bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cryptosporulation in Kurthia spp. forces a rethinking of asporogenesis in Firmicutes
Authors: Fatton Mathilda , Filippidou Sevasti , Junier Thomas , Cailleau Guillaume , Berge Matthieu , Poppleton Daniel , Blum Thorsten B. , Kaminek Marek , Odriozola Adolfo , Blom Jochen , Johnson Shannon L. , Abrahams Jan Pieter , Chain Patrick S. , Gribaldo Simonetta , Tocheva Elitza I. , Zuber Benoît , Viollier Patrick H. , Junier Pilar 
Published: August 2022

AbstractEndosporulation is a complex morphophysiological process resulting in a more resistant cellular structure that is produced within the mother cell and is called endospore. Endosporulation evolved in the common ancestor of Firmicutes, but it is lost in descendant lineages classified as asporogenic. While Kurthia spp. is considered to comprise only asporogenic species, we show here that strain 11kri321, which was isolated from an oligotrophic geothermal reservoir, produces phase‐bright spore‐like structures. Phylogenomics of strain 11kri321 and other Kurthia strains reveals little similarity to genetic determinants of sporulation known from endosporulating Bacilli. However, morphological hallmarks of endosporulation were observed in two of the four Kurthia strains tested, resulting in spore‐like structures (cryptospores). In contrast to classic endospores, these cryptospores did not protect against heat or UV damage and successive sub‐culturing led to the loss of the cryptosporulating phenotype. Our findings imply that a cryptosporulation phenotype may have been prevalent and subsequently lost by laboratory culturing in other Firmicutes currently considered as asporogenic. Cryptosporulation might thus represent an ancestral but unstable and adaptive developmental state in Firmicutes that is under selection under harsh environmental conditions.
Lasiodiplodia theobromae protein LtScp1 contributes to fungal virulence and protects fungal mycelia against hydrolysis by grapevine chitinase
Authors: Peng Junbo , Li Xinghong , Li Yonghua , Zhang Wei , Zhou Ying , Yan Jiye 
Published: August 2022

AbstractThe LysM proteins have been reported to be important for the virulence and host immunity suppression in herbaceous plant pathogens, whereas far less information is documented in the woody plant pathogen Lasiodiplodia theobromae. To investigate the functional mechanism of LysM protein in L. theobromae, one gene LtScp1 was cloned and characterized detailedly in the current study. Transcription profiling revealed that LtScp1 was highly expressed at the infectious stages. Compared to wild type, overexpression and silencing of LtScp1 in L. theobromae led to significantly increased and decreased lesion areas, respectively. Moreover, LtScp1 was determined to be a secreted protein via a yeast signal peptide trapping system. Interestingly, LtScp1 was confirmed to be modified by the N‐glycosylation, which is necessary for the homodimerization of LtScp1 molecules. Furthermore, it was found that LtScp1 interacted with the grapevine chitinase VvChi4 and interfered the ability of VvChi4 to bind chitin. Collectively, these results suggest that LtScp1 functions as a virulence factor to protect the fungus from degradation during the infection.
Enhanced ability of freshwater bacteria to secrete extracellular vesicles upon interaction with virus
Authors: Silva Thiago P. , Gamalier Juliana P. , Zarantonello Victor , Soares Caique R. , Resende Nathália S. , Barros Nathan O. , Melo Rossana C. N. 
Published: August 2022

AbstractThe ability of freshwater bacteria to secrete extracellular vesicles (EVs) upon interaction with viruses remains to be established. Here, we investigated for the first time if freshwater virus‐infected bacteria release EVs in both natural ecosystems and virus‐like particles (VLPs)‐enriched cultures. We performed a systematic study using transmission electron microscopy to visualize viruses and EVs at high resolution and single‐cell imaging analyses to quantitate nascent EVs at the surface of gram‐negative bacteria. First, by analysing freshwater samples from a tropical ecosystem (Negro River/Amazon Basin/Brazil), we captured bacteriophages‐infected bacteria releasing EVs from their outer membrane. Next, VLPs isolated from these samples and inoculated in bacterial cultures not only impacted bacteria growth and viability but also led them to a significant release of EVs (~300% increase in numbers/cell section) compared to controls. The numbers of both budding and free EVs and EVs per linear micrometre of cell envelope were significantly higher in infected bacteria. Our findings identify a yet‐not recognized capability of freshwater bacteria in generating EVs (overvesiculation) in response to viral infection. Since viruses are abundant members of aquatic ecosystems and bacteria are natural hosts for them, such interaction is an interesting event for microbial communities to be explored in freshwater ecosystems.
ProX from marine Synechococcus spp. show a sole preference for glycine‐betaine with differential affinity between ecotypes
Authors: Ford Benjamin A. , Ranjit Pramita , Mabbutt Bridget C. , Paulsen Ian T. , Shah Bhumika S. 
Published: August 2022

