, we characterized the biosynthetic process of a natural human IgM, SAM-6, using a recombinant HEK293 cell system. By creating a series of mutant subunits that differentially disrupt specific sets of inter-chain disulfide bonds, we assessed their effects on various aspects of IgM biosynthesis in 48 different mutant subunit combinations. The analysis included the visualization of intracellular biosynthetic events such as steady-state subcellular subunit distribution, secretory trafficking bottlenecks, and the ER-associated Russell body formation by fluorescent microscopy. We also characterized various extracellular events including secreted IgM product quality, secretion output, and the release of various assembly intermediates using biochemical and biophysical assays. In this combinatorial mutagenesis approach, we unexpectedly found that the loss of multiple inter-chain disulfide bonds, including the one between μHC and λLC subunits, was tolerated in polymeric IgM formation and secretion. This finding revealed the vital role of underlying non-covalent protein-protein association not only during the orchestration of initial subunit interactions but also in maintaining the polymeric IgM product integrity during ER quality control steps, secretory pathway trafficking, and secretion. We suggest that the IgM assembly process is inherently robust and has a stopgap that permits the secretion of polymeric IgM even when not all the prescribed inter-chain disulfide bonds are formed. This study holistically presents the requirements and exemptions in polymeric IgM biosynthesis by encompassing the characterization of intracellular and extracellular events and the roles of covalent and non-covalent interactions. These findings can guide antibody engineering strategy when designing IgM-based multivalent modalities.
Gemcitabine therapeutically disrupts essential SIRT1-mediated p53 repression in Atypical Teratoid/Rhabdoid Tumors
Authors: Metselaar Dennis S. , Meel Michaël H. , Goulding Joshua R. , Waranecki Piotr , de Gooijer Mark C. , Breur Marjolein , Koster Jan , Veldhuijzen van Zanten Sophie E.M. , Bugiani Marianna , Wesseling Pieter , Kaspers Gertjan J.L. , Hulleman Esther
Published: September 2023

Background

Atypical Teratoid/Rhabdoid Tumors (ATRT) are highly malignant embryonal tumors of the central nervous system with a dismal prognosis. Despite recent advances in understanding the molecular characteristics and subclasses of these tumors, effective therapeutic options remain scarce.

Methods

In this study, we developed and validated a novel patient-derived ATRT culture and xenograft model, which we used alongside a panel of other primary ATRT models for large-scale drug discovery assays. The identified hits were mechanistically and therapeutically investigated using an array of molecular assays and two orthotopic xenograft murine models.

Results

We found that ATRT are selectively sensitive to the nucleoside analogue gemcitabine, with additional efficacy in Sonic Hedgehog (SHH)-subtype ATRT. Gene expression profiles and protein analyses indicated that gemcitabine treatment causes degradation of Sirtuin 1 (SIRT1), resulting in cell death through activation of NF-kB and p53. Furthermore, we discovered that gemcitabine-induced loss of SIRT1 results in a nucleus-to-cytoplasm translocation of the SHH signaling activator GLI2, explaining the additional gemcitabine sensitivity in SHH-subtype ATRT. Treatment of SHH-subgroup ATRT xenograft-bearing mice with gemcitabine resulted in a >30% increase in median survival (p<0.005, log-rank test) and yielded long-term survivors in two independent patient-derived xenograft models.

Conclusions

These findings demonstrate that ATRT are highly sensitive to gemcitabine treatment, and we propose that gemcitabine may form part of a future multimodal treatment strategy for ATRT.

Key points

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ATRT are specifically sensitive to gemcitabine treatment

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SIRT1 may serve as a novel therapeutic target in ATRT

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Gemcitabine should be considered for clinical use in ATRT patients

Importance of the study

Atypical Teratoid/Rhabdoid Tumors (ATRT) are highly malignant pediatric brain tumors with a 5-year survival of merely 30%, for which effective treatment options are limited. In this study, we propose a potential novel treatment strategy for ATRT patients. We show that ATRT are highly sensitive to the chemotherapeutic gemcitabine, that takes advantage of ATRT-specific SIRT1 overexpression and disrupts p53 suppression and hedgehog signaling. Importantly, we show that gemcitabine significantly prolongs survival of ATRT patient-derived xenograft models, prolonging survival by over 30%. This effect was achieved using gemcitabine concentrations that are achievable in human brain and well-tolerated in pediatric patients. As such, gemcitabine could be readily incorporated into clinical treatment protocols and expand the still very limited therapeutic options for ATRT-patients.
Route Retracing: Way-pointing in Trail Following Ants
Authors: Freas Cody A , Spetch Marcia L
Published: September 2023

