Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of tigurilysin, a novel human CD59-specific cholesterol-dependent cytolysin, reveals a role for host specificity in augmenting toxin activity

Cholesterol-dependent cytolysins (CDCs) are a large family of pore-forming toxins, produced by numerous Gram-positive pathogens. CDCs depend on host membrane cholesterol for pore formation; some CDCs also require surface-associated human CD59 (hCD59) for binding, conferring specificity for human cells. We purified a recombinant version of a putative CDC encoded in the genome of Streptococcus oralis subsp . tigurinus , tigurilysin (TGY), and used CRISPR/Cas9 to construct hCD59 knockout (KO) HeLa and JEG-3 cell lines. Cell viability assays with TGY on wild-type and hCD59 KO cells showed that TGY is a hCD59-dependent CDC. Two variants of TGY exist among S. oralis subsp . tigurinus genomes, only one of which is functional. We discovered that a single amino acid change between these two TGY variants determines its activity. Flow cytometry and oligomerization Western blots revealed that the single amino acid difference between the two TGY isoforms disrupts host cell binding and oligomerization. Furthermore, experiments with hCD59 KO cells and cholesterol-depleted cells demonstrated that TGY is fully dependent on both hCD59 and cholesterol for activity, unlike other known hCD59-dependent CDCs. Using full-length CDCs and toxin constructs differing only in the binding domain, we determined that having hCD59 dependence leads to increased lysis efficiency, conferring a potential advantage to organisms producing hCD59-dependent CDCs.
The MODY-associated TALK-1 L114P mutation causes islet α-cell overactivity and β-cell inactivity resulting in transient neonatal diabetes and glucose dyshomeostasis in adults

The gain-of-function mutation in the TALK-1 K+ channel (p.L114P) is associated with maturity-onset diabetes of the young (MODY). TALK-1 is a key regulator of β-cell electrical activity and glucose-stimulated insulin secretion. The KCNK16 gene encoding TALK-1 is the most abundant and β-cell–restricted K+ channel transcript. To investigate the impact of KCNK16 L114P on glucose homeostasis and confirm its association with MODY, a mouse model containing the Kcnk16 L114P mutation was generated. Heterozygous and homozygous Kcnk16 L114P mice exhibit increased neonatal lethality in the C57BL/6J and the CD-1(ICR) genetic background, respectively. Lethality is likely a result of severe hyperglycemia observed in the homozygous Kcnk16 L114P neonates due to lack of glucose-stimulated insulin secretion and can be reduced with insulin treatment. Kcnk16 L114P increased whole-cell β-cell K+ currents resulting in blunted glucose-stimulated Ca2+ entry and loss of glucose-induced Ca2+ oscillations. Thus, adult Kcnk16 L114P mice have reduced glucose-stimulated insulin secretion and plasma insulin levels, which significantly impairs glucose homeostasis. Taken together, this study shows that the MODY-associated Kcnk16 L114P mutation disrupts glucose homeostasis in adult mice resembling a MODY phenotype and causes neonatal lethality by inhibiting islet insulin secretion during development. These data suggest that TALK-1 is an islet-restricted target for the treatment for diabetes. Graphical Summary
The F pilus serves as a conduit for the DNA during conjugation between physically distant bacteria

Horizontal transfer of F-like plasmids by bacterial conjugation is responsible for disseminating antibiotic resistance and virulence determinants among pathogenic Enterobacteriaceae species, a growing health concern worldwide. Central to this process is the conjugative F pilus, a long extracellular filamentous polymer that extends from the surface of plasmid donor cells, allowing it to probe the environment and make contact with the recipient cell. It is well established the F pilus can retract to bring mating pair cells in tight contact before DNA transfer. However, whether DNA transfer can occur through the extended pilus has been a subject of active debate. In this study, we use live-cell microscopy to show that the F pilus can indeed serve as a conduit for the DNA during transfer between physically distant cells. Our findings enable us to propose a new model for conjugation that revises our understanding of the DNA transport mechanism and the dissemination of drug resistance in complex bacterial communities. One-Sentence Summary: Plasmid DNA passes through the F pilus during conjugational transfer between physically distant bacteria.
From asexuality to sexual reproduction: cyclical switch of gametogenic pathways in hybrids depends on ploidy level

