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10 p.-6 fig.-3 tb., Functional pairing between cellular glyco-con-ju-gates and tissue lectins like galectins has wide (patho)physio-logical significance. Their study is facilitated by non-hydrolyzable deri-va-tives of the natural O-glycans, such as S- and Se-glycosides. The latter en-able extensive analyses by specific 77 Se NMR spectroscopy, but still remain under-explored. By the example of seleno--digalac-to-side (SeDG) and the human galectins 1 and 3, we evaluate diverse 77 Se NMR detec-tion methods and pro-pose selec-tive 1 H, 77 Se hetero-nuclear Hartmann-Hahn transfer for efficient use in com-peti-tive NMR screening against a seleno-glycoside spy ligand. By fluores-cence aniso-tropy, circular dichroism, and isothermal titra-tion calori-metry (ITC) we show that affinity and thermodynamics of SeDG bind-ing by galectins are similar to thiodi-galac-toside (TDG) and N-acetyl-lactos-amine (LacNAc), con-firm-ing that Se substitution has no major impact. ITC data in D 2 O vs. H 2 O are similar for TDG and LacNAc binding by both galectins, but a solvent effect, indicating solvent rearrangement at the binding site, is hinted for SeDG and clearly observed for LacNAc dimers with extend-ed chain length., We are much indebted to L. Szilágyi (University of Debrecen,Hungary) for kindly providing selenoglycosides for this study. We are grateful for inspiring discussions to Drs. B. Friday, A. Leddoz and A. W. L. Nose as well as for generous funding from the Spanish Ministry of Economy and Competitiveness (grant BFU2016-77835-R; to A.R.), the Department of Industry, Tourism and Trade of the Government of the Autonomous Community of the Basque Country (Elkartek BG2019; to T.D.), the Severo Ochoa Excellence Accreditation from MCIU (SEV-2016-0644; to T.D.), the Science Foundation of Ireland (grants 13/IA/1959 and 16/RC/3889;to S.O.), National Institute of Health (NIH) grant CA242351 to M.Cudic, and the COST Action CA 18103 (InnoGly; to H.-J.G.).

Chronic myeloid leukemia (CML) is a hematological malignancy characterized by BCR-ABL1-derived permanent proliferation of myeloid progenitor cells. BCR-ABL1 tyrosine kinase inhibitors (TKI) are effective first-line therapeutic options to suppress tumor proliferation. However, TKI therapy is not always curative and drug-related side effects as well as drug resistance may evolve over time, necessitating salvage therapies. In this case report we present a 68-year-old woman who developed second- and third-generation TKI therapy resistance with BCR-ABL1T315I and BCR-ABL1E255V mutation. Considering contraindication for hematopoietic stem cell transplantation, we treated the patient in an individual treatment attempt with a third-generation TKI ponatinib in combination with palbociclib, a CDK4/CDK6 inhibitor, which has been shown to effectively inhibit proliferation of BCR-ABL1T315I-mutated cells in vitro. Our case study shows strong antineoplastic effects using this combination in an advanced CML patient resistant to ponatinib monotherapy as a fourth-line treatment. Combined administration of ponatinib/palbociclib at full dose showed almost a tenfold decrease (42.6 to 4.4 IS%) of BCR-ABL1-positive cells but with simultaneous hematopoietic toxicity, necessitating dose reduction. This combination treatment showed high clinical activity. However, biological activity needs to be further characterized in prospective clinical trials.

The high sensitivity of beans to herbicides is one of the limiting factors regarding the management of dicot weeds in bean crops. Protoporphyrinogen oxidase (PPO) inhibition is an important mechanism of action that has unregistered molecules with potential use in bean crops. The objectives of this study were to investigate the tolerance of Brazilian bean cultivars to distinct PPO inhibitors and to determine the existence of cross-tolerance in cultivars to the different PPO inhibitor chemical groups. In the first and second experiments, the BRSMG Talismã, Jalo Precoce, BRS Esplendor, and IPR 81 cultivars were subjected to saflufenacil doses pre- (0, 9.6, 14.1, 20.5, 30.0, and 43.8 g a.i. ‧ ha–1) and post-emergence (0, 0.7, 1.0, 1.5, 2.1, and 3.1 g a.i. ‧ ha–1). In the third experiment, the tolerance of 28 bean genotypes to saflufenacil (20.5 g a.i. ‧ ha–1) in pre-emergence was determined. In the fourth, fifth, sixth and seventh experiments, we investigated the cross-tolerance of bean to the fomesafen, flumioxazin, sulfentrazone, and saflufenacil herbicides, respectively. Even very low saflufenacil doses in post-emergence caused plants of all cultivars to die rapidly; therefore, the tolerance was much lower at this application time than in pre-emergence. There was high tolerance variability to saflufenacil among the 28 cultivars. The bean tolerance to fomesafen, flumioxazin, sulfentrazone, and saflufenacil applied pre-emergence depended on the cultivar and dose. Fomesafen was highlighted owing to its higher selectivity in relation to the different cultivars. No cross-tolerance pattern to the PPO inhibitor chemical groups applied in pre-emergence was observed among the evaluated bean cultivars. The results of this study could be of significance to farmers and technical assistance personnel, as well as for future research on cultivar breeding and the elucidation of biochemical and genetic mechanisms involved in herbicide tolerance.

Autoimmune conditions can occur in a temporary relationship with any malignant lymphoma. In many instances, treatment at diagnosis is not required, but symptomatic autoimmune conditions represent an indication for treatment, particularly in chronic lymphoproliferative diseases. Treatment is selected depending on the predominant condition: autoimmune disease (immunosuppression) or lymphoma (antilymphoma therapy). Steroids and anti-CD20 antibodies are effective against both conditions and may suppress the autoimmune complication for a prolonged period. The efficacy of B-cell receptor inhibitors has provided us with novel insights into the pathophysiology of antibody-producing B cells. Screening for underlying autoimmune conditions is part of the lymphoma workup, because other drugs, such as immunomodulators and checkpoint inhibitors, should be avoided or used with caution. In this article, we discuss diagnostic challenges and treatment approaches for different situations involving lymphomas and autoimmune cytopenias.

Tisagenlecleucel is indicated for pediatric and young adult patients with relapsed/refractory (r/r) B-cell acute lymphoblastic leukemia (B-ALL) and adult patients with r/r diffuse large B-cell lymphoma (DLBCL). The tisagenlecleucel chimeric antigen receptor (CAR) contains a murine single-chain variable fragment domain; we examined the effects of humoral and cellular immune responses to tisagenlecleucel on clinical outcomes using 2 validated assays. Data were pooled from the ELIANA (registered at www.clinicaltrials.gov as #NCT02435849) and ENSIGN (#NCT02228096) trials in r/r B-ALL (N = 143) and the JULIET trial (#NCT02445248) in r/r DLBCL (N = 115). Humoral responses were determined by flow cytometric measurement of anti-murine CAR19 (mCAR19) antibodies in serum. Cellular responses were determined using T-cell production of interferon-γ in response to 2 different pools of mCAR19 peptides. Pretreatment anti-mCAR19 antibodies were detected in 81% of patients with r/r B-ALL and 94% of patients with r/r DLBCL. Posttreatment anti-mCAR19 antibodies were higher than patient-specific baseline in 42% of r/r B-ALL and 9% of r/r DLBCL patients. Pretreatment and posttreatment anti-mCAR19 antibodies did not affect tisagenlecleucel cellular kinetics, including maximum concentration and persistence (r2 < 0.05), clinical response (day-28 response, duration of response, and event-free survival), and safety. T-cell responses were consistent over time, with net responses