Maintaining positional estimates of goal locations is a fundamental task for navigating animals. Diverse animal groups, including both vertebrates and invertebrates, can accomplish this through path integration (PI). During PI, navigators integrate movement changes, tracking both distance and direction, to generate a spatial estimate of their start location, or global vector, allowing efficient direct return travel without retracing the outbound route. In ants, PI is accomplished through the coupling of pedometer and celestial compass estimates. Within the PI system, it has been theorized navigators may segment the global vector into local-vectors for way-pointing. However, this is controversial, as these navigators may instead be homing via the view alignment. Here, we present evidence trail-following ants can attend to segments of their global vector to retrace their non-straight pheromone trails, without the confound of familiar views.Veromessor pergandeiforagers navigate via directionally distinct segments of their PI by orienting along separate legs of their inbound route at unfamiliar locations, indicating these changes are not triggered by familiar external cues, but by the PI state. These findings contrast with the view of path integration as a singular memory estimate and underscore the system’s ability to way-point to intermediate goals along the inbound route. We discuss how the foraging ecology of ant species that rely on non-straight pheromone-marked trails may support attending vector segments to remain on the pheromone rather than attempting straight-line shortcuts back to the nest.
Sensitivity of BA.2.86 to prevailing neutralising antibody responses
Authors: Sheward Daniel J , Yang Yiqiu , Westerberg Michelle , Öling Sofia , Muschiol Sandra , Sato Kenta , Peacock Thomas P , Karlsson Hedestam Gunilla B , Albert Jan , Murrell Ben
Published: September 2023

A new SARS-CoV-2 variant, designated BA.2.86, has recently emerged with over 30 spike mutations relative to its parental BA.2, raising questions about its degree of resistance to neutralising antibodies. Using a spike-pseudotyped virus model we characterise neutralisation of BA.2.86 by clinically relevant monoclonal antibodies and by two cohorts of serum sampled from Stockholm, including both a recent cohort, and one sampled prior to the arrival of XBB in Sweden.
SARS-CoV-2 quarantine mandated by contact tracing: burden and infection rate among close contacts in Zurich, Switzerland, 2020-2021
Authors: Aschmann Hélène E. , Domenghino Anja , Jung Ruedi , Ballouz Tala , Menges Dominik , Fehr Jan , Puhan Milo A.
Published: September 2023

Objectives

Before vaccines and effective treatments were available, quarantine of close contacts was important to limit the spread of SARS-CoV-2. To evaluate potential benefits and harms of quarantine, we aimed to estimate infection rates and describe experiences and mental health among persons in mandated quarantine during the early SARS-CoV-2 pandemic.

Methods

We invited adults in mandated quarantine after an exposure to SARS-CoV-2 identified through contact tracing of the Canton of Zurich, Switzerland, between August 2020 and January 2021. Participants completed two questionnaires and received up to two SARS-CoV-2 polymerase chain reaction tests, during and at the end of quarantine.

Results

Among 395 participants, quarantine duration ranged from 2 to 20 days. By day 11 since the last contact, 11.1% [95% CI 8.4%–14.7%] were infected with SARS-CoV-2. The proportion of participants with symptoms of depression doubled from 9.3% before quarantine to 18.9% during quarantine, and 12.1% reported quarantine was very or extremely difficult.

Conclusions

Although quarantine was only moderately burdensome for most participants, some experienced significant difficulties and burden. Policymakers need to balance infection control with potential harms placed on individuals.
Cold-induced muscle atrophy in zebrafish: Insights from swimming activity and gene expression analysis
Authors: Ikeda Daisuke , Fujita Seina , Toda Kaito , Yaginuma Yuma , Kan-no Nobuhiro , Watabe Shugo
Published: September 2023

