bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplex profiling of developmental enhancers with quantitative, single-cell expression reporters
Authors: Lalanne Jean-Benoît , Regalado Samuel G. , Domcke Silvia , Calderon Diego , Martin Beth , Li Tony , Suiter Chase C. , Lee Choli , Trapnell Cole , Shendure Jay 
Published: December 2022

AbstractThe inability to scalably and precisely measure the activity of developmental enhancers in multicellular systems is a bottleneck in genomics. Here, we develop a dual RNA cassette that decouples the detection and quantification tasks inherent to multiplex single-cell reporter assays, resulting in accurate measurement of reporter expression over a >10,000-fold range of activity with a precision approaching the limit set by Poisson counting noise. Together with RNA barcode circularization, thesesingle-cellquantitativeexpressionreporters (scQers) provide high-contrast readouts analogous to classicin situassays, but entirely from sequencing. Screening >200 enhancers in a multicellularin vitromodel of early mammalian development, we identified numerous autonomous and cell-type-specific elements, including constituents of theSox2control region exclusively active in pluripotent cells, endoderm-specific enhancers, including nearFoxa2andGata4, and a compact pleiotropic enhancer at theLamc1locus. scQers can be mobilized in developmental systems to quantitatively characterize native, perturbed, and synthetic enhancers at scale, with high sensitivity and at single-cell resolution.
Evaluation of the safety, immunogenicity and efficacy of a new live-attenuated lumpy skin disease vaccine in India
Authors: Kumar Naveen , Barua Sanjay , Kumar Ram , Khandelwal Nitin , Kumar Amit , Verma Assim , Singh Lokender , Godara Bhagraj , Chander Yogesh , Riyesh Thachamvally , Sharma Deepak Kumar , Pathak Anubha , Kumar Sanjay , Dedar Ramesh Kumar , Mehta Vishal , Gaur Mitesh , Bhardwaj Bhupendra , Vyas Vithilesh , Chaudhary Sarjeet , Yadav Vijaypal , Bhati Adrish , Kaul Rakesh , Bashir Arif , Andrabi Anjum , Yousuf Raja Wasim , Koul Abhimanyu , Kachhawa Subhash , Gurav Amol , Gautam Siddharth , Tiwari Hari Audh , Gupta Madhurendu K. , Kumar Rajender , Misri Jyoti , Kumar Ashok , Mohanty Ashok Kumar , Nandi Sukdeb , Singh Karam Pal , Pal Yash , Dutt Triveni , Tripathi Bhupendra N. 
Published: December 2022

ABSTRACTLumpy skin disease (LSD) was reported for the first time in India in 2019 and since then, it has become endemic. Since a homologous (LSD-virus based) vaccine was not available in the country, goatpox virus (GPV)-based heterologous vaccine was authorized for mass immunization against LSD in cattle. This study describes the evaluation of safety, immunogenicity and efficacy of a new live-attenuated LSD vaccine developed using an Indian field strain (LSDV/India/2019/Ranchi). The virus was attenuated by continuous passage (P=50) in Vero cells. The vaccine (50thLSDV passage in Vero cells, named as Lumpi-ProVacInd) did not induce any local or systemic reaction upon its experimental inoculation in calves (n=10). At day 30 post-vaccination (pv), the vaccinated animals were shown to develop antibody- and cell-mediated immune response and exhibited complete protection upon virulent LSDV challenge. We observed a minimum Neethling response (0.018% animals; 5 out of 26940 animals) of the vaccine in field trials among 26940 animals. There was no significant reduction in the milk yield in lactating animals (n=10108), besides there was no abortion or any other reproductive disorder in the pregnant animals (n=2889). Sero-conversion was observed in 85.18% animals in the field by day 30 pv.
Patient-derived tumoroids of advanced high-grade neuroendocrine neoplasms mimic patient chemotherapy responses and guide the design of personalized combination therapies
Authors: April-Monn Simon L. , Detjen Katharina , Kirchner Philipp , Bräutigam Konstantin , Trippel Mafalda A. , Grob Tobias , Statzer Cyril , Maire Renaud S. , Kollàr Attila , Chouchane Aziz , Kunze Catarina A. , Horst David , Sadowski Martin C. , Schrader Jörg , Marinoni Ilaria , Wiedenmann Bertram , Perren Aurel 
Published: December 2022

