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ObjectiveOesophageal cancer (EC) is the sixth leading cause of cancer-related deaths. Oesophageal adenocarcinoma (EA), with Barrett’s oesophagus (BE) as a precursor lesion, is the most prevalent EC subtype in the Western world. This study aims to contribute to better understand the genetic causes of BE/EA by leveraging genome wide association studies (GWAS), genetic correlation analyses and polygenic risk modelling.DesignWe combined data from previous GWAS with new cohorts, increasing the sample size to 16 790 BE/EA cases and 32 476 controls. We also carried out a transcriptome wide association study (TWAS) using expression data from disease-relevant tissues to identify BE/EA candidate genes. To investigate the relationship with reported BE/EA risk factors, a linkage disequilibrium score regression (LDSR) analysis was performed. BE/EA risk models were developed combining clinical/lifestyle risk factors with polygenic risk scores (PRS) derived from the GWAS meta-analysis.ResultsThe GWAS meta-analysis identified 27 BE and/or EA risk loci, 11 of which were novel. The TWAS identified promising BE/EA candidate genes at seven GWAS loci and at five additional risk loci. The LDSR analysis led to the identification of novel genetic correlations and pointed to differences in BE and EA aetiology. Gastro-oesophageal reflux disease appeared to contribute stronger to the metaplastic BE transformation than to EA development. Finally, combining PRS with BE/EA risk factors improved the performance of the risk models.ConclusionOur findings provide further insights into BE/EA aetiology and its relationship to risk factors. The results lay the foundation for future follow-up studies to identify underlying disease mechanisms and improving risk prediction.

Anaerobic toluene degradation proceeds by fumarate addition to produce (R)-benzylsuccinate as first intermediate, which is further degraded via β-oxidation by five enzymes encoded in the conserved bbs operon. This study characterizes two enzymes of this pathway, (E)-benzylidenesuccinyl-CoA hydratase (BbsH), and (S,R)-2-(α-hydroxybenzyl)succinyl-CoA dehydrogenase (BbsCD) from Thauera aromatica. BbsH, a member of the enoyl-CoA hydratase family, converts (E)-benzylidenesuccinyl-CoA to 2-(α-hydroxybenzyl)succinyl-CoA and was subsequently used in a coupled enzyme assay with BbsCD, which belongs to the short-chain dehydrogenases/reductase (SDR) family. The BbsCD crystal structure shows a C2-symmetric heterotetramer consisting of BbsC2 and BbsD2 dimers. BbsD subunits are catalytically active and capable of binding NAD+ and substrate, whereas BbsC subunits represent built-in pseudoenzyme moieties lacking all motifs of the SDR family required for substrate binding or catalysis. Molecular modeling studies predict that the active site of BbsD is specific for conversion of the (S,R)-diastereomer of 2-(α-hydroxybenzyl)succinyl-CoA to (S)-2-benzoylsuccinyl-CoA by hydride transfer to the re-face of nicotinamide adenine dinucleotide (NAD)+ . Furthermore, BbsC subunits are not engaged in substrate binding and merely serve as scaffold for the BbsD dimer. BbsCD represents a novel clade of related enzymes within the SDR family, which adopt a heterotetrameric architecture and catalyze the β-oxidation of aromatic succinate adducts.

Bulk tank milk (BTM) is regularly used for surveillance on dairy farms for disease conditions such as mastitis and Johne's disease. In this study, we used 16S rRNA sequencing and bait-capture enrichment to characterize the microbiota and resistome of BTM, and investigate potential differences between the cream or pellet fractions. A total of 12 BTM samples were taken from 12 Prince Edward Island dairy farms, in Atlantic Canada, in duplicates. The DNA was analyzed by high-throughput sequencing of the 16S rRNA gene and a suite of antimicrobial resistance (AMR) genes. Target-capture enrichment of AMR genes was conducted before shotgun sequencing. The bioinformatics pipelines QIIME 2 and AMR++ were used for microbiota and resistome analysis, respectively. Differences between microbiotae were evaluated qualitatively with nonmetric multidimensional scaling and quantitatively with permutational ANOVA of UniFrac distances. A total of 47 phyla were present across the BTM samples. Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria were the most abundant phyla. At the genus level, Corynebacterium, Acinetobacter, Lactobacillus, and Turicibacter were the most abundant. There was no significant difference in the Faith's phylogenetic diversity between the cream and pellet fraction. Faith's phylogenetic diversity differed marginally by stall type. There were 10,217 hits across 80 unique AMR genes, with tetracycline resistance being the most common class.

Normalmente, as águas superficiais e das chuvas são insuficientes para atender às demandas dos produtores regionais no Norte de Minas Gerais. Assim, aqueles que possuem recursos hídricos subterrâneos satisfatórios vêm utilizando tal fonte para atender às necessidades hídricas das frutíferas regionais. No entanto, essas frutíferas comumente possuem teores elevados de carbonato e bicarbonato de cálcio, os quais promovem alterações nas características químicas dos solos, com elevação do pH e dos teores de Ca, após alguns anos de cultivo, proporcionando complicações no estado nutricional dos bananais. Nas áreas em que se tem excesso de Ca, proveniente das águas de irrigação, normalmente, esse induz deficiência de Mg e K nas plantas, comprometendo a produtividade e a longevidade dos bananais. O presente trabalho teve como objetivo definir a melhor combinação entre doses de KCl e MgSO4, em solos cultivados com bananeira ‘Nanica’, em sistema de cultivo irrigado com água de natureza calcária, no Norte de Minas Gerais. Os tratamentos foram definidos pela combinação de 0, 10, 20, 30 e 50 g de MgSO4 /família/trimestre e de 0, 40, 80, 120 e 160 g de KCl/família/mês, utilizando a matriz experimental Quadrado Duplo. Foram avaliadas características de desenvolvimento vegetativo e de produção da bananeira. Apenas as doses de KCl influenciaram as características de desenvolvimento vegetativo e de produção. Não existiu efeito da adubação com MgSO4, mesmo a análise inicial do solo tendo apontado deficiência da referida base. A duração do ciclo do plantio à colheita foi em média 486 dias. Palavras-chave: Musa sp. Equilíbrio Nutricional. Adubação Potássica e Magnesiana. Qualidade de Água para Irrigação. Abstract Normally, surface and rainwater are insufficient to meet the demands of regional producers in northern Minas Gerais. Thus, those who have satisfactory groundwater resources have been using this source to meet the water needs of regional fruit trees. However, they commonly have high levels of calcium carbonate and bicarbonate, which promote changes in the soils chemical characteristics , with an increase in pH and Ca levels, after some years of cultivation, providing complications in the banana trees’ nutritional status. In areas where there is an excess of Ca, from irrigation water, it usually induces deficiency of Mg and K in plants, compromising the f banana trees productivity and longevity. The present work had as objective to define the best combination between doses of KCl and MgSO4 in soils cultivated with banana 'Nanica' in a cultivation system irrigated with limestone water, in the northern Minas Gerais. The treatments were defined by the combination of 0, 10, 20, 30 and 50 g of MgSO4 / family / quarter and 0, 40, 80, 120 and 160 g of KCl / family / month, using the experimental Double Square matrix. Banana vegetative development and production characteristics were evaluated. Only KCl doses influenced the characteristics of vegetative development and production. There was no effect of fertilization with MgSO4, even though the initial soil analysis showed a deficiency of the referred base. The cycle duration from planting to harvest was on average 486 days. Keywords: Musa sp. Nutritional Balance. Potassium and Magnesium Fertilization. Water Quality for Irrigation.

This study was conducted to determine the occurrence of antimicrobial resistance to the extended-spectrum cephalosporins (ESC) in Escherichia coli isolates. The isolates were collected from retail meat products collected in the Maritime Provinces of Canada. Our analyses involved the use of both selective and traditional culture methods; we also conducted genotype analyses using multiplex polymerase chain reactions. ESC-resistant (ESC-R) E. coli were detected in 33 of 559 samples (5.9%) using the traditional culture method, compared with 151 of 557 samples (27.1%) using the selective culture method. We recovered more isolates of ESC-R E. coli from poultry compared with beef and pork (P < 0.001). Multidrug resistance, extended-spectrum β-lactamase (ESBL), and AmpC phenotypes were more common in chicken-derived isolates than other retail meat products (P < 0.001). From the 98 isolates examined, 76 isolates (77.6%) were positive for either ESBL and AmpC β-lactamases or both. Among the 76 isolates, blaCMY-2 (78.9%), blaCTXM (46.1%), blaTEM (21.1%), and blaSHV (1.3%) genes were detected. Among the blaCTXM-producing isolates, blaCTXM-1, blaCTXM-2, and blaCTXM-9 phylogenetic groups were detected. β-lactamase genes were more commonly detected in chicken-derived isolates compared with other meat types (P < 0.01). This study demonstrates the occurrence of ESBL- and AmpC-resistance genes in retail meat products in the Maritime Provinces of Canada. We found that selective culture significantly improved the recovery of ESC-R E. coli isolates from retail meat samples.