The investigation into the effects of cold acclimation on fish skeletal muscle function and its potential implications for muscle atrophy is of great interest to us. This study examines how rearing zebrafish at low temperatures affects their locomotor activity and the expression of genes associated with muscle atrophy. Zebrafish were exposed to temperatures ranging from 10 °C to 25 °C, and their swimming distance was measured. The expression levels of important muscle atrophy genes, Atrogin-1 and MuRF1, were also evaluated. Our findings show that swimming activity significantly decreases when the water temperature ranges from 10 °C to 15 °C, indicating a decrease in voluntary movement. Additionally, gene expression analysis shows a significant increase in the expression of Atrogin-1 and MuRF1 at 10 °C. This up-regulation could lead to muscle atrophy caused by decreased activity in cold temperatures. To investigate the effects of exercise on reducing muscle atrophy, we subjected zebrafish to forced swimming at a temperature of 8 °C for ten days. This treatment significantly reduced the expression of Atrogin-1 and MuRF1, emphasizing the importance of muscle stimulation in preventing muscle atrophy in zebrafish. These findings suggest that zebrafish can serve as a valuable model organism for studying muscle atrophy and can be utilized in drug screening for muscle atrophy-related disorders. Cold-reared zebrafish provide a practical and ethical approach to inducing disuse muscle atrophy, providing valuable insights into potential therapeutic strategies for addressing skeletal muscle atrophy.
Small Extracellular Vesicles from Failing Heart Accelerate Tumor Growth
Authors: Caller Tal , Rotem Itai , Shaihov–Teper Olga , Lendengolts Daria , Schary Yeshai , Shai Ruty , Glick-Saar Efrat , Dominissini Dan , Motie Menachem , Katzir Idan , Popovtzer Rachela , Nahmoud Merav , Boomgarden Alex , D’Souza-Schorey Crislyn , Naftali-Shani Nili , Leor Jonathan
Published: September 2023

Background

Myocardial infarction (MI) and heart failure (HF) are associated with an increased incidence of cancer. The mechanism is complex and unclear. Here, we aimed to test our hypothesis that cardiac small extracellular vesicles (sEVs), particularly cardiac mesenchymal stromal cells-derived sEVs (cMSC-sEVs), contribute to the link between post-MI HF and cancer.

Methods

We purified and characterized sEVs from the whole heart and cultured cMSCs. Then, we analyzed cMSC-EV cargo and pro-neoplastic effects on several types of cancer cell lines, macrophages, and endothelial cells. Next, we modeled post-MI HF along with heterotopic and orthotopic lung and breast cancer tumors in mice. We used cMSC-sEV transfer to assess sEV biodistribution and its effect on tumor growth. Finally, we tested the effects of sEV depletion and spironolactone treatment on cMSC-EV release and tumor growth.

Results

Post-MI hearts, particularly cMSCs, produced more sEVs with pro-neoplastic cargo than non-failing hearts did. Proteomic analysis revealed unique protein profiles and higher quantities of tumor-promoting cytokines, proteins, and microRNAs in cMSC-sEVs from failing hearts. The pro-neoplastic effects of cMSC-sEVs varied with different types of cancer cells, substantially affecting lung cancer cells relative to other more aggressive cancer cell lines. We also found that post-MI cMSC-sEVs activated resting macrophages into pro-angiogenic and pro-tumorigenic states in vitro. At 28-day follow-up analysis, mice with post-MI HF developed larger lung tumors than did sham-MI mice. Adoptive transfer of cMSC-sEVs from failing hearts accelerated lung tumor growth, and biodistribution analysis revealed an accumulating cMSC- sEVs in tumor cells along with accelerated tumor cell proliferation. Significantly, sEV depletion reduced the tumor-promoting effects of HF, and adoptive transfer of cMSC-sEVs from failing hearts partially restored it. Finally, post-MI spironolactone treatment reduced the number of cMSC-sEVs and suppressed tumor growth during post-MI HF.

