bluuebunny/crossref_metadata_2025_split huggingface dataset:
A transcriptome atlas ofStriga hermonthicagermination
Authors: Irafaha Gilles , Mutinda Sylvia , Mobegi Fredrick , Hale Brett , Omwenga George , Wijeratne Asela J. , Wicke Susann , Bellis Emily S. , Runo Steven 
Published: December 2022

AbstractSocietal Impact StatementWitchweeds, parasitic plants of the genusStriga, are nicknamed “cereal killers” because of their devasting destruction of Africa’s most staple cereals, including maize, sorghum, millets, and upland rice. The parasite relies on biomolecules emitted from the host roots to germinate and therefore initiate its infectious lifecycle. Some sorghum varieties have evolved to not produce effective germination stimulants, making them resistant to the parasite. Here, we assess genetic factors that underpinStrigagermination. We discuss how such knowledge can be used to develop newStrigamanagement strategies through the disruption of host-parasite communication exchange.SummarySeeds of the parasitic plantStrigaare dormant. They only germinate in response to biomolecules emitted from the host’s root exudate, strigolactones (SL). But, it is now emerging thatStrigagermination is a much more complex process regulated by crosstalk of hormone signaling pathways.To further understand the genetic basis of the communication exchange betweenStrigaand its host sorghum, we performed a comparative transcriptomic analysis. We sought to identify major transcriptomic changes that define the germination process inStrigaand a set of genes that may contribute to the differences in germination rates.Results showed that germination proceeds immediately after SL perception and is marked by a wave of transcriptional reprogramming to allow for metabolic processes of energy mobilization. Cluster analysis using self-organizing maps (SOMs) revealed a time-phased and genotype-differentiated response to germination stimulation. The variation in germination was also a function of hormonal crosstalk. The early germination stage was associated with significant repression of genes in the abscisic acid (ABA) biosynthesis pathway. Other hormones influenced germination as follows: (i) ABA and auxin repressed germination, (ii) brassinosteroid, ethylene and jasmonic acid promoted germination, and (iii) cytokinin had a more prominent role post-germination rather than during germination. Perception of SL sets the germination programme leading to different rates of germination in sorghum followed by a complex hormonal regulation network that acts to either repress or enhance germination. These results have far-reaching implications for developingStrigamanagement strategies by disrupting hormonal communication exchange.
Human intestinal epithelial cells can internalize luminal fungi via LC3-associated phagocytosis
Authors: Cohen-Kedar Sarit , Barda Efrat Shaham , Rabinowitz Keren Masha , Keizer Danielle , Abu-Taha Hannan , Schwartz Shoshana , Kaboub Kawsar , Baram Liran , Sadot Eran , White Ian , Wasserberg Nir , Wolff-Bar Meirav , Levy-Barda Adva , Dotan Iris 
Published: December 2022

AbstractIntestinal epithelial cells (IECs) are the first to encounter luminal microorganisms and actively participate in intestinal immunity. We reported that IECs express the β-glucan receptor Dectin-1, and respond to commensal fungi and β-glucans. In phagocytes, Dectin-1 mediates LC3 associated phagocytosis (LAP) utilizing autophagy components to process extracellular cargo. Dectin-1 can mediate phagocytosis of β-glucan-containing particles by non-phagocytic cells. We aimed to determine whether human IECs phagocytose β-glucan-containing fungal particles via LAP. Zymosan (β-glucan particle) and Heat-killed and UV inactivatedC. albicanswere phagocytosed by monolayers of human colonic (n=18) and ileal (n=4) organoids and IEC lines. LAP was identified by LC3 and Rubicon recruitment to phagosomes and lysosomal processing of internalized particles was demonstrated by co-localization with lysosomal dyes and LAMP2. Phagocytosis was significantly diminished by blockade of Dectin-1, actin polymerization and NAPDH oxidases. Our results show that human IECs sense luminal fungal particles and internalize them via LAP. This novel mechanism of luminal sampling suggests that IECs may contribute to the maintenance of mucosal tolerance towards commensal fungi.
Nested circuits mediate the decision to vocalize
Authors: Xiao Shuyun , Michael Valerie , Mooney Richard 
Published: December 2022