The cellular and molecular mechanisms governing sexual reproduction is highly conserved across eukaryotes. Nevertheless, hybridization can disrupt such machinery leading to asexual reproduction. To investigate how hybridization and polyploidization affect gametogenesis and reproductive outcomes of asexual hybrids, we conducted a comprehensive study on diploid and triploid hybrids along with their sexual parental species from the freshwater fish family Cobitidae. In diploid and triploid hybrids, most gonocytes maintain their original ploidy level. During meiosis, such gonocytes experience abnormal chromosome pairing preventing progression beyond pachytene. Diploid hybrid females regain fertility through premeiotic genome endoreplication, resulting in the rare emergence of tetraploid gonocytes. Tetraploid gonocytes bypass meiosis and lead to clonal diploid gametes. In contrast, triploid hybrids lack genome endoreplication but utilize premeiotic genome elimination of a single-copy parental genome forming diploid gonocytes that undergo meiosis and produce haploid gametes. Therefore, the interplay of parental genomes leads to diverse gametogenic outcomes in hybrids dependent on their ploidy and genome dosage. These alterations in gametogenic pathways can persist across generations, potentially enabling the cyclic maintenance of asexual/polyploid hybrids in natural populations.
Novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field

Iron oxidizing Zetaproteobacteria are well-known to colonize deep-sea hydrothermal vent fields around the world where iron-rich fluids are discharged into oxic seawater. How inter-field and intra-field differences in geochemistry influence the diversity of Zetaproteobacteria, however, remains largely unknown. Here, we characterize Zetaproteobacteria phylogenomic diversity, metabolic potential, and morphologies of the iron oxides they form, with a focus on the recently discovered Fåvne vent field. Located along the Mohns ridge in the Arctic, this vent field is a unique study site with vent fluids containing both iron and hydrogen with thick iron microbial mats (Fe mats) covering porously venting high-temperature (227-267 °C) black smoker chimneys. Through genome-resolved metagenomics and microscopy, we demonstrate that the Fe mats at Fåvne are dominated by tubular iron oxide sheaths, likely produced by Zetaproteobacteria of genus Ghiorsea. With these structures, Ghiorsea may provide a surface area for members of other abundant taxa such as Campylobacterota, Gammaproteobacteria and Alphaproteobacteria. Furthermore, Ghiorsea likely oxidizes both iron and hydrogen present in the fluids, with several Ghiorsea populations co-existing in the same niche. Homologues of Zetaproteobacteria Ni,Fe hydrogenases and iron oxidation gene cyc2 were found in genomes of other community members, suggesting exchange of these genes could have happened in similar environments. Our study provides new insights into Zetaproteobacteria in hydrothermal vents, their diversity, energy metabolism and niche formation. Importance Knowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of Ghiorsea, an iron- and hydrogen oxidizing Zetaproteobacteria representative belonging to ZetaOTU9. The study proposes that Ghiorsea exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.
A genome-wide overexpression screen reveals Mycobacterium smegmatis growth inhibitors encoded by mycobacteriophage Hammy