The ability to use the protoporphyrinogen oxidase (PPO)-inhibiting herbicides fomesafen, flumioxazin, and sulfentrazone in potato is limited regionally or by soil texture, largely because of crop injury noted in research in the 1990s. With that in mind, we evaluated whether reducing the herbicide rates could maintain weed control while providing more consistent crop safety. Studies were conducted on a silt loam and a coarse-textured loamy sand soil. Soil texture played a greater than anticipated role in PPO-inhibitor herbicide injury risk as it relates to high-precipitation events. For example, in 2020 at the silt loam location, there were five precipitation events across the season that exceeded 2.5 cm, including one 6 d after treatment (DAT), and a seasonal total precipitation that was over 10 cm greater than the previous year. Despite excessive moisture and initial potato injury as high as 27% where flumioxazin was applied at the high rate with S-metolachlor, by 29 DAT injury was less than 10% in all treatments, and marketable tuber yield was similar among treatments. In contrast, in 2020 at the loamy sand location, there were four precipitation events across the season that exceeded 2.5 cm, and potato injury was as much as 60%. In 2020 the high amount of injury from flumioxazin was hypothesized to be caused by precipitation before herbicide application and not after, suggesting a need for more research in this area. This work documents the fine line between yield reduction presumably caused by reduced weed control and yield reduction assumed to be related to herbicide injury. This delineation between adequate weed control and consistent crop safety may differ by soil texture and environmental conditions, supporting the notion that custom-tailored weed management may become more necessary as high-precipitation events become more common in upper midwestern U.S. agricultural systems.

It is known that microorganisms are essential for the functioning of ecosystems, but the extent to which microorganisms respond to different environmental variables in their natural habitats is not clear. In the current study, we present a methodological framework to quantify the covariation of the microbial community of a habitat and environmental variables of this habitat. It is built on theoretical considerations of systems ecology, makes use of state-of-the-art machine learning techniques and can be used to identify bioindicators. We apply the framework to a data set containing operational taxonomic units (OTUs) as well as more than twenty physicochemical and geographic variables measured in a large-scale survey of European lakes. While a large part of variation (up to 61%) in many environmental variables can be explained by microbial community composition, some variables do not show significant covariation with the microbial lake community. Moreover, we have identified OTUs that act as "multitask" bioindicators, i.e., that are indicative for multiple environmental variables, and thus could be candidates for lake water monitoring schemes. Our results represent, for the first time, a quantification of the covariation of the lake microbiome and a wide array of environmental variables for lake ecosystems. Building on the results and methodology presented here, it will be possible to identify microbial taxa and processes that are essential for functioning and stability of lake ecosystems.

Objectives For many years, tumor development has been viewed as a cell-autonomous process; however, today we know that the tumor microenvironment (TME) and especially cancer-associated fibroblasts (CAFs) significantly contribute to tumor progression. Caveolin-1 (Cav-1) is a scaffolding protein which is involved in several cancer-associated processes as important component of the caveolae. Our goal was to shed light on the expression of the two different isoforms of Cav-1 in normal fibroblasts (NFs) and CAFs of patients with oral squamous cell carcinoma (OSCC). Materials and methods Fibroblasts from normal mucosa and CAFs were isolated and propagated in vitro. Gene expression of the different Cav-1 isoforms was assessed via quantitative real-time PCR (qPCR) and supplemented by protein expression analysis. Results We could show that the Cav-1β isoform is more highly expressed in NFs and CAFs compared to Cav-1α. Furthermore, the different Cav-1 isoforms tended to be differently expressed in different tumor stages. However, this trend could not be seen consistently, which is in line with the ambiguous role of Cav-1 in tumor progression described in literature. Western blotting furthermore revealed that NFs and CAFs might differ in the oligomerization profile of the Cav-1 protein. Conclusion These differences in expression of Cav-1 between NFs and CAFs of patients with OSCC confirm that the protein might play a role in tumor progression and is of interest for further analyses. Clinical relevance Our findings support a possible role of the two isoforms of Cav-1 in the malignant transformation of OSCC.

Teratomas are the most common tumors in the ovary during childhood. Previous studies suggested that they may be derived from germ cells at any developmental stage from premeiotic oogonia through meiotic oocytes to post-meiotic ova. The majority of mature teratomas reveal normal karyotypes and immature teratomas show higher frequency of chromosomal abnormalities. We analyzed fresh tissue samples from 25 primary ovarian teratomas and three extraovarian deposits using whole genome single nucleotide polymorphism (SNP) array and karyotype. SNP array detected five patterns of copy neutral loss of heterozygosity (CN-LOH): failure of meiosis I (type I) in 12 tumors, failure of meiosis II (type II) in six tumors, endoreduplication of a haploid ovum (type III) in two tumors, premeiotic error (type IV) in four tumors, and both meiotic I and meiotic II errors in one tumor (type V). Three tumors with type I error had a single chromosome showing meiotic II error, and two tumors with type II error had a single chromosome showing premature sister-chromatid separation in meiosis I. Lack of recombination in multiple chromosomes in meiosis I were common, chromosomes 17, 7, 8, 21, and 22 were most commonly involved. Abnormal karyotypes were observed in four teratomas including +3, del(3q), +7, +8, +12, and i(18q). The extraovarian deposits revealed the same CN-LOH pattern as the primary teratoma. In summary, SNP array reveals the origin of ovarian teratoma and we propose a new mechanism that consecutive meiotic I and II errors occur frequently in ovarian teratomas.

Background Sequencing of marker genes amplified from environmental samples, known as amplicon sequencing, allows us to resolve some of the hidden diversity and elucidate evolutionary relationships and ecological processes among complex microbial communities. The analysis of large numbers of samples at high sequencing depths generated by high throughput sequencing technologies requires efficient, flexible, and reproducible bioinformatics pipelines. Only a few existing workflows can be run in a user-friendly, scalable, and reproducible manner on different computing devices using an efficient workflow management system. Results We present Natrix, an open-source bioinformatics workflow for preprocessing raw amplicon sequencing data. The workflow contains all analysis steps from quality assessment, read assembly, dereplication, chimera detection, split-sample merging, sequence representative assignment (OTUs or ASVs) to the taxonomic assignment of sequence representatives. The workflow is written using Snakemake, a workflow management engine for developing data analysis workflows. In addition, Conda is used for version control. Thus, Snakemake ensures reproducibility and Conda offers version control of the utilized programs. The encapsulation of rules and their dependencies support hassle-free sharing of rules between workflows and easy adaptation and extension of existing workflows. Natrix is freely available on GitHub (https://github.com/MW55/Natrix) or as a Docker container on DockerHub (https://hub.docker.com/r/mw55/natrix). Conclusion Natrix is a user-friendly and highly extensible workflow for processing Illumina amplicon data.

[Image: see text] Glycogen synthase kinase-3β (GSK3β) is involved in many pathological conditions and represents an attractive drug target. We previously reported dual GSK3β/p38α mitogen-activated protein kinase inhibitors and identified N-(4-(4-(4-fluorophenyl)-2-methyl-1H-imidazol-5-yl)pyridin-2-yl)cyclopropanecarboxamide (1) as a potent dual inhibitor of both target kinases. In this study, we aimed to design selective GSK3β inhibitors based on our pyridinylimidazole scaffold. Our efforts resulted in several novel and potent GSK3β inhibitors with IC(50) values in the low nanomolar range. 5-(2-(Cyclopropanecarboxamido)pyridin-4-yl)-4-cyclopropyl-1H-imidazole-2-carboxamide (6g) displayed very good kinase selectivity as well as metabolical stability and inhibited GSK3β activity in neuronal SH-SY5Y cells. Interestingly, we observed the importance of the 2-methylimidazole’s tautomeric state for the compound activity. Finally, we reveal how this crucial tautomerism effect is surmounted by imidazole-2-carboxamides, which are able to stabilize the binding via enhanced water network interactions, regardless of their tautomeric state.

