bluuebunny/crossref_metadata_2025_split huggingface dataset:
Geography and environmental pressure are predictive of class-specific radioresistance in black fungi
Authors: Aureli Lorenzo , Coleine Claudia , Delgado-Baquerizo Manuel , Ahren Dag , Cemmi Alessia , Sarcina Ilaria Di , Onofri Silvano , Selbmann Laura 
Published: February 2023

AbstractBlack fungi are among the most resistant organisms to ionizing radiation on Earth. However, our current knowledge is based on studies on a few isolates, while the overall radioresistance limits across this microbial group and the relationship with local environmental conditions remains largely undetermined. To address this knowledge gap, we assessed the survival of 101 strains of black fungi isolated across a worldwide spatial distribution to gamma radiation doses up to 100 kGy. We found that intra and inter-specific taxonomy, UV radiation and precipitation levels primarily influence the radioresistance in black fungi. Altogether, this study provides insights into the adaptive mechanisms of black fungi to extreme environments and highlights the role of local adaptation in shaping the survival capabilities of these extreme-tolerant organisms.Originality statementAlthough previous studies showed the extraordinary ability of a few strains of black fungi to survive ionizing radiation, the overall radioresistance of this group of organisms has not been defined yet. Moreover, how and why radioresistance shifts across environmental gradients remain virtually unknown. Here, we collected black fungi from locations across the globe and found that biogeography shapes the responses of black fungi to environmental stress with UV light being significantly correlated with radiotolerance. Our study provides a clear picture of the boundaries of life for black fungi under ionizing radiation; further, we demonstrate, for the first time, that this ability in such microorganisms, not only is related to taxonomy, but also may be a consequence of their adaptation to various factors encountered in the environment where they live.
Sex-specific declines in cholinergic-targeting tRNA fragments in the nucleus accumbens in Alzheimer’s disease
Authors: Shulman Dana , Dubnov Serafima , Zorbaz Tamara , Madrer Nimrod , Paldor Iddo , Bennett David A. , Seshadri Sudha , Mufson Elliott J. , Greenberg David S. , Loewenstein Yonatan , Soreq Hermona 
Published: February 2023

AbstractIntroductionFemales with Alzheimer’s disease (AD) suffer accelerated dementia and loss of cholinergic neurons compared to males, but the underlying mechanisms are unknown. Seeking causal contributors to both these phenomena, we pursued changes in tRNA fragments (tRFs) targeting cholinergic transcripts (CholinotRFs).MethodsWe analyzed small RNA-sequencing data from thenucleus accumbens(NAc) brain region which is enriched in cholinergic neurons, compared to hypothalamic or cortical tissues from AD brains; and explored small RNA expression in neuronal cell lines undergoing cholinergic differentiation.ResultsNAc CholinotRFs of mitochondrial genome origin showed reduced levels that correlated with elevations in their predicted cholinergic-associated mRNA targets. Single cell RNA seq from AD temporal cortices showed altered sex-specific levels of cholinergic transcripts in diverse cell types; inversely, human-originated neuroblastoma cells under cholinergic differentiation presented sex-specific CholinotRF elevations.DiscussionOur findings support CholinotRFs contributions to cholinergic regulation, predicting their involvement in AD sex-specific cholinergic loss and dementia.
Enhancer-promoter interactions are reconfigured through the formation of long-range multiway chromatin hubs as mouse ES cells exit pluripotency
Authors: Lando D. , Ma X. , Cao Y. , Jartseva A. , Stevens T. J. , Boucher W. , Reynolds N. , Montibus B. , Hall D. , Lackner A , Ragheb R. , Leeb M , Hendrich B. D. , Laue E. D. 
Published: February 2023