Tham Wiman Nakin or “Snake Cave” has so far been recognized as being the only late Middle Pleistocene Homo-bearing fauna, dated to older than 169 ka, in mainland Southeast Asia. Since the last two decades, the highly diversified mammal fauna found from this cave has been widely used as standard references for several studies, though the majority of fossil primates, carnivores, and ungulates have never been described in detail. This paper presents taxonomic descriptions of unpublished fossil specimens from the long-known collection of Tham Wiman Nakin. As a result, the fauna of Tham Wiman Nakin consisted of at least 28 large mammal taxa. Although several previously described specimens are re-assigned to different tooth elements and/or mammal taxa, our taxonomic study confirms the existence of most of the species identified from the previous work and describes three additional taxa for the locality: an Asian badger, a tiger, and a Himalayan goral. The Tham Wiman Nakin fauna is one of the most diverse Pleistocene mammals, including a hominin, in mainland Southeast Asia and documents long-term survivors of living species since the late Middle Pleistocene. Based on several recent dates of fossil sites in mainland Southeast Asia, biochronological data imply a possible faunal age up to the maximum of 300 ka for the Tham Wiman Nakin fauna, but younger than that of Pha Bong where Gigantopithecus was present. Fossil records in the region also suggest a relatively stable fauna through Pleistocene glacial-interglacial cycles, at least from the late Middle to latest Pleistocene. The extinction occurring in the mainland varied across taxa and likely resulted in less impacted biodiversity loss prior to the Holocene, compared to other continents, as indicated by the small proportion of species becoming extinct during each interval. The importance of stable mosaic habitats through time may provide clues to the long-term survival of several large mammal taxa in the region.

Background: Cryopreservation of ovarian tissue is one of the strategies offered to girls and women needing gonadotoxic treatment, as a means of preserving their fertility. There are two methods of ovarian tissue cryopreservation: slow freezing, the reference method, and vitrification, an alternative method. The aim of the present study was to evaluate which of the two is the best method for human ovarian tissue cryopreservation. Each ovary was divided into 3 groups: Fresh, Slow freezing and Vitrification. In each group a histological study to evaluate follicular density and quality; and an evaluation of 6 gene expression (CYP11A, STAR, GDF9, ZP3, CDK2, CDKN1A) were performed. Results: We observed no significant difference in follicular density within these 3 groups. Slow freezing altered the pool of primordial follicles compared to the Fresh tissue (31.8% vs 55.9%, p = 0.046, respectively). The expression of genes involved in steroidogenesis varied after cryopreservation compared to the fresh group; CYP11A was under-expressed in both freezing groups compared to the fresh group and significantly under-expressed in the slow freezing group (p = 0.01), STAR was over-expressed in the slow freezing group and significantly under-expressed in the vitrification group (p = 0.01). Regarding the expression of genes involved in cell cycle regulation, CDKN1A was significantly under-expressed in both freezing groups (slow freezing: p = 0.0008; vitrification: p = 0.03) compared to the fresh group. Conclusion: Vitrification had no effect on the histological quality of the follicles at any stage of development compared to Fresh tissue. There was no significant difference in gene expression between the two techniques.

Plant growth and fertility strongly depend on environmental conditions such as temperature. Remarkably, temperature also influences meiotic recombination and thus, the current climate change will affect the genetic make-up of plants. To better understand the effects of temperature on meiosis, we followed male meiocytes in Arabidopsis thaliana by live cell imaging under three temperature regimes: at 21°C; at heat shock conditions of 30°C and 34°C; after an acclimatization phase of 1 week at 30°C. This work led to a cytological framework of meiotic progression at elevated temperature. We determined that an increase from 21°C to 30°C speeds up meiosis with specific phases being more amenable to heat than others. An acclimatization phase often moderated this effect. A sudden increase to 34°C promoted a faster progression of early prophase compared to 21°C. However, the phase in which cross-overs mature was prolonged at 34°C. Since mutants involved in the recombination pathway largely did not show the extension of this phase at 34°C, we conclude that the delay is recombination-dependent. Further analysis also revealed the involvement of the ATAXIA TELANGIECTASIA MUTATED kinase in this prolongation, indicating the existence of a pachytene checkpoint in plants, yet in a specialized form.

The lack of samples for generating standardized DNA datasets for setting up a sequencing pipeline or benchmarking the performance of different algorithms limits the implementation and uptake of cancer genomics. Here, we describe reference call sets obtained from paired tumor–normal genomic DNA (gDNA) samples derived from a breast cancer cell line—which is highly heterogeneous, with an aneuploid genome, and enriched in somatic alterations—and a matched lymphoblastoid cell line. We partially validated both somatic mutations and germline variants in these call sets via whole-exome sequencing (WES) with different sequencing platforms and targeted sequencing with >2,000-fold coverage, spanning 82% of genomic regions with high confidence. Although the gDNA reference samples are not representative of primary cancer cells from a clinical sample, when setting up a sequencing pipeline, they not only minimize potential biases from technologies, assays and informatics but also provide a unique resource for benchmarking ‘tumor-only’ or ‘matched tumor–normal’ analyses.

Background A considerable proportion of SARS-CoV-2 transmission occurs from asymptomatic and pre-symptomatic cases. Therefore, different polymerase chain reaction (PCR)- or rapid antigen test (RAT)-based approaches are being discussed and applied to identify infectious individuals that would have otherwise gone undetected. In this article, we provide a framework to estimate the time-dependent risk of being infectious after a negative SARS-CoV-2 test, and we simulate the number of expected infectious individuals over time in populations who initially tested negative. Methods A Monte Carlo approach is used to simulate asymptomatic infections over a 10-days period in populations of 1000 individuals following a negative SARS-CoV-2 test. Parameters representing the application of PCR tests or RATs are utilized, and SARS-CoV-2 cumulative 7-day incidences between 25 and 200 per 100,000 people are considered. Simulation results are compared to case numbers predicted via a mathematical equation. Results The simulations showed a continuous increase in infectious individuals over time in populations of individuals who initially tested SARS-CoV-2 negative. The interplay between false negative rates of PCR tests or RATs, and the time that has passed since testing determines the number of infectious individuals. The simulated and the mathematically predicted number of infectious individuals were comparable. However, Monte Carlo simulations highlight that, due to random variation, theoretically observed infectious individuals can considerably exceed predicted case numbers even shortly after a test was conducted. Conclusions This study demonstrates that the number of infectious individuals in a screened group of asymptomatic people can be effectively reduced, and this effect can be described mathematically. However, the false negative rate of a test, the time since the negative test and the underlying SARS-CoV-2 incidence are critical parameters in determining the observed subsequent number of cases in tested population groups.

