Sex chromosomes are evolutionarily labile in many animals and sometimes fuse with autosomes, creating so-called neo-sex chromosomes. Fusions between sex chromosomes and autosomes have been proposed ...to reduce sexual conflict and to promote adaptation and reproductive isolation among species. Recently, advances in genomics have fuelled the discovery of such fusions across the tree of life. Here, we discovered multiple fusions leading to neo-sex chromosomes in the sapho subclade of the classical adaptive radiation of Heliconius butterflies. Heliconius butterflies generally have 21 chromosomes with very high synteny. However, the five Heliconius species in the sapho subclade show large variation in chromosome number ranging from 21 to 60. We find that the W chromosome is fused with chromosome 4 in all of them. Two sister species pairs show subsequent fusions between the W and chromosomes 9 or 14, respectively. These fusions between autosomes and sex chromosomes make Heliconius butterflies an ideal system for studying the role of neo-sex chromosomes in adaptive radiations and the degeneration of sex chromosomes over time. Our findings emphasize the capability of short-read resequencing to detect genomic signatures of fusion events between sex chromosomes and autosomes even when sex chromosomes are not explicitly assembled.
Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important species for bioconversion of organic material into animal feed. We generated a high-quality ...chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudochromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 16,478 protein-coding genes using the BRAKER2 pipeline. We analyzed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of the lab population by assessing runs of homozygosity. This provided evidence for inbreeding events including long runs of homozygosity on chromosome 5. The release of this novel chromosome-scale BSF genome assembly will provide an improved resource for further genomic studies, functional characterization of genes of interest and genetic modification of this economically important species.
Summary
Background
Tonsillectomy is one of the most common pediatric procedures in the United States. An optimal perioperative pain control regimen remains a challenge. Intravenous ibuprofen ...administered at induction of anesthesia may be a safe and efficacious option for postoperative tonsillectomy pain.
Objectives
To determine whether preoperative administration of intravenous ibuprofen (IV‐ibuprofen) can significantly decrease the number of doses of postoperative fentanyl when compared with placebo in pediatric tonsillectomy surgical patients.
Methods
This was a multicenter, randomized, double‐blind placebo‐controlled trial conducted at six hospitals in the United States. A total of 161 pediatric patients aged 6–17 years undergoing tonsillectomy were randomized to receive either a single preoperative dose of 10 mg·kg−1 IV‐ibuprofen or placebo (normal saline). Postoperative pain was managed with intravenous fentanyl (0.5 μg·kg−1) on an as needed basis when the visual analog scale (VAS) was >30 mm and deemed appropriate by recovery room nurse/physician. The primary endpoint was the number of doses and amount of postoperative fentanyl administered postoperatively for rescue analgesia.
Results
There was a significant reduction in the number of postoperative doses and the amount of fentanyl administered after surgery in the IV‐ibuprofen group compared with the placebo group (P = 0.021). There were no differences in the time to first analgesia request or the number of patients who required postoperative analgesia. There were no significant differences in the incidence of serious adverse events, surgical blood loss (P = 0.662), incidence of postoperative bleeding, or a need for surgical re‐exploration between the treatment groups.
Conclusion
Administration of IV‐ibuprofen, 10 mg·kg−1, significantly reduced fentanyl use in pediatric tonsillectomy patients.
We present spectroscopic redshifts for the first 466 X-ray- and radio-selected AGN targets in the 2 deg super(2) COSMOS field. Spectra were obtained with the IMACS instrument on the Magellan (Baade) ...telescope, using the nod-and-shuffle technique. We identify a variety of type 1 and type 2 AGNs, as well as red galaxies with no emission lines. Our redshift yield is 72% down to i sub(ab) = 24, although the yield is >90% for i sub(ab) < 22. We expect the completeness to increase as the survey continues. When our survey is complete and additional redshifts from the zCOSMOS project are included, we anticipate similar to 1100 AGNs with redshifts over the entire COSMOS field. Our redshift survey is consistent with an obscured AGN population that peaks at z similar to 0.7, although further work is necessary to disentangle the selection effects.