Stable and sufficient food supplies are increasingly threatened by climatic variability, in particular extreme heat events. Intraspecific crop diversity may be an important biological resource to both understand and maintain crop resilience to extreme conditions. Here using data from a mass field experiment screening for heat tolerance in sweet potato (Ipomoea batatas), we identify 132 heat-tolerant cultivars and breeding lines (6.7%) out of 1,973 investigated. Sweet potato is the world's fifth most important food crop, and mean conditions experienced by sweet potato by 2070 are predicted to be 1 to 6 °C warmer, negatively impacting most genotypes. We identify canopy temperature depression, chlorophyll content and storage root-flesh colour as predictors of heat tolerance and, therefore, as potential traits for breeding consideration. These results highlight the role of intraspecific biodiversity for the productivity and resilience of food and agricultural systems in the face of climate change.

Landfill leachate is a potential environmental pollutant. Physicochemical analyses allow identifying its elements while the use of ecotoxicological tests aims to understand the relation with the environment. The germination assay of Senna macranthera in different substrates (filter paper, commercial-SCM, conventional-SCV and organic-SOR) was performed with different doses of leachate. The objective was to identify the potential impact of leachate by determining the concentration able to cause inhibition in 50% of the seeds (LC50) and the values of the no observable effect concentration (NOEC) and the lowest observed effect concentration (LOEC). The LC50 and LOEC occurred in the treatments with 6.25 while NOEC was with 3.125%. The test in substrates, It was not possible to identify the LC50 in the SCM. For the SCV was with 66 and in SOR with 25%. The NOEC and LOEC for SCM and SCV were 25 and 50% and in SOR with 50 and 100%.

Weed management in carrot is challenging, given slow and inconsistent crop emergence and early-season growth and the lack of practical season-long management tools such as herbicides. We investigated holistic carrot production systems with a focus on minimizing inputs while optimizing resource use. In an overall sense, results of this work were consistent between years, and stark. The choice of carrot variety had a moderate influence on carrot foliar canopy development and, subsequently, weed density. For example, ‘Cupar’ carrot formed a complete crop canopy sooner than the other dicer-type ‘Canada’ variety. Likely as a result, density of weed species such as spotted ladysthumb and common lambsquarters was less where ‘Cupar’ was grown compared with where ‘Canada’ was grown. Gibberellic acid as a foliar application was not successful in these studies and, in a few cases, may have even increased weed-seed germination and establishment. Adding two carrot rows to the current regional industry-standard three-row bed system not only enhanced competitiveness with weeds but also improved carrot yield without additional fertilizer, water, or pest management inputs. By far, though, the most successful strategy to reduce weed density while maintaining or improving carrot yield was to delay seeding by 17 to 19 d. We anticipate more holistic production system research that integrates low-input alternatives in other crops as herbicide-resistant weeds proliferate while few new herbicides are developed. As was demonstrated in this research, such novel approaches can be successful without adding significant economic burden to the farmer or increasing risk of crop failure.

Human cytosolic monothiol glutaredoxin-3 (GLRX3) is a protein essential for the maturation of cytosolic [4Fe–4S] proteins. We show here that dimeric cluster-bridged GLRX3 transfers its [2Fe–2S]2+ clusters to the human P-loop NTPase NUBP1, an essential early component of the cytosolic iron–sulfur assembly (CIA) machinery. Specifically, we observed that [2Fe–2S]2+ clusters are transferred from GLRX3 to monomeric apo NUBP1 and reductively coupled to form [4Fe–4S]2+ clusters on both N-terminal CX13CX2CX5C and C-terminal CPXC motifs of NUBP1 in the presence of glutathione that acts as a reductant. In this process, cluster binding to the C-terminal motif of NUBP1 promotes protein dimerization, while cluster binding to the N-terminal motif does not affect the quaternary structure of NUBP1. The cluster transfer/assembly process is not complete on both N- and C-terminal motifs and indeed requires a reductant stronger than GSH to increase its efficiency. We also showed that the [4Fe–4S]2+ cluster formed at the N-terminal motif of NUBP1 is tightly bound, while the [4Fe–4S]2+ cluster bound at the C-terminal motif is labile. Our findings provide the first evidence for GLRX3 acting as a [2Fe–2S] cluster chaperone in the early stage of the CIA machinery.

Background Buccal swab sampling constitutes an attractive noninvasive alternative to blood drawings for antibody serostatus assays. Here we describe a method to determine the cytomegalovirus immunoglobulin G (CMV IgG) serostatus from dried buccal swab samples. Methods Upon solubilization, CMV IgG is determined by an ELISA assay specifically adapted to cope with low IgG concentrations. The derived CMV titer is normalized against the total protein concentration to adjust for incorrectly or less efficiently sampled buccal swabs. Assay parameters were optimized on a set of 713 samples. Results Validation with 1784 samples revealed distinct results for > 80% of samples with 98.6% specificity and 99.1% sensitivity. Based on the analysis of 1.2 million samples we derived age- and sex-stratified CMV prevalence statistics for Germany, Poland, United Kingdom, and Chile. To confirm accuracy of the assay in routine operation, the CMV status of 6518 donors was reassessed by independent laboratories based on conventional blood samples revealing 96.9% specificity and 97.4% sensitivity. Conclusions The assay accurately delivers the CMV IgG serostatus from dried buccal swab samples for > 80% of the participants. Thereby it provides a noninvasive alternative to plasma-based CMV monitoring for nondiagnostic purposes such as hematopoietic stem cell transplantation donor screening or population studies., We developed an assay to determine the CMV IgG status based on dried buccal swab samples. Assay validation on a set of 1784 samples revealed 99% sensitivity and specificity. We describe CMV prevalence statistics for Germany, Poland, United Kingdom, and Chile.

This study was carried out to determine the antimicrobial resistance (AMR) genes and mobile genetic elements of 4 fecal blaCMY-2-producing Escherichia coli isolated from Holstein dairy calves on the same farm using whole-genome sequencing. Genomic analysis revealed that 3 of the 4 isolates shared similar genetic features, including sequence type (ST), serotype, plasmid characteristics, insertion ST, and virulence genes. In addition to genes encoding for complex multidrug resistance efflux systems, all 4 isolates were carriers of genes conferring resistance to β-lactams (blaCMY-2, blaTEM-1B), tetracyclines (tetA, tetB, tetD), aminoglycosides [aadA1, aph(3")-lb, aph(6)-ld], sulfonamides (sul2), and trimethoprim (dfrA1). We also detected 4 incompatibility plasmid groups: Inc.F, Inc.N, Inc.I, and Inc.Q. A novel ST showing a new purA and mdh allelic combination was found. The 4 isolates were likely enterotoxigenic pathotypes of E. coli, based on serotype and presence of the plasmid Inc.FII(pCoo). This study provides information for comparative genomic analysis of AMR genes and mobile genetic elements. This analysis could give some explanation to the multidrug resistance characteristics of bacteria colonizing the intestinal tract of dairy calves in the first few weeks of life.

Self-transferable plasmids of the incompatibility group P-1 (IncP-1) are considered important carriers of genes for antibiotic resistance and other adaptive functions. In the laboratory, these plasmids have a broad host range; however, little is known about their in situ host profile. In this study, we discovered that Thauera aromatica K172T, a facultative denitrifying microorganism capable of degrading various aromatic compounds, contains a plasmid highly similar to the IncP-1 ε archetype pKJK5. The plasmid harbours multiple antibiotic resistance genes and is maintained in strain K172T for at least 1000 generations without selection pressure from antibiotics. In a subsequent search, we found additional nine IncP-type plasmids in a total of 40 sequenced genomes of the closely related genera Aromatoleum and Thauera. Six of these plasmids form a novel IncP-1 subgroup designated θ, four of which carry genes for anaerobic or aerobic degradation of aromatic compounds. Pentanucleotide sequence analyses (k-mer profiling) indicated that Aromatoleum spp. and Thauera spp. are among the most suitable hosts for the θ plasmids. Our results highlight the importance of IncP-1 plasmids for the genetic adaptation of these common facultative denitrifying bacteria, and provide novel insights into the in situ host profile of these plasmids.