AbstractVocalizations facilitate mating and social affiliation, but may also inadvertently alert predators and rivals. Consequently, the decision to vocalize depends on brain circuits that can weigh and compare these potential benefits and risks. Male mice produce ultrasonic vocalizations (USVs) during courtship to facilitate mating and female mice produce USVs to promote social affiliation with each other. Previously we showed that a specialized set of neurons in the midbrain periaqueductal gray (PAG) are an obligatory gate for USV production in both male and female mice, and that both PAG-USV neurons and USVs can be switched on by their inputs from the preoptic area (POA) of the hypothalamus and switched off by their inputs from neurons on the border between the central and medial amygdala (AmgC/M-PAGneurons) (Michael et al., 2020). Here we show that the USV-suppressing AmgC/M-PAGneurons are strongly activated by predator cues or during social contexts that suppress USV production in male and female mice. Furthermore, a subset of USV-promoting POA neurons that provide input to the PAG-USV region also extend axon collaterals to the amygdala, where they directly inhibit AmgC/M-PAGneurons. Accordingly, AmgC/M-PAGneurons, along with POAPAGand PAG-USV neurons, form a nested hierarchical circuit in which environmental and social information converges to influence the decision to vocalize.
A spatial code for temporal cues is necessary for sensory learning
Authors: Bagur Sophie , Bourg Jacques , Kempf Alexandre , Tarpin Thibault , Bergaoui Khalil , Guo Yin , Ceballo Sebastian , Schwenkgrub Joanna , Verdier Antonin , Puel Jean Luc , Bourien Jérôme , Bathellier Brice 
Published: December 2022

AbstractThe temporal structure of sensory inputs contains essential information for their interpretation by the brain1–9. Sensory systems represent these temporal cues through two codes: the temporal sequences of neuronal activity and the spatial patterns of neuronal firing rate3,7,10–20. However, it is still unknown which of these two coexisting codes causally drives sensory decisions3,10,20,21. To separate their contributions, we designed an optogenetic stimulation paradigm in the mouse auditory cortex to generate neuronal activity patterns differing exclusively along their temporal or spatial dimensions. Training mice to discriminate these patterns shows that they efficiently learn to discriminate spatial but not temporal patterns, indicating that spatial representations are necessary for sensory learning. In line with this result, we observed, based on large-scale neuronal recordings of the auditory system, that the auditory cortex is the first region in which spatial patterns efficiently represent temporal auditory cues varying over several hundred milliseconds. This feature is shared by the deep layers of neural networks trained to categorise time-varying sounds. Therefore, the emergence of a spatial code for temporal sensory cues is a necessary condition to associate temporally structured stimuli to decisions. We expect this constraint to be crucial for re-engineering perception by cortical stimulation.
PyDESeq2: a python package for bulk RNA-seq differential expression analysis
Authors: Muzellec Boris , Teleńczuk Maria , Cabeli Vincent , Andreux Mathieu 
Published: December 2022

AbstractSummaryWe present PyDESeq2, a python implementation of the DESeq2 workflow for differential expression analysis on bulk RNA-seq data. This implementation achieves better precision, allows speed improvements on large datasets, as shown in experiments on TCGA data, and can be more easily interfaced with modern python-based data science tools.Availability and ImplementationPyDESeq2 is released as an open-source software under the MIT license. The source code is available on GitHub athttps://github.com/owkin/PyDESeq2.Contactboris.muzellec@owkin.com
A bibliometric analysis of gender in microbiology collaborations
Authors: Wheatley Rachel M. , Ogunlana Lois 
Published: December 2022

AbstractWomen are underrepresented in senior academic positions within microbiology globally. Studies show that gender bias affects the progression of women in academia, but there is evidence that improving conscious awareness of bias can improve equity in this regard. Here we carry out a bibliometric analysis of review articles within the microbiology field to investigate the statistical associations with author gender. We analyse the publication data from 1857 review articles published between 2010 and 2022 in three leading microbiology review journals: Nature Reviews Microbiology, Trends in Microbiology, and Annual Review of Microbiology. We find a significant association between the gender of the lead author and the gender of co-authors in multi-author publications. Review articles with men lead authors have a significantly reduced proportion of women co-authors compared to reviews with women lead authors. Given the existing differences in the proportions of men and women in lead author positions, this association may have important consequences for the relative visibility of women in microbiology, along with potential negative impacts on scientific output relating to reduced collaboration diversity. We further probe associations between gender and citation metrics, acknowledgement of contributions, and publishing during the Covid-19 pandemic within microbiology reviews.
Genome and Genetic Engineering of the House Cricket (Acheta domesticus): Applications for Sustainable Agriculture
Authors: Dossey Aaron T. , Oppert Brenda , Chu Fu-Chyun , Lorenzen Marcé D. , Scheffler Brian , Simpson Sheron , Koren Sergey , Johnston J. Spencer , Kataoka Kosuke , Ide Keigo 
Published: December 2022

