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Crop yield loss due to flooding is a threat to food security. Submergence-induced hypoxia in plants results in stabilization of group VII ETHYLENE RESPONSE FACTORs (ERF-VIIs), which aid survival under these adverse conditions. ERF-VII stability is controlled by the N-end rule pathway, which proposes that ERF-VII N-terminal cysteine oxidation in normoxia enables arginylation followed by proteasomal degradation. The PLANT CYSTEINE OXIDASEs (PCOs) have been identified as catalysts of this oxidation. ERF-VII stabilization in hypoxia presumably arises from reduced PCO activity. We directly demonstrate that PCO dioxygenase activity produces Cys-sulfinic acid at the N terminus of an ERF-VII peptide, which then undergoes efficient arginylation by an arginyl transferase (ATE1). This provides molecular evidence of N-terminal Cys-sulfinic acid formation and arginylation by N-end rule pathway components, and a substrate of ATE1 in plants. The PCOs and ATE1 may be viable intervention targets to stabilize N-end rule substrates, including ERF-VIIs, to enhance submergence tolerance in agriculture. The N-end rule pathway targets substrate proteins for proteasomal degradation. Here, White et al . show that Arabidopsis PLANT CYSTEINE OXIDASEs show dioxygenase activity producing Cys-sulfinic acid at the N-terminus of target proteins, which then act as direct substrates for arginyl transferase.

The fission yeast clade—comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus—occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade.

Whether obesity is associated with recurrent venous thromboembolism (VTE) in elderly patients is unknown. To examine the association between two obesity measures, the body mass index (BMI) and the waist circumference (WC), and recurrent VTE in elderly patients. We studied 986 patients aged ≥65 years with an acute VTE from a prospective multicenter cohort study (09/2009-12/2013). The BMI was determined and categorized as <25, 25 to <30, or ≥30 kg/m2. The WC was categorized as <80 cm in women (w)/<94 cm in men (m), 80 to <88 cm (w)/94 to <102 cm (m), or ≥88 cm (w)/≥102 cm (m). We examined the association between the BMI and the WC and the time to a first symptomatic recurrent VTE using competing risk regression, adjusting for known risk factors of VTE recurrence and periods of anticoagulation. The mean follow-up was 28 months. The 3-year cumulative incidence of recurrent VTE did not vary by BMI and was 17.6% for a BMI <25 kg/m2, 11.5% for a BMI 25 to <30 kg/m2, and 16.9% for a BMI ≥30 kg/m2 (P = 0.09). The 3-year cumulative incidence of recurrent VTE did not vary by WC. After adjustment, neither the BMI (sub-hazard ratio [SHR] 1.02, 95% confidence interval [CI 0.98-1.05]) nor the WC (SHR 1.01, 95% CI 0.99-1.02) was associated with recurrent VTE. Measures of body weight were not associated with recurrent VTE in our cohort. Obesity does not appear to be a predictor of recurrent VTE in the elderly.