Coccidia (Chromista: Miozoa: Eimeriidae) of columbiform birds (Aves: Columbiformes) have been described since the end of the nineteenth century; however, some of these descriptions were poorly detailed or inconclusive. In this sense, the current work makes a detailed taxonomic revision reconsidering and organizing 18 Eimeria spp. and two Isospora spp. previously described or reported of Columbiformes. Along with this, a new species of Eimeria is morphologically and molecularly identified by the mitochondrial cytochrome c oxidase subunit 1 (COI) gene and by the 18S small subunit ribosomal RNA (18S) gene from the ruddy ground-dove Columbina talpacoti (Temminck, 1809) in the Médio Paraíba region of the State of Rio de Janeiro, southeastern Brazil. Eimeria columbinae n. sp. has subspheroidal oocysts, 14.7 × 13.2 μm, with smooth, bi-layered wall, ~ 1.1 μm and length/width ratio of 1.1. Micropyle and oocyst residuum are present, but polar granule is absent. Sporocysts are ellipsoidal to slightly asymmetrical, 9.0 × 5.1 μm, with both Stieda and sub-Stieda bodies. Sporocyst residuum present and sporozoites with refractile body and nucleus. This is the 19th description of an eimerian from Columbiformes in the World, and the second to have a molecular identification of the COI and 18S genes.

Previous studies have shown that Ginkgo biloba extract (GbE) reduces food intake and body mass gain and regulates proteins related to lipid metabolism in obese rats. In ovariectomized rats, GbE restored the hippocampal and hypothalamic serotonergic system activity, favoring the spontaneous feeding decrement. Considering the promising hypophagic effect of GbE, this study aimed to investigate the effect of a single acute dose on hypothalamic pathways that regulate feeding behavior in male rats. Four-month-old Wistar male rats received either a single acute oral GbE dose (500 mg/kg) or vehicle. Food intake and body mass were measured after 1, 4, 12, and 24 h. Rats were euthanized, and hypothalami were removed for mRNA quantification of anorexigenic (POMC/CART) and orexigenic (AgRP/NPY) neuropeptides, leptin/serotonin receptors (5HT1A, 5HT1B, 5HT2C), and serotonin transporters. We also investigated POMC, 5-HT1B, and 5-HT2C protein levels. A single acute GbE dose induced the hypothalamic POMC, CART, and 5-HT2C gene expression but failed to modify orexigenic effectors. No alterations in food intake, body mass, and hypothalamic protein levels were observed. In summary, the present findings demonstrate the rapid stimulation of pivotal hypothalamic anorexigenic pathways in response to a single GbE administration, reinforcing the GbE hypophagic activity. However, more studies are necessary to evaluate its potential as an appetite modulator.

Rhinoviruses (RV) and inhaled allergens, such as house dust mite (HDM) are the major agents responsible for asthma onset, exacerbations and progression to the severe disease, but the mechanisms of these pathogenic reciprocal virus-allergen interactions are not well understood. To address this, we analyzed mechanisms of airway epithelial sensing and response to RV infection using controlled experimental in vivo RV infection in healthy controls and patients with asthma and in vitro models of HDM exposure and RV infection in primary airway epithelial cells. We found that intranasal RV infection in patients with asthma led to the highly augmented inflammasome-mediated lower airway inflammation detected in bronchial brushes, biopsies and bronchoalveolar lavage fluid. Mechanistically, RV infection in bronchial airway epithelium led to retinoic acid-inducible gene I (RIG-I), but not via NLR family pyrin domain containing 3 (NLRP3) inflammasome activation, which was highly augmented in patients with asthma, especially upon pre-exposure to HDM. This excessive activation of RIG-I inflammasomes was responsible for the impairment of antiviral type I/III interferons (IFN), prolonged viral clearance and unresolved inflammation in asthma in vivo and in vitro. Pre-exposure to HDM amplifies RV-induced epithelial injury in patients with asthma via enhancement of pro-IL1β expression and release, additional inhibition of type I/III IFNs and activation of auxiliary proinflammatory and pro-remodeling proteins. Finally, in order to determine whether RV-induced activation of RIG-I inflammasome may play a role in the susceptibility to severe acute respiratory syndrome coronavirus (SARS-CoV-2) infection in asthma, we analyzed the effects of HDM exposure and RV/SARS-CoV-2 coinfection. We found that prior infection with RV restricted SARS-CoV-2 replication, but co-infection augmented RIG-I inflammasome activation and epithelial inflammation in patients with asthma, especially in the presence of HDM. Timely inhibition of epithelial RIG-I inflammasome activation may lead to more efficient viral clearance and lower the burden of RV and SARS-CoV-2 infections.

Microbes are essential for element cycling and ecosystem functioning. However, many questions central to understanding the role of microbes in ecology are still open. Here, we analyze the relationship between lake microbiomes and the lakes' land cover. By applying machine learning methods, we quantify the covariance between land cover categories and the microbial community composition recorded in the largest amplicon sequencing dataset of European lakes available to date. Our results show that the aggregation of environmental features or microbial taxa before analysis can obscure ecologically relevant patterns. We observe a comparatively high covariation of the lakes' microbial community with herbaceous and open spaces surrounding the lake; nevertheless, the microbial covariation with land cover categories is generally lower than the covariation with physico-chemical parameters. Combining land cover and physico-chemical bioindicators identified from the same amplicon sequencing dataset, we develop analytical data structures that facilitate insights into the ecology of the lake microbiome. Among these, a list of the environmental parameters sorted by the number of microbial bioindicators we have identified for them points towards apparent environmental drivers of the lake microbial community composition, such as the altitude, conductivity, and area covered herbaceous vegetation surrounding the lake. Furthermore, the response map, a similarity matrix calculated from the Jaccard similarity of the environmental parameters' lists of bioindicators, allows us to study the ecosystem's structure from the standpoint of the microbiome. More specifically, we identify multiple clusters of highly similar and possibly functionally linked ecological parameters, including one that highlights the importance of the calcium-bicarbonate equilibrium for lake ecology. Taken together, we demonstrate the use of machine learning approaches in studying the interplay between microbial diversity and environmental factors and introduce novel approaches to integrate environmental molecular diversity into monitoring and water quality assessments.

Anaplastic sarcoma of the kidney (ASK) is a rare renal tumor for which less than thirty cases have been described in the literature to date. Diagnosis of ASK is primarily based on histology, which features solid spindle cell neoplastic islands arranged in a fascicular pattern, prominent anaplastic nuclear morphology, brisk mitoses, and multiple multiloculated cysts lined by hobnail epithelium reminiscent of cystic nephroma. Chondroid or rhabdomyocytic differentiation is often present within the sarcoma. It has been recently suggested that this tumor entity belongs to the DICER1 syndrome tumors based on identification of DICER1 mutations. We report on a case of this rare tumor found in a twenty-month-old female. In addition to the typical histologic findings of ASK, this case also displayed heterologous neuroblastic-gangliocytic differentiation, which has not been previously described in the literature. TP53 and BRAF v600E had aberrant immunostaining. Chromosomal microarray and genomic sequencing revealed loss of chromosome 10 p15.3-p11.2 and both somatic and germline DICER1 mutations, consistent with recent research and further supporting the classification of this tumor within the DICER1 syndrome associated tumors.