AbstractThe house cricket,Acheta domesticus, is one of the most farmed insects worldwide and the foundation of an emerging industry for the use of insects as a sustainable food source. Edible insects present a promising alternative for protein production amid a plethora of recent reports on climate change and biodiversity loss largely driven by agriculture. As with other agricultural crops, genetic resources are needed to improve crickets for food and other applications. We present the first high quality annotated genome assembly ofA. domesticuswhich was assembled from long read data and scaffolded to chromosome level from long range data, providing information on promoters and genes needed for genetic manipulation. Gene groups that may be useful for improving the value of these insects to farmers were manually annotated, mainly genes related to immunity. Metagenome scaffolds in theA. domesticusassembly, including those from bacteria, other microbes and viruses such as Invertebrate Iridescent Virus 6 (IIV6), were submitted in a separate accession as host-associated sequences. We demonstrate both CRISPR/Cas9-mediated knock-in and knock-out of selected genes and discuss implications for the food, pharmaceutical and other industries. RNAi was demonstrated to disrupt the function of thevermilioneye-color gene to produce a useful white-eye biomarker phenotype. We are utilizing these data to develop base technologies and methodologies for downstream commercial applications, including the generation of more nutritious and disease resistant crickets as well as lines producing valuable bioproducts such as vaccines and antibiotics. We also discuss how this foundational research can play a critical role in utilizing the largest, most diverse yet almost entirely untapped biological resource on Earth: Class Insecta.Significance StatementSequencing and assembly of the genome of the house cricket has led to improvements in farmed insects for food, pharmaceutical and other applications.
Monitoring the battlefield: Antimicrobial resistance, antibiofilm patterns and virulence factors ofAcinetobacter baumanniiisolates from hospital system
Authors: Awour Silas Onyango 
Published: December 2022

ABSTRACTHospital-acquired contagions are on the increase and are a substantial cause of clinical and financial burden for healthcare systems. While contagion control plays a major role in curtailing the spread of outbreak organisms, it is not always effective. One organism of particular concern isAcinetobacter baumannii, due to both its persistence in the hospital setting and its ability to acquire antibiotic resistance.A. baumanniihas appeared as a nosocomial pathogen that displays high levels of resistance to antibiotics, and remains resilient against traditional cleaning measures with resistance to Colistin increasingly reported. Given the costs associated and magnitude with hospital acquired infections, and the rise in multidrug-resistant organisms, it is worth re-evaluating our current approaches and observing for substitutes or aides-de-camp to traditional antibiotics therapies. The aims of this study was to determine antimicrobial resistance, antibiofilm patterns and virulence factors ofAcinetobacter baumanniiisolates from hospital system. Among the five drugs used (Amikacin, Gentamicin, Meropenem, Tigecycline and Tazobactam) it was revealing that all the isolates show resistance to all the drugs. It was revealed that 3 isolates show resistance at difference antimicrobial classes in isolate05/JOOTRH/22and17/JOOTRH/22were able to produce all type of the virulence enzymes while isolate11/JOOTRH/22was able to produce all except protease enzyme. The isolates showed that the biofilm formation inhibitory effects of the various concentrations (0.5, 0.25, 0.125, 0.0625 and 0.03125 mg ml−1) were significantly lower than that of the positive control, an indication that biofilm formation was inhibited at these concentrations
Neurodegeneration Risk Factor,EIF2AK3(PERK), Influences Tau Protein Aggregation
Authors: Park Goonho , Xu Ke , Chea Leon , Kim Kyle , Safarta Lance , Song Keon-Hyoung , Wu Jian , Park Soyoung , Min Hyejung , Hiramatsu Nobuhiko , Han Jaeseok , Lin Jonathan H. 
Published: December 2022

