bluuebunny/crossref_metadata_2025_split huggingface dataset:
A natural ANI gap that can define intra-species units of bacteriophages and other viruses
Authors: Aldeguer-Riquelme Borja , Conrad Roth E , Antón Josefa , Rossello-Mora Ramon , Konstantinidis Konstantinos T. 
Published: April 2024

AbstractDespite the importance of intra-species variants of viruses for causing disease and/or disrupting ecosystem functioning, there is no universally applicable standard to define these. A 95% whole-genome average nucleotide identity (ANI) gap is commonly used to define species, especially for bacteriophages, but whether a similar gap exists within species that can be used to define intra-species units has not been evaluated yet. Whole-genome comparisons among members of 1,016 bacteriophage species revealed a region of low frequency of pairs around 99.2-99.8% ANI, showing 3-fold or fewer pairs than expected for an even or normal distribution. This second gap is prevalent in viruses infecting various cultured or uncultured hosts, and from a variety of environments, although a few exceptions to this pattern were also observed (∼3.7% of the total species evaluated) and are likely attributed to cultivation biases. Similar results were observed for a limited set of eukaryotic viruses that are adequately sampled including SARS-CoV-2, whose ANI-based clusters matched well the WHO-defined Variants of Concern, indicating that they represent functionally and/or ecologically distinct units. The existence of sequence-discrete units appears to be predominantly driven by (high) ecological cohesiveness coupled to either recombination frequency for bacteriophages or selection and clonal evolution for other viruses such as SARS-CoV-2. These results indicate that fundamentally different underlying mechanisms could lead to similar diversity patterns. Based on these results, we propose the 99.5% ANI as a practical, standardized, and data-supported threshold for defining viral intra-species units of bacteriophages, for which we propose the term genomovars.ImportanceViral species are composed of an ensemble of intra-species variants whose dynamic may have major implications for human and animal health and/or ecosystem functioning. However, the lack of universally-accepted standards to define these intra-species variants has led researchers to use different approaches for this task, creating inconsistent intra-species units across different viral families and confusion in communication. By comparing hundreds of viral bacteriophage genomes, we show that there is a nearly universal natural gap in whole-genome average nucleotide identities (ANI) among genomes at around 99.5%, which can be used to define intra-species units. Therefore, these results advance the molecular toolbox for tracking viral intra-species units and should facilitate future epidemiological and environmental studies.
Extended period of selection for antimicrobial resistance due to persistency of antimicrobials in broilers
Authors: Swinkels Aram F. , Berendsen Bjorn J.A. , Fischer Egil A.J. , Zomer Aldert L. , Wagenaar Jaap A. 
Published: April 2024

AbstractAntimicrobials can select for antimicrobial resistant bacteria. After treatment the active compound is excreted through urine and faeces. As some antimicrobials are chemically stable and very persistent, recirculation of sub-inhibitory concentrations of antimicrobials may occur due to coprophagic behaviour of animals such as chickens.The persistence of three antimicrobials over time and their potential effects on antimicrobial resistance were determined in four groups of broilers. Groups were left untreated (control) or were treated with amoxicillin (non-persistent), doxycycline or enrofloxacin (persistent). Antimicrobials were extracted from the faecal samples and concentrations were measured by LC-MS/MS. We determined the resistome genotypically using shotgun metagenomics and phenotypically by usingEscherichia colias indicator microorganism.Up to 37 days after treatment, persistent antimicrobials (doxycycline and enrofloxacin) had concentrations in faeces equal to or higher than the minimal selective concentration (MSC), in contrast to the non-persistent (amoxicillin) treatment. The amoxicillin treatment showed a significant difference (p ≤ 0.01 and p ≤ 0.0001) in the genotypic resistance only directly after treatment. On the other hand, the doxycycline treatment showed approximately 52% increase in phenotypic and a significant difference (p ≤ 0.05 and p ≤ 0.0001) in genotypic resistance throughout the trial. Furthermore, the enrofloxacin treatment resulted in a complete enrofloxacin-resistantE. colipopulation but the quantity of resistance genes was similar to the control group, likely because resistance is mediated by point mutations.Based on our findings, we suggest that persistency of antimicrobials should be taken into consideration in the assessment of priority classification of antimicrobials in livestock.
Toxicity assessment of 3-O-[6-deoxy-3-O-methyl-β-D-allopyranosyl-(1→4)-β-D-oleandropyranosyl]-17β–marsdenin isolated fromGongronema latifoliumleaf on selected brain and kidney function indices in mice
Authors: Ani Onyedika Gabriel , Medayedupin Oluwatobi Ayodeji , Azeez Aminat Abike , Gyebi Gideon Ampoma , Boateng Isaac Duah , Adebayo Joseph Oluwatope 
Published: April 2024