In most bacteria and archaea, filaments of FtsZ protein organize cell division. FtsZ forms a ring structure at the division site and starts the recruitment of 10 to 20 downstream proteins that together form a multiprotein complex termed the divisome. The divisome is thought to facilitate many of the steps required to make two cells out of one. FtsQ and FtsB are part of the divisome, with FtsQ being a central hub, interacting with most of the other divisome components. Here we show for the first time in detail how FtsQ interacts with its downstream partner FtsB and show that mutations that disturb the interface between the two proteins effectively inhibit cell division. Most bacteria and archaea use the tubulin homologue FtsZ as its central organizer of cell division. In Gram-negative Escherichia coli bacteria, FtsZ recruits cytosolic, transmembrane, periplasmic, and outer membrane proteins, assembling the divisome that facilitates bacterial cell division. One such divisome component, FtsQ, a bitopic membrane protein with a globular domain in the periplasm, has been shown to interact with many other divisome proteins. Despite its otherwise unknown function, it has been shown to be a major divisome interaction hub. Here, we investigated the interactions of FtsQ with FtsB and FtsL, two small bitopic membrane proteins that act immediately downstream of FtsQ. We show in biochemical assays that the periplasmic domains of E. coli FtsB and FtsL interact with FtsQ, but not with each other. Our crystal structure of FtsB bound to the β domain of FtsQ shows that only residues 64 to 87 of FtsB interact with FtsQ. A synthetic peptide comprising those 24 FtsB residues recapitulates the FtsQ-FtsB interactions. Protein deletions and structure-guided mutant analyses validate the structure. Furthermore, the same structure-guided mutants show cell division defects in vivo that are consistent with our structure of the FtsQ-FtsB complex that shows their interactions as they occur during cell division. Our work provides intricate details of the interactions within the divisome and also provides a tantalizing view of a highly conserved protein interaction in the periplasm of bacteria that is an excellent target for cell division inhibitor searches. IMPORTANCE In most bacteria and archaea, filaments of FtsZ protein organize cell division. FtsZ forms a ring structure at the division site and starts the recruitment of 10 to 20 downstream proteins that together form a multiprotein complex termed the divisome. The divisome is thought to facilitate many of the steps required to make two cells out of one. FtsQ and FtsB are part of the divisome, with FtsQ being a central hub, interacting with most of the other divisome components. Here we show for the first time in detail how FtsQ interacts with its downstream partner FtsB and show that mutations that disturb the interface between the two proteins effectively inhibit cell division.

Within the past decade, microplastic (MP) particles (<5 mm in size) became the focus of both scientific and public attention, on one hand due to their cumulative industrial application and global presence, on the other hand due to their size range allowing the interaction with organisms at the base of the marine food web. Along with the growing evidence of their ubiquitous distribution, the ingestion of MP fibers and fragments has been verified for a variety of marine biota, with fish species being among the group of organisms most intensively studied both in the laboratory and in the field. While the gross of scientific literature focuses on the quantification and chemical characterization of MP in the gastrointestinal tract of fish, in-depth investigations on the impacts or a contextualization of ingestion are rarely accomplished. Yet, the constant media-coverage and omnipresence of the topic present a (threat) scenario among civil society which might lack a solid scientific foundation. This review, therefore, analyses the scientific output of 90 field studies covering 487 different fish taxa with due regard to explanatory variables for MP ingestion. Additionally, it highlights persistent knowledge gaps in relation to the examination of in-situ ingestion effects and proposes measures how to approach them in future research initiatives. Moreover, the potential existence of a publication bias and a consequent distortion of the perception of the topic is evaluated.

Background Comparative genomics is a formidable tool to identify functional elements throughout a genome. In the past ten years, studies in the budding yeast Saccharomyces cerevisiae and a set of closely related species have been instrumental in showing the benefit of analyzing patterns of sequence conservation. Increasing the number of closely related genome sequences makes the comparative genomics approach more powerful and accurate. Results Here, we report the genome sequence and analysis of Saccharomyces arboricolus , a yeast species recently isolated in China, that is closely related to S. cerevisiae . We obtained high quality de novo sequence and assemblies using a combination of next generation sequencing technologies, established the phylogenetic position of this species and considered its phenotypic profile under multiple environmental conditions in the light of its gene content and phylogeny. Conclusions We suggest that the genome of S. arboricolus will be useful in future comparative genomics analysis of the Saccharomyces sensu stricto yeasts.

Replication of eukaryotic genomes is highly stochastic, making it difficult to determine the replication dynamics of individual molecules with existing methods. We report a sequencing method for the measurement of replication fork movement on single molecules by detecting nucleotide analog signal currents on extremely long nanopore traces (D-NAscent). Using this method, we detect 5-bromodeoxyuridine (BrdU) incorporated by Saccharomyces cerevisiae to reveal, at a genomic scale and on single molecules, the DNA sequences replicated during a pulse-labeling period. Under conditions of limiting BrdU concentration, D-NAscent detects the differences in BrdU incorporation frequency across individual molecules to reveal the location of active replication origins, fork direction, termination sites, and fork pausing/stalling events. We used sequencing reads of 20–160 kilobases to generate a whole-genome single-molecule map of DNA replication dynamics and discover a class of low-frequency stochastic origins in budding yeast. The D-NAscent software is available at https://github.com/MBoemo/DNAscent.git.Replication initiation is stochastic and obscured in population sequencing; D-NAscent reports the use of long nanopore reads to detect base analogs and thus to assess replication initiation at the individual molecule level.

