AsnI: A novel class II restriction endonuclease from Arthrobacter sp., strain N-CM, recognizing 5′-AT/TAAT-3′

AbstractA new class II restriction endonuclease, AsnI, with a novel sequence specificity was isolated from the Gram-positive eubacterium Arthrobacter species, strain N-CM. AsnI recognizes the unambiguously defined palindromic hexanucleotide consisting of A- and T-residues. The novel enzyme in the presence of Mg2+ cleaves specifically both strands as indicated by the arrows. The staggered cuts generate 5′-protruding ends with single-stranded 5′-TA-3′ dinucleotide extensions. The novel enzyme may be a useful tool for cloning experiments by complementation of the few enzymes such as PstI and PvuI cutting only once in the Ampr-gene of plasmids pBR322 and pBR328

Automated vessel centerline extraction and diameter measurement in OCT Angiography

Optical Coherence Tomography Angiography (OCTA) is a non-invasive imaging technique that enables the visualizationof perfused vasculature in vivo. In ophthalmology,it allows the physician to monitor diseases affecting the vascular networks of the retina such as age-related macular degeneration or diabetic retinopathy. Due to the complexity of the vasculature in the retina,it is of interest to automatically extract vascular parameters which describe the condition of the vessels. Suitable parameters could improve the diagnosis and the treatment during the course of therapy.We present an automated algorithm tocompute the diameters of the vessels in en face OCTA images. After segmentingthe images, the vessel centerlinewascomputed using a thinningalgorithm.The centerline wasrefined by detecting invalid pixelssuch as spursandbycontinuing the centerline until the endsof the vessels. Lastly, the diameter wascomputed by dilating a discrete circle at the position of the centerline or by measuring the distance between both borders of the vessels. The developed algorithms were applied to in vivo images of human eyes. Certainly, no ground truth was available. Hence, a plausibility check was performed by comparing the measured diameters of two different layers of the retina (Superficial Vascular Complex (SVC) and Deep Vascular Complex (DVC)). Each layer exhibits a different characteristic vasculature.The algorithm clearly reflectedthe differences from both retinal layers. The measured diameters demonstrate that the DVC consists of more capillaries and considerably smaller vessels compared to the SVC.The presented method enables automated analysis of the retinal vasculature and forms thereby the basis for monitoringdiseases influencing the vasculature of the retina. The validation of the method using an artificial ground truth is still neede

Dietary Silicon Deficiency Does Not Exacerbate Diet-Induced Fatty Lesions in Female ApoE Knockout Mice.

BACKGROUND: Dietary silicon has been positively linked with vascular health and protection against atherosclerotic plaque formation, but the mechanism of action is unclear. OBJECTIVES: We investigated the effect of dietary silicon on 1) serum and aorta silicon concentrations, 2) the development of aortic lesions and serum lipid concentrations, and 3) the structural and biomechanic properties of the aorta. METHODS: Two studies, of the same design, were conducted to address the above objectives. Female mice, lacking the apolipoprotein E (apoE) gene, and therefore susceptible to atherosclerosis, were separated into 3 groups of 10-15 mice, each exposed to a high-fat diet (21% wt milk fat and 1.5% wt cholesterol) but with differing concentrations of dietary silicon, namely: silicon-deprived (-Si; <3-μg silicon/g feed), silicon-replete in feed (+Si-feed; 100-μg silicon/g feed), and silicon-replete in drinking water (+Si-water; 115-μg silicon/mL) for 15-19 wk. Silicon supplementation was in the form of sodium metasilicate (feed) or monomethylsilanetriol (drinking water). RESULTS: The serum silicon concentration in the -Si group was significantly lower than in the +Si-feed (by up to 78%; P < 0.003) and the +Si-water (by up to 84%; P < 0.006) groups. The aorta silicon concentration was also lower in the -Si group than in the +Si-feed group (by 65%; P = 0.025), but not compared with the +Si-water group. There were no differences in serum and aorta silicon concentrations between the silicon-replete groups. Body weights, tissue wet weights at necropsy, and structural, biomechanic, and morphologic properties of the aorta were not affected by dietary silicon; nor were the development of fatty lesions and serum lipid concentrations. CONCLUSIONS: These findings suggest that dietary silicon has no effect on atherosclerosis development and vascular health in the apoE mouse model of diet-induced atherosclerosis, contrary to the reported findings in the cholesterol-fed rabbit model