The transcription factor Zinc finger E-box binding 1 (ZEB1) displays a range of regulatory activities in cell function and embryonic development, including driving epithelial-mesenchymal transition. Several aspects of ZEB1 function can be regulated by its functional interactions with noncoding RNA types, namely microRNAs (miRNAs) and long noncoding RNAs (lncRNAs). Increasing evidence indicates that ZEB1 importantly influences cancer initiation, tumor progression, metastasis, and resistance to treatment. Cancer is the main disease-related cause of death in children and adolescents. Although the role of ZEB1 in pediatric cancer is still poorly understood, emerging findings have shown that it is expressed and regulates childhood solid tumors including osteosarcoma, retinoblastoma, neuroblastoma, and central nervous system tumors. Here, we review the evidence supporting a role for ZEB1, and its interplays with miRNAs and lncRNAs, in pediatric cancers.

Measuring biomass and leaf area using non-destructive methods is of great interest to avoid plant degradation. These data are necessary for biomass allocation and estimation of carbon distribution in trees using functional and structural growth models such as GREENLAB. Organ biomass and leaf area are important parameters in plant physiology and production. They are used in structural and functional plant models to simulate tree architecture but are difficult to determine rapidly. Using stem length and internode diameter and leaf length and width to estimate them is a rapid, non-destructive field approach. We used the method on Khaya senegalensis, Pterocarpus erinaceus and Parkia biglobosa in Cote d'Ivoire. Internodes and leaves of the three species were sampled in 2019 and 2020 on three categories of axis in the architecture of individuals of different ages to maximize size variability. All statistical relationships found in the linear, logarithmic, polynomial and power models used to estimate the dry biomass of organs and leaf area were significant in all three species (P = 0.0001). The best models were obtained with the logarithmic transformation of the data. Three equation (linear, power and polynomial) were sufficient to estimate internode dry biomass (IDM), leaf dry biomass (LDM) and leaf area (LA) from the dimensions of the internodes (Volume: VL) and leaves (rachis length: RCL, number of primary leaflets: NLt, length: LLtL and width: LLtW of the largest primary leaflet in Khaya senegalensis and Pterocarpus erinaceus, then number of secondary leaflets: NSeLt, length: LSeLtL and width: LSeLtW of the largest secondary leaflet in Parkia biglobosa). In the field, the scientist will therefore make a choice according to his convenience among these proposed models. The best relationships between the measured organ dimensions and estimated parameters were defined by the following equations: IDM = 0.45*VL + 0.02, LDM = 1.07*NLt*LLtL*LLtW-2.74 and LA = 0.83*NLt*LLtL*LLtW or LA = 0.08*[NLt*LLtL*LLtW]2 + 1.13*[NLt*LLtL*LLtW]-0.27 for Khaya senegalensis; IDM = 1.15*VL0.26, LDM = 0.71*RCL*LLtL*LLtW-1.64 and LA = 0.74*NLt*LtL*LtW + 0.15 or LA = 0.03*[NLt*LLtL*LLtW]2 + 0.65*[NLt*LLtL*LLtW] + 0.23 for Pterocarpus erinaceus then IDM = 1.45*VL0.39, LDM = 0.23*[NSeLt*LSeLtL*LSeLtW*NLt]2–0.4*[NSeLt*LSeLtL*LSeLtW*NLt]-0.11 and LA = 1.81*[NSeLt*LSeLtL*LSeLtW*NLt]0.65 for Parkia biglobosa. This method can be applied to estimate the organ biomass and leaf area of species of the same family as the target species in an agroforestry system.

This paper analyzes the effects of weight-based pricing on municipal waste generation in Flanders (Belgium) by applying the bias-corrected least squares dummy variables estimation model to account for the dynamic relationship. The study also considers yearly weight-based pricing dummy variables to clarify the annual effects after its introducing and price elasticities of weight-based pricing systems from the both viewpoints of short and long terms. The results by the dynamic panel estimations showed that the continuous participation of weight-based pricing decreases the amount of residual waste significantly by approximately 10.4%. However, the remarkable decrease (approximately 21.4%) was observed only in the first year after the introduction and the reduction effect gradually decreases following its introduction and it disappears in five years. The study also showed that price elasticities of weight-based pricing were smaller than that of volume-based pricing for five years after its introduction and consequently the difference between them disappeared in five years. In addition, the study indicated that the estimation results by the non-dynamic fixed effects model overestimated the long-term effects in weight-based pricing and price effects while underestimating the short-term effect by its introduction. The study suggested that we should consider dynamic effects and remove the bias from the least squares dummy variables estimators when we examine the effects of weight-based pricing. ispartof: Waste Management vol:128 pages:132-141 ispartof: location:United States status: published

Bone marrow (BM) angiogenesis significantly influences disease progression in multiple myeloma (MM) patients and correlates with adverse prognosis. The present study shows a statistically significant correlation of the AP-1 family member JunB with VEGF, VEGFB, and IGF1 expression levels in MM. In contrast to the angiogenic master regulator Hif-1α, JunB protein levels were independent of hypoxia. Results in tumor-cell models that allow the induction of JunB knockdown or JunB activation, respectively, corroborated the functional role of JunB in the production and secretion of these angiogenic factors (AFs). Consequently, conditioned media derived from MM cells after JunB knockdown or JunB activation either inhibited or stimulated in vitro angiogenesis. The impact of JunB on MM BM angiogenesis was finally confirmed in a dynamic 3D model of the BM microenvironment, a xenograft mouse model as well as in patient-derived BM sections. In summary, in continuation of our previous study (Fan et al., 2017), the present report reveals for the first time that JunB is not only a mediator of MM cell survival, proliferation, and drug resistance, but also a promoter of AF transcription and consequently of MM BM angiogenesis. Our results thereby underscore worldwide efforts to target AP-1 transcription factors such as JunB as a promising strategy in MM therapy.

B-cell receptor (BCR) signaling and T-cell interactions play a pivotal role in chronic lymphocytic leukemia (CLL) pathogenesis and disease aggressiveness. CLL cells can use microRNAs (miRNAs) and their targets to modulate microenvironmental interactions in the lymph node niches. To identify miRNA expression changes in the CLL microenvironment, we performed complex profiling of short noncoding RNAs in this context by comparing CXCR4/CD5 intraclonal cell subpopulations (CXCR4dimCD5bright vs CXCR4brightCD5dim cells). This identified dozens of differentially expressed miRNAs, including several that have previously been shown to modulate BCR signaling (miR-155, miR-150, and miR-22) but also other candidates for a role in microenvironmental interactions. Notably, all 3 miR-29 family members (miR-29a, miR-29b, miR-29c) were consistently down-modulated in the immune niches, and lower miR-29(a/b/c) levels associated with an increased relative responsiveness of CLL cells to BCR ligation and significantly shorter overall survival of CLL patients. We identified tumor necrosis factor receptor–associated factor 4 (TRAF4) as a novel direct target of miR-29s and revealed that higher TRAF4 levels increase CLL responsiveness to CD40 activation and downstream nuclear factor-κB (NF-κB) signaling. In CLL, BCR represses miR-29 expression via MYC, allowing for concurrent TRAF4 upregulation and stronger CD40–NF-κB signaling. This regulatory loop is disrupted by BCR inhibitors (bruton tyrosine kinase [BTK] inhibitor ibrutinib or phosphatidylinositol 3-kinase [PI3K] inhibitor idelalisib). In summary, we showed for the first time that a miRNA-dependent mechanism acts to activate CD40 signaling/T-cell interactions in a CLL microenvironment and described a novel miR-29–TRAF4–CD40 signaling axis modulated by BCR activity.