Ethylbenzene dehydrogenase (EbDH), the initial enzyme of anaerobic ethylbenzene degradation from the beta-proteobacterium Aromatoleumaromaticum, is a soluble periplasmic molybdenum enzyme consisting of three subunits. It contains a Mo-bis-molybdopterin guanine dinucleotide (Mo-bis-MGD) cofactor and an 4Fe–4S cluster (FS0) in the α-subunit, three 4Fe–4S clusters (FS1 to FS3) and a 3Fe–4S cluster (FS4) in the β-subunit and a heme b cofactor in the γ-subunit. Ethylbenzene is hydroxylated by a water molecule in an oxygen-independent manner at the Mo-bis-MGD cofactor, which is reduced from the MoVI to the MoIV state in two subsequent one-electron steps. The electrons are then transferred via the Fe–S clusters to the heme b cofactor. In this report, we determine the midpoint redox potentials of the Mo-bis-MGD cofactor and FS1–FS4 by EPR spectroscopy, and that of the heme b cofactor by electrochemically induced redox difference spectroscopy. We obtained relatively high values of > 250 mV both for the MoVI–MoV redox couple and the heme b cofactor, whereas FS2 is only reduced at a very low redox potential, causing magnetic coupling with the neighboring FS1 and FS3. We compare the results with the data on related enzymes and interpret their significance for the function of EbDH. Graphical abstract

The hexaploid sweet potato is one of the most important root crops worldwide. However, its genetic origins, especially that of its tetraploid progenitor, are unclear. In this study, we conceived a pipeline consisting of a genome-wide variation-based phylogeny and a novel haplotype-based phylogenetic analysis (HPA) to determine that the tetraploid accession CIP695141 of Ipomoea batatas 4x from Peru is the tetraploid progenitor of sweet potato. We detected biased gene exchanges between subgenomes. The B1 to B2 subgenome conversions were almost 3-fold higher than the B2 to B1 subgenome conversions. Our analyses revealed that the genes involved in storage root formation, sugar transport, stress resistance, and maintenance of genome stability have been selected during the speciation and domestication of sweet potato. This study sheds lights on the evolution of sweet potato and paves a way for the improvement of sweet potato.

Circulating tumor-derived DNA (ctDNA) can be used to monitor cancer dynamics noninvasively. Detection of ctDNA can be challenging in patients with low-volume or residual disease, where plasma contains very few tumor-derived DNA fragments. We show that sensitivity for ctDNA detection in plasma can be improved by analyzing hundreds to thousands of mutations that are first identified by tumor genotyping. We describe the INtegration of VAriant Reads (INVAR) pipeline, which combines custom error-suppression methods and signal-enrichment approaches based on biological features of ctDNA. With this approach, the detection limit in each sample can be estimated independently based on the number of informative reads sequenced across multiple patient-specific loci. We applied INVAR to custom hybrid-capture sequencing data from 176 plasma samples from 105 patients with melanoma, lung, renal, glioma, and breast cancer across both early and advanced disease. By integrating signal across a median of >105 informative reads, ctDNA was routinely quantified to 1 mutant molecule per 100,000, and in some cases with high tumor mutation burden and/or plasma input material, to parts per million. This resulted in median area under the curve (AUC) values of 0.98 in advanced cancers and 0.80 in early-stage and challenging settings for ctDNA detection. We generalized this method to whole-exome and whole-genome sequencing, showing that INVAR may be applied without requiring personalized sequencing panels so long as a tumor mutation list is available. As tumor sequencing becomes increasingly performed, such methods for personalized cancer monitoring may enhance the sensitivity of cancer liquid biopsies.

Computational investigations into the structure and function of metalloenzymes with transition metal cofactors require proper preparation of the model, which requires obtaining reliable force field parameters for the cofactor. Here, we present a test case where several methods were used to derive amber force field parameters for a bonded model of the Fe(II) cofactor of ectoine synthase. Moreover, the spin of the ground state of the cofactor was probed by DFT and post-HF methods, which consistently indicated the quintet state is lowest in energy and well separated from triplet and singlet. The performance of the obtained force field parameter sets, derived for the quintet spin state, was scrutinized and compared taking into account metrics focused on geometric features of the models as well as their energetics. The main conclusion of this study is that Hessian-based methods yield parameters which represent the geometry around the metal ion, but poorly reproduce energy variance with geometrical changes. On the other hand, the energy-based method yields parameters accurately reproducing energy-structure relationships, but with bad performance in geometry optimization. Preliminary tests show that admixing geometrical criteria to energy-based methods may allow to derive parameters with acceptable performance for both energy and geometry.

Compounds simultaneously inhibiting two targets that are involved in the progression of the same complex disease may exhibit additive or even synergistic therapeutic effects. Here we unveil 2,4,5-trisubstituted imidazoles as dual inhibitors of p38α mitogen-activated protein kinase and glycogen synthase kinase 3β (GSK3β). Both enzymes are potential therapeutic targets for neurodegenerative disorders, like Alzheimer's disease. A set of 39 compounds was synthesized and evaluated in kinase activity assays for their ability to inhibit both target kinases. Among the synthesized compounds, potent dual-target-directed inhibitors showing IC50 values down to the low double-digit nanomolar range, were identified. One of the best balanced dual inhibitors presented in here is N-(4-(2-ethyl-4-(4-fluorophenyl)-1H-imidazol-5-yl)pyridin-2-yl)cyclopropanecarboxamide (20c) (p38α, IC50 = 16 nM; GSK3β, IC50 = 35 nM) featuring an excellent metabolic stability and an appreciable isoform selectivity over the closely related GSK3α. Our findings were rationalized by computational docking studies based on previously published X-ray structures.

Caenorhabditis elegans possesses a rudimentary innate immune response that serves as a model for various aspects of the human innate immune response. To date, a nematode response to pathogenic cytoplasmic DNA has not been identified... Innate immune responses protect organisms against various insults, but may lead to tissue damage when aberrantly activated. In higher organisms, cytoplasmic DNA can trigger inflammatory responses that can lead to tissue degeneration. Simpler metazoan models could shed new mechanistic light on how inflammatory responses to cytoplasmic DNA lead to pathologies. Here, we show that in a DNase II-defective Caenorhabditis elegans strain, persistent cytoplasmic DNA leads to systemic tissue degeneration and loss of tissue functionality due to impaired proteostasis. These pathological outcomes can be therapeutically alleviated by restoring protein homeostasis, either via ectopic induction of the ER unfolded protein response or N-acetylglucosamine treatment. Our results establish C. elegans as an ancestral metazoan model for studying the outcomes of inflammation-like conditions caused by persistent cytoplasmic DNA and provide insight into potential therapies for human conditions involving chronic inflammation.

The gnateaters Conopophaga spp. are insectivorous passerines commonly observed in high and humid forests, where they remain lodged in thin branches and, sometimes, they fly to the ground to catch insects. The insectivorous feeding habit is related to low prevalence and density of coccidians in passerines; however, several coccidian species are recorded for families of insectivorous passerines. This study aimed to examine the feces from gnateaters Conopophaga spp. captured in the municipality of Barra Mansa and in the Itatiaia National Park, State of Rio de Janeiro, Southeastern Brazil, to determine what coccidian parasites were present. Nine gnateaters were captured with mist nets. Coccidian oocysts were recovered from the fecal samples by flotation in Sheather’s saturated solution. Morphological observations, line drawings, photomicrographs and measurements were made in optical microscopy and digitally edited. The molecular analysis included the study of the sequence of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene, with phylogenetic reconstructions based on the neighbor-joining and maximum likelihood analysis. Four Conopophaga spp. were positive for oocysts. An Isospora sp. considered as new to science is described and identified from Conopophaga melanops (Vieillot, 1818) and Conopophaga lineata (Wied, 1831). Isospora borbai n. sp. has oocysts that are subspheroidal, 17–22 × 15–22 (20.2 × 19.1) µm, with rough, bilayered wall, c.1.7 μm thick. Micropyle present, but without micropyle cap. Oocyst residuum absent, but one or two polar granules are present. Sporocysts are ellipsoidal, 12–15 × 8–11 (14.1 × 9.1) µm. The Stieda body is knob-like to half-moon-shaped and sub-Stieda body is rounded. Sporocyst residuum is present, composed of scattered spherules of different sizes. Sporozoites are vermiform with refractile body and nucleus. Molecular analysis at the cox1 gene exhibited similarity greater than 99% with Isospora spp. isolates from other Neotropical passerine birds. Based on the morphological and molecular features, I. borbai is considered as new to science and the first coccidian species recorded from Conopophagidae.