AbstractOsmotic stress, caused by high or fluctuating salt concentrations, is a crucial abiotic factor affecting microbial growth in aquatic habitats. Many organisms utilize common responses to osmotic stress, generally requiring active extrusion of toxic inorganic ions and accumulation of compatible solutes to protect cellular machinery. We heterologously expressed and purified predicted osmoprotectant, proline/glycine betaine‐binding proteins (ProX) from two phylogenetically distinct Synechococcus spp. MITS9220 and WH8102. Homologues of this protein are conserved only among Prochlorococcus LLIV and Synechococcus clade I, III and CRD1 strains. Our biophysical characterization show Synechococcus ProX exists as a dimer, with specificity solely for glycine betaine but not to other osmoprotectants tested. We discovered that MITS9220_ProX has a 10‐fold higher affinity to glycine betaine than WH8102_ProX, which is further elevated (24‐fold) in high salt conditions. The stronger affinity and effect of ionic strength on MITS9220_ProX glycine betaine binding but not on WH8102_ProX alludes to a novel regulatory mechanism, providing critical functional insights into the phylogenetic divergence of picocyanobacterial ProX proteins that may be necessary for their ecological success.
Profiling of bacterial transcriptome from ultra‐low input with MiniBac‐seq
Authors: Wang Tianmin , Shen Ping , Chai Ruochen , He Yihui , Liu Jintao 
Published: August 2022

AbstractThere is a lack of appropriate methods for preparing bacterial RNA‐seq library with ultra‐low amount of RNA. To address this issue, we developed miniBac‐seq, a strand‐specific method for high‐quality library construction from sub‐nanogram of total RNA, which is 100‐fold lower than the current benchmark kit and dramatically reduces preparation cost ($28 + $15 × samples). We further demonstrated the high sensitivity of miniBac‐seq via detecting more than 500 genes from amount of total RNA equivalent to that of a single bacterial cell. Finally, we profiled the transcriptome of growth‐arrested bacteria in isogenic culture of Escherichia coli. This subpopulation of bacteria is generally low in abundance but is a potent reservoir of antibiotic persistence, and their gene expression has been largely unknown due to technical limitations. Using miniBac‐seq, we identified potential molecular driver towards arrested growth as well as antibiotic tolerance. Our method thus expands the capacity to quantify bacterial transcriptome in situ, which is useful to the understanding of bacterial physiology and regulation in their native contexts.
Redefining the phylogenetic and metabolic diversity of phylum Omnitrophota
Authors: Perez‐Molphe‐Montoya Eugenio , Küsel Kirsten , Overholt Will A. 
Published: August 2022

AbstractThe candidate phylum Omnitrophica—recently termed Omnitrophota, and originally known as OP3—is an understudied bacterial clade that has primarily been found in aquatic ecosystems. To characterize the diversity and ecology of this phylum, we reconstructed 55 Omnitrophota metagenome‐assembled genomes (MAGs) from a well‐characterized groundwater system within central Germany and placed them within the context of publicly available genomes. Seven clades were identified, four of which contained novel genomes obtained from our groundwater system. All clades exhibited the capacity for type IV pili, type II secretion systems, glycogen storage, and carbohydrate degradation. Only the characterized Cand. Omnitrophus magneticus genome exhibited functions associated with magnetosome construction. Clades were characterized by sets of traits rather than unique pathways, which were then used to infer ecological strategies. These lifestyles consisted of mixotrophs, obligate fermenters, and versatile respiratory heterotrophs. Patterns in 16S rRNA gene amplicons from a 6 years, monthly sampled groundwater time‐series dataset reflected the persistent and widespread occurrence of Clade 7 Wood–Ljungdahl utilizing mixotrophs and highlight this group as a core member of the groundwater community. Overall, this study uncovered, characterized, and contextualized the metabolic and phylogenetic diversity within phylum Omnitrophota, and predicts that environmental populations may mediate both nitrogen and sulfur cycling, along with organic matter production and degradation within aquatic ecosystems.
Whose policy uncertainty affects commodity trade between Australia and the United States?
Authors: Bahmani‐Oskooee Mohsen , Nouira Ridha , Saafi Sami 
Published: August 2022

