Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.

Improvements in genome sequencing and assembly are enabling high-quality reference genomes for all species. However, the assembly process is still laborious, computationally and technically demanding, lacks standards for reproducibility, and is not readily scalable. Here we present the latest Vertebrate Genomes Project assembly pipeline and demonstrate that it delivers high-quality reference genomes at scale across a set of vertebrate species arising over the last ~500 million years. The pipeline is versatile and combines PacBio HiFi long-reads and Hi-C-based haplotype phasing in a new graph-based paradigm. Standardized quality control is performed automatically to troubleshoot assembly issues and assess biological complexities. We make the pipeline freely accessible through Galaxy, accommodating researchers even without local computational resources and enhanced reproducibility by democratizing the training and assembly process. We demonstrate the flexibility and reliability of the pipeline by assembling reference genomes for 51 vertebrate species from major taxonomic groups (fish, amphibians, reptiles, birds, and mammals).

Structural basis for an unprecedented enzymatic alkylation in cylindrocyclophane biosynthesis.

The cyanobacterial enzyme CylK assembles the cylindrocyclophane natural products by performing two unusual alkylation reactions, forming new carbon-carbon bonds between aromatic rings and secondary alkyl halide substrates. This transformation is unprecedented in biology, and the structure and mechanism of CylK are unknown. Here, we report X-ray crystal structures of CylK, revealing a distinctive fusion of a Ca2+-binding domain and a ß-propeller fold. We use a mutagenic screening approach to locate CylK's active site at its domain interface, identifying two residues, Arg105 and Tyr473, that are required for catalysis. Anomalous diffraction datasets collected with bound bromide ions, a product analog, suggest that these residues interact with the alkyl halide electrophile. Additional mutagenesis and molecular dynamics simulations implicate Asp440 in activating the nucleophilic aromatic ring. Bioinformatic analysis of CylK homologs from other cyanobacteria establishes that they conserve these key catalytic amino acids, but they are likely associated with divergent reactivity and altered secondary metabolism. By gaining a molecular understanding of this unusual biosynthetic transformation, this work fills a gap in our understanding of how alkyl halides are activated and used by enzymes as biosynthetic intermediates, informing enzyme engineering, catalyst design, and natural product discovery.

Using social autopsy to understand maternal, newborn, and child mortality in low-resource settings: a systematic review of the literature.

BACKGROUND: Social, cultural, and behavioral factors are often potent upstream contributors to maternal, neonatal, and child mortality, especially in low- and middle-income countries (LMICs). Social autopsy is one method of identifying the impact of such factors, yet it is unclear how social autopsy methods are being used in LMICs. OBJECTIVE: This study aimed to identify the most common social autopsy instruments, describe overarching findings across populations and geography, and identify gaps in the existing social autopsy literature. METHODS: A systematic search of the peer-reviewed literature from 2005 to 2016 was conducted. Studies were included if they were conducted in an LMIC, focused on maternal/neonatal/infant/child health, reported on the results of original research, and explicitly mentioned the use of a social autopsy tool. RESULTS: Sixteen articles out of 1950 citations were included, representing research conducted in 11 countries. Five different tools were described, with two primary conceptual frameworks used to guide analysis: Pathway to Survival and Three Delays models. Studies varied in methods for identifying deaths, and recall periods for respondents ranged from 6 weeks to 5+ years. Across studies, recognition of danger signs appeared to be high, while subsequent care-seeking was inconsistent. Cost, distance to facility, and transportation issues were frequently cited barriers to care-seeking, however, additional barriers were reported that varied by location. Gaps in the social autopsy literature include the lack of: harmonized tools and analytical methods that allow for cross-study comparisons, discussion of complexity of decision making for care seeking, qualitative narratives that address inconsistencies in responses, and the explicit inclusion of perspectives from husbands and fathers. CONCLUSION: Despite the nascence of the field, research across 11 countries has included social autopsy methods, using a variety of tools, sampling methods, and analytical frameworks to determine how social factors impact maternal, neonatal, and child health outcomes.

Efficacy of fenbendazole and levamisole treatments in captive Houston toads (Bufo [Anaxyrus] houstonensis).

Effective disease monitoring and prevention is critical to the success of captive amphibian care. Nematodes, including the genera Rhabdias and Strongyloides, are known to contribute to mortality in captive amphibians and have been identified in the Houston Zoo's endangered Houston toad (Bufo [Anaxyrus] houstonensis) captive assurance colony. Five years of fecal data for the toad colony were compiled and analyzed in order to investigate the efficacy of two anthelminthic medications, fenbendazole (FBZ) and levamisole (LMS), which were used to control nematode infections. Both FBZ (dusted onto food items) and topical LMS (6.5 to 13.5 mg/kg) significantly reduced the number of nematode eggs, larvae, and adults observed by fecal parasitologic examination. There were no significant differences between treatments, and egg reappearance periods were difficult to compare as a result of low sample size. No adverse effects from either anthelminthic treatment were observed. Both topical LMS and oral FBZ appear to be safe and efficacious treatments for the reduction of the internal nematode burden in captive Houston toads.

Yuri gagarin is required for actin, tubulin and basal body functions in Drosophila spermatogenesis.

Males of the genus Drosophila produce sperm of remarkable length. Investigation of giant sperm production in Drosophila melanogaster has demonstrated that specialized actin and microtubule structures play key roles. The gene yuri gagarin (yuri) encodes a novel protein previously identified through its role in gravitaxis. A male-sterile mutation of yuri has revealed roles for Yuri in the functions of the actin and tubulin structures of spermatogenesis. Yuri is a component of the motile actin cones that individualize the spermatids and is essential for their formation. Furthermore, Yuri is required for actin accumulation in the dense complex, a microtubule-rich structure on the sperm nuclei thought to strengthen the nuclei during elongation. In the yuri mutant, late clusters of syncytial nuclei are deformed and disorganized. The basal bodies are also mispositioned on the nuclei, and the association of a specialized structure, the centriolar adjunct (CA), with the basal body is lost. Some of these nuclear defects might underlie a further unexpected abnormality: sperm nuclei occasionally locate to the wrong ends of the spermatid cysts. The structure of the axonemes that grow out from the basal bodies is affected in the yuri mutant, suggesting a possible role for the CA in axoneme formation.

Strategic planning for post-disaster temporary housing.

Temporary housing programmes suffer from excessively high cost, late delivery, poor location, improper unit designs and other inherent issues. These issues can be attributed in part to a prevalence of ad hoc tactical planning, rather than pre-disaster strategic planning, for reconstruction undertaken by governments and non-governmental organisations (NGOs) in the chaotic post-disaster environment. An analysis of the process and outcomes from six case studies of temporary housing programmes after disasters in Turkey and Colombia in 1999, Japan in 1995, Greece in 1986, Mexico in 1985, and Italy in 1976 yields information about the extent to which strategic planning is employed in temporary housing programmes, as well as common issues in temporary housing. Based on an understanding of these common issues, this paper proposes a framework for strategic planning for temporary housing that identifies organisational designs and available resources for temporary housing before the disaster, but allows modifications to fit the specific post-disaster situation.