Las sociedades humanas que habitaron las zonas áridas y semiáridas de todo el planeta han tenido en elpasado, igual que en la actualidad, al agua como unrecurso crítico en su toma de decisiones. Desde lasciencias humanas y naturales se han hecho aportespara comprender los patrones de uso del espacio deestos grupos y el manejo (en un sentido amplísimodel término, desde lo estrictamente económico a losimbólico) que tuvieron del recurso hídrico. En estetrabajo buscamos entender el uso del espacio y lamovilidad de los grupos humanos que habitaron unsector de la Diagonal Árida Sudamericana ubicadoen el centro de Argentina, desde la interface de lasciencias geológicas, hidrológicas y ecológicas. El áreade estudio fue conocida como ?Las Travesías? desdeel tiempo de contacto hispano-indígena debido a lasdificultades que imponían para atravesarla, la carencia de agua y el bajo poblamiento. Esta noción europea del paisaje resulta inapropiada a la luz de lasevidencias arqueológicas de pueblos originarios enel territorio desde hace ca. 8000 años AP, que indicarían la presencia de recursos hídricos previamentesubestimados. Combinando el análisis geomorfológico e hidrológico de los paisajes de dunas prevalentesen gran parte de Las Travesías con las evidenciasarqueológicas y etnográficas existentes, proponemosun modelo de ocupación del espacio de la región conmayor déficit hídrico de Sudamérica, en el que estospaisajes funcionaron como eco-refugios. Estos sistemas de dunas suelen albergar aguas subterráneas debajo contenido de sales y poca profundidad, graciasal alto drenaje del sustrato arenoso que permite queuna fracción apreciable de las lluvias, aun en climasáridos, escape de la evapotranspiración y recargue elacuífero freático. Evidencia actual y etnográfica sugiere que la ocupación y disturbio persistente de estossistemas de dunas aumenta su capacidad de proveeragua al deteriorar la cubierta vegetal y así (i) restringir la evapotranspiración y aumentar la recarga y (ii)deprimir zonas del terreno por erosión, acortando laprofundidad al manto freático. Un conjunto relativamente limitado pero eficiente de estrategias para lacosecha de agua, sumado a una movilidad estacionaly el conocimiento profundo del espacio, se planteancomo estrategias que permitieron no solo la exploración y colonización inicial de Las Travesías sino, posteriormente también, su ocupación definitiva. Both in the past as in the present, the native peoples who inhabited the arid and semi-arid zones of the entire planet have had water as a critical resource in their decision-making. From the human and natural sciences, contributions have been made to understand the patterns of the use of space of these groups and the management (in a very broad sense of the term, from the strictly economic to the symbolic one) of the water resource. The aim of this work is to understand the use of space and mobility of the human groups that inhabited a sector of the Arid South American Diagonal, located in the center of Argentina, from the interface of the geological, hydrological, and ecological sciences. The study area was known as “Las Travesías” from the time of the Hispanic-Indigenous contact due to the difficulties of crossing it, because of the lack of water and the low population. This European notion of the landscape is inappropriate in the light of the archaeological evidence of indigenous peoples in the territory since ca. 8000 years BP. These occupations suggest the presence of previously underestimated water resources. Combining the geomorphological and hydrological analyses of the dune landscapes, prevalent in a large part of Las Travesías, with the existing archaeological and ethnographic evidences, we propose a model of space occupation with greatest water deficit in South America and, in which, these landscapes have functioned as eco-shelters. These systems of dunes tend to hold groundwater with low salt content and shallowness due to the high drainage of the sandy substrate that allows a considerable fraction of the rains, even in arid climates, escape evapotranspiration and recharge the phreatic aquifer. Modern and ethnographic evidence suggests that the persistent occupation and disturbance of these dune systems increases their ability to provide water by damaging the vegetation cover, restricting evapotranspiration, increasing recharge, and depressing areas of the land by erosion, shortening the depth to the water table. A relatively small but efficient set of strategies for harvesting water, together with seasonal mobility and a deep knowledge of the space, are proposed as the strategies that allowed not only the exploration and initial colonization of Las Travesías but also the definitive occupation of this space. Fil: Heider, Guillermo. Universidad Nacional de San Luis; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis; Argentina Fil: Jobbagy Gampel, Esteban Gabriel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina Fil: Tripaldi, Alfonsina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Geociencias Básicas, Aplicadas y Ambientales de Buenos Aires. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Geociencias Básicas, Aplicadas y Ambientales de Buenos Aires; Argentina

Linuron herbicide has been a mainstay of carrot weed management for years, but uncertainty around regulatory registration review and an increased prevalence of herbicide-resistant weeds have spurred interest in identifying alternatives that can be readily adopted in production. With this context in mind, herbicide programs were evaluated on a coarse-textured, low organic matter soil in 2015 and 2016. Season-long weed control without compromising yield was possible with weed management programs that included prometryn POST instead of linuron. With that said, a PRE herbicide such as pendimethalin was critical to establish an early-season competitive advantage for carrot plants over weeds, and careful attention should be paid to the prometryn rate, as selectivity is marginal. Carrot is often interseeded with a grain nurse crop to mitigate risk of wind erosion. Nurse crop injury was minimal where S-metolachlor, pendimethalin, or prometryn was applied at rates labeled for PRE use in carrot, with the exception of where prometryn was applied at rates above 1.1 kg ai ha−1.

Sweet potato (Ipomoea batatas, Lam.) is an important root vegetable in developing countries. After its domestication in Neotropical America, human migration led to the distribution of the sweet potato plant throughout the world. Both leaf and storage root are high in compounds of nutritional value. Yet, the storage roots are of particular value due to their significant content of provitamin A (β-carotene). The breeding effort for elite sweet potato lines led to the reduction of genetic diversity and the potential to improve other traits. The focus of the present study was to assess the metabolic diversity of 27 sweet potato cultivars including landraces and improved varieties. A metabolite profiling approach was optimised for sweet potato leaf and storage root tissue and 130 metabolites identified with three different analysis platforms. The data highlighted a lack of correlation between storage root phenotype and leaf metabolism. Furthermore, the metabolic diversity of storage roots was based on the secondary metabolism, including phenylpropanoids and carotenoids. Three cultivars of three different flesh colouration (yellow, orange and purple) showed a significant difference of the primary metabolism. This data demonstrates the value of metabolite profiling to breeding programs as a means of identifying differences in phenotypes/chemotypes and characterising parental material for future pre-breeding resources., Food crops: Assessing the metabolic diversity of sweet potato Understanding the metabolic variations of different types of sweet potato could help improve their nutritional value. Sweet potato is one of the world’s major food crops but recurrent breeding of high yielding lines is reducing their genetic diversity. A study led by Paul D. Fraser, Royal Holloway University of London, UK, examined the chemical differences between 25 types of sweet potato, including orange and purple varieties. They show that there is little correlation between the chemicals found in the leaves and storage root material and that there are significant differences in metabolism between varieties that produce different pigments in their storage roots. Their findings highlight the importance of metabolite profiling for identifying those varieties that produce the highest levels of starch and health-promoting compounds such as carotenoids.

Highlights • CPPV-1 was found in all females of the study, tested with qPCR. • Was found CPPV-1 in fetal/maternal tissue in the post-mortem examination. • Feline females (with and without Reproductive Failures) were negative for commonly-occurring RF viruses in the same (FIV, FeLV e FHV-1). • Females showed clinical signs only related to RF and abnormalities WBCC. • These results provide the first description of an FPV agent causing only RF-related clinical signs in queens., Although reproductive failures (RF) such as abortion, stillbirth and neonatal mortality in cats are still under researched, it is known that many RF are caused by viral agents. This research surveyed the viral agent prevalence in queens with RF. Queens were excluded from the study if their RF was caused by issues other than infection, such as genetic, traumatic, hormonal or nutritional problems, or if they had a history of RF. Blood samples from 26 pregnant females with RF were collected for complete blood counts (BCC), renal/hepatic biochemistry and glycaemic analysis. Ultrasonography was performed to evaluate gestational age and foetal viability. When possible, placentas, humours and foetal tissues were collected. Blood samples were tested by PCR and qPCR for feline leukaemia virus (FeLV), feline immunodeficiency virus (FIV), feline alphaherpesvirus 1 (FeHV-1) and carnivore protoparvovirus 1 (CPPV-1). All maternal samples were negative for FeLV, FIV and FeHV-1 and positive for CPPV-1. In addition, foetuses from one queen and three females were positive for CPPV-1 by qPCR and for feline panleukopenia virus (FPV) through DNA sequencing. The BCC and biochemistry results revealed significant neutrophilia, lymphopenia, monocytosis, and liver enzymes. These results provide the first description of an FPV agent causing only RF-related clinical signs in queens.