Understanding mechanisms of promiscuity is increasingly important from a fundamental and application point of view. As to enzyme structural dynamics, more promiscuous enzymes generally have been recognized to also be more flexible. However, examples for the opposite received much less attention. Here, we exploit comprehensive experimental information on the substrate promiscuity of 147 esterases tested against 96 esters together with computationally efficient rigidity analyses to understand the molecular origin of the observed promiscuity range. Unexpectedly, our data reveal that promiscuous esterases are significantly less flexible than specific ones, are significantly more thermostable, and have a significantly increased specific activity. These results may be reconciled with a model according to which structural flexibility in the case of specific esterases serves for conformational proofreading. Our results signify that an esterase sequence space can be screened by rigidity analyses for promiscuous esterases as starting points for further exploration in biotechnology and synthetic chemistry.

BackgroundInterleukin(IL)-1 signaling is of major importance in human innate cytokine responses. Common variants in related genes have been linked to various inflammation-mediated diseases and stimulation-induced cytokine responses, but the role of rare variants remains to be elucidated.MethodsIn this study, we characterize the role of rare and common genetic variation, as identified by molecular inversion probe-based sequencing, in 48 genes related to the IL-1 pathway. Using a systems biology approach, we examined the inter-individual variability of in vitro stimulation-specific human cytokine responses from 463 healthy individuals of the Human Functional Genomics Project and assessed the role of rare and common genetic variants, separately and combined, by means of the Sequence Kernel Association Test.ResultsWe identified strong associations for rare genetic variants in NCF4 (adjP=7.2E−05) and CASP1 (adjP=3.0E−05) with IL-6 production in response to PHA and LPS stimulation, respectively. In addition, common variants in IL36A and IL38 were associated to both C. albicans-induced IL-1β (IL36AadjP=0.0442; IL38adjP=0.0092) and IL-6 production (IL36AadjP=0.0037; IL38adjP=0.0082), an effect that was stronger at the subpathway level both for IL-1β (adjP=0.0017) and IL-6 (adjP=1.8E−04). The common variant signature for the IL-1β and IL-6 response to C. albicans was confirmed by an association with all anti-inflammatory genes (adjP=1.87E−03 and adjP=5.75E−04), and we validated this finding for non-coding common variants. Lastly, we identified a burden of rare variants in pro-inflammatory genes and LPS-induced IL-6 production (adjP=2.42E−04), and a new role for anti-inflammatory rare variants on S. aureus-stimulated IL-6 production (adjP=6.71E−03).ConclusionsIn conclusion, we show that both common and rare genetic variation in genes of the IL-1 pathway, separately and combined, differentially influence in vitro cytokine responses to various stimuli in healthy individuals. This study therefore accentuates potential mechanisms that are translatable into new hypothesis-driven characterization of common and rare variant involvement in a wide variety of inflammatory and immunological mechanisms and diseases.

Population bottlenecks can reduce genetic diversity and may lead to inbreeding depression. However, some studies have provided evidence that long lifespans buffer negative genetic effects of bottlenecks. Others have cautioned that longevity might merely mask the effects of genetic drift, which will still affect long-term population viability. We used microsatellite data from actual populations of tuatara (Sphenodon punctatus) and eastern massasaugas (Sistrurus catenatus) as a starting point for simulated population declines to evaluate the performance of bottleneck tests under a range of scenarios. We quantified losses in genetic diversity for each scenario and assessed the power of commonly used tests (i.e., M-ratio, heterozygosity excess, and mode-shift) to detect known bottlenecks in these moderate- to long-lived species. Declines in genetic diversity were greater in bottlenecks simulated for eastern massasaugas, the shorter-lived species, and mode-shift and heterozygosity excess tests were more sensitive to population declines in this species. Conversely, M-ratio tests were more sensitive to bottlenecks simulated in tuatara. Despite dramatic simulated population declines, heterozygosity excess and mode-shift tests often failed to detect bottlenecks in both species, even when large losses in genetic diversity had occurred (both allelic diversity and heterozygosity). While not eliminating type II error, M-ratio tests generally performed best and were most reliable when a critical value (Mc) of 0.68 was used. However, in tuatara simulations, M-ratio tests had high rates of type I error when Mc was calculated assuming θ = 10. Our results suggest that reliance on these tests could lead to misguided species management decisions.

Multi-dimensional omics profiling continues to illuminate the complexity of cellular processes. Because of difficult mechanistic interpretation of phenotypes induced by slow perturbation, fast experimental setups are increasingly used to dissect causal interactions directly in cells. Here we review a growing body of studies that leverage rapid pharmacological perturbation to delineate causality in gene control. When coupled with kinetically matched readouts, fast chemical genetic tools allow recording of primary phenotypes before confounding secondary effects manifest. The toolbox encompasses directly acting probes, such as active-site inhibitors and proteolysis-targeting chimeras, as well as strategies using genetic engineering to render target proteins chemically tractable, such as analog-sensitive and degron systems. We anticipate that extrapolation of these concepts to single-cell setups will further transform our mechanistic understanding of transcriptional control in the future. Importantly, the concept of leveraging speed to derive causality should be broadly applicable to many aspects of biological regulation.

International audience; The study and reanalysis of late Oligocene and middle Miocene dental material from Thailand provides evidence for long-distance stratigraphic correlations, and thus sheds new light on past terrestrial connections between Southeastern Asia and Europe. Here we report the oldest occurrence of Ursidae in southern Asia – a late Oligocene fossil from Nong Ya Plong previously referred to Mustelida but reattributed here to Cephalogale aff. geoffroyi (Ursidae, Hemicyoninae, Cephalogalini). We also describe a new Viverridae, Semigenetta cf. steinheimensis, from the middle Miocene carnivoran-rich locality of Mae Moh. The presence of these two taxa in Western Europe reinforces stratigraphic correlations of the MP29 and MN7–8 fossil sites with Southeast Asian localities. Members of the tribe Cephalogalini may have migrated several times from Asia to Europe, or vice-versa, during the Oligocene and early Miocene via either a northern route across northern China, or a southern route traversing southern Asia and the Middle East. Semigenetta could have dispersed along a corridor through Central Asia or a southern Asian route into Thailand during the middle Miocene. Our study thus indicates that medium- or large-sized carnivorans constitute a useful tool for reconstructing the paleobiogeography of extinct species.

Item does not contain fulltext Sudan, a northeastern African country, is characterized by high levels of cultural, linguistic, and genetic diversity, which is believed to be affected by continuous migration from neighboring countries. Consistent with such demographic effect, genome-wide SNP data revealed a shared ancestral component among Sudanese Afro-Asiatic speaking groups and non-African populations, mainly from West Asia. Although this component is shared among all Afro-Asiatic speaking groups, the extent of this sharing in Semitic groups, such as Sudanese Arab, is still unknown. Using genotypes of six polymorphic human leukocyte antigen (HLA) genes (i.e., HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1), we examined the genetic structure of eight East African ethnic groups with origins in Sudan, South Sudan, and Ethiopia. We identified informative HLA alleles using principal component analysis, which revealed that the two Semitic groups (Gaalien and Shokrya) constituted a distinct cluster from the other Afro-Asiatic speaking groups in this study. The HLA alleles that distinguished Semitic Arabs co-exist in the same extended HLA haplotype, and those alleles are in strong linkage disequilibrium. Interestingly, we find the four-locus haplotype "C*12:02-B*52:01-DRB1*15:02-DQB1*06:01" exclusively in non-African populations and it is widely spread across Asia. The identification of this haplotype suggests a gene flow from Asia, and likely these haplotypes were brought to Africa through back migration from the Near East. These findings will be of interest to biomedical and anthropological studies that examine the demographic history of northeast Africa.

