Resolving the chromatin impact of mosaic variants with targeted Fiber-seq.

Accurately quantifying the functional consequences of noncoding mosaic variants requires the pairing of DNA sequences with both accessible and closed chromatin architectures along individual DNA molecules-a pairing that cannot be achieved using traditional fragmentation-based chromatin assays. We demonstrate that targeted single-molecule chromatin fiber sequencing (Fiber-seq) achieves this, permitting single-molecule, long-read genomic, and epigenomic profiling across targeted >100 kb loci with ∼10-fold enrichment over untargeted sequencing. Targeted Fiber-seq reveals that pathogenic expansions of the CTG repeat that underlie Myotonic Dystrophy 1 are characterized by somatic instability and disruption of multiple nearby regulatory elements, both of which are repeat length-dependent.

3-hour genome sequencing and targeted analysis to rapidly assess genetic risk.

Purpose: Rapid genetic testing in the critical care setting may guide diagnostic evaluation, direct therapies, and help families and care providers make informed decisions about goals of care. We tested whether a simplified DNA extraction and library preparation process would enable us to perform ultra-rapid assessment of genetic risk for a Mendelian condition, based on information from an affected sibling, using long-read genome sequencing and targeted analysis.

Methods: Following extraction of DNA from cord blood and rapid library preparation, genome sequencing was performed on an Oxford Nanopore PromethION.

Resolving the chromatin impact of mosaic variants with targeted Fiber-seq.

Accurately quantifying the functional consequences of non-coding mosaic variants requires the pairing of DNA sequence with both accessible and closed chromatin architectures along individual DNA molecules-a pairing that cannot be achieved using traditional fragmentation-based chromatin assays. We demonstrate that targeted single-molecule chromatin fiber sequencing (Fiber-seq) achieves this, permitting single-molecule, long-read genomic and epigenomic profiling across targeted >100 kilobase loci with ~10-fold enrichment over untargeted sequencing. Targeted Fiber-seq reveals that pathogenic expansions of the CTG repeat that underlie Myotonic Dystrophy 1 are characterized by somatic instability and disruption of multiple nearby regulatory elements, both of which are repeat length-dependent.

DNA-m6A calling and integrated long-read epigenetic and genetic analysis with .

Long-read DNA sequencing has recently emerged as a powerful tool for studying both genetic and epigenetic architectures at single-molecule and single-nucleotide resolution. Long-read epigenetic studies encompass both the direct identification of native cytosine methylation and the identification of exogenously placed DNA -methyladenine (DNA-m6A). However, detecting DNA-m6A modifications using single-molecule sequencing, as well as coprocessing single-molecule genetic and epigenetic architectures, is limited by computational demands and a lack of supporting tools.

Pomegranate peel, chokeberry leaves and Ironwort extract as novel natural inhibitors of amylin aggregation and cellular toxicity in pancreatic β cells.

Impeding or reducing human amylin aggregation and/or its toxicity can be key to preventing pancreatic islet amyloidosis and β-cell loss in patients with Type 2 Diabetes Mellitus (T2DM). Here, Punica granatum (pomegranate) peel, Sideritis raeseri (ironwort) and Aronia melanocarpa (chokeberry) leaf extracts, were tested for their novel anti-aggregative and antitoxic properties in human amylin (hIAPP) treated rat pancreatic insulinoma (INS) cells. The protein aggregation (Th-T) assay revealed an inhibitory trend of all three plant extracts against amylin aggregates.

DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools.

Long-read DNA sequencing has recently emerged as a powerful tool for studying both genetic and epigenetic architectures at single-molecule and single-nucleotide resolution. Long-read epigenetic studies encompass both the direct identification of native cytosine methylation as well as the identification of exogenously placed DNA -methyladenine (DNA-m6A). However, detecting DNA-m6A modifications using single-molecule sequencing, as well as co-processing single-molecule genetic and epigenetic architectures, is limited by computational demands and a lack of supporting tools.

Saccharomyces cerevisiae DNA polymerase IV overcomes Rad51 inhibition of DNA polymerase δ in Rad52-mediated direct-repeat recombination.