AbstractRecent studies are assessing the impact of news‐based policy uncertainty measure on trade flows between countries. In this paper we add to this new literature by investigating the symmetric and asymmetric effects of Australian policy uncertainty index and the U.S. index on trade flows of 63 two‐digit industries that trade between the two countries. When we estimated a symmetric and linear model for each industry, we found short‐run effects of both uncertainty measures on 30% of the industries' trade flows. However, this number increased to 70% when an asymmetric and nonlinear model was estimated. The long‐run effects of both policy uncertainty followed similar pattern. Less than 10% of trade was affected by the estimates of the linear models. However, estimates of the nonlinear models predicted that 41.20% (26.53%) of the U.S. exports to Australia was affected by the U.S. uncertainty (Australian uncertainty). As for the Australian exports to the United States, 6.72% (5.5%) of its exports were affected by the changes in the U.S. policy uncertainty (Australian uncertainty). In almost all industries, increased uncertainty was found to hurt the trade and decreased uncertainty was found to boost it at different rate or asymmetrically. In sum, the U.S. and Australian policy uncertainty measure affects U.S. exports to Australia much more than they affect Australian exports to the United States.
Company and the mysteries of a dugout canoe
Authors: Pina‐Cabral João 
Published: August 2022

AbstractThis article examines the mysterious side of ‘company’, a fundamental aspect of human existence, exemplifying it with an ethnographic vignette about a dugout canoe in the mangroves of southern Bahia (Northeast Brazil). Inspired by Kant's proposal concerning aspects of world, the article distinguishes company both from empathy and from community, as distinct registers of human sociality. Being in company necessarily engages more than two persons inhabiting a common space; it involves an intersubjective encounter that has implications not only for what we do, but also for who we are and where we are. As they emerge into personhood from within company, persons necessarily experience the presence of third parties as a possible threat, inevitably giving rise to contradictory emotions: there is as much fear and conflict as peace within company, for it brings together entities with divergent interests and combines persons and objects in the world. The article addresses the way in which companionship engages power relations, by reference both to gender and to control over land.
Hot air‐assisted radio frequency drying of grated potato (Solanum tuberosum L.): Drying behavior and the associated effect on characteristics of potato flour
Authors: Kemal Ezgi , Özbek Hatice Neval , Göğüş Fahrettin , Yanık Derya Koçak 
Published: August 2022

AbstractIn this study, drying of grated potato in a hot air‐assisted radio frequency system (HA‐RF) and the associated effects on the final potato flour quality were studied. The drying behavior of the grated potatoes at different electrode distances (70–90 mm) and sample thickness (2–4 cm) was investigated. The safe drying (without burning tendency) of the maximum amount of sample (1000 g) in a reasonable drying time was carried out at 80 mm of electrode gap and 4 cm of sample thickness. HA‐RF drying kinetics were studied and compared with hot air (HA) and radio frequency (RF) (without hot air) drying methods. HA‐RF drying increased drying rate and shortened drying time by about 58% and 70% compared to HA and RF drying, respectively. The properties of the final potato flour obtained after HA‐RF drying were also compared with those produced by RF, HA, and freeze drying. The flour obtained by HA‐RF was superior to RF and HA dried samples with better retention of cellular microstructure and color. The drying method significantly affected the functional properties, thermal characteristics, pasting properties, and other characteristics of potato flours.Practical ApplicationHA‐RF as an alternative drying technology was used for the first time to produce potato flour. The functional, thermal, and structural properties of the HA‐RF dried product were compared with those dried by HA, RF, and freeze drying. The results of this study ensured very useful information for the use of potato flour obtained by different drying methods in the development of products with specific functional and rheological properties.
Global shocks and international policy coordination
Authors: Goyal Ashima , Pal Rupayan 
Published: August 2022