During infection, bacteriophages produce diverse gene products to overcome bacterial anti-phage defenses, to outcompete other phages, and take over cellular processes. Even in the best-studied model phages, the roles of most phage-encoded gene products are unknown, and the phage population represents a largely untapped reservoir of novel gene functions. Considering the sheer size of this population, experimental screening methods are needed to sort through the enormous collection of available sequences and identify gene products that can modulate bacterial behavior for downstream functional characterization. Here, we describe the construction of a plasmid-based overexpression library of 94 genes encoded by Hammy, a Cluster K mycobacteriophage closely related to those infecting clinically important mycobacteria. The arrayed library was systematically screened in a plate-based cytotoxicity assay, identifying a diverse set of 24 gene products (representing 25% of the Hammy genome) capable of inhibiting growth of the host bacterium Mycobacterium smegmatis. Half of these are related to growth inhibitors previously identified in related phage Waterfoul, supporting their functional conservation; the other genes represent novel additions to the list of known anti-mycobacterial growth inhibitors. This work, conducted as part of the HHMI-supported Science Education Alliance Gene-function Elucidation by a Network of Emerging Scientists (SEA-GENES) project, highlights the value of parallel, comprehensive overexpression screens in exploring genome-wide patterns of phage gene function and novel interactions between phages and their hosts.
Detection of threshold-level stimuli modulated by temporal predictions of the cerebellum

The cerebellum has the reputation of being a primitive part of the brain that mostly is involved in motor coordination and motor control. Older lesion studies and more recent electrophysiological studies have, however, indicated that it is involved in temporal perception and temporal expectation-building. An outstanding question is whether this temporal expectation-building cerebellar activity has functional relevance. In this study, we collected magnetoencephalographic data from 30 healthy participants performing a detection task on at-threshold stimulation that was presented at the end of a sequence of temporally regular or irregular above-threshold stimulation. We found that behavioural detection rates depended on the degree of irregularity in the sequence preceding it. We also found cerebellar responses evoked by above-threshold and at-threshold stimulation. The evoked responses to at-threshold stimulation differed significantly, depending on whether it was preceded by a regular or an irregular sequence. Finally, we found that detection performance across participants correlated significantly with the differences in cerebellar evoked responses to the at-threshold stimulation, demonstrating the functional relevance of cerebellar activity in sensory expectation-building. We furthermore found evidence of thalamic involvement, as indicated by responses in the beta band (14-30 Hz) and by significant modulations of cerebello-thalamic connectivity by the regularity of the sequence and the kind of stimulation terminating the sequence. These results provide evidence that the temporal expectation-building mechanism of the cerebellum, what we and others have called an internal clock, shows functional relevance by regulating behaviour and performance in sensory action that requires acting and integrating evidence over precise time-scales.
Biomarkers to predict steroid resistance in idiopathic nephrotic syndrome: a systematic review

In this systematic review we have sought to summarise the current knowledge concerning biomarkers that can distinguish between steroid-resistant nephrotic syndrome and steroid-sensitive nephrotic syndrome. Additionally, we aim to select biomarkers that have the best evidence-base and should be prioritised for further research. Pub med and web of science databases were searched using “steroid resistant nephrotic syndrome AND biomarker”. Papers published between 01/01/2012 and 10/05/2022 were included. Papers that did not compare steroid resistant and steroid sensitive nephrotic syndrome, did not report sensitivity/specificity or area under curve and reviews/letters were excluded. The selected papers were then assessed for bias using the QUADAS-2 tool. The source of the biomarker, cut off, sensitivity/specificity, area under curve and sample size were all extracted. Quality assessment was performed using the BIOCROSS tool. 17 studies were included, comprising 15 case-control studies and 2 cross-sectional studies. Given the rarity of nephrotic syndrome and difficulty in recruiting large cohorts, case-control studies were accepted despite their limitations. Haptoglobin and suPAR were identified as the most promising biomarkers based on their ability to predict rather than assess steroid resistance in nephrotic syndrome, their respective sample sizes and specificity and sensitivity. None of the selected papers stated whether the authors were blinded to the patient’s disease when assessing the index test in the cohort. These candidate biomarkers must now be tested with much larger sample sizes. Using new biobanks such as the one built by the NURTuRE-INS team will be very helpful in this regard.
Physiological phenotypes differ among color morphs in introduced populations of the common wall lizard, Podarcis muralis