AbstractTauopathies are neurodegenerative diseases caused by pathologic misfolded tau protein aggregation in the nervous system. Population studies implicateEIF2AK3(eukaryotic translation initiation factor 2 alpha kinase 3), better known asPERK(protein kinase R-like endoplasmic reticulum kinase), as a genetic risk factor in several tauopathies. PERK is a key regulator of intracellular proteostatic mechanisms – Unfolded Protein Response (UPR) and Integrated Stress Response (ISR). Previous studies found that tauopathy-associated PERK variants encoded functional hypomorphs with reduced signalingin vitro. But, it remained unclear how altered PERK activity led to tauopathy. Here, we chemically or genetically modulated PERK signaling in cell culture models of tau aggregation and found that PERK pathway activation prevented tau aggregation while inhibition exacerbated tau aggregation. In primary tauopathy patient brain tissues, we found that reduced PERK signaling correlated with increased tau neuropathology. We found that tauopathy-associated PERK variants targeted the ER luminal domain; and two of these variants damaged hydrogen bond formation. Our studies support that PERK activity protects against tau aggregation and pathology. This may explain why people carrying hypomorphic PERK variants have increased risk for developing tauopathies. Finally, our studies identify small molecule augmentation of PERK signaling as an attractive therapeutic strategy to treat tauopathies by preventing tau pathology.
A set of orthogonal versatile interacting peptide tags for imaging cellular proteins
Authors: Suyama Alexa , Devlin Kaylyn L. , Macias-Contreras Miguel , Doh Julia K. , Shinde Ujwal , Beatty Kimberly E. 
Published: December 2022

AbstractGenetic tags are transformative tools for investigating the function, localization, and interactions of cellular proteins. Most studies today are reliant on selective labeling of more than one protein to obtain comprehensive information on a protein’s behavior in situ. Some proteins can be analyzed by fusion to protein tag, such as green fluorescent protein, HaloTag, or SNAP-Tag. Other proteins benefit from labeling via small peptide tags, such as the recently reported versatile interacting peptide (VIP) tags. VIP tags enable observations of protein localization and trafficking with bright fluorophores or nanoparticles. Here we expand the VIP toolkit by presenting two new tags: TinyVIPER and PunyVIPER. These two tags were designed for use with MiniVIPER for labeling up to three distinct proteins at once in living cells. Labeling is mediated by the formation of a high affinity, biocompatible heterodimeric coiled coil. Each tag was validated by fluorescence microscopy, including observation of transferrin receptor 1 trafficking in live cells. We verified that labeling via each tag is highly specific, with no cross-reactivity between the three VIP tags under cellular conditions. Lastly, the self-sorting tags were used for simultaneous labeling of three protein targets (i.e., TOMM20, histone 2B, and actin), highlighting their utility for multicolor microscopy. MiniVIPER, TinyVIPER, and PunyVIPER are small and robust peptide tags for selective labeling of cellular proteins.
ARID1A-deficient cells promote endometrial carcinoma progression and dissemination by reprograming tumor microenvironment
Authors: Megino-Luque Cristina , Matias-Guiu Xavier , Eritja Núria 
Published: December 2022

AbstractAT-rich interactive domain-containing protein 1A (ARID1A) loss-of-function mutation accompanied by a loss of ARID1A protein expression is frequently observed in endometrial carcinomas (EC). However, the mechanisms underlying this loss of ARID1A involved in the progression and dissemination of EC have been poorly studied and understood. Tumor microenvironment (TME) is reprogramed by cancer cells and have a high influence in aggressive behaviours of solid tumors. TME, and specially the stromal component, has a clear impact on the progression and aggressiveness of EC, but little is known about its activation, signalling and functions. Thus, the main aim of this study was to analyse the role of EC ARID1A loss in TME reprograming and its implication in endometrial tumor progression and aggressiveness. Here, using different endometrialin vitroandin vivomodels, we show that endometrial tumor cells with altered expression ofARID1Apromote the modulation and activation of the TME. We demonstrate that ARID1A depleted endometrial tumor cells induce aggressive behaviour in neighbouring endometrial tumor cells with wild-type ARID1A expression and the recruitment and activation of endometrial stromal cells (ESC). Interestingly, these pro-tumoral signals spread through the bloodstream supporting ARID1A wild-type EC cells aggressiveness. Finally, we show that ARID1A altered tumor cells display a different secretion profile and express significative high levels of chemokines in the TME. Taken together, our data demonstrate ARID1A depleted endometrial tumor cells reprograms TME promoting progression and dissemination of EC through chemokine secretion.
Changing patterns of cigarette and ENDS transitions in the US: a multistate transition analysis of youth and adults in the PATH Study in 2015–17 vs 2017–2019
Authors: Brouwer Andrew F. , Jeon Jihyoun , Jimenez-Mendoza Evelyn , Land Stephanie R. , Holford Theodore R. , Friedman Abigail S. , Tam Jamie , Mistry Ritesh , Levy David T. , Meza Rafael 
Published: December 2022