ABSTRACTThere are no therapeutic predictive biomarkers or representative preclinical models for high-grade gastroenteropancreatic neuroendocrine neoplasms (GEP-NEN), a highly aggressive, fatal, and heterogeneous epithelial malignancy. We established patient-derived (PD) tumoroids from biobanked tissue samples of advanced high-grade GEP-NEN patients and applied this model for targeted rapidex vivopharmacotyping, next-generation sequencing, and perturbational profiling. We used tissue-matched PD tumoroids to profile individual patients, comparedex vivodrug response to patients’ clinical response to chemotherapy, and investigated treatment-induced adaptive stress responses.PD tumoroids recapitulated biological key features of high-grade GEP-NEN and mimicked clinical response to cisplatin and temozolomideex vivo. When we investigated treatment-induced adaptive stress responses in PD tumoroids in silico, we discovered and functionally validated Lysine demethylase 5A and interferon-beta, which act synergistically in combination with cisplatin. Sinceex vivodrug response in PD tumoroids matched clinical patient responses to standard-of-care chemotherapeutics for GEP-NEN, our rapid and functional precision oncology approach could expand personalized therapeutic options for patients with advanced high-grade GEP-NEN.
eEF2 improves dense connective tissue repair and healing outcome by regulating cellular death, autophagy, apoptosis, proliferation and migration
Authors: Chen Junyu , Wang Jin , Wu Xinjie , Simon Nils , Svensson Camilla I , Yuan Juan , Hart David A , Ahmed Aisha S , Ackermann Paul W 
Published: December 2022

AbstractOutcomes following human dense connective tissue (DCT) repair are often variable and suboptimal, resulting in compromised function and development of chronic painful degenerative diseases. Moreover, biomarkers and mechanisms that guide good clinical outcomes after DCT injuries are mostly unknown. Here, we characterize the proteomic landscape of DCT repair following human tendon rupture and its association with long-term patient-reported outcome. Moreover, the regulatory mechanisms of relevant biomarkers were assessed partly by gene silencing experiments. A Mass-Spectrometry based proteomic approach quantified a large number (769) of proteins, including 51 differentially expressed proteins among 20 good versus 20 poor outcome patients. A novel biomarker, elongation factor-2 (eEF2) was identified as being strongly prognostic of the 1-year clinical outcome. Further bioinformatic and experimental investigation revealed that eEF2 positively regulated autophagy, cell proliferation and migration, as well as reduced cell death and apoptosis, leading to improved DCT repair and outcomes. Findings of eEF2 as novel prognostic biomarker could pave the way for new targeted treatments to improve healing outcomes after DCT injuries.
Ocean currents drive the worldwide colonization of the most widespread marine plant, eelgrass (Zostera marina)
Authors: Yu Lei , Khachaturyan Marina , Matschiner Michael , Healey Adam , Bauer Diane , Cameron Brenda , Cusson Mathieu , Duffy J. Emmet , Fodrie F. Joel , Gill Diana , Grimwood Jane , Hori Masakazu , Hovel Kevin , Hughes A. Randall , Jahnke Marlene , Jenkins Jerry , Keymanesh Keykhosrow , Kruschel Claudia , Mamidi Sujan , Moksnes Per-Olav , Nakaoka Masahiro , Pennacchio Christa , Reiss Katrin , Rossi Francesca , Ruesink Jennifer L. , Schultz Stewart , Talbot Sandra , Unsworth Richard , Dagan Tal , Schmutz Jeremy , Stachowicz John J. , Van de Peer Yves , Olsen Jeanine L. , Reusch Thorsten B. H. 
Published: December 2022

AbstractCurrents are unique drivers of oceanic phylogeography and so determine the distribution of marine coastal species, along with past glaciations and sea level changes. Here, we reconstruct the worldwide colonization history of eelgrass (Zostera marinaL.), the most widely distributed marine flowering plant or seagrass from its origin in the Northwest Pacific, based on nuclear and chloroplast genomes. We identified two divergent Pacific clades with evidence for admixture along the East Pacific coast. Multiple west to east (trans-Pacific) colonization events support the key role of the North Pacific Current. Time-calibrated nuclear and chloroplast phylogenies yielded concordant estimates of the arrival ofZ. marinain the Atlantic through the Canadian Arctic, suggesting that eelgrass-based ecosystems, hotspots of biodiversity and carbon sequestration, have only been present since ∼208 Kya (thousand years ago). Mediterranean populations were founded ∼53 Kya while extant distributions along western and eastern Atlantic shores coincide with the end of the Last Glacial Maximum (∼20 Kya). The recent colonization and 5-to 7-fold lower genomic diversity of Atlantic compared to the Pacific populations raises concern and opportunity about how Atlantic eelgrass might respond to rapidly warming coastal oceans.
De novo design of high-affinity protein binders to bioactive helical peptides
Authors: Vázquez Torres Susana , Leung Philip J. Y. , Lutz Isaac D. , Venkatesh Preetham , Watson Joseph L. , Hink Fabian , Huynh Huu-Hien , Yeh Andy Hsien-Wei , Juergens David , Bennett Nathaniel R. , Hoofnagle Andrew N. , Huang Eric , MacCoss Michael J , Expòsit Marc , Lee Gyu Rie , Levine Paul M. , Li Xinting , Lamb Mila , Korkmaz Elif Nihal , Nivala Jeff , Stewart Lance , Rogers Joseph M. , Baker David 
Published: December 2022