AbstractWe show as emerging markets (EMs) size crosses a threshold it is in advanced economies (AEs) own interest to reduce negative spillovers to EMs. It follows the potential for international cooperation in macroeconomic and prudential policy increases. But entrenched perceptions and historical advantages are obstacles. These blocks are explored as well as possibilities in macroeconomic policies and in prudential regulation. Export of capital is a major way AEs earn a share in EM income. AE macroeconomic policy and volatile capital outflows from AEs are a source of negative spillovers for EMs, but preventive prudential regulation is not adequate in AEs. More regulation is likely to reduce short‐term returns to capital flows but not long‐term, since with fewer crises both AE and EM income streams would rise. Moreover, there is some evidence excess capital flow volatility has adverse effects on AEs themselves. It follows universal macro‐prudential polices would benefit both country groups.
Correlates of optimism among patients in substance use disorder inpatient treatment
Authors: Provost Scott E. , Griffin Margaret L. , Hilton Blake T. , McHugh R. Kathryn , Taghian Nadine R. , Trinh Catherine D. , Weiss Roger D. 
Published: August 2022

AbstractBackground and ObjectivesEarly recovery from substance use disorder (SUD) is often characterized by hopelessness and despair about the future. Optimism, or the expectation that good things will happen, may provide a buffer against despair, and motivate adaptive goal engagement and coping. Study objectives were to (1) compare levels of optimism among individuals in substance use disorder inpatient treatment to other populations and (2) examine correlates of optimism.MethodsThis exploratory study utilized a cross‐sectional survey design. Participants (n = 355) completed self‐report measures assessing sociodemographic and clinical characteristics. The main variable of interest, optimism, was assessed by Life Orientation Test‐Revised scores. Multivariate regression was used to examine the association among sociodemographic and clinical variables and optimism.ResultsOur sample (n = 342) scored lower on optimism (mean = 11.7) than general population and SUD patients reported in the literature (range = 13.0–18.5). Optimism was higher for SUD inpatients who were college‐educated and those with higher scores on the recovery protection factor, while greater anxiety severity was associated with lower optimism scores.Conclusions and Scientific SignificanceThis study contributes to emerging research on the association between optimism and SUDs. Optimism has not been previously studied among patients in acute, short‐term inpatient SUD treatment and doing so may be clinically useful in addressing low optimism as an obstacle to motivation for treatment. Bolstering optimism may be a promising target for intervention and future research.
Sectoral wage gaps and gender in rural India†
Authors: Merfeld Joshua D. 
Published: August 2022

AbstractUsing detailed monthly household panel data from rural India, I analyze sectoral wage gaps for men and women. I show that the wage gap across the non‐farm and farm sectors is much higher for women than for men. Relative to men, women also work less time in non‐farm wage employment than in farm wage employment. Taken together, these findings suggest that constraints are preventing women from reallocating their time to more remunerative wage employment opportunities. Women are less likely to work outside of their own village in the non‐farm sector, yet the wage gap is driven by higher caste and married women. These results are consistent with a lack of local non‐farm employment opportunities interacting with barriers to labor mobility for women but not men.
Does Affective Polarization Undermine Democratic Norms or Accountability? Maybe Not
Authors: Broockman David E. , Kalla Joshua L. , Westwood Sean J. 
Published: August 2022

AbstractScholars warn that affective polarization undermines democratic norms and accountability. They speculate that if citizens were less affectively polarized, they would be less likely to endorse norm violations, overlook copartisan politicians’ shortcomings, oppose compromise, adopt their party's views, or misperceive economic conditions. We advance reasons to doubt that affective polarization influences political choices. We support this argument with five experiments that manipulate citizens’ affective polarization with multiple approaches. We then trace the downstream consequences of manipulating citizens’ affective polarization, such as their reactions to information about their actual representatives in Congress. In our experiments (total N = 12,341), we “rewind” the equivalent of three decades of change in affective polarization but find no evidence that these changes influence many political outcomes, only general questions about interpersonal attitudes. Our results suggest caution when assuming that reducing affective polarization would meaningfully bolster democratic norms or accountability.
Defining complexity in anaesthesia: description and validation of the Oxford Anaesthetic Complexity (OxAnCo) score
Authors: Ridgeon E. , Wilson K. , Wilkinson D. , Douglass P. , Elrefaey A. 
Published: August 2022