Conclusions

For the first time, we show that cardiac sEVs, specifically cMSC-sEVs from post-MI failing hearts, carry multiple pro-tumorigenic factors. Uptake of cMSC-sEVs by cancer cells accelerates tumor growth. Post-MI spironolactone treatment reduces the associated tumor growth. Thus, we provide new insight into the link between post-MI HF and cancer and propose a translational option to mitigate this deadly association.
Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma
Authors: Sehgal Manas , Nayak Sonali Priyadarshini , Sahoo Sarthak , Somarelli Jason A , Jolly Mohit Kumar
Published: September 2023

Neuroblastoma is the most frequent extracranial pediatric tumor and leads to 15% of all cancer-related deaths in children. Tumor relapse and therapy resistance in neuroblastoma are driven by phenotypic plasticity and heterogeneity between noradrenergic (NOR) and mesenchymal (MES) cell states. Despite the importance of this phenotypic plasticity, however, the dynamics and molecular patterns associated with these bidirectional cell-state transitions remain relatively poorly understood. Here, we analyze multiple RNA-seq datasets at both bulk and single-cell resolution, to understand the association between NOR- and MES-specific factors. We observed that NOR-specific and MES-specific expression patterns are largely mutually exclusive, exhibiting a “teams-like” behavior among the genes involved, reminiscent of our earlier observations in lung cancer and melanoma. This antagonism was noticed also in the association of NOR and MES phenotypes with metabolic reprogramming and with immunotherapy targets PD-L1 and GD2, and in experimental perturbations driving the NOR-MES and/or MES-NOR transition. Further, this “teams-like” patterns was seen only among the NOR- and MES-specific genes, but not in housekeeping genes, possibly highlighting a hallmark of network topology enabling cancer cell plasticity.
Predictors of voluntary uptake of modern contraceptive methods in rural Sindh, Pakistan
Authors: Memon Zahid , Ahmed Wardah , Mian Abeer , Jawwad Muhammad , Muhammad Shah , Noorani Abdul Qayyum , Bhutta Zulfiqar , Soltani Hora
Published: September 2023

Introduction

The use of modern contraceptive methods (MCMs) in Pakistan has been stagnant for the last decade. In Sindh, current contraceptive use is at 28.9%, of which 25% is MCMs use. Such a low uptake translates into high unmet need 17% amongst married women. To bridge the gap between the health system and beneficiaries, there is a need to assess predictors that influence voluntary uptake of MCMs among women, at the health services and individual levels.

Methods

A cross-sectional household survey was conducted in two districts of Sindh, Pakistan namely Matiari and Badin. In total, 1684 Married Women of Reproductive Age (MWRA) 15-49 years were interviewed. For the selection of eligible respondents, a two-stage stratified cluster sampling strategy was used. Univariate and multivariable logistic regression was used to determine the predictive factors for the increase in the use of MCM.

Results

Mean age was 32.3 ±SD 7.1 years. Average number of children per woman was 4.0 ± 2.0. Use of modern methods of contraceptive was 26.1% [n=441).Statistically significant socio demographic predictors of MCM included: Number of children 4 or more (AOR 5.234 95%CI 2.78-9.84), Mother having primary education (AOR 1.730 95% CI 1.26-2.36), and Husband having middle education [AOR 1.69 95% CI 1.03 – 2.76).Maternal health services indicators included postnatal checkup of mother (AOR 1.46 95% CI 1.09 – 2.05); women who were visited by Lady Health Workers in their postnatal period and were counseled on family planning (AOR 1.83 95% CI 1.386 - 2.424).

Conclusion

Voluntary uptake of modern contraceptive methods is higher in women having 2 or more children, having primary education and husband having middle education. Significantly, receiving post-natal checkup at facility, and Lady Health Worker visit after delivery have more likelihood to opt for contraception. Additionally, young couple counseling on family planning is imperative to bridge the gap between knowledge and its translation into practice. There is also a need to focus on the provision of integrated family planning and maternal, newborn, and child health services through facility-based and community engagement platforms.
Kin selection underpins family dynamics in rural China
Authors: He Qiao-Qiao , Wang Ming-Yang , Wu Jia-Jia , Feng Tian-Jiao , Zheng Xiu-Deng , Yu Jie-Ru , Tang Song-Hua , Deng Ling-Ling , Fu Chang , Mace Ruth , Tao Yi , Ji Ting
Published: September 2023