AbstractMany peptide hormones form an alpha-helix upon binding their receptors1–4, and sensitive detection methods for them could contribute to better clinical management.De novoprotein design can now generate binders with high affinity and specificity to structured proteins5,6. However, the design of interactions between proteins and short helical peptides is an unmet challenge. Here, we describe parametric generation and deep learning-based methods for designing proteins to address this challenge. We show that with the RFdiffusiongenerative model, picomolar affinity binders can be generated to helical peptide targets either by noising and then denoising lower affinity designs generated with other methods, or completelyde novostarting from random noise distributions; to our knowledge these are the highest affinity designed binding proteins against any protein or small molecule target generated directly by computation without any experimental optimization. The RFdiffusiondesigns enable the enrichment of parathyroid hormone or other bioactive peptides in human plasma and subsequent detection by mass spectrometry, and bioluminescence-based protein biosensors. Capture reagents for bioactive helical peptides generated using the methods described here could aid in the improved diagnosis and therapeutic management of human diseases.7,8
Structural basis for BIRC6 to balance apoptosis and autophagy
Authors: Liu Shuo-Shuo , Jiang Tian-Xia , Bu Fan , Zhao Ji-Lan , Wang Guang-Fei , Yang Guo-Heng , Kong Jie-Yan , Qie Yun-Fan , Wen Pei , Fan Li-Bin , Li Ning-Ning , Gao Ning , Qiu Xiao-Bo 
Published: December 2022

ABSTRACTCaspase-9 is the initiator caspase for the intrinsic apoptotic cell death pathway, and is critical to the activation of effector caspases during apoptosis, but how its levels and activities are maintained remains unclear. The gigantic Inhibitor of Apoptosis Protein (IAP) BIRC6/BRUCE/Apollon not only inhibits apoptosis, but also promotes ubiquitination of the key autophagic protein LC3 and inhibits autophagy. Here we show that BIRC6 forms an anti-parallel U-shaped dimer in a 3.6-Å cryo-EM structure with multiple previously unannotated domains, including a ubiquitin-like domain, and discover that the mitochondria-derived pro-apoptotic factor Smac/DIABLO binds BIRC6 by interacting with one BIR domain, two carbohydrate-binding modules and two helices in the central cavity. Notably, Smac outcompetes the effector caspase 3 and the pro-apoptotic protease HtrA2, but not caspase 9, for binding BIRC6. BIRC6 strongly inhibits cellular activity of caspase 9, but weakly suppresses that of caspase 3. Meanwhile, BIRC6 binds LC3 through an LC3-interacting region, probably following dimer disruption of this BIRC6 region. Deficiency in LC3 ubiquitination promotes autophagy and autophagic degradation of BIRC6, and inhibits apoptosis. Moreover, induction of autophagy promotes autophagic degradation of both procaspase-9 and active caspase-9, but not of effector caspases. These results are important to understand how the balance between apoptosis and autophagy is regulated under pathophysiological conditions.
Comprehensive Evaluation of Rapamycin’s Specificity as an mTOR Inhibitor
Authors: Artoni Filippo , Grützmacher Nina , Demetriades Constantinos 
Published: December 2022

