Characterization of the sheep Complement Factor B gene (CFB)

The Complement Factor B gene (CFB) of the alternative complement pathway has been identified in the sheep Major Histocompatibility Complex (MHC) and its genomic sequence determined. CFB is located approximately 600bp upstream of the complement C2 gene, contains 18 exons, and manifests the domain signature characteristic of CFB protein. Thirteen single nucleotide polymorphisms were identified in merino sheep and interbreed variation was identified by comparison with International Sheep Genomics Consortium data. Two predicted non synonymous substitutions were observed and in-silico analysis indicates that these are likely to have a destabilising effect on the protein structure. Sheep and cattle CFB were compared and shown to contain a common nine nucleotide deletion in exon 18 relative to human CFB. Predicted CFB amino acid sequences for these two species contain 761 aa relative to 764 aa in the human orthologue. Sequencing of the cosmid and BAC clones used in this study permitted the relative positions of three adjacent loci to be determined and showed that the previously described microsatellite locus (BfMs) is located within SKIV2L

Polymorphism of sheep MHC Class IIb gene TAPASIN

The Major Histocompatibility Complex (MHC) is one of the most gene dense regions in the genome and studies in several species have shown significant associations between the MHC and disease. The endoplasmic reticular glycoprotein, tapasin, is involved in the MHC class I antigen presentation pathway. Sheep TAPASIN is located in the class IIb region of the MHC. Sheep TAPASIN was subcloned from BAC and cosmid genomic clones and DNA sequenced. TAPASIN is 9549 bp in length and encodes a protein of 447 amino acids. The structure of sheep TAPASIN was similar to other mammals and consisted of eight exons with a distinctively larger intron between exon three and four. Sheep TAPASIN gene had high sequence identity with other mammalian TAPASINs. The TAPASIN gene sequence is conserved across many mammalian species and is possibly maintained through purifying selection with the average ratio of ds/dn of 3.9. Twenty-six SNPs in sheep TAPASIN were identified

Antibiotic Prophylaxis with Trimethoprim-Sulfamethoxazole versus No Treatment after Mid-to-Distal Hypospadias Repair: A Prospective, Randomized Study

Purpose. To evaluate the impact of prophylactic antibiotics after distal hypospadias repair on postoperative bacteriuria, symptomatic urinary tract infection, and postoperative complications in a prospective, randomized trial. Materials and Methods. Consecutive patients aged 6 months to 2 years were enrolled at our institution between June 2013 and May 2017. Consenting patients were randomized to antibiotic prophylaxis with trimethoprim-sulfamethoxazole versus no antibiotic. Patients had catheterized urine samples obtained at surgery and 6–10 days postoperatively. The primary outcome was bacteriuria and pyuria at postoperative urine collection. Secondary outcomes included symptomatic urinary tract infection and postoperative complications. Results. 70 patients consented to the study, of which 35 were randomized to receive antibiotics compared to 32 who did not. Demographics, severity of hypospadias, and type of repair were similar between the groups. Patients in the treatment group had significantly less pyuria (18%) and bacteriuria (11%) present at stent removal compared to the nontreatment group (55% and 63%; p=0.01 and p<0.001, resp.). No patient had a symptomatic urinary tract infection. There were 11 postoperative complications. Conclusions. Routine antibiotic prophylaxis appears to significantly decrease bacteriuria and pyuria in the immediate postoperative period; however, no difference was observed in symptomatic urinary tract infection or postoperative complications. Clinical Trial Registration Number NCT02593903

Probabilistic classification of acute myocardial infarction from multiple cardiac markers

Logistic regression and Gaussian mixture model (GMM) classifiers have been trained to estimate the probability of acute myocardial infarction (AMI) in patients based upon the concentrations of a panel of cardiac markers. The panel consists of two new markers, fatty acid binding protein (FABP) and glycogen phosphorylase BB (GPBB), in addition to the traditional cardiac troponin I (cTnI), creatine kinase MB (CKMB) and myoglobin. The effect of using principal component analysis (PCA) and Fisher discriminant analysis (FDA) to preprocess the marker concentrations was also investigated. The need for classifiers to give an accurate estimate of the probability of AMI is argued and three categories of performance measure are described, namely discriminatory ability, sharpness, and reliability. Numerical performance measures for each category are given and applied. The optimum classifier, based solely upon the samples take on admission, was the logistic regression classifier using FDA preprocessing. This gave an accuracy of 0.85 (95% confidence interval: 0.78–0.91) and a normalised Brier score of 0.89. When samples at both admission and a further time, 1–6 h later, were included, the performance increased significantly, showing that logistic regression classifiers can indeed use the information from the five cardiac markers to accurately and reliably estimate the probability AMI

MTHFD1 controls DNA methylation in Arabidopsis.

