Bradysia (Sciara) coprophila larvae up-regulate DNA repair pathways and down-regulate developmental regulators in response to ionizing radiation.

The level of resistance to radiation and the developmental and molecular responses can vary between species, and even between developmental stages of one species. For flies (order: Diptera), prior studies concluded that the fungus gnat Bradysia (Sciara) coprophila (sub-order: Nematocera) is more resistant to irradiation-induced mutations that cause visible phenotypes than the fruit fly Drosophila melanogaster (sub-order: Brachycera). Therefore, we characterized the effects of and level of resistance to ionizing radiation on B.

Correction: Yamamoto, Y.; Gerbi, S.A. Development of Transformation for Genome Editing of an Emerging Model Organism. 2022, , 1108.

There was a typographical error in the original publication [...

Development of Transformation for Genome Editing of an Emerging Model Organism.

With the advances in genomic sequencing, many organisms with novel biological properties are ripe for use as emerging model organisms. However, to make full use of them, transformation methods need to be developed to permit genome editing. Here, we present the development of transformation for the fungus fly () ; this may serve as a paradigm for the development of transformation for other emerging systems, especially insects.

High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing.

Background: The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination in Sciara was the first observation of imprinting, though the mechanism remains a mystery.

Anatomy and evolution of a DNA replication origin.

DNA amplification occurs at the DNA puff II/9A locus in the fungus fly Sciara coprophila. As a foundation to study the molecular mechanism for the initiating events of II/9A DNA re-replication, we have sequenced 14 kb spanning a DNase hypersensitive site (DHS) upstream of the 1 kb amplification origin and through transcription units II/9-1 and II/9-2 downstream of the origin. These elements are annotated as well as the ORC binding site at the origin and the transition point (TP) between continuous and discontinuous DNA syntheses that marks the origin of bidirectional replication at the nucleotide level.

Accuracy and comparison of two rapid multiplex PCR tests for gastroenteritis pathogens: a systematic review and meta-analysis.

Objectives: The primary aim is to provide a summary of evidence for the diagnostic accuracies of multiplex PCR gastrointestinal (GI) panels-BioFire FilmArray and Luminex xTAG on the detection of gastroenteritis pathogens. The secondary aim is to compare the performance of these GI panels head to head.

Methods: A comprehensive search up to 1 December 2019 was conducted on PubMed, Embase, Ovid Medline and Web of Science for studies that used FilmArray or Luminex xTAG Gastrointestinal Pathogen Panel (GPP) for diagnosis of acute gastroenteritis.

Heterogeneity of outcomes for intraoperative music interventions: a scoping review and evidence map.

Background: Over the past 30 years, numerous studies have been performed that assess the efficacy of intraoperative music as an adjunctive means to regional and local anaesthesia to improve clinical outcomes. Despite an emerging body of evidence and growing adoption of music in surgical settings, the variety of interventions studied, and the heterogeneity of outcomes and outcome measurement tools applied makes difficult the task of aggregating evidence.

Objective: This study assesses the state of the field of intraoperative musical interventions by documenting and visualising the breadth of outcomes measured in studies.

Left atrial cross-sectional area is a novel measure of atrial shape associated with cardioembolic strokes.

Objective: Cardioembolic (CE) stroke carries significant morbidity and mortality. Left atrial (LA) size has been associated with CE risk. We hypothesised that differential LA remodelling impacts on pathophysiological mechanism of major CE strokes.

Perspectives on Wnt Signal Pathway in the Pathogenesis and Therapeutics of Chronic Obstructive Pulmonary Disease.

Chronic obstructive pulmonary disease (COPD) is a chronic lung disease with progressive airflow limitation and functional decline. The pathogenic mechanisms for this disease include oxidative stress, inflammatory responses, disturbed protease/antiprotease equilibrium, apoptosis/proliferation imbalance, senescence, autophagy, metabolic reprogramming, and mitochondrial dysfunction. The Wnt signaling pathway is an evolutionarily conserved signaling pathway that is abnormal in COPD, including chronic bronchitis and pulmonary emphysema.

Making ends meet: targeted integration of DNA fragments by genome editing.