AbstractRapamycin is a macrolide antibiotic that functions as an immunosuppressive and anti-cancer agent, and displays robust anti-ageing effects in multiple organisms including humans. Importantly, rapamycin analogs (rapalogs) are of clinical importance against certain cancer types and neurodevelopmental diseases. Although rapamycin is widely perceived as an allosteric inhibitor of mTOR (mechanistic target of rapamycin), the master regulator of cellular and organismal physiology, its specificity has not been thoroughly evaluated so far. In fact, previous studies in cells and in mice suggested that rapamycin may be also acting independently from mTOR to influence various cellular functions. Here, we generated a gene-edited cell line, that expresses a rapamycin-resistant mTOR mutant (mTORRR), and assessed the effects of rapamycin treatment on the transcriptome and proteome of control or mTORRR-expressing cells. Our data reveal a striking specificity of rapamycin towards mTOR, demonstrated by virtually no changes in mRNA or protein levels in rapamycin-treated mTORRRcells, even following prolonged drug treatment. Overall, this study provides the first comprehensive and conclusive assessment of rapamycin’s specificity, with important potential implications for ageing research and human therapeutics.
Network analysis of chromophore binding site in LOV domain
Authors: Panda Rishab , Panda Pritam Kumar , Krishnamoorthy Janarthanan , Kar Rajiv K. 
Published: December 2022

AbstractPhotoreceptor proteins are versatile toolbox for developing biosensors for optogenetic applications. These molecular tools get activated upon illumination of blue light, which in turn offers a non-invasive method for gaining high spatiotemporal resolution and precise control of cellular signal transduction. The Light-Oxygen-Voltage (LOV) domain family of proteins is a well-recognized system for constructing optogenetic devices. Translation of these proteins into efficient cellular sensors is possible by tuning their photochemistry lifetime. However, the bottleneck is the need for more understanding of the relationship between the protein environment and photocycle kinetics. Significantly, the effect of the local environment also modulates the electronic structure of chromophore, which perturbs the electrostatic and hydrophobic interaction within the binding site. This work highlights the critical factors hidden in the protein networks, linking with their experimental photocycle kinetics. It presents an opportunity to quantitatively examine the alternation in chromophore’s equilibrium geometry and identify details which have substantial implications in designing synthetic LOV constructs with desirable photocycle efficiency.
Strategic control of location and ordinal context in visual working memory
Authors: Fulvio Jacqueline M. , Yu Qing , Postle Bradley R. 
Published: December 2022

AbstractWorking memory (WM) requires encoding stimulus identity and context (e.g., where or when stimuli were encountered). To explore the neural bases of the strategic control of context binding in WM, we acquired fMRI while subjects performed delayed recognition of three orientation patches presented serially and at different locations. The recognition probe was an orientation patch with a superimposed digit, and pretrial instructions directed subjects to respond according to its location (location-relevant), to the ordinal position corresponding to its digit (order-relevant), or to just its orientation (relative to all three samples;context-irrelevant). Delay-period signal in PPC was greater for context-relevant than forcontext-irrelevanttrials, and multivariate decoding revealed strong sensitivity to context binding requirements (relevant vs.irrelevant) and to context domain (location-vs.order-relevant) in both occipital cortex and PPC. At recognition, multivariate inverted encoding modeling revealed markedly different patterns in these two regions, suggesting different context-processing functions. In occipital cortex, an active representation of the location of each of the three samples was reinstated, regardless of trial type. The pattern in PPC, in contrast, suggested a trial type-dependent filtering of sample information. These results indicate that PPC exerts strategic control over the representation of stimulus context in visual WM.
Regulation of Nuclear Transcription by Mitochondrial RNA
Authors: Sriram Kiran , Qi Zhijie , Yuan Dongqiang , Malhi Naseeb K. , Liu Xuejing , Calandrelli Riccardo , Luo Yingjun , Jin Shengyan , Shi Ji , Salas Martha , Dang Runrui , Armstrong Brian , Priceman Saul J. , Wang Ping , Liao Jiayu , Natarajan Rama , Zhong Sheng , Chen Zhen B. 
Published: December 2022

AbstractChromatin-associated RNAs (caRNAs) form a relatively poorly recognized layer of the epigenome. The caRNAs reported to date are transcribed from the nuclear genome. Here, leveraging a recently developed assay for detection of caRNAs and their genomic association, we report that mitochondrial RNAs (mtRNAs) are attached to the nuclear genome and constitute a subset of caRNA, which we termed mt-caRNA. In four human cell types analyzed, mt-caRNAs preferentially attach to promoter regions. In human endothelial cells (ECs), the level of mt-caRNA-promoter attachment changes in response to environmental stress that mimics diabetes. Suppression of a non-coding mt-caRNA in ECs attenuates stress-induced nascent RNA transcription from the nuclear genome, including that of critical genes regulating cell adhesion, and abolishes stress-induced monocyte adhesion, a hallmark of dysfunctional ECs. Finally, we report increased nuclear localization of multiple mtRNAs in the ECs of human diabetic donors, suggesting many mtRNA translocate to the nucleus in a cell stress and disease-dependent manner. These data nominate mt-caRNAs as messenger molecules responsible for mitochondrial-nuclear communication and connect the immediate product of mitochondrial transcription with the transcriptional regulation of the nuclear genome.
Cleavage of the Jaw1 C-terminal region enhances its augmentative effect on the Ca2+release via inositol 1,4,5-trisphosphate receptors
Authors: Kozono Takuma , Jogano Chifuyu , Okumura Wataru , Sato Hiroyuki , Matsui Hitomi , Takagi Tsubasa , Okumura Nobuaki , Takao Toshifumi , Tonozuka Takashi , Nishikawa Atsushi 
Published: December 2022