SummaryEnhancers are genomic DNA sequences that bind transcription factors, chromatin regulators and non-coding transcripts to modulate the expression of target genes. They have been found to act from different locations relative to a gene and to modulate the activity of promoters up to ∼1 Mb away. Here we report the first 3D genome structures of single mouse ES cells as they are induced to exit pluripotency, transition through a formative stage and undergo neuroectodermal differentiation. In order to directly study how interactions between enhancers and promoters are reconfigured genome wide we have determined 3D structures of haploid cells using single cell Hi-C, where we can unambiguously map the contacts to particular chromosomes. We find that there is a remarkable reorganisation of 3D genome structure where inter-chromosomal intermingling increases dramatically in the formative state. This intermingling is associated with the formation of a large number of multiway hubs that bring together enhancers and promoters with similar chromatin states from typically 5-8 distant chromosomal sites that are often separated by many Mb from each other. Genes important for pluripotency exit establish contacts with emerging enhancers within multiway chromatin hubs as cells enter the formative state, consistent with these structural changes playing an important role in establishing new cell identities. Furthermore, we find that different multiway chromatin hubs, and thus different enhancer-promoter interactions, are formed in different individual cells. Our results suggest that studying genome structure in single cells will be important to identify key changes in enhancer-promoter interactions that occur as cells undergo developmental transitions.
Genetic investigation of honeybee populations in Kazakhstan
Authors: Gritsenko D. , Temirbayeva K. , Taskuzhina A. , Kostuykova V. , Pozharskiy A. , Khusnitdinova M. , Krupskiy O. , Mayer A. , Nuralieva U. 
Published: February 2023

AbstractBeekeeping as a staple of agriculture in Kazakhstan is believed to have emerged when external bee specimens were introduced into the country. The Central Russian bee (Apis mellifera mellifera) has been present throughout Kazakhstanian apiaries for a long time since its import into Eastern Kazakhstan at the end of the 18thcentury. To date, six subspecies have been distributed across the country (A.m. sossimai,A.m. carpatica,A.m. mellifera,A.m. ligustica, А.m. caucasica, andA.m. carnica). According to mitochondrial haplotype analysis based on DraI mtDNA COI-COII (DmCC) test, local samples were represented by C2 (316), C1 (99), and M4 (7) haplotypes. The results of simple sequence repeats (SSR) genotyping revealed a large polymorphism at nine microsatellite loci, with the number of alleles amounting to 35 (AP55), 32 (AP43), 25 (A124), 18 (A113), 13 (A88), 12 (A43), 11 (A007), 7 (A28), and 5 (A24). Relative to the expected heterozygosity (He), the observed heterozygosity (Ho) was slightly higher for most markers considering both the overall samples and individual populations. The inbreeding coefficient confirmed the excess outbreeding for the geographical populations of car-Shym-T (−0,105), car-zham-A (−0,114), Zhet-Alakol (−0,008), and Zhet-Ushbulak (−0,028). The admixture of honeybee local populations was confirmed by the research presented here.The differentiation of populations was only possible by geographical location according to clustering analysis. A considerable degree of genetic admixtures among subspecies was identified in every population. The subspecies were not separated from each other. None of the groups formed by the neighbor-joining tree based on Nei’s genetic distance included a precise subspecies or population. All groups represented an admixture of subspecies from different populations.Unregulated cross-breeding for the past 50 years has laid the foundation for the promiscuous genetic nature of honeybee populations in Kazakhstan. It could be concluded that some samples were the result of cross-breeding with endemic beeApis mellifera pomonellasince most apiaries were located in areas of endemic bee distribution.
Transcription activator WCC recruits deacetylase HDA3 to control transcription dynamics and bursting in Neurospora
Authors: Oehler Michael , Diernfellner Axel C.R. , Brunner Michael 
Published: February 2023

ABSTRACTRNA polymerase II initiates transcription either randomly or in bursts. We examined the light-dependent transcriptional activator White Collar Complex (WCC) ofNeurosporato characterize the transcriptional dynamics of the strongvivid(vvd) promoter and the weakerfrequency(frq) promoter. We show that WCC is not only an activator but also represses transcription by recruiting histone deacetylase 3 (HDA3). Our data suggest that bursts offrqtranscription are governed by a long-lived refractory state established and maintained by WCC and HDA3 at the core promoter, whereas transcription ofvvdis determined by WCC binding dynamics at an upstream activating sequence. Thus, in addition to stochastic binding of transcription factors, transcription factor-mediated repression may also influence transcriptional bursting.TEASERBalanced interaction of transcription factor with coactivator and corepressors determines transcription dynamics and bursting.
A simple mechanism for integration of quorum sensing and cAMP signalling inV. cholerae
Authors: Walker Lucas M. , Haycocks James R.J. , van Kessel Julia C. , Dalia Triana N. , Dalia Ankur B. , Grainger David C. 
Published: February 2023