Targeted insertion of large pieces of DNA is an important goal of genetic engineering. However, this goal has been elusive since classical methods for homology-directed repair are inefficient and often not feasible in many systems. Recent advances are described here that enable site-specific genomic insertion of relatively large DNA with much improved efficiency.

Universal and domain-specific sequences in 23S-28S ribosomal RNA identified by computational phylogenetics.

Comparative analysis of ribosomal RNA (rRNA) sequences has elucidated phylogenetic relationships. However, this powerful approach has not been fully exploited to address ribosome function. Here we identify stretches of evolutionarily conserved sequences, which correspond with regions of high functional importance.

Whole Organism Genome Editing: Targeted Large DNA Insertion via ObLiGaRe Nonhomologous End-Joining in Vivo Capture.

Targeted gene insertion is a goal of genome editing and has been performed in cultured cells but only in a handful of whole organisms. The existing method to integrate foreign DNA using the homologous recombination pathway is inherently low efficiency, and many systems are refractory to this method. Several additional manipulations have been developed to gain greater efficiency by suppressing the competing dominant repair pathway of nonhomologous end-joining.

Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins.

Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (λ-exo) to efficiently digest parental DNA while leaving RNA-primer protected nascent strands intact. We used genomics and biochemical approaches to determine if λ-exo digests all parental DNA sequences equally.

Mullerian inhibiting substance levels at the time of HCG administration in IVF cycles predict both ovarian reserve and embryo morphology.

Background: Pre-antral and early antral follicles secrete Müllerian inhibiting substance (MIS), suggesting that MIS may directly reflect ovarian reserve. Since little is known about how ovarian reserve affects oocyte quality, we attempt here to assess the predictive value of MIS on embryo morphology and IVF outcome. To do so, we measured MIS at the time of HCG administration 36 h prior to oocyte retrieval.

Initiation of DNA replication in multicellular eukaryotes.

Three questions central to understanding the initiation of DNA replication in eukaryotes are: (1) Does DNA synthesis begin at a defined place? (2) What determines replication initiation sites? (3) What regulates an origin to fire only once per cell cycle? A key player in this is the origin recognition complex (ORC), required for assembly of the pre-replication complex (pre-RC), that is converted later to the initiation complex (IC). In both yeast ARS1 and DNA puff II/9A of the metazoan fly Sciara, there is a defined start site of replication adjacent to an ORC-binding site. Although ORC has some inherent preference for certain DNA sequences, other factors may also modulate its binding to DNA.

Developmental changes in the Sciara II/9A initiation zone for DNA replication.

Developmentally regulated initiation of DNA synthesis was studied in the fly Sciara at locus II/9A. PCR analysis of nascent strands revealed an initiation zone that spans approximately 8 kb in mitotic embryonic cells and endoreplicating salivary glands but contracts to 1.2 to 2.

Maintenance of the DNA puff expanded state is independent of active replication and transcription.

The maintenance of the expanded state of DNA puffs II/2B and II/9A in polytene chromosomes from stage 14 x 7 Sciara coprophila salivary glands was assayed after inhibition of RNA synthesis, DNA synthesis, or both processes together. Heat shock conditions were established in order to inhibit transcription. Polypeptides of Mr 72,000 and 36,000 were produced in Sciara after heat shock.

Changes in 7SL RNA conformation during the signal recognition particle cycle.

The structure of 7SL RNA has been probed by chemical modification followed by primer extension, using four substrates: (i) naked 7SL RNA; (ii) free signal recognition particle (SRP); (iii) polysome bound SRP; and (iv) membrane bound SRP. Decreasing sensitivity to chemical modification between these different substrates suggests regions on 7SL RNA that: bind proteins associated with SRP might interact with ribosomes; and are protected by binding to membranes. Other areas increase in chemical sensitivity, exemplified by a tertiary interaction present in naked 7SL RNA but not in free SRP.

Splenic artery ligation for splenic salvage: clinical experience and immune function.

Documentation of overwhelming post-splenectomy sepsis, characterized by infection from encapsulated organisms, has led to development of surgical techniques for preservation of the injured spleen to maintain splenic clearance of encapsulated, opsonized organisms from the circulation. In this study splenic artery ligation (SAL) was performed as an adjunct to successful splenorrhaphy in 20 adults suffering blunt splenic injury. There were no deaths and no reoperations.