AbstractIntroductionIt is unknown how recent changes in the tobacco product marketplace have impacted transitions in cigarette and electronic nicotine delivery system (ENDS) use.MethodsA multistate transition model was applied to 24,242 adults and 12,067 youth in Waves 2–4 (2015–2017) and 28,061 adults and 12,538 youth in Waves 4–5 (2017–2019) of the Population Assessment of Tobacco and Health (PATH) Study. Hazards for initiation, cessation, and product transitions were estimated in multivariable models, accounting for gender, age group, race/ethnicity, and daily vs non-daily product use.ResultsChanges in ENDS initiation/relapse rates from never, non-current, and cigarette-only use depended on age group, including among adults. Among youth never users, the 1-year probability of ENDS initiation increased after 2017 from 1.6% (95%CI: 1.4-1.8%) to 3.8% (95%CI: 3.4-4.2). Persistence of ENDS-only use (1-year probability of remaining an ENDS-only user) increased for youth from 40.7% (95%CI: 34.4-46.9%) to 65.7% (95%CI: 60.5-71.1%) and for adults from 57.8% (95%CI: 54.4-61.3%) to 78.2% (95%CI: 76.080.4%). Persistence of dual use similarly increased for youth from 48.3% (95%CI: 37.4-59.2%) to 60.9% (95%CI: 43.0-78.8%) and for adults from 40.1% (95%CI: 37.0-43.2%) to 63.8% (95%CI: 59.6-67.6%). Youth and young adult dual users became more likely to transition to ENDS-only use but middle-aged and older adults did not.ConclusionsENDS and dual use have become more persistent. Middle-aged and older adult dual users have become less likely to transition to cigarette-only use but not more likely to discontinue cigarettes. Youth and young adults are more likely to transition to ENDS-only use.
High-dimensional single-cell definition of CLL T cells identifies Galectin-9 as novel immunotherapy target
Authors: Llaó Cid L , Wong JKL , Fernandez Botana I , Paul Y , Wierz M , Flörchinger A , Gonder S , Pagano G , Chazotte M , Bestak K , Schifflers C , Iskar M , Roider T , Czernilofsky F , P-M Bruch , Mallm JP , Cosma A , Campton DE , Gerhard-Hartmann E , Rosenwald A , Colomer D , Campo E , Schapiro D , Dietrich S , Lichter P , Moussay E , Paggetti J , Zapatka M , Seiffert M 
Published: December 2022

AbstractFailure of cancer immunotherapy is linked to T cell exhaustion. To decipher the underlying mechanisms, we explored the T cell landscape in blood, bone marrow and lymph node samples of patients with chronic lymphocytic leukemia (CLL), and spleen samples of a CLL mouse model. By single-cell RNA-sequencing, mass cytometry (CyTOF), and multiplex image analysis of tissue microarrays, we identified a disease-specific accumulation of distinct regulatory T cell subsets and T cell exhaustion stages and their trajectories in CLL lymph nodes. Integration of T cell receptor sequencing data revealed a clonal expansion of CD8+precursor exhausted T cells (TPEX), suggesting their CLL reactivity. Interactome analyses identified the TIM3 ligand Galectin-9 as a novel immunoregulatory molecule in CLL. Blocking of Galectin-9 in CLL-bearing mice slowed down disease development and reduced the number of TIM3-expressing T cells. Galectin-9 expression correlated with shorter survival of patients with CLL, renal cell carcinoma or glioma.Statement of significanceOur findings for the first time define the T cell landscape in CLL lymph nodes and reshape the current understanding of T cell exhaustion in this malignancy. They further introduce Galectin-9 as novel immune checkpoint with a high potential to overcome resistance to PD1 targeting drugs in CLL and beyond.