AbstractThe safety of bioactive compounds, especially those isolated from medicinal plants, is a major concern for health authorities, pharmaceutical industries, and the public. Of recent, anti-tumor pregnane glycosides were isolated fromGongronema latifoliumleaf, of which the toxicity of one, 3-O-[6-deoxy-3-O-methyl-β-D-allopyranosyl-(1→4)-β-D-oleandropyranosyl]-17β–marsdenin (3DMAOM), has not been evaluated. This study, therefore, evaluated the effects of 3DMAOM on selected brain and kidney function indices in mice. Female Swiss albino mice were randomly administered 5% dimethyl sulphoxide and different doses of 3DMAOM (0.5, 1, 2, and 4 mg/kg body weight) for fourteen (14) days, and their blood, brains, and kidneys were collected for biochemical analysis. There was no significant alteration in the activities of alkaline phosphatase (ALP), acetylcholinesterase, creatine kinase, Na+/K+-ATPase, Ca2+/Mg2+-ATPase, and Mg2+-ATPase in the brain of the treated groups compared to control. Also, no significant changes in the activities of ALP, gamma-glutamyltransferase, Na+/K+-ATPase, Ca2+/Mg2+-ATPase, and Mg2+-ATPase in the kidney of the treated groups compared to control. The plasma concentrations of Na+, K+, Cl-, PO43-, creatinine, and urea of mice were not significantly altered at all doses of the 3DMAOM compared to controls. However, the plasma concentration of Ca2+was significantly reduced (p<0.05) at all doses of the 3DMAOM, and the plasma concentration of uric acid was significantly reduced (p<0.05) at 2 mg/kg body weight of the 3DMAOM compared to controls. These findings suggest that 3DMAOM isolated fromGongronema latifoliumleaf may not adversely affect brain function but may affect calcium ion homeostasis in subjects.
Phosphorylation of KRP3, a KIP-related protein by MPK3 modulates rice tiller and seed number by fine-tuning cell division
Authors: Banerjee Gopal , Jonwal Sarvesh , Pal Uttam , Rengasamy Balakrishnan , Singh Dhanraj , Sinha Alok Krishna 
Published: April 2024

AbstractDuring the cell cycle process, multiple inhibitors function as checkpoint regulators ensuring an impeccable duplication of genetic material. Kip-Related Proteins (KRPs) are a group of plant-specific cell cycle inhibitors and are known to regulate plant architecture and yield by differentially regulating cell division. KRPs, though functionally conserved, are dynamic in their amino acid composition. Interestingly, some KRPs are specific to dicots, and some are for monocots. In this study, we have identified that the presence of KRP3 and KRP6 is specific to the Poaceae family of monocots. An in-depth study ofKRP3showed a strict regulation of its expression in actively dividing cells during the G1-S phase progression of cell division. Our study identified KRP3 as a phosphorylation target of MPK3. The phosphorylation enhances KRP3 protein stability, which leads to strong inhibition of cell proliferation. By generating knock-out lines ofkrp3,mpk3and double knock-outkrp3mpk3, our study demonstrated that the MPK3-KRP3 module regulates rice root and shoot development as well as tiller and seed numbers. It was observed that KRP3 regulate the rate of cell division in a dose-dependent manner. The study, in a nutshell, establishes the role of KRP3 as an important regulator of rice vigor and yield.
Keetia gordoniisp. nov. (Rubiaceae - Vanguerieae) a new species of threatened forest liana from the littoral forest of Gabon
Authors: Cheek Martin , Bissiengou Pulchérie 
Published: April 2024