The P-Loop Domain of Yeast Clp1 Mediates Interactions Between CF IA and CPF Factors in Pre-mRNA 3′ End Formation

Cleavage factor IA (CF IA), cleavage and polyadenylation factor (CPF), constitute major protein complexes required for pre-mRNA 3′ end formation in yeast. The Clp1 protein associates with Pcf11, Rna15 and Rna14 in CF IA but its functional role remained unclear. Clp1 carries an evolutionarily conserved P-loop motif that was previously shown to bind ATP. Interestingly, human and archaean Clp1 homologues, but not the yeast protein, carry 5′ RNA kinase activity. We show that depletion of Clp1 in yeast promoted defective 3′ end formation and RNA polymerase II termination; however, cells expressing Clp1 with mutant P-loops displayed only minor defects in gene expression. Similarly, purified and reconstituted mutant CF IA factors that interfered with ATP binding complemented CF IA depleted extracts in coupled in vitro transcription/3′ end processing reactions. We found that Clp1 was required to assemble recombinant CF IA and that certain P-loop mutants failed to interact with the CF IA subunit Pcf11. In contrast, mutations in Clp1 enhanced binding to the 3′ endonuclease Ysh1 that is a component of CPF. Our results support a structural role for the Clp1 P-loop motif. ATP binding by Clp1 likely contributes to CF IA formation and cross-factor interactions during the dynamic process of 3′ end formation

Early Switch from Intravenous to Oral Antibiotics in Skin- and Soft-tissue Infections: An Algorithm-based Prospective Multicentre Pilot Trial.

BACKGROUND: In hospitalized patients with skin and soft tissue infections (SSTIs), intravenous (IV) empiric antibiotic treatment is initiated. The best time point for switching from IV to oral treatment is unknown. We used an algorithm-based decision tree for the switch from IV to oral antibiotics within 48 hours and aimed to investigate the treatment outcome of this concept. METHODS: In a nonrandomized trial, we prospectively enrolled 128 patients hospitalized with SSTI from July 2019 to May 2021 at 3 institutions. Clinical and biochemical response data during the first week and at follow-up after 30 days were analyzed. Patients fulfilling criteria for the switch from IV to oral antibiotics were assigned to the intervention group. The primary outcome was a composite definition consisting of the proportion of patients with clinical failure or death of any cause. RESULTS: Ninety-seven (75.8%) patients were assigned to the intervention group. All of them showed signs of clinical improvement (ie, absence of fever or reduction of pain) within 48 hours of IV treatment, irrespective of erythema finding or biochemical response. The median total antibiotic treatment duration was 11 (interquartile range [IQR], 9–13) days in the invention group and 15 (IQR, 11–24) days in the nonintervention group (P < .001). The median duration of hospitalization was 5 (IQR, 4–6) days in the intervention group and 8 (IQR, 6–12) days in the nonintervention group (P < .001). There were 5 (5.2%) failures in the intervention group and 1 (3.2%) in the nonintervention group after a median follow-up of 37 days. CONCLUSIONS: In this pilot trial, the proposed decision algorithm for early switch from IV to oral antibiotics for SSTI treatment was successful in 95% of cases. Clinical Trials Registration. ISRCTN1524549

Dopamine transporter (DAT1) and dopamine receptor D4 (DRD4) genotypes differentially impact on electrophysiological correlates of error processing

Peer reviewedPublisher PD

Hereditary thrombotic thrombocytopenic purpura and COVID-19: Impacts of vaccination and infection in this rare disease.