Synopsis Artificial light at night (ALAN) functions as a novel environmental stimulus that has the potential to disrupt interactions among species. Despite recent efforts to explain nocturnal pollinators’ responses to this stimulus, the likelihood and associated mechanisms of attraction toward artificial light and potential consequences on fitness for diurnal pollinators are still largely unclear. Here, we took advantage of the obligate mutualism between yucca moths (Tegeticula maculata maculata) and yucca plants (Hesperoyucca whipplei) to understand how direct light exposure and skyglow can influence a pairwise plant–pollinator interaction. To surmise whether adult moths exhibit positive phototaxis, we deployed a set of field-placed light towers during the peak of yucca flowering and compared the number of moths caught in traps between dark-controlled and light-treated trials. Adult moth abundance was much higher when light was present, which suggests that ALAN may alter this diurnal moth’s activity patterns to expand their temporal niche into the night. To evaluate ALAN effects on yucca fruit set and moth larva recruitment, we measured skyglow exposure above yucca plants and direct light intensity from a second set of light towers. Both larva and fruit recruitment increased with skyglow, and fruit set also increased with direct lighting, but the relationship was weaker. Contrarily, larva recruitment did not change when exposed to a gradient of direct light, which may instead reflect effects of ALAN on moth physiology, such as disrupted female oviposition, or misdirecting behaviors essential to oviposition activity. Our results suggest that ALAN can positively influence the fitness of both plants and moths in this tightly co-evolved mutualism, but the benefits to each species may depend on whether night lighting is direct or indirect. Whether such effects and mechanisms could relate to susceptibility to the presence of ALAN on this or other plant–pollinator relationships will remain an important focus of future research.

The fetal and neonatal immune systems are uniquely poised to generate tolerance to self, maternal, and environmental antigens encountered in the womb and shortly after birth. However, the tolerogenic nature of fetal and neonatal immunity can be detrimental in the context of pathogens, leading to overwhelming bacterial infections or chronic viral infections. A variety of mechanisms contribute to fetal and neonatal tolerance, including a propensity to generate Foxp3+ regulatory T cells (Treg cells). However, the mechanism(s) of fetal Foxp3+ T cell differentiation, the specific antigen-presenting cells required, and factors that inhibit Treg generation after the neonatal period are poorly understood. Here, we demonstrate that a subset of CD14+ monocytes expressing the scavenger molecule, CD36, can generate CD4+ and CD8+ T cells that co-express Foxp3 and T-bet from both umbilical cord blood. These Foxp3+ T-bet+ T cells potently suppress T cell proliferation and ameliorate xenogeneic graft versus host disease. CD14+ CD36+ monocytes provide known Treg-inducing signals: membrane-bound transforming growth factor-beta and retinoic acid. Unexpectedly, adult peripheral blood monocytes are also capable of inducing Foxp3+ T cells from both cord blood and adult peripheral naive T cells. The induction of Foxp3+ T cells in umbilical cord blood by monocytes was inhibited by the lymphoid fraction of adult peripheral blood cells. These studies highlight a novel immunoregulatory role of monocytes and suggest that antigen presentation by CD36hi monocytes may contribute to the peripheral development of Foxp3+ T-bet+ T cells with regulatory functions in both neonates and adults.

GNRA tetraloop-binding receptor interactions are key components in the macromolecular assembly of a variety of functional RNAs. In nature, there is an apparent bias for GAAA/11nt receptor and GYRA/helix interactions, with the former interaction being thermodynamically more stable than the latter. While past in vitro selections allowed isolation of novel GGAA and GUGA receptors, we report herein an in vitro selection that revealed several novel classes of specific GUAA receptors with binding affinities comparable to those from natural GAAA/11nt interactions. These GUAA receptors have structural homology with double-locked bulge RNA modules naturally occurring in ribosomal RNAs. They display mutational robustness that enables exploration of the sequence/phenotypic space associated to GNRA/receptor interactions through epistasis. Their thermodynamic self-assembly fitness landscape is characterized by a rugged neutral network with possible evolutionary trajectories toward natural GNRA/receptor interactions. High throughput sequencing analysis revealed synergetic mutations located away from the tertiary interactions that positively contribute to assembly fitness. Our study suggests that the repertoire of GNRA/receptor interactions is much larger than initially thought from the analysis of natural stable RNA molecules and also provides clues for their evolution towards natural GNRA/receptors.

Introduction HIV infection has become a chronic, well-treatable disease and the focus of caretakers has shifted to diagnosis and treatment of comorbidities. Hypogonadism in elderly men with HIV might be of particular relevance, however, little is known about its epidemiology in contrast to non-infected peers and men with other chronic medical conditions, such as type 2 diabetes. This study aimed at comparing the prevalence of testosterone deficiency and functional hypogonadism in men ≥ 50 years in these three groups. Patients and Methods Multi-center, cross-sectional substudy of the German-wide 50/2010 study, including men aged 50 years or older with HIV-infection, type 2 diabetes, and controls. Results Altogether, 322 men were included (mean age: 62 years (SD±7.9)). The prevalence of testosterone deficiency in men living with HIV, type 2 diabetes, and controls was 34.5, 44.9, and 35.0%, respectively; the prevalence of functional hypogonadism was 7.7, 14.3 and 3.5%, respectively. Single-factor ANOVA demonstrated significant differences between the groups for total testosterone (p Discussion Despite a comparable prevalence of testosterone deficiency, functional hypogonadism was more frequent in men living with HIV when compared to non-infected controls. This was the result of a higher burden of symptoms that might, however, also be secondary to other conditions. Number of comorbidities was a more important factor than belonging to one of the groups.

The negative effects of roads on wildlife populations are a growing concern. Movement corridors and road-kill data are typically used to prioritize road segments for mitigation measures. Some research suggests that locations where animals move across roads following corridors coincide with locations where they are often killed by vehicles. Other research indicates that corridors and road-kill rarely occur in the same locations. We compared movement corridor and road mortality models as means of prioritizing road segments for mitigation for five species of felids in Brazil: tiger cats (Leopardus tigrinus and Leopardus guttulus were analyzed together), ocelot (Leopardus pardalis), jaguarundi (Herpailurus yagouaroundi), and puma (Puma concolor). We used occurrence data for each species and applied circuit theory to identify potential movement corridors crossed by roads. We used road-kill records for each species and applied maximum entropy to determine where mortality was most likely to occur on roads. Our findings suggest that movement corridors and high road mortality are not spatially associated. We suggest that differences in the behavioral state of the individuals in the species occurrence and road-kill data may explain these results. We recommend that the road segments for which the results from the two methods agree (~5300 km for all studied species combined at 95th percentile) should be high-priority candidates for mitigation together with road segments identified by at least one method in areas where felids occur in low population densities or are threatened by isolation effects.