Genome-wide DNA polymerase usage maps determined in fission yeast, using a new sequencing strategy based on ribonucleotide misincorporation, track the division of labor between replicative polymerases and reveal locations and efficiencies of replication origins. Three eukaryotic DNA polymerases are essential for genome replication. Polymerase (Pol) α–primase initiates each synthesis event and is rapidly replaced by processive DNA polymerases: Polɛ replicates the leading strand, whereas Polδ performs lagging-strand synthesis. However, it is not known whether this division of labor is maintained across the whole genome or how uniform it is within single replicons. Using Schizosaccharomyces pombe, we have developed a polymerase usage sequencing (Pu-seq) strategy to map polymerase usage genome wide. Pu-seq provides direct replication-origin location and efficiency data and indirect estimates of replication timing. We confirm that the division of labor is broadly maintained across an entire genome. However, our data suggest a subtle variability in the usage of the two polymerases within individual replicons. We propose that this results from occasional leading-strand initiation by Polδ followed by exchange for Polɛ.

Milk urea concentration is an indicator for dietary nitrogen (N)-supply and urinary N-excretion. Dairy cows with high (HMU) compared to low milk urea (LMU) concentration have greater plasma urea, creatinine and uric acid concentrations, but if the liver metabolism accounts for these differences is unknown. Eighteen HMU and 18 LMU cows were fed a diet with a low (LP) or normal (NP) crude protein concentration. A N balance study was performed and a 13 C-urea bolus was administered to measure urea pool size. Liver samples were analyzed by 2D-gel-based proteomics and RT-qPCR. Although HMU cows had a greater urea pool, plasma urea, uric acid, and hippuric acid concentrations, these differences were not associated with altered expressions of genes related to urea cycling or N-metabolism. Instead, HMU cows had higher oxidative stress levels. Conclusively, other factors than hepatic urea metabolism account for milk urea concentrations. Despite higher plasma urea concentrations and argininosuccinate synthase 1 protein expression on the LP diet, urea cycle mRNA expressions were not affected, indicating that its activity is not controlled at transcriptional level. Feeding the LP diet resulted in increased expressions of enzymes catabolizing fatty acids, but the reason remains to be investigated in future studies.

BackgroundEndometriosis is a chronic, inflammatory, and hormone-dependent disease that affects approximately 10% of women in reproductive age. Endometriosis is categorized into different types, as superficial, deep, and ovarian endometriosis. When deep endometriosis occurs, the sigmoid and rectum are often affected (Becker et al. in Hum Reprod Open, 2022, https://doi.org/10.1093/hropen/hoac009). In the following article, we aim to demonstrate stepwise surgery for stage IV endometriosis involving the anterior rectosigmoid.MethodsWe present the case of a 26-year-old obese (BMI 35.87) woman with severe posterior pelvic compartment endometriosis, persistent abdominal pain, and constipation. On preoperative MRI of the pelvis, a 13 cm conglomerate incorporating both ovaries (kissing ovaries), uterine serosa, and the anterior rectosigmoid was observed (Fig. 1). Accordingly, interdisciplinary laparoscopic surgery with a gynecologist and colorectal surgeon was planned.ResultsThe total laparoscopic approach is demonstrated step by step in the video.ConclusionsDeep endometriosis is a rare condition. When involvement of other organs (e.g., the bowel) is suspected, preoperative endometriosis-specific imaging should be performed for optimal surgical planning. Experienced endometriosis multidisciplinary surgical teams can provide specialized and high-quality care for patients suffering from this debilitating disease (Luna Russo et al. in Minerva Ginecol, 2020, https://doi.org/10.23736/S0026-4784.20.04544-X).