ABSTRACTMany bacteria use quorum sensing to control changes in lifestyle. The process is regulated by microbially derived “autoinducer” signalling molecules, that accumulate in the local environment. Individual cells sense autoinducer abundance, to infer population density, and alter their behaviour accordingly. InVibrio cholerae, quorum sensing signals are transduced by phosphorelay to the transcription factor LuxO. Unphosphorylated LuxO permits expression of HapR, which alters global gene expression patterns. In this work, we have mapped the genome-wide distribution of LuxO and HapR inV. cholerae. Whilst LuxO has a small regulon, HapR targets 32 loci. Many HapR targets coincide with sites for the cAMP receptor protein (CRP) that regulates the transcriptional response to carbon starvation. This overlap, also evident in otherVibriospecies, results from similarities in the DNA sequence bound by each factor. At shared sites, HapR and CRP simultaneously contact the double helix and binding is stabilised by direct interaction of the two factors. Importantly, this involves a CRP surface that usually contacts RNA polymerase to stimulate transcription. As a result, HapR can block transcription activation by CRP. Thus, by interacting at shared sites, HapR and CRP integrate information from quorum sensing and cAMP signalling to control gene expression. This likely allowsV. choleraeto regulate subsets of genes during the transition between aquatic environments and the human host.
Surf4 deficiency reduces intestinal lipid absorption and secretion and decreases metabolism in mice
Authors: Tao Geru , Wang Hao , Shen Yishi , Zhai Lei , Liu Boyan , Wang Bingxiang , Chen Wei , Xing Sijie , Chen Yuan , Gu Hong-mei , Qin Shucun , Zhang Da-wei 
Published: February 2023

AbstractBackgroundPostprandial dyslipidemia is a causative risk factor for cardiovascular disease. The majority of absorbed dietary lipids are packaged into chylomicron and then delivered to circulation. Previous studies showed that Surfeit4 (Surf4) mediates very low-density lipoprotein secretion from hepatocytes. Silencing hepatic Surf4 markedly reduces the development of atherosclerosis in different mouse models of atherosclerosis without causing hepatic steatosis. However, the role of Surf4 in chylomicron secretion is unknown.MethodsWe developed inducible intestinal-specificSurf4knockdown mice (Surf4IKO) usingVil1Cre-ERT2andSurf4floxmice. Metabolic cages were used to monitor mouse metabolism. Enzymatic kits were employed to measure serum and tissue lipid levels. The expression of target genes was detected by qRT-PCR and Western Blot. Transmission electron microscopy and radiolabeled oleic acid were used to assess the structure of enterocytes and intestinal lipid absorption and secretion, respectively. Proteomics was performed to determine changes in protein expression in serum and jejunum.ResultsSurf4IKOmice, especially maleSurf4IKOmice, displayed significant body weight loss, increased mortality, and reduced metabolism.Surf4IKOmice exhibited lipid accumulation in enterocytes and impaired fat absorption and secretion. Lipid droplets and small lipid vacuoles were accumulated in the cytosol and the endoplasmic reticulum lumen of the enterocytes ofSurf4IKOmice, respectively. Surf4 colocalized with apoB and co-immunoprecipitated with apoB48 in differentiated Caco-2 cells. Intestinal Surf4 deficiency also significantly reduced serum triglyceride, cholesterol and free fatty acid levels in mice. Proteomics data revealed that diverse pathways were altered inSurf4IKOmice. In addition,Surf4IKOmice had mild liver damage, decreased liver size and weight, and reduced hepatic triglyceride levels.ConclusionOur findings demonstrate that intestinal Surf4 plays an essential role in lipid absorption and chylomicron secretion and suggest that the therapeutic use of Surf4 inhibition requires highly cell/tissue-specific targeting.HighlightsIntestinal Surf4 deficiency reduces chylomicron secretion.Lack of intestinal Surf4 reduces absorption of dietary lipids.Silencing intestinal Surf4 reduces serum lipid levels.Intestinal Surf4 deficiency leads to lipid accumulation in intestinal villi.Intestinal Surf4 is essential for dietary lipid absorption and secretion.
Gender quota in the civil service and female participation: Evidence from Nepal
Authors: Upadhaya Hari Prasad , Kwon Illoong 
Published: February 2023