The ventromedial (VM)/ventro-anterior-lateral (VAL) motor thalamus is a key junction within the brain circuits sustaining normal and pathologic motor control functions and decision-making. In this area of thalamus, on one hand, the inhibitory nigro-thalamic pathway provides a main output from the basal ganglia, and, on the other hand, motor thalamo-cortical loops are involved in the maintenance of ramping preparatory activity before goal-directed movements. To better understand the nigral impact on thalamic activity, we recorded electrophysiological responses from VM/VAL neurons while male and female mice were performing a delayed right/left decision licking task. Analysis of correct (corr) and error trials revealed that thalamic ramping activity was stronger for premature licks (impulsive action) and weaker for trials with no licks [omission (omi)] compared with correct trials. Suppressing ramping activity through optogenetic activation of nigral terminals in the motor thalamus during the delay epoch of the task led to a reduced probability of impulsive action and an increased amount of omissions trials. We propose a parsimonious model explaining our data and conclude that a thalamic ramping mechanism contributes to the control of proper timing of action release and that inhibitory nigral inputs are sufficient to interrupt this mechanism and modulate the amount of motor impulsivity in this task.SIGNIFICANCE STATEMENTCoordinated neural activity in motor circuits is essential for correct movement preparation and execution, and even slight imbalances in neural processing can lead to failure in behavioral tasks or motor disorders. Here we focused on how failure to regulate the control of activity balance in the motor thalamus can be implicated in impulsive action release or omissions to act, through an activity ramping mechanism that is required for proper action release. Using optogenetic activation of inhibitory basal ganglia terminals in motor thalamus we show that basal ganglia input is well positioned to control this ramping activity and determine the timing of action initiation.

The metallo-β-lactamase fold is an ancient protein structure present in numerous enzyme families responsible for diverse biological processes. The crystal structure of the hyperthermostable crenarchaeal enzyme Igni18 from Ignicoccus hospitalis was solved at 2.3 Å and could resemble a possible first archetype of a multifunctional metallo-β-lactamase. Ancestral enzymes at the evolutionary origin are believed to be promiscuous all-rounders. Consistently, Igni18´s activity can be cofactor-dependently directed from β-lactamase to lactonase, lipase, phosphodiesterase, phosphotriesterase or phospholipase. Its core-domain is highly conserved within metallo-β-lactamases from Bacteria, Archaea and Eukarya and gives insights into evolution and function of enzymes from this superfamily. Structural alignments with diverse metallo-β-lactamase-fold-containing enzymes allowed the identification of Protein Variable Regions accounting for modulation of activity, specificity and oligomerization patterns. Docking of different substrates within the active sites revealed the basis for the crucial cofactor dependency of this enzyme superfamily., The structure of Igni18, ancient enzyme from the Crenarchaean species Ignicoccus hospitalis, is solved and characterized by Pérez-García, Chow and colleagues. This structure provides insight as to the evolution of metallo-beta-lactamases and their functions.

The primary photochemistry is similar among the flavin-bound sensory domains of light–oxygen–voltage (LOV) photoreceptors, where upon blue-light illumination a covalent adduct is formed on the microseconds time scale between the flavin chromophore and a strictly conserved cysteine residue. In contrast, the adduct-state decay kinetics vary from seconds to days or longer. The molecular basis for this variation among structurally conserved LOV domains is not fully understood. Here, we selected PpSB2-LOV, a fast-cycling (τrec 3.5 min, 20 °C) short LOV protein from Pseudomonas putida that shares 67% sequence identity with a slow-cycling (τrec 2467 min, 20 °C) homologous protein PpSB1-LOV. Based on the crystal structure of the PpSB2-LOV in the dark state reported here, we used a comparative approach, in which we combined structure and sequence information with molecular dynamic (MD) simulations to address the mechanistic basis for the vastly different adduct-state lifetimes in the two homologous proteins. MD simulations pointed toward dynamically distinct structural region, which were subsequently targeted by site-directed mutagenesis of PpSB2-LOV, where we introduced single- and multisite substitutions exchanging them with the corresponding residues from PpSB1-LOV. Collectively, the data presented identify key amino acids on the Aβ-Bβ, Eα-Fα loops, and the Fα helix, such as E27 and I66, that play a decisive role in determining the adduct lifetime. Our results additionally suggest a correlation between the solvent accessibility of the chromophore pocket and adduct-state lifetime. The presented results add to our understanding of LOV signaling and will have important implications in tuning the signaling behavior (on/off kinetics) of LOV-based optogenetic tools.

The number of effective breeders (Nb) has been touted as a means to monitor freshwater fishes, but the realized application of Nbhas been limited. Using genetic monitoring data for two Arctic grayling (Thymallus arcticus) populations of conservation concern, we describe temporal trends in genetic variation and Nb, determine how sampling and variance in reproductive success influence estimates of Nb, and quantify the relationship among Nb, effective population size (Ne), and adult abundance (Nc). Temporal trends in allelic richness (AR) and Nbtracked known or suspected population trajectories. Nbincreased in one population where there has been extensive conservation action, and both Nband ARtracked a decline in the other population where harsh winter conditions have resulted in overwinter mortality events. After accounting for population demography, Neestimates for each population were 190.7 and 308.8. Overall, this study demonstrates that temporal genetic data effectively resolve demographic and evolutionary status and trend in Arctic grayling, provides insight into the demographic factors that influence genetic variation, and emphasizes the value of temporal genetic data for conservation and management.

Aims: The aim of this work was to evaluate the optimal radiation dose to maintain the antioxidant capacity of conventional and organic acaí freeze-dried pulps. Study Design: All analyses were conducted in sextuplicate for each experiment. Place and Duration of Study: Were conducted at the LATAIA and the irradiation processes at the Laboratory of Nuclear Instrumentation, UFRJ, Rio de Janeiro, Brazil. The study was carried out from July, 2018 to March, 2020. Methodology: Frozen acaí pulps from two commercial brands, one of them organic and other conventional were used and purchased in the city of Rio de Janeiro, packed in plastic bags containing 1 kg. For each brand, frozen pulps (5 kg) were thawed at 4ºC, opened and homogenized. Samples were subdivided into aliquots ranging from 20 to 300 g for the assays and frozen inside the plastic bags until analyses. A Cobalt 60, Gammacell irradiator was used and doses of 1.25. 2.5. 3.75 and 5 kGy were applied in the in natura pulps. Antioxidant capacity was performed by the ORAC and DPPH methods and, phenolic compounds by Folin Ciocalteau method and, total anthocyanins and majority anthocyanidins by HPLC. Results: Anthocyanins increases at irradiaton dose up to 3.75 kGy in organic açaí but it was not significant in conventional acaí irradiated at low doses (1.25 to 3.75 kGy). Our results suggested that irradiation doses up to 5 kGy do not decrease total phenolic or anthocyanin contents nor the pulp antioxidant activity compared with non-irradiated pulps. The results showed irradiation did not reduce these analytes, and even increased in the organic acaí. Conclusion: The study evidenced that gamma irradiation can be an alternative safe process for fruit pulps preservation. We conclude that irradiation doses up to 5 kGy can be used in acaí without harming its antioxidant properties.