A novel acyl-CoA dehydrogenase involved in degradation of the auxin indoleacetate by Aromatoleum aromaticum was identified as a decarboxylating benzylmalonyl-CoA dehydrogenase (IaaF). It is encoded within the iaa operon coding for enzymes of indoleacetate catabolism. Using enzymatically produced benzylmalonyl-CoA, the reaction was characterized as simultaneous oxidation and decarboxylation of benzylmalonyl-CoA to cinnamoyl-CoA and CO2. Oxygen served as electron acceptor and was reduced to H2O2, whereas electron transfer flavoprotein or artificial dyes serving as electron acceptors for other acyl-CoA dehydrogenases were not used. The enzyme is homotetrameric, contains an FAD cofactor and is enantiospecific in benzylmalonyl-CoA turnover. It shows high catalytic efficiency and strong substrate inhibition with benzylmalonyl-CoA, but otherwise accepts only a few medium-chain alkylmalonyl-CoA compounds as alternative substrates with low activities. Its reactivity of oxidizing 2-carboxyacyl-CoA with simultaneous decarboxylation is unprecedented and indicates a modified reaction mechanism for acyl-CoA dehydrogenases, where elimination of the 2-carboxy group replaces proton abstraction from C2.

The goal of yam bean improvement in Africa is to develop superior high yielding and high dry matter cultivars that are preferred for adoption. In this study, the estimates of variance components, heritability and response to selection were studied in F3 yam bean families selected from interspecies crosses targeting improvement of storage root dry matter and associated traits. Breeding populations were generated using North Carolina II (NC II) mating design involving high dry matter P. tuberosus chuin cultivar, low dry matter P. ahipa and the high yielding P. erosus yam beans. The progenies were advanced through selfing from F1 to F2 population and then exposed to selection at 10% selection intensity to obtain 83 high dry matter lines. The selected lines were evaluated in an F3 trial using a randomized complete block design (RCBD) with three replications at the National Crops Resources Research Institute (NaCRRI) Namulonge, in Central Uganda. The results revealed significant (P P

Summary The complex architecture of transmembrane proteins requires quality control (QC) of folding, membrane positioning, and trafficking as prerequisites for cellular homeostasis and intercellular communication. However, it has remained unclear whether transmembrane protein-specific QC hubs exist. Here we identify cereblon (CRBN), the target of immunomodulatory drugs (IMiDs), as a co-chaperone that specifically determines chaperone activity of HSP90 toward transmembrane proteins by means of counteracting AHA1. This function is abrogated by IMiDs, which disrupt the interaction of CRBN with HSP90. Among the multiple transmembrane protein clients of CRBN-AHA1-HSP90 revealed by cell surface proteomics, we identify the amino acid transporter LAT1/CD98hc as a determinant of IMiD activity in multiple myeloma (MM) and present an Anticalin-based CD98hc radiopharmaceutical for MM radio-theranostics. These data establish the CRBN-AHA1-HSP90 axis in the biogenesis of transmembrane proteins, link IMiD activity to tumor metabolism, and nominate CD98hc and LAT1 as attractive diagnostic and therapeutic targets in MM., Graphical abstract, Highlights • CRBN functions as a transmembrane protein-specific co-chaperone of HSP90 • Disruption of CRBN-HSP90 interaction determines the anti-tumor activity of IMiDs • The CD98hc/LAT1 complex is a central target of IMiDs in multiple myeloma • CD98hc-Anticalin is a theranostic tool in multiple myeloma, Heider et al. investigate the molecular function of immunomodulatory drugs (IMiDs) and describe their target, CRBN, as a transmembrane protein (TP)-specific co-chaperone of the HSP90-AHA1 axis. By disrupting CRBN-HSP90 interaction, IMiDs lead to destabilization of various TPs as CD98hc/LAT1, which serve as therapeutic targets in multiple myeloma.

This trial evaluated average daily gain (ADG) effects of heifer calves (< 1 year old) from affordable housing improvements to the roof and flooring on 150 randomly allocated smallholder dairy farms. During the 16-month data collection period, bimonthly farm visits were used to measure weight and other animal- and farm-level factors on the 187 study calves. Multivariable linear regression was used to model ln ADG and ADG during pre-weaning and post-weaning periods, respectively. Median pre-weaning and post-weaning ADGs were 0.307 (interquartile range (IQR): 0.227–0.398) and 0.487 (IQR: 0.354–0.675) kg/d, respectively. In the final pre-weaning model (p

While several pieces of evidence link obesity and mood disorders in menopause, the mechanisms involved are not yet fully understood. We have previously demonstrated that Ginkgo biloba extract (GbE) both attenuated diet-induced obesity of male rats and restored serotonin-induced hypophagia in ovariectomized female rats. The present study aimed at exploring whether GbE treatment ameliorates ovariectomy-related obesity and anxious/depressive-like behaviours. Wistar female rats were either ovariectomized (OVX) or sham-operated (Sham). After 2 months, either 500 mg/kg of GbE or vehicle were administered daily by gavage for 14 days. Anxious/depressive-like behaviours were assessed by the Elevated Plus Maze and the Forced Swim Tests, respectively. Ovariectomy caused high visceral adiposity, hyperleptinemia, and hypercholesterolemia, and increased the anxiety index (p = 0.048 vs. Sham + GbE) while it decreased the latency to immobility (p = 0.004 vs. Sham). GbE treatment in OVX rats improved body composition, adiponectin levels and blood lipid profile. It also reduced the anxiety index (p = 0.004) and increased the latency to immobility (p = 0.003) of OVX rats. Linear regression analysis demonstrated that leptin (p = 0.047) and total cholesterol levels (p = 0.022) were associated with anxious-like behaviours while body adiposity (p = 0.00005) was strongly associated with depressive-like behaviours. The results showed that GbE therapy was effective in attenuating the deleterious effects of ovariectomy on body composition, lipid profile, and anxious/depressive-like behaviours. Further studies are warranted to better understand the therapeutic potential of GbE in menopause.

Staphylococcus aureus is the main causative pathogen of subcutaneous, bone, and implant-related infections, forming structures known as staphylococcal abscess communities (SACs) within tissues that also contain immunosuppressive myeloid-derived suppressor cells (MDSCs). Although both SACs and MDSCs are present in chronic S. aureus infections, it remains unknown whether SACs directly trigger MDSC expansion. To investigate this, a previously developed 3D in vitro SAC model was co-cultured with murine and human bone marrow cells. Subsequently, it was shown that SAC-exposed human CD11blow/− myeloid cells or SAC-exposed murine CD11b+ Gr-1+ cells were immunosuppressive mainly by reducing absolute CD4+ and CD8α+ T cell numbers, as shown in T cell proliferation assays and with flow cytometry. Monocytic MDSCs from mice with an S. aureus bone infection also strongly reduced CD4+ and CD8α+ T cell numbers. Using protein biomarker analysis and an immunoassay, we detected in SAC–bone marrow co-cultures high levels of GM-CSF, IL-6, VEGF, IL-1β, TNFα, IL-10, and TGF-β. Furthermore, SAC-exposed neutrophils expressed Arg-1 and SAC-exposed monocytes expressed Arg-1 and iNOS, as shown via immunofluorescent stains. Overall, this study showed that SACs cause MDSC expansion from bone marrow cells and identified possible mediators to target as an additional strategy for treating chronic S. aureus infections.

Anaerobic toluene degradation is initiated by adding toluene to fumarate via the glycyl radical enzyme benzylsuccinate synthase (BSS). We developed a recombinant production system producing active BSS and present data on the effects of some active-site mutants. A single substitution of Ile617 to Val inside a hydrophobic pocket of the active site leads to an extended substrate range of the variant, which includes conversion of m-xylene, but not of o- or p-xylene. Moreover, a mutation of the conserved Arg508, which participates in fumarate binding, to Lys or Gln decreases or eliminates BSS activity, proving its catalytic importance. Surprisingly, the Arg508Lys mutant gained the ability to synthesize a small amount of the product 3-benzyl-4-ketopentanoate from toluene and the fumarate analogue 3-acetyl acrylate. This study provides insight into substrate recognition by BSS and opens avenues for possible broader biotechnological applications in C-C bond formation.