AbstractFemale quotas for high‐ranking positions in corporations and governments should (i) increase the hiring of women and (ii) inspire more women to apply for these positions. The goal will be that eventually, (iii) even without the quota, more women will apply to and succeed in high‐ranked positions. This paper exploits the variations of female quotas in Nepalese civil service exams across years, services, ranks and exams within the same service to investigate these three effects. Empirical results show that female quotas in a given exam increase applications and the hiring of women. Even in exams without a quota, the female quotas of other exams within the same service increase the number of female applicants.
Surface layer proteins in species of the family Lactobacillaceae
Authors: Palomino M. Mercedes , Allievi Mariana C. , Gordillo Tania B. , Bockor Sabrina S. , Fina Martin Joaquina , Ruzal Sandra M. 
Published: February 2023

AbstractThe S‐layer or surface layer protein (SLP) is the most ancient biological envelope, highly conserved in several Bacteria and Archaea. In lactic acid bacteria (LAB), SLP is only found in species belonging to the Lactobacillaceae family, many of them considered probiotic microorganisms. New reclassification of members within the Lactobacillaceae family (International Journal of Systematic and Evolutionary Microbiology, 2020, 70, 2782) and newly sequenced genomes demands an updated revision on SLP genes and domain organization. There is growing information concerning SLP occurrence, molecular biology, biophysical properties, and applications. Here, we focus on the prediction of slp genes within the Lactobacillaceae family, and specifically, on the neat interconnection between the two different modular SLP domain organizations and the new reclassified genera. We summarize the results in a concise tabulated manner to review the present knowledge on SLPs and discuss the most relevant and updated concepts regarding SLP sequence clustering. Our assessment is based on sequence alignments considering the new genera classification and protein domain definition with post‐translational modifications. We analyse the difficulties encountered to resolve the SLPs 3D structure, describing the need for structure prediction approaches and the relation between protein structure and its anchorage mechanism to the cell wall. Finally, we enumerate new SLP applications regarding heterologous display, pathogen exclusion, immunostimulation, and metal binding.
Indigenous sustainable finance as a research field: A systematic literature review on indigenising ESG, sustainability and indigenous community practices
Authors: Poyser Andre , Daugaard Dan 
Published: February 2023

AbstractSustainable finance research has come into its own as an established area in the finance literature. The increased awareness of sustainability and global concerns around environmental, social and governance (ESG) issues, particularly among institutional investors, has catalysed a shift towards greater research and publications in this area. Accompanying this is the emerging body of work being produced on indigenous investments and indigenous community practices. These nascent strands of literature tell a story of the shift that is taking place within the finance field. To chart this shift and create a harmonised view of these bodies of work, this paper conducts a systematic literature review of the significant nexus between sustainable investments and indigenous approaches to sustainability. We present a framework for conceptualising and characterising the various stands of literature and, in so doing, make the case for Indigenous Sustainable Finance (ISF) as a distinct disciplinary field. This paper argues that ISF is distinct from mainstream sustainable finance and other social and management sciences and constitutes a legitimate, well‐defined sub‐field of research in its own right.
The TH22‐mediated IL‐22 deficiency associated with premature ovarian insufficiency
Authors: Zhang Wenzhe , Xu Shiru , Zhang Rongrong , Li Zhuqing , Li Nianyu , Zhang Xiruo , Lu Yueshuang , Bian Yuehong , Yang Ping , Fang Fang , Qin Yingying , Jiao Xue 
Published: February 2023