The IL‐1 family member IL‐38 (IL1F10) suppresses inflammatory and autoimmune conditions. Here, we report that plasma concentrations of IL‐38 in 288 healthy Europeans correlate positively with circulating memory B cells and plasmablasts. IL‐38 correlated negatively with age (p = 0.02) and was stable in 48 subjects for 1 year. In comparison with primary keratinocytes, IL1F10 expression in CD19+ B cells from PBMC was lower, whereas cell‐associated IL‐38 expression was comparable. In vitro, IL‐38 is released from CD19+ B cells after stimulation with rituximab. Intravenous LPS in humans failed to induce circulating IL‐38, compared to 100‐fold induction of IL‐6 and IL‐1 receptor antagonist. In a cohort of 296 subjects with body mass index > 27 at high risk for cardiovascular disease, IL‐38 plasma concentrations were significantly lower than in healthy subjects (p < 0.0001), and lowest in those with metabolic syndrome (p < 0.05). IL‐38 also correlated inversely with high sensitivity C‐reactive protein (p < 0.01), IL‐6, IL‐1Ra, and leptin (p < 0.05). We conclude that a relative deficiency of the B cell product IL‐38 is associated with increased systemic inflammation in aging, cardiovascular and metabolic disease, and is consistent with IL‐38 as an anti‐inflammatory cytokine., We propose that circulating B cells are a major source of the anti‐inflammatory cytokine interleukin 38 (IL‐38). Circulating IL‐38 concentrations are reduced by old age, being overweight and having metabolic syndrome. In overweight subjects, a relative IL‐38 deficiency is associated with chronic inflammation and increased cardiovascular disease risk.

Zeolitic imidazolate framework (ZIF) hybrid fluorescent nanoparticles and ZIF antibody conjugates have been synthesized, characterized, and employed in lateral‐flow immunoassay (LFIA). The bright fluorescence of the conjugates and the possibility to tailor their mobility gives a huge potential for diagnostic assays. An enzyme‐linked immunosorbent assay (ELISA) with horseradish peroxidase (HRP) as label, proved the integrity, stability, and dispersibility of the antibody conjugates, LC‐MS/MS provided evidence that a covalent link was established between these metal‐organic frameworks and lysine residues in IgG antibodies., Framing an assay: We present nanosized zeolitic imidazolate frameworks (ZIFs) conjugated to immunoglobulin G (IgG) antibodies by using a strong and flexible covalent amino‐alkyl link. These nanoZIF‐IgG particles display good mobility and an excellent behaviour in dispersion. Their application to antibody‐based bioanalytical assays, including enzyme‐linked immunosorbent assay (ELISA) and lateral flow immunoassay (LFIA), was examined.

The majority of plants use C3 photosynthesis, but over sixty independent lineages of angiosperms have evolved the C4 pathway. In most C4 species, photosynthesis gene expression is compartmented between mesophyll and bundle sheath cells. We performed DNaseI-SEQ to identify genome-wide profiles of transcription factor binding in leaves of the C4 grasses Zea mays, Sorghum bicolor and Setaria italica as well as C3Brachypodium distachyon. In C4 species, while bundle sheath strands and whole leaves shared similarity in the broad regions of DNA accessible to transcription factors, the short sequences bound varied. Transcription factor binding was prevalent in gene bodies as well as promoters, and many of these sites could represent duons that impact gene regulation in addition to amino acid sequence. Although globally there was little correlation between any individual DNaseI footprint and cell-specific gene expression, within individual species transcription factor binding to the same motifs in multiple genes provided evidence for shared mechanisms governing C4 photosynthesis gene expression. Furthermore, interspecific comparisons identified a small number of highly conserved transcription factor binding sites associated with leaves from species that diverged around 60 million years ago. These data therefore provide insight into the architecture associated with C4 photosynthesis gene expression in particular and characteristics of transcription factor binding in cereal crops in general.One sentence summaryGenome-wide patterns of transcription factor binding in vivo defined by DNaseI for leaves of C3 and C4 grasses

Summary Ibrutinib, a Bruton tyrosine kinase inhibitor, is approved for treatment of various B‐cell malignancies. In ibrutinib clinical studies, low‐grade haemorrhage was common, whereas major haemorrhage (MH) was infrequent. We analysed the incidence of and risk factors for MH from 15 ibrutinib clinical studies (N = 1768), including 4 randomised controlled trials (RCTs). Rates of any‐grade bleeding were similar for single‐agent ibrutinib and ibrutinib combinations (39% and 40%). Low‐grade bleeding was more common in ibrutinib‐treated than comparator‐treated patients (35% and 15%), and early low‐grade bleeding was not associated with MH. The proportion of MH in RCTs was higher with ibrutinib than comparators (4.4% vs. 2.8%), but after adjusting for longer exposure with ibrutinib (median 13 months vs. 6 months), the incidence of MH was similar (3.2 vs. 3.1 per 1000 person‐months). MH led to treatment discontinuation in 1% of all ibrutinib‐treated patients. Use of anticoagulants and/or antiplatelets (AC/AP) during the study was common (~50% of patients) and had an increased exposure‐adjusted relative risk for MH in both the total ibrutinib‐treated population (1.9; 95% confidence interval, 1.2–3.0) and RCT comparator‐treated patients (2.4; 95% confidence interval, 1.0–5.6), indicating that ibrutinib may not alter the effect of AC/AP on the risk of MH in B‐cell malignancies.

Currently, researchers rely on generalized methods to quantify transposable element (TE) RNA expression, such as RT-qPCR and RNA-seq, that do not distinguish between TEs expressed from their own promoter (bona fide) and TEs that are transcribed from a neighboring gene promoter such as within an intron or exon. This distinction is important owing to the differing functional roles of TEs depending on whether they are independently transcribed. Here we report a simple strategy to examine bona fide TE expression, termed BonaFide-TEseq. This approach can be used with any template-switch based library such as Smart-seq2 or the single-cell 5′ gene expression kit from 10x, extending its utility to single-cell RNA-sequencing. This approach does not require TE-specific enrichment, enabling the simultaneous examination of TEs and protein-coding genes. We show that TEs identified through BonaFide-TEseq are expressed from their own promoter, rather than captured as internal products of genes. We reveal the utility of BonaFide-TEseq in the analysis of single-cell data and show that short-interspersed nuclear elements (SINEs) show cell type–specific expression profiles in the mouse hippocampus. We further show that, in response to a brief exposure of home-cage mice to a novel stimulus, SINEs are activated in dentate granule neurons in a time course that is similar to that of protein-coding immediate early genes. This work provides a simple alternative approach to assess bona fide TE transcription at single-cell resolution and provides a proof-of-concept using this method to identify SINE activation in a context that is relevant for normal learning and memory.