Introduction Severe COVID-19 is associated with an important increase of von Willebrand factor and mild lowering of ADAMTS13 activity that may, in the presence of a strong inflammatory reaction, increase the risk of acute thrombotic thrombocytopenic purpura (TTP). Although acute episodes of immune-mediated TTP associated with COVID-19 or SARS-CoV-2 vaccination have been reported, data about clinical evolution of hereditary TTP (hTTP) during the pandemic are scarce. Method We conducted a survey among adult patients of the International Hereditary TTP Registry about SARS-CoV-2 vaccination, COVID-19, and occurrence of acute hTTP episodes. Results Of 122 adult hTTP patients invited to participate, 86 (70.5%) responded. Sixty-five had been vaccinated (75.6%), of which 14 had received in addition a booster, resulting in 139 individual vaccine shots. Although vaccinations in patients on plasma prophylaxis were done within 1 week of the last plasma infusion, all 23 patients treated with plasma on demand were vaccinated without prior plasma infusions. One patient on uninterrupted weekly plasma infusions presented within 3 days from his second vaccination with neurological symptoms and computed tomography scan 9 days later showed subacute ischemic/hemorrhagic frontal lobe infarction. A second male patient developed acute myocarditis after his second dose of mRNA-1273 vaccine. Twelve (14%) patients had COVID-19, associated with an acute hTTP episode in three of them: one patient had a transient ischemic attack, one a stroke, and a pregnant woman was hospitalized to intensify plasma treatment. Discussion The risk of an acute episode triggered by COVID-19 seems higher than following vaccination in hTTP patients, who can be safely vaccinated against SARS-CoV-2

No evidence for intervention-associated DNA methylation changes in monocytes of patients with posttraumatic stress disorder.

DNA methylation patterns can be responsive to environmental influences. This observation has sparked interest in the potential for psychological interventions to influence epigenetic processes. Recent studies have observed correlations between DNA methylation changes and therapy outcome. However, most did not control for changes in cell composition. This study had two aims: first, we sought to replicate therapy-associated changes in DNA methylation of commonly assessed candidate genes in isolated monocytes from 60 female patients with post-traumatic stress disorder (PTSD). Our second, exploratory goal was to identify novel genomic regions with substantial pre-to-post intervention DNA methylation changes by performing whole-genome bisulfite sequencing (WGBS) in two patients with PTSD. Equivalence testing and Bayesian analyses provided evidence against physiologically meaningful intervention-associated DNA methylation changes in monocytes of PTSD patients in commonly investigated target genes (NR3C1, FKBP5, SLC6A4, OXTR). Furthermore, WGBS yielded only a limited set of candidate regions with suggestive evidence of differential DNA methylation pre- to post-therapy. These differential DNA methylation patterns did not prove replicable when investigated in the entire cohort. We conclude that there is no evidence for major, recurrent intervention-associated DNA methylation changes in the investigated genes in monocytes of patients with PTSD

Repeated pulses of vertical methane flux recorded in glacial sediments from the southeast Bering Sea

Author Posting. © American Geophysical Union, 2011. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Paleoceanography 26 (2011): PA2210, doi:10.1029/2010PA001993.There is controversy over the role of marine methane hydrates in atmospheric methane concentrations and climate change during the last glacial period. In this study of two sediment cores from the southeast Bering Sea (700 m and 1467 m water depth), we identify multiple episodes during the last glacial period of intense methane flux reaching the seafloor. Within the uncertainty of the radiocarbon age model, the episodes are contemporaneous in the two cores and have similar timing and duration as Dansgaard-Oeschger events. The episodes are marked by horizons of sediment containing 13C-depleted authigenic carbonate minerals; 13C-depleted archaeal and bacterial lipids, which resemble those found in ANME-1 type anaerobic methane oxidizing microbial consortia; and changes in the abundance and species distribution of benthic foraminifera. The similar timing and isotopic composition of the authigenic carbonates in the two cores is consistent with a region-wide increase in the upward flux of methane bearing fluids. This study is the first observation outside Santa Barbara Basin of pervasive, repeated methane flux in glacial sediments. However, contrary to the “Clathrate Gun Hypothesis” (Kennett et al., 2003), these coring sites are too deep for methane hydrate destabilization to be the cause, implying that a much larger part of the ocean's sedimentary methane may participate in climate or carbon cycle feedback at millennial timescales. We speculate that pulses of methane in these opal-rich sediments could be caused by the sudden release of overpressure in pore fluids that builds up gradually with silica diagenesis. The release could be triggered by seismic shaking on the Aleutian subduction zone caused by hydrostatic pressure increase associated with sea level rise at the start of interstadials.Support for this project was from the National Science Foundation Office of Polar Programs, United States Department of Energy, Oak Foundation, and MARUM at University of Bremen