The number of co-resident members is an important characteristic of human families and thus plays an important role in human evolution. However, an inclusive fitness model of how many members should co-reside has not been explicitly tested. Here we use an evolutionary game model and a decade of family dynamic data from a rural population of southwestern China (1,110 households) to show that the existence of an evolutionary stable family size can be understood by considering the average local relatedness and average inclusive fitness of the family. Empirical data analyses show that average relatednessdecreased with increasing family size, andwas associated with helping behavior (especially for the elders) in the family, so the family tended to keep a higher level of average relatedness by adjusting the number of co-resident members. These findings are helpful to understand the variation in family size in different cultures and to demonstrate the importance of kin selection in regulating family dynamics.
A developmental ontology for the colonial architecture of salps
Authors: Damian-Serrano Alejandro , Sutherland Kelly R.
Published: September 2023

Colonial animals are composed of clonal individuals that remain physically connected and physiologically integrated. Salps are urochordates with a dual life cycle including an asexual solitary stage that buds sexual colonies composed of jet-propelling zooids that efficiently swim together as a single unit by multi-jet propulsion. Colonies from different species develop distinct architectures characterized by their zooid arrangement patterns, but this diversity has received little attention. Thus, these architectures have never been formally defined using a framework of variables and axes that would allow comparative analyses. We set out to define an ontology of the salp colony architecture morphospace and describe the developmental pathways that build the different architectures. To inform these definitions, we collected and photographed live specimens of adult and developing colonies through offshore SCUBA diving. Since all salp colonies begin their development as a transversal double chain, we characterized each adult colonial architecture as a series of developmental transitions, such as rotations and translations of zooids, relative to their orientation at this early shared stage. We hypothesize that all adult architectures are either final or intermediate stages within three developmental pathways towards either bipinnate, cluster, or helical forms. This framework will enable comparative studies on the biomechanical implications, ecological functions, evolutionary history, and engineering applications of the diversity of salp colony architectures.
Defining RNA oligonucleotides that reverse deleterious phase transitions of RNA-binding proteins with prion-like domains
Authors: Guo Lin , Mann Jacob R. , Mauna Jocelyn C. , Copley Katie E. , Wang Hejia , Rubien Jack D. , Odeh Hana M. , Lin JiaBei , Lee Bo Lim , Ganser Laura , Robinson Emma , Kim Kevin M. , Murthy Anastasia C. , Paul Tapas , Portz Bede , Gleixner Amanda M. , Diaz Zamia , Carey Jenny L. , Smirnov Ashleigh , Padilla George , Lavorando Ellen , Espy Carolann , Shang Yulei , Huang Eric J. , Chesi Alessandra , Fawzi Nicolas L. , Myong Sua , Donnelly Christopher J. , Shorter James
Published: September 2023

RNA-binding proteins with prion-like domains, such as FUS and TDP-43, condense into functional liquids, which can transform into pathological fibrils that underpin fatal neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS)/frontotemporal dementia (FTD). Here, we define short RNAs (24-48 nucleotides) that prevent FUS fibrillization by promoting liquid phases, and distinct short RNAs that prevent and, remarkably, reverse FUS condensation and fibrillization. These activities require interactions with multiple RNA-binding domains of FUS and are encoded by RNA sequence, length, and structure. Importantly, we define a short RNA that dissolves aberrant cytoplasmic FUS condensates, restores nuclear FUS, and mitigates FUS proteotoxicity in optogenetic models and human motor neurons. Another short RNA dissolves aberrant cytoplasmic TDP-43 condensates, restores nuclear TDP-43, and mitigates TDP-43 proteotoxicity. Since short RNAs can be effectively delivered to the human brain, these oligonucleotides could have therapeutic utility for ALS/FTD and related disorders.
Eta-secretase-like processing of the amyloid precursor protein (APP) by RHBDL4
Authors: Ylauna Christine Megane Penalva , Paschkowsky Sandra , Recinto Sherilyn Junelle , Duchesne Anthony , Levet Clemence , Charron François , Freeman Matthew , McKinney R. Anne , Trempe Jean-Francois , Munter Lisa Marie
Published: September 2023