DNA methylation is an epigenetic mechanism that has important functions in transcriptional silencing and is associated with repressive histone methylation (H3K9me). To further investigate silencing mechanisms, we screened a mutagenized Arabidopsis thaliana population for expression of SDCpro-GFP, redundantly controlled by DNA methyltransferases DRM2 and CMT3. Here, we identify the hypomorphic mutant mthfd1-1, carrying a mutation (R175Q) in the cytoplasmic bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase (MTHFD1). Decreased levels of oxidized tetrahydrofolates in mthfd1-1 and lethality of loss-of-function demonstrate the essential enzymatic role of MTHFD1 in Arabidopsis. Accumulation of homocysteine and S-adenosylhomocysteine, genome-wide DNA hypomethylation, loss of H3K9me and transposon derepression indicate that S-adenosylmethionine-dependent transmethylation is inhibited in mthfd1-1. Comparative analysis of DNA methylation revealed that the CMT3 and CMT2 pathways involving positive feedback with H3K9me are mostly affected. Our work highlights the sensitivity of epigenetic networks to one-carbon metabolism due to their common S-adenosylmethionine-dependent transmethylation and has implications for human MTHFD1-associated diseases

Polyketide synthesis genes associated with toxin production in two species of Gambierdiscus (Dinophyceae)

Background Marine microbial protists, in particular, dinoflagellates, produce polyketide toxins with ecosystem-wide and human health impacts. Species of Gambierdiscus produce the polyether ladder compounds ciguatoxins and maitotoxins, which can lead to ciguatera fish poisoning, a serious human illness associated with reef fish consumption. Genes associated with the biosynthesis of polyether ladder compounds are yet to be elucidated, however, stable isotope feeding studies of such compounds consistently support their polyketide origin indicating that polyketide synthases are involved in their biosynthesis. Results Here, we report the toxicity, genome size, gene content and transcriptome of Gambierdiscus australes and G. belizeanus. G. australes produced maitotoxin-1 and maitotoxin-3, while G. belizeanus produced maitotoxin-3, for which cell extracts were toxic to mice by IP injection (LD50 = 3.8 mg kg-1). The gene catalogues comprised 83,353 and 84,870 unique contigs, with genome sizes of 32.5 ± 3.7 Gbp and 35 ± 0.88 Gbp, respectively, and are amongst the most comprehensive yet reported from a dinoflagellate. We found three hundred and six genes involved in polyketide biosynthesis, including one hundred and ninty-two ketoacyl synthase transcripts, which formed five unique phylogenetic clusters. Conclusions Two clusters were unique to these maitotoxin-producing dinoflagellate species, suggesting that they may be associated with maitotoxin biosynthesis. This work represents a significant step forward in our understanding of the genetic basis of polyketide production in dinoflagellates, in particular, species responsible for ciguatera fish poisoning.Postprin

Igneous seismic geomorphology of buried lava fields and coastal escarpments on the Vøring volcanic rifted margin

Voluminous igneous complexes are commonly present in sedimentary basins on volcanic rifted margins, and they represent a challenge for petroleum explorationists. A 2500 km2 industry-standard 3D seismic cube has recently been acquired on the Vøring Marginal High offshore mid-Norway to image subbasalt sedimentary rocks. This cube also provides a unique opportunity for imaging top- and intrabasalt structures. Detailed seismic geomorphological interpretation of the top-basalt horizon, locally calibrated with high-resolution P-Cable wide-azimuth data, reveals new insight into the late-stage development of the volcanic flow fields and the kilometer-high coastal Vøring Escarpment. Subaerial lava flows with compressional ridges and inflated lava lobes cover the marginal high, with a comparable structure and size to modern subaerial lava fields. Pitted surfaces, likely formed by lava emplaced in a wet environment, are present in the western part of the study area near the continent-ocean boundary. The prominent Vøring Escarpment formed when eastward-flowing lava reached the coastline. The escarpment morphology is influenced by preexisting structural highs, and these highs are locally bypassed by the lava. Volcanogenic debris flows are well-imaged on the escarpment horizon, along with large-scale large slump blocks. Similar features exist in active volcanic environments, e.g., on the south coast of Hawaii. Numerous postvolcanic extensional faults and incised channels cut into the marginal high and the escarpment, and we found that the area was geologically active after the volcanism ceased. In summary, igneous seismic geomorphology and seismic volcanostratigraphy are two very powerful methods to understand the volcanic deposits and development of rifted margins. Our study demonstrates great promise for further understanding the igneous development of offshore basins as more high-quality 3D seismic data become available