SummaryIncreasing demand for surgery and anaesthesia has created an imperative to manage anaesthetic workforce and caseload. This may include changes to distribution of cases amongst anaesthetists of different grades, including non‐physician anaesthetists. To achieve this safely, an assessment of case complexity is essential. We present a novel system for scoring complexity of cases in anaesthesia, the Oxford Anaesthetic Complexity score. This integrates patient, anaesthetic, surgical and systems factors, and is different from assessments of risk. We adopted an end‐user development approach to the design of the score, and validated it using a dataset of anaesthetic cases. Across 688 cases, the median (IQR [range]) complexity score was 19 (17–22 [15–33]). Cases requiring a consultant anaesthetist had a significantly higher median (IQR [range]) score than those requiring a senior trainee at 22 (20–25 [15–33]) vs. 19(17–21 [15–28]), p < 0.001. Cases undertaken in a tertiary acute hospital had a significantly higher score than those in a district general hospital, the median (IQR [range]) scores being 20 (17–22 [15–33]) vs. 17 (16–19 [17–28]), p < 0.001. Receiver‐operating characteristic analysis showed good prediction of complexity sufficient to require a consultant anaesthetist, with area under the curve of 0.84. Any rise in complexity above baseline (score > 15) was strongly predictive of a case too complex for a junior trainee (positive predictive value 0.93). The Oxford Anaesthetic Complexity score can be used to match cases to different grades of anaesthetist, and can help in defining cases appropriate for the expanding non‐physician anaesthetist workforce.
Chicken ovalbumin upstream promoter transcription factor type II interacts and functionally cooperates with GATA4 to regulate anti‐Müllerian hormone receptor type 2 transcription in mouse MA‐10 Leydig cells
Authors: Mehanovic Samir , Pierre Kenley Joule , Viger Robert S. , Tremblay Jacques J. 
Published: August 2022

AbstractBackgroundLeydig cells produce testosterone and insulin‐like 3, two hormones essential for male sex differentiation and reproductive function. The orphan nuclear receptor, chicken ovalbumin upstream promoter transcription factor type II (COUP‐TFII), and the zinc finger factor GATA4 are two transcription factors involved in Leydig cell differentiation, gene expression, and function.ObjectivesSeveral Leydig cell gene promoters contain binding motifs for both GATA factors and nuclear receptors. The goal of the present study is to determine whether GATA4 and COUP‐TFII cooperate to regulate gene expression in Leydig cells.Materials and methodsThe transcriptomes from GATA4‐ and COUP‐TFII‐depleted MA‐10 Leydig cells were analyzed using bioinformatic tools. Functional cooperation between GATA4 and COUP‐TFII, and other related family members, was assessed by transient transfections in Leydig (MA‐10 and MLTC‐1) and fibroblast (CV‐1) cell lines on several gene promoters. Recruitment of GATA4 and COUP‐TFII to gene promoters was investigated by chromatin immunoprecipitation. Co‐immunoprecipitation was used to determine whether GATA4 and COUP‐TFII interact in MA‐10 Leydig cells.ResultsTranscriptomic analyses of GATA4‐ and COUP‐TFII‐depleted MA‐10 Leydig cells revealed 44 commonly regulated genes including the anti‐Müllerian hormone receptor type (Amhr2) gene. GATA4 and COUP‐TFII independently activated the Amhr2 promoter, and their combination led to a stronger activation. A GC‐rich element, located in the proximal Amhr2 promoter was found to be essential for GATA4‐ and COUP‐TFII‐dependent activation as well as for the COUP‐TFII/GATA4 cooperation. COUP‐TFII and GATA4 directly interacted in MA‐10 Leydig cell extracts. Chromatin immunoprecipitation revealed that GATA4 and COUP‐TFII are recruited to the proximal Amhr2 promoter, which contains binding sites for both factors in addition to the GC‐rich element. Cooperation between COUP‐TFII and GATA6, but not GATA1 and GATA3, was also observed.Discussion and conclusionOur results establish the importance of physical and functional cooperation between COUP‐TFII/GATA4 in the regulation of gene expression in MA‐10 Leydig cells, and more specifically the Amhr2 gene.