Saccharomyces cerevisiae DNA polymerase IV (Pol4) like its homolog, human DNA polymerase lambda (Polλ), is involved in Non-Homologous End-Joining and Microhomology-Mediated Repair. Using genetic analysis, we identified an additional role of Pol4 also in homology-directed DNA repair, specifically in Rad52-dependent/Rad51-independent direct-repeat recombination. Our results reveal that the requirement for Pol4 in repeat recombination was suppressed by the absence of Rad51, suggesting that Pol4 counteracts the Rad51 inhibition of Rad52-mediated repeat recombination events.

Evaluation of -methyldeoxyadenosine antibody-based genomic profiling in eukaryotes.

Low-level DNA -methyldeoxyadenosine (DNA-m6A) has recently been reported across various eukaryotes. Although anti-m6A antibody-based approaches are commonly used to measure DNA-m6A levels, this approach is known to be confounded by DNA secondary structures, RNA contamination, and bacterial contamination. To evaluate for these confounding features, we introduce an approach for systematically validating the selectivity of antibody-based DNA-m6A methods and use a highly selective anti-DNA-m6A antibody to reexamine patterns of DNA-m6A in , , and Our findings raise caution about the use of antibody-based methods for endogenous m6A quantification and mapping in eukaryotes.

Inducible degradation of dosage compensation protein DPY-27 facilitates isolation of Caenorhabditis elegans males for molecular and biochemical analyses.

Biological sex affects numerous aspects of biology, yet how sex influences different biological processes have not been extensively studied at the molecular level. Caenorhabditis elegans, with both hermaphrodites (functionally females as adults) and males, is an excellent system to uncover how sex influences physiology. Here, we describe a method to isolate large quantities of C.

The Relational Self-Schema Measure: Assessing Psychological Needs in Multiple Self-with-Other Representations.

Modern self-schema theory posits multiple representations in memory of the self, with each individual self-schema possessing associative connections to relational contexts (i.e., self-with-other).

Maternal exercise before and during pregnancy alleviates metabolic dysfunction associated with high-fat diet in pregnant mice, without significant changes in gut microbiota.

Although maternal exercise before and during pregnancy is beneficial, the effects of exercise on microbiota changes during pregnancy are unknown. Here we tested the hypothesis that maternal exercise before and during pregnancy would positively affect glucose homeostasis, pancreatic cell function, and gut microbiota dysbiosis in high-fat diet (HFD) fed dams. Female C57BL/6 mice were fed either a HFD or a low-fat diet (LFD) for 12 weeks.

Same-Day Discharge Following Laparoscopic Appendectomy for Uncomplicated Acute Appendicitis as a Measure of Quality in the Pediatric Population.

Background: Acute appendicitis remains the most common surgical emergency in children, with laparoscopic appendectomy (LA) now the standard of care. Same-day discharge (SD) after LA is both feasible and safe in children treated for uncomplicated appendicitis. This study aims to determine if SD following LA for children with uncomplicated appendicitis would improve the quality of care with respect to cost of treatment, patient satisfaction, and complications when compared with a cohort admitted postoperatively.

Tibiotalocalcaneal Arthrodesis Using Retrograde Intramedullary Nail Fixation: Comparison of Patients With and Without Diabetes Mellitus.

Retrograde intramedullary nailing for tibiotalocalcaneal arthrodesis is a salvage procedure reserved for severe cases of deformity. The aim of the present study was to compare the outcomes of this technique in patients with and without diabetes mellitus (DM). A total of 61 patients with and 56 without DM underwent retrograde intramedullary nailing and had a minimum follow-up period of 12 months.

State of the practice for pediatric surgery--career satisfaction and concerns. A report from the American Pediatric Surgical Association Task Force on Family Issues.

Background: There has been increasing interest and concern raised in the surgical literature regarding changes in the culture of surgical training and practice, and the impact these changes may have on surgeon stress and the appeal of a career in surgery. We surveyed pediatric surgeons and their partners to collect information on career satisfaction and work-family balance.