SummaryKeetia gordoniisp. nov. (Rubiaceae - Vanguerieae) a new species of forest liana from the littoral forest of Gabon is formally described and illustrated as the first endemic species of the genus from that country. On current evidence, the species appears to have three locations and is threatened by forest clearance. It is provisionally assessed using the IUCN 2012 standard as Endangered (EN B2a,b(i-iv). The new species is extremely distinctive within the genus, showing several character states previously unrecorded inKeetia. Keetia gordoniiis currently unique in its genus for the massively thick, coriaceous leaf blades seen in the fruiting axillary branches (in this respect resembling aPsydraxGaertn., vs papery or rarely thinly coriaceous in otherKeetiaspecies), and also for the globose, smooth pyrenes (vs ovoid, colliculose in other species), in which the lid crest is so vestigial that it is almost imperceptible (vs lid crest conspicuous in other species). The tanniferous seed endosperm shows a new character state for the genus being present in a continuous, solid layer in the outer part of the seed, rather than being in radial bands or diffuse as in other species of the genus. However, there is no doubt that this taxon is best placed inKeetiaas opposed toPsydraxdue to the disc concealed deep inside the calyx tube (vs exposed), the presence of a pyrene cap (vs none) and the stipules that lack a well-developed keel (vs keel present). Further, the presence of tanniniferous seed endosperm is not recorded in any other genus of the tribe.Keetia gordoniiis currently assigned to theK. hispidaspecies group of Guineo-Congolian Africa.
A Sequential Binding Mechanism for 5’ Splice Site Recognition and Modulation for the Human U1 snRNP
Authors: White David S. , Dunyak Bryan M. , Vaillancourt Frédéric H. , Hoskins Aaron A. 
Published: April 2024

AbstractSplice site recognition is essential for defining the transcriptome. Drugs like risdiplam and branaplam change how U1 snRNP recognizes particular 5’ splice sites (5’SS) and promote U1 snRNP binding and splicing at these locations. Despite the therapeutic potential of 5’SS modulators, the complexity of their interactions and snRNP substrates have precluded defining a mechanism for 5’SS modulation. We have determined a sequential binding mechanism for modulation of -1A bulged 5’SS by branaplam using a combination of ensemble kinetic measurements and colocalization single molecule spectroscopy (CoSMoS). Our mechanism establishes that U1-C protein binds reversibly to U1 snRNP, and branaplam binds to the U1 snRNP/U1-C complex only after it has engaged a -1A bulged 5’SS. Obligate orders of binding and unbinding explain how reversible branaplam interactions cause formation of long-lived U1 snRNP/5’SS complexes. Branaplam is a ribonucleoprotein, not RNA duplex alone, targeting drug whose action depends on fundamental properties of 5’SS recognition.
Comparative root transcriptome analysis suggests down-regulation of nitrogen assimilation in DJ123, a highly phosphorus-efficient rice genotype
Authors: Prodhan M. Asaduzzaman , Ueda Yoshiaki , Wissuwa Matthias 
Published: April 2024

AbstractMany cultivable lands across the globe are characteristically low for plant-available phosphorus (P). This necessitates application of P fertilisers, but this increases farming costs beyond the affordability of marginal farmers. Thus, developing cultivars with high P-use efficiency (PUE) is necessary in high-yielding modern rice varieties, which are typically inefficient in P usage. However, the molecular and physiological bases to increase PUE in crops remain elusive. Here, we studied root transcriptomes of two breeding parents contrasting in PUE via RNA-seq to elucidate key physiological and molecular mechanisms that underlies efficient use of P in rice. Examination of transcriptome data obtained from plants grown under P-sufficient and P-deficient hydroponic conditions in DJ123 (an upland rice genotype adapted to low P soils) and IR64 (a modern rice variety less efficient in P use) revealed that the genes encoding nitrogen assimilation-related enzymes such as glutamine synthetase [EC. 6.3.1.2], glutamate synthase [EC. 1.4.1.13], and asparagine synthetase [EC. 6.3.5.4] were down-regulated only in DJ123 roots while it was not significantly affected in IR64 under low P conditions. In addition, DJ123 roots had a lower total nitrogen (N) concentration than IR64 irrespective of P conditions. Taken together, we surmise that the low level of N concentration together with down-regulation of the N assimilation-related genes allow DJ123 to operate at a low level of N, thus leading to formation of root tissues with lower metabolic investment and a greater PUE.
Periodic dietary restriction of animal products induces metabolic reprogramming in humans with effects on health
Authors: Rouskas Konstantinos , Bocher Ozvan , Simistiras Alexandros , Emmanouil Christina , Mantas Panagiotis , Skoulakis Anargyros , Park Y.C. , Dimopoulos Alexandros , Glentis Stavros , Kastenmüller Gabi , Zeggini Eleftheria , Dimas Antigone S. 
Published: April 2024