Many species exhibit color polymorphisms which have distinct physiological and behavioral characteristics. However, the consistency of morph trait covariation patterns across species, time, and ecological contexts remains unclear. This trait covariation is especially relevant in the context of invasion biology and urban adaptation. Specifically, physiological and behavioral traits pertaining to energy maintenance are crucial to fitness, given their immediate ties to individual reproduction, growth, and population establishment. We investigated the physiological and behavioral traits of Podarcis muralis, a versatile color polymorphic species that thrives in urban environments (including invasive populations in Ohio, USA). We measured five physiological and behavioral traits (circulating corticosterone and triglycerides, hematocrit, body condition, and field body temperature) which compose an integrated multivariate phenotype. We then tested variation among stable color polymorphisms in the context of establishment in an urban environment. We found that the traits describing physiological status and strategy shifted across the active season in a morph-dependent manner-the white and yellow morphs exhibited clearly different multivariate physiological phenotypes, characterized primarily by differences in circulating corticosterone. This suggests that morphs have different strategies in physiological regulation, the flexibility of which is crucial to urban adaptation. The white-yellow morph exhibited an intermediate phenotype, suggesting an intermediary energy maintenance strategy. Orange morphs also exhibited distinct phenotypes, but the low prevalence of this morph in our study populations precludes clear interpretation. Our work provides insight into how differences among stable polymorphisms exist across axes of the phenotype and how this variation may aid in establishment within novel environments. Epigraph: “If you are only moved by color relationships, you are missing the point. ” – Mark Rothko, Latvian-American abstract painter
Effects of intelligence and approximate number system on the non-symbolic division ability in preschoolers

Recently, it has become evident that cognitive abilities such as the approximate number system (ANS), number knowledge, and intelligence affect individuals’ fundamental mathematical ability. However, it is unclear which of these cognitive abilities have the greatest impact on the non-symbolic division ability in preschoolers. Therefore, in the present study, we included 4- to 6-year-old Korean preschoolers without prior formal education of division in order to test their ability to solve non-symbolic division problems, ANS acuity, and intelligence, and to determine the interrelationships among those functions (N = 38). We used the Panamath Dot Comparison Paradigm to measure the ANS acuity, employed non-symbolic division tasks to measure the ability to solve non-symbolic division problems, and measured the intelligence using the Korean version of the WPPSI-IV (Wechsler Preschool Primary Scale of Intelligence-IV). Our results showed that, in all conditions of the non-symbolic division tasks, the 4- to 6-years old children were able to perform better than chance level. Additionally, in a relatively easy condition, the children’s performance showed a significant positive correlation with full-scale intelligence quotient (FSIQ) and ANS acuity; however, in a more complex condition, only FSIQ was significantly correlated with their performance. Overall, we found significant relationships between the children’s performance in the non-symbolic division tasks and verbal comprehension, fluid reasoning, and processing speed index. Taken together, our findings demonstrate that preschoolers without formal education on the arithmetic problem solving can solve non-symbolic division problems. Moreover, we suggest that both FSIQ and ANS ability play essential roles in children’s ability to solve non-symbolic division problems, highlighting the significance of intelligence on children’s fundamental mathematical ability.
Azathioprine as an adjuvant therapy in severe Graves’ disease: a randomized controlled open-label clinical trial