Thyroid carcinoma incidence rates in western societies are among the fastest rising, compared to all malignant tumors over the past two decades. While risk factors such as age and exposure to ionizing radiation are known, early-state carcinogenic processes or pre-lesions are poorly understood or unknown. This study aims at the identification and characterization of early-state radiation-associated neoplastic processes by histologic and transcriptomic analyses of thyroid tissues derived from a mouse model. Comprehensive histological examination of 246 thyroids (164 exposed, 82 non-exposed) was carried out. Proliferative and normal tissues from exposed cases and normal tissue from non-exposed cases were collected by laser-capture microdissection, followed by RNAseq transcriptomic profiling using a low input 3′-library preparation protocol, differential gene expression analysis and functional association by gene set enrichment analysis. Nine exposed samples exhibited proliferative lesions, while none of the non-exposed samples showed histological abnormalities, indicating an association of ionizing radiation exposure with histological abnormalities. Activated immune response signaling and deregulated metabolic processes were observed in irradiated tissue with normal histology compared to normal tissue from non-exposed samples. Proliferative lesions compared to corresponding normal tissues showed enrichment for mainly proliferation-associated gene sets. Consistently, proliferative lesion samples from exposed mice showed elevated proliferation-associated signaling and deregulated metabolic processes compared to normal samples from non-exposed mice. Our findings suggest that a molecular deregulation may be detectable in histologically normal thyroid tissues and in early proliferative lesions in the frame of multi-step progression from irradiated normal tissue to tumorous lesions.

Graphical abstract, The surveillance of wastewater for the Covid-19 virus during this unprecedented pandemic and mapped to the distribution and magnitude of the infected in the population near real-time exemplifies the importance of tracking rapidly changing trends of pathogens or public health problems at a large scale. The rising trends of antimicrobial resistance (AMR) with multidrug-resistant pathogens from the environmental water have similarly gained much attention in recent years. Wastewater-based epidemiology from water samples has shown that a wide range of AMR-related genes is frequently detected. Albeit sewage is treated before release and thus, the abundance of pathogens should be significantly reduced or even pathogen-free, several studies indicated the contrary. Pathogens are still measurable in the released water, ultimately entering freshwaters, such as rivers and lakes. Furthermore, socio-economic and environmental factors, such as chemical industries and animal farming nearby, impact the presence of AMR. Many bacterial species from the environment are intrinsically resistant and also contribute to the resistome of freshwater lakes. This study collected the most extensive standardized freshwater data set from hundreds of European lakes and conducted a comprehensive multi-omics analysis on antimicrobial resistance from these freshwater lakes. Our research shows that genes encoding for AMR against tetracyclines, cephalosporins, and quinolones were commonly identified, while for some, such as sulfonamides, resistance was less frequently present. We provide an estimation of the characteristic resistance of AMR in European lakes, which can be used as a comprehensive resistome dataset to facilitate and monitor temporal changes in the development of AMR in European freshwater lakes.

Recently, extruded rice as a functional ingredient has been a hot area of research in food processing. In this study, extruded rice with purple sweet potato (ERPSP) was prepared. Moreover, the effects of extrusion and added purple sweet potato on the structure and in vitro digestibility of extruded rice were studied via numerous detection methods, such as scanning electron microscopy (SEM), water absorption index (WAI), water solubility index (WSI), differential scanning calorimetry (DSC), X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FT-IR). SEM results showed that there were numerous pits and bubbles in the extruded rice. In particular, compared with raw rice, the WAI and WSI of ERPSP was higher, and the thermal properties also changed noticeably. The results of XRD and FT-IR spectroscopy showed that the semicrystalline structure of extruded rice changed from A-type to A + V-type mixture, and the relative crystallinity of extruded rice changed accordingly. In addition, a significantly lower equilibrium hydrolysis (C∞) and kinetic constant (k) were observed in ERPSP. The novel rice product made from broken rice by extrusion processing and addition of the purple sweet potato exhibited improved structural properties and reduced digestibility, which increased the potential value and application of broken rice in the food industry.

Background: Experimental and clinical data suggest that reducing inflammation without affecting lipid levels may reduce the risk of cardiovascular disease. Yet, the inflammatory hypothesis of atherothrombosis has remained unproved. Methods: We conducted a randomized, double-blind trial of canakinumab, a therapeutic monoclonal antibody targeting interleukin-1β, involving 10,061 patients with previous myocardial infarction and a high-sensitivity C-reactive protein level of 2 mg or more per liter. The trial compared three doses of canakinumab (50 mg, 150 mg, and 300 mg, administered subcutaneously every 3 months) with placebo. The primary efficacy end point was nonfatal myocardial infarction, nonfatal stroke, or cardiovascular death. RESULTS: At 48 months, the median reduction from baseline in the high-sensitivity C-reactive protein level was 26 percentage points greater in the group that received the 50-mg dose of canakinumab, 37 percentage points greater in the 150-mg group, and 41 percentage points greater in the 300-mg group than in the placebo group. Canakinumab did not reduce lipid levels from baseline. At a median follow-up of 3.7 years, the incidence rate for the primary end point was 4.50 events per 100 person-years in the placebo group, 4.11 events per 100 person-years in the 50-mg group, 3.86 events per 100 person-years in the 150-mg group, and 3.90 events per 100 person-years in the 300-mg group. The hazard ratios as compared with placebo were as follows: in the 50-mg group, 0.93 (95% confidence interval [CI], 0.80 to 1.07; P = 0.30); in the 150-mg group, 0.85 (95% CI, 0.74 to 0.98; P = 0.021); and in the 300-mg group, 0.86 (95% CI, 0.75 to 0.99; P = 0.031). The 150-mg dose, but not the other doses, met the prespecified multiplicity-adjusted threshold for statistical significance for the primary end point and the secondary end point that additionally included hospitalization for unstable angina that led to urgent revascularization (hazard ratio vs. placebo, 0.83; 95% CI, 0.73 to 0.95; P = 0.005). Canakinumab was associated with a higher incidence of fatal infection than was placebo. There was no significant difference in all-cause mortality (hazard ratio for all canakinumab doses vs. placebo, 0.94; 95% CI, 0.83 to 1.06; P = 0.31). Conclusions: Antiinflammatory therapy targeting the interleukin-1β innate immunity pathway with canakinumab at a dose of 150 mg every 3 months led to a significantly lower rate of recurrent cardiovascular events than placebo, independent of lipid-level lowering. (Funded by Novartis; CANTOS ClinicalTrials.gov number, NCT01327846.)

Existing methods to improve detection of circulating tumor DNA (ctDNA) have focused on genomic alterations but have rarely considered the biological properties of plasma cell-free DNA (cfDNA). We hypothesized that differences in fragment lengths of circulating DNA could be exploited to enhance sensitivity for detecting the presence of ctDNA and for noninvasive genomic analysis of cancer. We surveyed ctDNA fragment sizes in 344 plasma samples from 200 patients with cancer using low-pass whole-genome sequencing (0.4×). To establish the size distribution of mutant ctDNA, tumor-guided personalized deep sequencing was performed in 19 patients. We detected enrichment of ctDNA in fragment sizes between 90 and 150 bp and developed methods for in vitro and in silico size selection of these fragments. Selecting fragments between 90 and 150 bp improved detection of tumor DNA, with more than twofold median enrichment in >95% of cases and more than fourfold enrichment in >10% of cases. Analysis of size-selected cfDNA identified clinically actionable mutations and copy number alterations that were otherwise not detected. Identification of plasma samples from patients with advanced cancer was improved by predictive models integrating fragment length and copy number analysis of cfDNA, with area under the curve (AUC) >0.99 compared to AUC 0.91 compared to AUC < 0.5 without fragmentation features. Fragment size analysis and selective sequencing of specific fragment sizes can boost ctDNA detection and could complement or provide an alternative to deeper sequencing of cfDNA.

This study was conducted to determine the occurrence of antimicrobial resistance to the extended-spectrum cephalosporins (ESC) in Escherichia coli isolates recovered from retail meat products collected in the Maritime Provinces of Canada using both selective and traditional culture methods, and genotypically using multiplex polymerase chain reactions.ESC-R E. coli was detected in 33/559 (5.9%) samples using the traditional culture compared to 151/557 (27.1%) samples using the selective culture method. The recovery of ESC-R E. coli isolates was more common in poultry compared to beef and pork (PblaCMY-2 (78.9%), blaCTXM (46.1%), blaTEM (21.1%), and blaSHV (1.3%) were detected. Among the blaCTXM-producing isolates; blaCTXM-1, blaCTXM-2, and blaCTXM-9 phylogenetic groups were detected. β-lactamase genes were detected more in chicken-derived isolates compared to other meat types (PE. coli isolates from retail meat samples.