AbstractObjectivesDietary interventions can be a powerful tool for the prevention and treatment of diseases, but the molecular mechanisms through which diet affects health remain underexplored in humans. Generating robust evidence on the molecular impact of specific dietary patterns in humans will help us harness the power of dietary interventions to improve health.MethodsHere, we compare plasma metabolomic and proteomic profiles between dietary states for a unique group of individuals (N=200) who alternate between omnivory and restriction of animal products for religious reasons. We also contrast findings to a control group of continuously omnivorous individuals (N=211).ResultsWe find that short-term animal product restriction drives reductions in levels of lipid classes and of branched-chain amino acids, not detected in the control group, and results in metabolic profiles associated with decreased risk for all-cause mortality. We show that 23% of restriction-associated proteins are druggable targets and reveal that pro-longevity hormone FGF21 and seven additional proteins (FOLR2, SUMF2, HAVCR1, PLA2G1B, OXT, HPGDS, SPP1) display the greatest magnitude of change upon restriction. Through Mendelian randomization we demonstrate potentially causal effects of FGF21 and HAVCR1 on risk for type 2 diabetes, of HPGDS on BMI, and of OXT on risk for lacunar stroke.ConclusionsWe demonstrate that short-term restriction of animal products results in metabolic reprogramming with mostly positive effects on health and emphasise high-value targets for pharmacological intervention.
Conducting a survey of abortion-related knowledge, attitudes and practices amongst health professionals in Britain, strategies adopted and lessons learned: evidence from the SACHA Study
Authors: French RS , Palmer MJ , McCarthy O , Salaria N , Meiksin R , Shawe J , Lewandowska M , Scott R , Wellings K ,   the SACHA Study Team
Published: April 2024

AbstractBackgroundMost surveys examining health professionals’ knowledge, attitudes and practices around abortion have used convenience samples and have targeted doctors. Our goal in the SACHA Study, drawing on evidence-based strategies to maximise response rates, was to achieve a representative sample of a wider range of health professionals, working in general practice, maternity services, pharmacies, sexual and reproductive health (SRH) clinics and specialist abortion services in Britain, to explore the knowledge, attitudes and experience of abortion care and views on future models of delivery.MethodsA cross-sectional questionnaire-based survey of midwives, doctors, nurses and pharmacists in England, Scotland and Wales was undertaken between November, 2021 and July, 2022. We used a stratified cluster sampling approach to select a random sample of sites and all eligible staff within those services were asked to respond to the survey. Evidence-based strategies to maximise completion rates were adopted, including postal delivery of the one-page questionnaire with personal letter of invitation and a stamped address envelope for return, inclusion of an unconditional voucher and follow-up.ResultsOverall, 147 of the 314 (46.8%) health service sites randomly selected took part in the survey. Reasons for non-participation included local Research and Development (R&D) Department non-response, lack of resources or insufficient time to support or approve the study, lack of interest in or perceived relevance of the topic and insufficient capacity to take part, exacerbated by work demands during the COVID epidemic. Of the 1370 questionnaires sent to eligible identified participants within these services, 771 were completed and returned (56.3%). At the service level the highest proportion of returns was from SRH clinics (81.0%) and the lowest from general practice (32.4%). In relation to profession, returns were highest amongst midwives (69.6%) and lowest amongst pharmacists (36.5%).ConclusionsObtaining information about health professional knowledge, attitudes and practices is key to guide service development and policy and to identify gaps in training and service provision in abortion. Despite our attempts to gain a representative sample of health professionals, the challenges we experienced limited the representativeness of the sample, despite the use of an evidence-based strategy.
The B-box protein BBX13/COL15 suppresses photoperiodic flowering by attenuating the action of CONSTANS in Arabidopsis
Authors: Rahul Puthan Valappil , Yadukrishnan Premachandran , Sasidharan Anagha , Datta Sourav 
Published: April 2024