The amyloid precursor protein (APP) has been extensively studied with regards to its contribution to the pathology of Alzheimer’s disease. APP is an ubiquitously expressed type I transmembrane protein synthesized in the endoplasmic reticulum (ER) and translocated to the plasma membrane where it undergoes proteolytic cleavages by several identified proteases. Conversely to other known proteases, we previously elucidated human rhomboid protease RHBDL4 as a novel APP processing enzyme where several cleavages likely occur already in the ER. Interestingly, the pattern of RHBDL4-derived large APP C-terminal fragments resemble those generated by the η-secretase or MT5-MMP, which was described to generate so called Aη fragments. The similarity in large APP C-terminal fragments between both proteases raised the question whether RHBDL4 may contribute to η-secretase activity and Aη-like fragments. Here, we identified two cleavage sites of RHBDL4 in APP by mass spectrometry, which, intriguingly, lie in close proximity to the cleavage sites of MT5-MMP. Indeed, we observed that RHBDL4 generates Aη-like fragmentsin vitrowithout contributions of α-, β-, or γ-secretases. Such Aη-like fragments are likely generated in the ER since RHBDL4-derived APP-C-terminal fragments do not reach the cell surface. Inherited, familial APP mutations appear to not affect this processing pathway. In RHBDL4 knockout mice, we observed increased cerebral full length APP levels in comparison to WT brains in support of RHBDL4 being a physiologically relevant protease for APP. Furthermore, we found secreted Aη fragments in dissociated mixed cortical cultures from wild type mice, however significantly less Aη fragments in cultures from RHBDL4 knockout mice. Our data underscores that RHBDL4 contributes to η-secretease-like processing of APP and that RHBDL4 is a physiologically relevant protease for APP.
Investigating the genetic control of plant development under speed breeding conditions
Authors: Rossi Nicola , Powell Wayne , Mackay Ian , Hickey Lee , Maurer Andreas , Pillen Klaus , Halliday Karen , Sharma Rajiv
Published: September 2023

Speed breeding is a powerful tool to accelerate breeding and research programmes by shortening generation time and has been widely adopted for a range of crop species. Despite its success and growing popularity with breeders the genetic basis of plant development under speed breeding remains unknown. In this study, we explored how genotypes respond in terms of developmental advancement under different photoperiod regimes in the context of speed breeding. A subset of the barley HEB-25 Nested Association Mapping population was evaluated for days to heading and maturity under two contrasting photoperiod conditions: 1) Speed Breeding (SB) consisting of 22 hours of light and 2 hours of darkness), and 2) Normal Breeding (NB) consisting of 16 hours of light and 8 hours of darkness. GWAS revealed that developmental responses under both conditions were largely controlled by two loci:PPDH-1andELF3. Allelic variants at these genes determine whether plants display early flowering and maturity under both NB and SB. At key QTL regions, domesticated alleles were associated with late flowering and maturity in NB and early flowering and maturity in SB, whereas wild alleles were associated with early flowering under both conditions. We hypothesise that this may be related to the dark dependent repression ofPPD-H1byELF3which might be more prominent in NB conditions. Furthermore, by comparing development under two contrasting photoperiod regimes, we were able to derive an estimate of plasticity for the two traits. Interestingly, plasticity in development was largely attributed to allelic variation at ELF3. Our results have important implications for our understanding and optimisation of speed breeding protocols particularly when incorporating genetics from wild relatives into breeding programmes and the design of breeding programmes to support the delivery of climate resilient crops.
Palmitoylation of proteolipid protein M6 promotes tricellular junction assembly in epithelia ofDrosophila
Authors: Schleutker Raphael , Luschnig Stefan
Published: September 2023

Tricellular junctions (TCJs) provide essential adhesive and occluding functions at epithelial cell vertices and play key roles for tissue integrity and physiology, but how TCJs are assembled and maintained is poorly understood. InDrosophila, the transmembrane proteins Anakonda (Aka), Gliotactin (Gli), and M6 constitute tricellular occluding junctions. Aka and M6 localize in an interdependent manner to vertices and are required jointly to localize Gli, but how these proteins interact to assemble TCJs was not known. Here, we show that the tetraspan proteolipid protein M6 physically interacts with Aka and with itself. M6 is palmitoylated on a conserved juxta-membrane cysteine cluster. This modification promotes efficient vertex localization of M6 and binding to Aka, but not to itself, and becomes essential when TCJ protein levels are reduced. Abolishing M6 palmitoylation leads to delayed accumulation of M6 and Aka at vertices but does not affect the rate of TCJ growth or mobility of M6 or Aka. Our findings suggest that palmitoylation-dependent recruitment of Aka by M6 promotes initiation of TCJ assembly, while subsequent TCJ growth relies on different mechanisms independent of M6 palmitoylation.
High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing
Authors: Jensen Thomas BN , Dall Sebastian M , Knutsson Simon , Karst Søren M , Albertsen Mads
Published: September 2023