AbstractJaw1, a tail-anchored protein with 39 carboxyl (C)-terminal amino acids, is oriented to the lumen of the endoplasmic reticulum and outer nuclear membrane. We previously reported that Jaw1, as a member of the KASH protein family, plays a role in maintaining nuclear shape via its C-terminal region. Furthermore, we recently reported that Jaw1 functions as an augmentative effector of Ca2+release from the endoplasmic reticulum by interacting with the inositol 1,4,5-trisphosphate receptors (IP3Rs). Intriguingly, the C-terminal region is partially cleaved, meaning that Jaw1 exists in the cell in at least two forms: uncleaved and cleaved. However, the mechanism of the cleavage event and its physiological significance remain to be determined. In this study, we demonstrate that the C-terminal region of Jaw1 is cleaved after its insertion by the signal peptidase complex (SPC). Particularly, our results indicate that the SPC with the catalytic subunit SEC11A, but not SEC11C, specifically cleaves Jaw1. Furthermore, using a mutant with a deficit in the cleavage event, we demonstrate that the cleavage event enhances the augmentative effect of Jaw1 on the Ca2+release ability of IP3Rs.Summary statementThe C-terminal region of Jaw1, a tail-anchored protein, is cleaved by signal peptidase complex and this cleavage event enhances the augmentative effect of Jaw1 on the Ca2+release activity of inositol 1,4,5-trisphosphate receptors
Epidemiological transition in Australia: An analysis of immigration patterns in relation to circulatory system diseases and all-cause mortality in the mid-twentieth century
Authors: Kelleher Cecily C , Kelly Gabrielle E , Segurado Ricardo , Briody Jonathan , Sellers Alexander M , McCalman Janet S 
Published: December 2022

AbstractBackground and ObjectivesCirculatory System Diseases (CSD) patterns vary over time and between countries, related to lifestyle risk factors, associated in turn with socio-economic circumstances. Current global CSD epidemics in developing economies are similar in scale to those observed previously in the USA and Australasia. Australia exhibits an important macroeconomic phenomenon as a rapidly transitioning economy with high immigration throughout the 19thand 20thcenturies. We wished to examine how that historical immigration related to CSD patterns subsequently.Methods and SettingWe provide a novel empirical analysis employing census-derived place of birth by age bracket and sex from 1891 to 1986, in order to map patterns of immigration against CSD mortality rates from 1907 onwards. Age-specific generalised additive models for both CSD mortality in the general population, and all-cause mortality for the foreign-born (FB) only, from 1910 to 1980 were also devised for both males and females.ResultsThe % FB fell from 32% in 1891 to 9.8% in 1947. Rates of CSD rose consistently, particularly from the 1940s onwards, peaked in the 1960s, then declined sharply in the 1980s and showed a strong period effect across age groups and genders. The main effects of age and census year and their interaction were highly statistically significant for CSD mortality for males (p < 0.001, each term) and for females (p < 0.001, each term). The main effect of age was statistically significant for all-cause mortality minus net migration rates for the FB males (p =0.005) and for FB females, both age (p < 0.001) and the interaction term (p=0.002) were significant.ConclusionsWe argue our empirical calculations, supported by historical and socio-epidemiological evidence, employing immigration patterns as a proxy for epidemiological transition, affirm the lifecourse hypothesis that both early life circumstances and later life lifestyle drive CSD patterns.Article SummaryStrengthsAn original analysis employing census data and immigration patterns to reinterpret historical trends in CSD in AustraliaRelevant to modern public health policy for population approaches to CSD prevention, also integrates lifecourse and lifestyle drivers of trendsLimitationsHistorical databases do not categorise either all cause or CSD mortality according to country of origin.However, data for foreign-born mortality were inferred using novel actuarial type calculationsThere are no second-generation data by country of origin, unlike in USA.