AbstractResearch questionIs deficiency of IL‐22 associated with premature ovarian insufficiency (POI)?DesignLevels of IL‐22 and IL‐22BP, IL‐22‐producing T cells, and IL22RA1/IL10R2 expression were measured and compared among 29 patients with POI, 42 with precursor stage of POI (pre‐POI) and 46 control women. Correlation of serum IL‐22 and IL‐22+CD4+T subsets with ovarian reserve markers were further analyzed.ResultsIL‐22 levels in serum significantly differed among control women and patients with pre‐POI and POI, with the lowest concentrations in POI group (p = .019). Significant reduction of peripheral CD4+IL‐22+T cells was observed in patients with POI (p = .010), which mainly contributed by decrease of CD4+IL‐22+IL‐17− TH22 cells (p = .012) but not TH17 cells (p = .125). Levels of serum IL‐22 and IL‐22‐producing CD4+T subsets were significantly correlated with ovarian reserve markers, including AMH, bilateral AFC, follicle‐stimulating hormone (FSH), and E2 (p < .05). The specific receptor IL22RA1 expression was marginally reduced in granulosa cells from patients with pre‐POI (p = .051). No difference of IL‐22BP was observed either in serum (p = .216) or follicular fluid (p = .856) among groups.ConclusionsOur study first demonstrated the significant association between TH22‐mediated IL‐22 deficiency and ovarian insufficiency, which provide new insights into the autoimmune disturbance and opens new avenues for exogenous IL‐22 administration as potential intervention of POI.
Retinal vascular occlusions in ocular Behçet disease – a comparative analysis
Authors: Ostrovsky Michael , Ramon Dan , Iriqat Salam , Shteiwi Abdallah , Sharon Yael , Kramer Michal , Vishnevskia‐Dai Vicktoria , Sar Shaul , Boulos Yosif , Tomkins‐Netzer Oren , Lavee Natalie , Ben‐Arie‐Weintrob Yael , Pizem Hadas , Hareuveni‐Blum Tamar , Schneck Marina , Gepstein Raz , Masarwa Dua , Nakhoul Nakhoul , Bakshi Erez , Shulman Shiri , Goldstein Michaella , Anouk Marina , Rosenblatt Amir , Habot‐Wilner Zohar 
Published: February 2023

AbstractPurposeThe literature on retinal vascular occlusions in Behçet disease (BD) patients is limited. The aim of this study is to thoroughly investigate retinal vascular occlusions among ocular BD patients.MethodsRetrospective, multicentre case–control study. Three‐hundred and three eyes of 175 patients with ocular BD, from 13 hospitals in Israel and Palestine, were included. Patients were assigned into two groups according to the presence of retinal vascular occlusion. Epidemiology, systemic and ocular manifestations, treatments and outcomes were compared between the groups and risk factors for retinal vascular occlusions were identified.ResultsOne hundred twenty‐five patients (71.4%) were male. The mean age at presentation was 28.2 ± 0.86 years. Retinal vascular occlusions were found in 80 eyes of 54 (30.9%) patients, including branch retinal vein occlusion (51.3%), peripheral vessels occlusions (32.5%), central retinal vein occlusion (13.8%) and arterial occlusions (7.5%). Systemic manifestations were similar among both groups. Anterior uveitis was more common in non‐occlusive eyes (p < 0.01). Non‐occlusive retinal vasculitis (p = 0.03) and ocular complications were more common in occlusive eyes (p < 0.01). Treatments including mycophenolate mofetil, Infliximab or a combination therapy of anti‐metabolite and calcineurin inhibitor were more commonly used by occlusive patients (p < 0.05). Occlusive patients underwent more cataract surgeries (p = 0.03). The occlusive group had worse mean best‐corrected visual acuity (BCVA) throughout follow‐up (p < 0.01). Risk factors for retinal vascular occlusions included male sex and Jewish ethnicity (p < 0.05).ConclusionRetinal vascular occlusions were found in a third of ocular BD patients. Occlusive eyes had a worse prognosis. Risk factors for vascular occlusions were identified.
An integrated approach to reconstruct the role of the heat treatment within the reduction sequence of chert artefacts: The case of the early Neolithic site of Lugo di Grezzana (north‐eastern Italy)
Authors: Santaniello Fabio , Berloffa Angela , Grimaldi Stefano , Pedrotti Annaluisa , Gialanella Stefano 
Published: February 2023

AbstractThe lithic assemblage from the well‐known site of Lugo di Grezzana (Italy) attributable to the Fiorano group (5,300–4,900 BC cal) is analysed to shed new insights on the early Neolithic lithic technology in North‐Eastern Italy. Techno‐typological data are discussed allowing detailed reconstruction of the reduction sequence, thanks also to several refittings. A complex laminar production with several technical objectives has been identified. Whereas clues for the heat treatment of lithic materials have been identified, we verified it by a combined experimental approach. In the first place, we used density measurements, which already proved to be useful for prescreening analysis, to detect potentially heated artefacts. Afterward, we performed Fourier Transform Infrared (FT‐IR) spectroscopy tests to assess the actual (de)hydration condition of the siliceous materials. Reflectance spectra have been acquired, analysing any item and avoiding any constraint related to both morphology and thickness of the sample. The archaeometric results, combined with the reduction sequence reconstruction, provide new indications on the technical capabilities and knowledge of the human groups that inhabited the region during the early Neolithic.