Reductions in sequencing costs have enabled widespread use of shotgun metagenomics and amplicon sequencing, which have drastically improved our understanding of the microbial world. However, large sequencing projects are now hampered by the cost of library preparation and low sample throughput. Here, we benchmarked three high-throughput DNA extraction methods: ZymoBIOMICS™ 96 MagBead DNA Kit, MP BiomedicalsTMFastDNATM-96 Soil Microbe DNA Kit, and DNeasy® 96 PowerSoil® Pro QIAcube® HT Kit. The DNA extractions were evaluated based on length, quality, quantity, and the observed microbial community across five diverse soil types. DNA extraction of all soil types was successful for all kits, however DNeasy® 96 PowerSoil® Pro QIAcube® HT Kit excelled across all performance parameters. We further used the nanoliter dispensing robot I.DOT One to miniaturize Illumina amplicon and metagenomic library preparation volumes by a factor of 5 and 10, respectively, with no significant impact on the observed microbial communities. With these protocols, DNA extraction, metagenomic library preparation, or amplicon library preparation for one 96-well plate are approx. 3, 5, and 6 hours, respectively. Furthermore, the miniaturization of amplicon and metagenome library preparation reduces the chemical and plastic costs from 5.0 to 3.6 and 59 to 7.3 USD pr. sample.
Post-replicative lesion processing limits DNA damage-induced mutagenesis
Authors: Maslowska Katarzyna H. , Wong Ronald P. , Ulrich Helle D. , Pagès Vincent
Published: September 2023

DNA lesions are a threat to genome stability. To cope with them during DNA replication, cells have evolved lesion bypass mechanisms: Translesion Synthesis (TLS), which allows the cell to insert a nucleotide directly opposite the lesion, with the risk of introducing a mutation, and error-free Damage Avoidance (DA), which uses homologous recombination to retrieve the genetic information from the sister chromatid.

In this study, we investigate the timing of lesion bypass and its implications for the accuracy of the process. Our findings reveal that DNA polymerase η can bypass common, UV-induced TT-cyclobutane pyrimidine dimers at the fork, immediately after encountering the blocking lesion. In contrast, TLS at TT(6-4) photoproducts and bulky G-AAF adducts, mediated by Rev1 and Pol ζ, takes place behind the fork, at post-replicative gaps that are generated downstream of the lesion after repriming. We show that in this latter situation, TLS competes with the DA pathway, thus reducing overall mutagenicity of damage bypass. Additionally, our study demonstrates that Exo1 nuclease influences the balance between TLS and DA by modulating the size of the post-replicative gaps.
Alternative splicing coupled to nonsense-mediated decay coordinates downregulation of non-neuronal genes in developing neurons
Authors: Zhuravskaya Anna , Yap Karen , Hamid Fursham , Makeyev Eugene V.
Published: September 2023

The functional coupling between alternative pre-mRNA splicing (AS) and the mRNA quality control mechanism called nonsense-mediated decay (NMD) can modulate transcript abundance. Previous studies have identified several examples of such a regulation in developing neurons. However, the systems-level effects of AS-NMD in this context are poorly understood. We developed an R package, factR2, which offers a comprehensive suite of AS-NMD analysis functions. Using this tool, we conducted a longitudinal analysis of gene expression in pluripotent stem cells undergoing induced neuronal differentiation. Our analysis uncovered hundreds of AS-NMD events with significant potential to regulate gene expression. Notably, this regulation was significantly overrepresented in specific functional groups of developmentally downregulated genes. Particularly strong association with gene downregulation was detected for alternative cassette exons stimulating NMD (NS-CEs) upon their inclusion into mature mRNA. By combining bioinformatics analyses with CRISPR/Cas9 genome editing and other experimental approaches we show that NS-CEs regulated by the RNA-binding protein PTBP1 dampen the expression of their genes in developing neurons. We also provide evidence that the NS-CE activity is temporally coordinated with NMD-independent gene repression mechanisms. Our study provides an accessible workflow for the discovery and prioritization of AS-NMD targets. It further argues that the AS-NMD pathway plays a widespread role in developing neurons by facilitating the downregulation of functionally related non-neuronal genes.