SummaryThe optimal timing of transition from vegetative to floral reproductive phase is critical for plant productivity and agricultural yields. Light plays a decisive role in regulating this transition. The B-box (BBX) family of transcription factors regulates several light-mediated developmental processes in plants, including flowering. Here, we identify a previously uncharacterized group II member of the BBX family, BBX13/COL15, as a negative regulator of flowering under long-day conditions.BBX13is primarily expressed in the leaf vasculature, buds, and flowers. Its spatial expression pattern is similar to the major flowering time regulatorsCOandFT. bbx13mutants flower early, whileBBX13-overexpressors exhibit delayed flowering under long days. Genetic analyses showed thatBBX13acts upstream toCOandFTin the flowering pathway and negatively regulates their expression. We found that BBX13 physically interacts with CO and inhibits the CO-mediated transcriptional activation ofFT. In addition, BBX13 directly binds to theCORE2motif on theFTpromoter, a site where CO also binds. Furthermore, our ChIP data indicates that BBX13 reduces the in vivo binding of CO on theFTpromoter. Through luciferase assay, we found that BBX13 inhibits the CO-mediated transcriptional activation ofFT.All these data together suggest that BBX13/COL15 represses flowering in Arabidopsis by attenuating CO activity.Summary statementBBX13, a previously uncharacterized protein in the B-Box family of transcription factors, negatively regulates flowering time inArabidopsis thaliana. BBX13 physically and genetically interacts with CO and inhibits the CO-mediated transcriptional activation ofFT.
Microresonator Brillouin laser and multi-Stokes generation at
2µm
Authors: Pathak Kanad , Puri Satyam , Pant Ravi 
Published: April 2024

Brillouin scattering in microresonators has emerged as the driving process for developing high-coherence lasers for applications such as coherent optical communications, optical atomic clocks, microcomb solitons, and quantum communications. However, most of the demonstrations of microresonator Brillouin lasers have been limited to a 1550 nm wavelength regime, which benefits from the development of low-loss microresonator devices on different material platforms and the availability of tunable pump lasers. The development of wide bandwidth thulium-doped fiber amplifiers and low two-photon absorption in silicon around 2µm makes this wavelength region a potential candidate for applications in future optical communications, gravitation wave sensing, and atmospheric sensing. All these applications will benefit from the development of Brillouin lasers. However, there has not been much progress on microresonator-based 2µm Brillouin lasers. Here, we present a demonstration of a 2µm microresonator Brillouin laser. We use whispering gallery mode resonances in a ∼330µm silica microsphere to demonstrate a Brillouin lasing threshold of 35 mW. We achieve generation of second- and third-order Brillouin Stokes using pump powers of ∼60mW and 104 mW, respectively. By tuning the pump laser wavelength, we demonstrate high-resolution (∼10 pm) tuning of the Brillouin laser. From the beat signal of the first- and third-order Brillouin Stokes, we estimate a Brillouin laser linewidth of ∼135kHz, which is 15 times smaller than the pump linewidth. This work may find applications in optical communications, soliton combs, and atmospheric sensing in the 2µm wavelength region.

Published by the American Physical Society
2024
Multidimensional relative poverty alleviation of the targeted microcredit in rural China: a gendered perspective
Authors: Wu Benjian , Niu Linyi , Tan Ruiqi , Zhu Haibo 
Published: April 2024

PurposeThis study explores whether targeted microcredit can effectively alleviate households’ multidimensional relative poverty (MdRP) in rural China in the new era following the poverty elimination campaign and discusses it from a gendered perspective.Design/methodology/approachThis study applies a fixed-effects model, propensity score matching (PSM) and two-stage instrumental variable method to two-period panel data collected from 611 households in rural western China in 2018 and 2021 to explore the effects, mechanisms and heterogenous performance of targeted microcredit on households’ MdRP in the new era.Findings(i) Targeted microcredit can alleviate MdRP among rural households in the new era, mainly by reducing income and opportunity inequality. (ii) Targeted microcredit can promote women’s empowerment, mainly by enhancing their social participation, thereby helping alleviate households’ MdRP. The effect of the targeted microcredit on MdRP is more significant in medium-educated women households and non-left-behind women households. (iii) The MdRP alleviation effect is stronger in villages with a high degree of digitalization.Research limitations/implicationsLearn from the experience of targeted microcredit. Accurately identify poor groups and integrate loan design into financial health and women empowerment. Particularly, pay attention to less-educated and left-behind women households and strengthen coordination between targeted microcredit and digital village strategies.Originality/valueThis study clarifies the effect of targeted microcredit on women’s empowerment and households’ MdRP alleviation in the new era. It also explores its various effects on households with different female characteristics and regional digitalization levels, providing ideas for optimizing microcredit.