Methods: The American Pediatric Surgical Association Task Force on Family Issues developed separate survey instruments for both pediatric surgeons and their partners that requested demographic data and information regarding the impact of surgical training and practice on the surgeon's opportunity to be involved with his/her family.

Doxycycline sclerotherapy as primary treatment of head and neck lymphatic malformations in children.

Purpose: The authors report their experience with doxycycline sclerotherapy as primary treatment of head and neck lymphatic malformations (LMs) in children.

Methods: A retrospective chart review was used to collect data on 11 patients treated with doxycycline sclerotherapy for LMs of the head and neck at our institution since 2003. Radiographic imaging allowed classification of patient LM as macrocystic, microcystic, or mixed according to previously published guidelines.

Lymphangiogenesis in the developing lung promoted by VEGF-A.

Understanding the basic processes of late-stage pulmonary vascular development is essential as this period corresponds to the stage when preterm infants have increased chance of survival. During this period, refinement of the gas exchange unit leads to close apposition of the capillary vasculature and airway epithelium through thinning of the mesenchyme, formation of alveolar septae and functional adaptation of endothelial cells into vessels including pulmonary lymphatics. The pulmonary lymphatic network promotes efficient gas exchange through maintaining interstitial fluid balance.

Portal vein thrombosis after laparoscopic splenectomy: an ongoing clinical challenge.

Objectives: Portal vein thrombosis (PVT) following open splenectomy is a potentially lethal complication with an incidence of up to 6%. The objective of this report is to describe our management of a recent laparoscopic case, discuss current therapies, and consider antiplatelet therapy for prophylaxis.

Methods: Medical records, laboratory studies, and imaging studies pertaining to a recent case of a laparoscopic splenectomy were examined.

Laparoscopic femoral hernia repair using umbilical ligament as plug.

A novel technique for the laparoscopic repair of femoral hernia is described. An 11-year-old boy who had undergone previous open inguinal herniorrhaphy presented with a persistent bulge in the ipsilateral groin. At laparoscopic exploration, a small femoral hernia was discovered.

Mesenchymal expression of vascular endothelial growth factors D and A defines vascular patterning in developing lung.

The lung has specific vascular patterning requirements for effective gas exchange at birth, including alignment of airways and blood vessels and lymphatic vessels. Vascular endothelial growth factors (VEGF) are potent effectors of vascular development. We examined the temporal and spatial expression of VEGF-D and specific VEGF-A isoforms at each stage of lung development.

Characterisation of ISAV proteins from cell culture.

The characterisation of 2 infectious salmon anemia virus (ISAV) proteins is described. Proteins were harvested from ISAV-infected Chinook salmon embryo (CHSE)-214 cell culture by continuous elution denaturing gel electrophoresis, enabling the harvest of specific molecular weight fractions. Through the use of a polyclonal antiserum to ISAV, it was possible to identify a potentially autolytic major antigen of 72 kDa and a glycosylated protein of approximately 38 kDa which varied in size depending on cell line compatibility.

Polysaccharide biosynthesis locus required for virulence of Bacteroides fragilis.

Bacteroides fragilis, though only a minor component of the human intestinal commensal flora, is the anaerobe most frequently isolated from intra-abdominal abscesses. B. fragilis 9343 expresses at least three capsular polysaccharides-polysaccharide A (PS A), PS B, and PS C.

Inhibition of the transmembrane protein tyrosine phosphatase lar by 3S-peptide-I enhances insulin receptor phosphorylation in intact cells.

3S-peptide-I, a tris-sulfotyrosyl dodecapeptide that corresponds to the major autophosphorylation domain within the insulin receptor beta-subunit, selectively enhances insulin signal transduction by specifically inhibiting dephosphorylation of the insulin receptor catalyzed by protein tyrosine phosphatases (PTPases). Because of the potential role of the transmembrane PTPase LAR in the regulation of insulin signaling, we assessed the effect of 3S-peptide-I on recombinant LAR PTPase activity and in McA-RH7777 rat hepatoma cells overexpressing full-length LAR protein (McA4B/LAR). 3S-peptide-I significantly reduced insulin receptor dephosphorylation by recombinant LAR (p < 0.