Low dissolved oxygen, or hypoxia, is a common phenomenon in ice-covered lakes in winter. We measured dissolved oxygen (DO) before, during, and after ice-over to characterize the timing, severity, and spatial variability of winter hypoxia in Upper Red Rock Lake, Montana, home to one of the last remaining lacustrine populations of endemic Montana Arctic Grayling (Thymallus arcticus). Unlike most previous investigations of winterkill-prone lakes, we observed considerable horizontal spatial variability in DO, a non-linear winter oxygen depletion rate, and lake-wide re-oxygenation 2–4 weeks prior to spring ice loss. Parts of the upper 1 m of the lake and near stream mouths remained well-oxygenated even during late winter. DO levels were strongly associated with maximum daily air temperature. Our analysis of a 28-year weather record revealed large interannual variability in risk of winter hypoxia, with a slight declining trend in winter severity (number of days with maximum air temperatures ≤ 0°C) in Upper Red Rock Lake. The approach we used in our study provides a useful framework for quantifying and mapping the seasonal dynamics of the extent and severity of winter hypoxia, and for identifying critical winter habitats.

Genetic screens in Saccharomyces cerevisiae have allowed for the identification of many genes as sensors or effectors of DNA damage, typically by comparing the fitness of genetic mutants in the presence or absence of DNA-damaging treatments. However, these static screens overlook the dynamic nature of DNA damage response pathways, missing time-dependent or transient effects. Here, we examine gene dependencies in the dynamic response to ultraviolet radiation-induced DNA damage by integrating ultra-high-density arrays of 6144 diploid gene deletion mutants with high-frequency time-lapse imaging. We identify 494 ultraviolet radiation response genes which, in addition to recovering molecular pathways and protein complexes previously annotated to DNA damage repair, include components of the CCR4-NOT complex, tRNA wobble modification, autophagy, and, most unexpectedly, 153 nuclear-encoded mitochondrial genes. Notably, mitochondria-deficient strains present time-dependent insensitivity to ultraviolet radiation, posing impaired mitochondrial function as a protective factor in the ultraviolet radiation response.

The use of proximity-dependent biotin labelling (PDL) approaches coupled with mass spectrometry recently greatly advanced the identification of protein-protein interactions and study of protein complexation. PDL is based on the expression of a promiscuous biotin ligase (PBL), e.g. BirA* or a peroxidase fused to a bait protein of interest. In the presence of biotin as substrate, PBL enables covalent biotin labelling of proteins in the vicinity of the PBL-fused bait in vivo , allowing the subsequent capture and identification of interacting and neighbouring proteins without the need for the protein complex to remain intact during purification. To date, PDL has not been extensively used in plants. Here we present the results of a systematic multi-lab study applying a variety of PDL approaches in several plant systems under various conditions and bait proteins. We show that TurboID is the most promiscuous variant for PDL in plants and establish protocols for its efficient application. We demonstrate the applicability of TurboID in capturing membrane protein interactomes using the Lotus japonicus symbiotically active receptor kinases RLKs NOD FACTOR RECEPTOR 5 (NFR5) and LRR-RLK SYMBIOTIC RECEPTOR-KINASE (SYMRK) as test-cases. Furthermore, we benchmark the efficiency of various PBLs using the octameric endocytic TPLATE complex and compare PDL with one-step AP-MS approaches. Our results indicate that different PDL approaches in plants may differ in signal-to-noise ratio and robustness. We present a straightforward strategy to identify both non-biotinylated as well as biotinylated proteins in plants in a single experimental setup. Finally, we provide initial evidence that this technique has potential to infer structural information of protein complexes. Our methods, tools and adjustable pipelines provide a useful resource for the plant research community.

The gut microbiome is an ecosystem that involves complex interactions. Currently, our knowledge about the role of the gut microbiome in health and disease relies mainly on differential microbial abundance, and little is known about the role of microbial interactions in the context of human disease. Here, we construct and compare microbial co-abundance networks using 2,379 metagenomes from four human cohorts: an inflammatory bowel disease (IBD) cohort, an obese cohort and two population-based cohorts. We find that the strengths of 38.6% of species co-abundances and 64.3% of pathway co-abundances vary significantly between cohorts, with 113 species and 1,050 pathway co-abundances showing IBD-specific effects and 281 pathway co-abundances showing obesity-specific effects. We can also replicate these IBD microbial co-abundances in longitudinal data from the IBD cohort of the integrative human microbiome (iHMP-IBD) project. Our study identifies several key species and pathways in IBD and obesity and provides evidence that altered microbial abundances in disease can influence their co-abundance relationship, which expands our current knowledge regarding microbial dysbiosis in disease., Gut microbiome alterations have been linked to inflammatory bowel disease (IBD) and obesity. Here, the authors characterize the metagenomes of four large human cohorts and perform co-abundance network analysis showing that dysbiosis in disease is marked by the altered co-abundance relationships, suggesting that pathway coabundance networks are more heterogeneous than species network.

Spondweni virus (SPONV) is the most closely related known flavivirus to Zika virus (ZIKV). Its pathogenic potential and vector specificity have not been well defined. SPONV has been found predominantly in Africa, but was recently detected in a pool of Culex quinquefasciatus mosquitoes in Haiti. Here we show that SPONV can cause significant fetal harm, including demise, comparable to ZIKV, in a mouse model of vertical transmission. Following maternal inoculation, we detected infectious SPONV in placentas and fetuses, along with significant fetal and placental histopathology, together suggesting vertical transmission. To test vector competence, we exposed Aedes aegypti and Culex quinquefasciatus mosquitoes to SPONV-infected bloodmeals. Aedes aegypti could efficiently transmit SPONV, whereas Culex quinquefasciatus could not. Our results suggest that SPONV has the same features that made ZIKV a public health risk.

Background Recurrent vulvovaginal candidiasis (RVVC) affects up to 8% of women. The immunopathogenesis is poorly understood but it has been suggested that RVVC might be due to dysregulated innate immune response. The aim of this study was to compare cytokine profiles in stimulated primary mononuclear cells (PBMCs) from RVVC and healthy individuals. Methods PBMCs isolated from RVVC patients (n = 24) and healthy volunteers (n = 30) were stimulated with unspecific and pathogen-specific antigens. Cytokine production was assessed after 24 hours, 48 hours, and 7 days using ELISA. Results No significant differences in cytokine production were found in T helper 1 (Th1), Th2, and Th17 immunity in response to both unspecific and pathogen-specific stimulations. Tumor necrosis factor-α (TNF-α) production in response to C. albicans hyphae was significantly higher in patients than controls and within the patient group, a significant positive correlation was found between interleukin-1β (IL-1β) and both TNF-α and IL-6. Both IL-1β/IL-1Ra and TNF-α/IL-10 ratios in Candida hyphae-stimulated PBMCs were significantly higher in patients than controls. Conclusions Women affected by RVVC showed increased monocytes-derived cytokine production, which might contribute to an exaggerated vaginal immune response to Candida hyphae. RVVC patients show no defective Th-dependent adaptive immune response upon Candida stimulation.

International audience; The Mascarene Petrel Pseudobulweria aterrima is a critically endangered seabird endemic to Reunion Island, with an extremely small population suffering several threats. Fifteen polymorphic microsatellite loci were isolated from this species to analyse genetic diversity, estimate contemporary effective population size, search for evidence of a population bottleneck and see whether results support the hypothesis that life history traits could preserve allelic diversity in small populations. Results from 22 individuals found grounded as a consequence of light pollution highlight a surprisingly high genetic diversity, an absence of inbreeding, a contemporary effective population size estimated at approximately 1211 individuals and a probable bottleneck around 10 000 generations ago. Additional studies on genetic diversity and structure from a larger number of samples are thus required to evaluate the evolutionary potential of this critically endangered species.