Introduction Azathioprine (AZA) interferes with the activation of T and B lymphocytes, which are the main cells involved in the pathogenesis of Graves’ disease (GD). The aim of this study was to investigate the effectiveness of AZA as an adjuvant therapy to antithyroid drugs (ATDs) for moderate and severe GD. In addition, we conducted an incremental cost-effectiveness analysis of AZA to determine its cost-effectiveness. Methods We conducted a randomized, open-label, and parallel-group clinical trial. We randomized untreated hyperthyroid patients with severe GD into three groups. All patients received 45-mg carbimazole (CM) as the starting dose and propranolol 40–120 mg daily. The first group (AZA1) received an additional 1 mg/kg/day AZA, the second group (AZA2) received an additional 2 mg/kg/day AZA, and the third group (control group) received only CM and propranolol. We measured thyroid-stimulating hormone (TSH) and TSH-receptor antibody (TRAb) levels at baseline and every 3 months, while free triiodothyronine (FT3) and free thyroxine (FT4) levels were measured at the time of diagnosis, 1 month after initiation of therapy, and every 3 months thereafter until 2 years after remission. Thyroid volume (TV) was assessed by ultrasound at baseline and 1 year after remission. Results A total of 270 patients were included in this trial. By the end of follow-up, there was higher remission rate in the AZA1 and AZA2 groups compared with controls (87.5% and 87.5% vs. 33.4%, p = 0.002). Throughout the course of follow-up, FT3, FT4, TSH, and TRAb were significantly different between the AZA groups and the control group, but there was no significant difference regarding TV. The decline in the concentrations of FT4, FT3, and TRAb was significantly faster in the AZA2 group than in the AZA1 group. The relapse rate during the 12-month follow-up was insignificantly higher in the control group than in either the AZA1 or AZA2 group (10, 4.4, and 4.4%, p = 0.05, respectively). The median relapse time was 18 months for the control group and 24 months for the AZA1 and AZA2 groups. The incremental cost-effectiveness ratio for the AZA group compared with the conventional group was 27,220.4 Egyptian pounds per remission reduction for patients using AZA as an adjuvant for ATDs. Conclusion AZA could be a novel, affordable, cost-effective, and safe drug offering hope for patients with GD to achieve early and long-lasting medical remission. Trial registry The trial is registered at the Pan African Clinical Trial Registry (Registration number: PACTR201912487382180).
Identification, physical mechanisms and impacts of drought–flood abrupt alternation: a review

Climate change has led to an increase in the frequency of extreme events, such as droughts and floods. This study aims to review the literature on the newly proposed phenomenon known as drought-flood abrupt alternation (DFAA). A comprehensive summary is provided to round up the numerous approaches employed to identify DFAA events, as well as its mechanisms and impacts. To provide a reference for responding and managing the emerging intensity and frequency of DFAA events, we conclude the paper by listing the insufficiency of current research and suggesting possible future research directions. As for the impact of DFAA, besides the loss of life and property which can be caused by any natural disaster, a DFAA event severely threatens food security by making a lasting and profound impact on the land productivity through the alteration of the combining conditions of water, soil, and temperature. As for the future research directions, existing indexes developed for DFAA identification should be improved by downscaling the temporal and spatial scale, with interactions of neighboring drought and flood events taken into consideration. What’s more, to better protect human society from the losses caused by DFAA, researches on accurate DFAA prediction are encouraged.
Low vaccination and infection rate of Omicron in patients with inflammatory bowel disease: a comparative study of three unique cohorts

Background The SARS-CoV-2 Omicron variant caused a large-scale outbreak of COVID-19 in Shanghai, China. Patients with inflammatory bowel disease (IBD) are at high risk of infection due to immunosuppressive interventions. We aimed to investigate the vaccination information of patients with IBD and update a vaccination guide based on a comparison of vaccination in asymptomatic carriers and healthy individuals. Methods This retrospective study was conducted during an Omicron variant wave. We assessed the vaccination status in patients with IBD, asymptomatic carriers and healthy individuals. Factors with unvaccinated status and adverse events following vaccination were also determined in patients with IBD. Results The vaccination rate was 51.2% in patients with IBD, 73.2% in asymptomatic carriers, and 96.1% in healthy individuals. Female sex (p = 0.012), Crohn’s disease (p = 0.026), and disease behavior of B3 (p = 0.029) were factors that indicated a lower vaccination rate. A significantly higher proportion of healthy individuals had received one booster dose (76.8%) than asymptomatic carriers (43.4%) and patients with IBD (26.2%). Patients with IBD received vaccination without an increased risk of adverse events (p = 0.768). Conclusion The vaccination rate of patients with IBD remains much lower than that of asymptomatic carriers and healthy individuals. The COVID-19 vaccine has been found to be safe among all three groups and patients with IBD are not more susceptible to adverse events.