Over the past decade, there has been increasing interest in advanced secondary mobility aids for people with low vision, such as sensory substitution devices (SSDs) and electronic travelling aids ...(ETAs). However, these new modalities have not been able to reach end-users in significant numbers. We conducted an online survey to investigate the current uptake of mobility aids, as well as perspectives on emerging technologies from people with inherited retinal disease (IRD). The cross-sectional survey received 74 complete responses from Australians that self-reported as legally blind from IRD. Approximately half (57%) of respondents were aged over 55 years, with the cohort exhibiting above average education levels (with half holding a bachelor’s degree or above). Long canes (54%) are currently the most used primary mobility aids in this cohort. However, around half of the respondents have used ETAs or SSDs (51 %) for additional help. Respondents reported that their choice of mobility aid was often based on whether they were in a familiar or unfamiliar environment. Most respondents showed interest in SSDs, but were concerned about usability and aesthetics. This cohort of people living with IRD in Australia was interested in advanced technologies and showed willingness to try novel mobility aids if the device was easy to use and the quality of training was guaranteed. Respondents indicated a preference for devices which were portable, and had a minimally intrusive form-factor. Our results can inform the research and development of emerging assistive devices. They serve as valuable guidance for selecting aids tailored to the needs of individuals with visual impairments. Future assessments on the effectiveness of low vision aids should include not only the functional improvement, but also participant-reported assessments regarding usability and portability, as these aspects dictate integration of the device into regular use.
We present optical spectroscopy for an X-ray and optical flux-limited sample of 677 XMM-Newton selected targets covering the 2 deg2 Cosmic Evolution Survey field, with a yield of 485 high-confidence ...redshifts. The majority of the spectra were obtained over three seasons (2005-2007) with the Inamori Magellan Areal Camera and Spectrograph instrument on the Magellan (Baade) telescope. We also include in the sample previously published Sloan Digital Sky Survey spectra and supplemental observations with MMT/Hectospec. We detail the observations and classification analyses. The survey is 90% complete to flux limits of f 0.5-10 keV > 8 X 10-16 erg cm-2 s-1 and i + AB < 22, where over 90% of targets have high-confidence redshifts. Making simple corrections for incompleteness due to redshift and spectral type allows for a description of the complete population to i + AB < 23. The corrected sample includes a 57% broad emission line (Type 1, unobscured) active galactic nucleus (AGN) at 0.13 < z < 4.26, 25% narrow emission line (Type 2, obscured) AGN at 0.07 < z < 1.29, and 18% absorption line (host-dominated, obscured) AGN at 0 < z < 1.22 (excluding the stars that made up 4% of the X-ray targets). We show that the survey's limits in X-ray and optical fluxes include nearly all X-ray AGNs (defined by L 0.5-10 keV > 3 X 1042 erg s-1) to z < 1, of both optically obscured and unobscured types. We find statistically significant evidence that the obscured-to-unobscured AGN ratio at z < 1 increases with redshift and decreases with luminosity.
With a retinal prosthesis connected to a head-mounted camera, subjects can perform low vision tasks using a combination of electrode discrimination and head-directed localization. The objective of ...the present study was to investigate the contribution of retinotopic electrode discrimination (perception corresponding to the arrangement of the implanted electrodes with respect to their position beneath the retina) to visual performance for three recipients of a 24-channel suprachoroidal retinal implant. Proficiency in retinotopic discrimination may allow good performance with smaller head movements, and identification of this ability would be useful for targeted rehabilitation.
Three participants with retinitis pigmentosa performed localization and grating acuity assessments using a suprachoroidal retinal prosthesis. We compared retinotopic and nonretinotopic electrode mapping and hypothesized that participants with measurable acuity in a normal retinotopic condition would be negatively impacted by the nonretinotopic condition. We also expected that participants without measurable acuity would preferentially use head movement over retinotopic information.
Only one participant was able to complete the grating acuity task. In the localization task, this participant exhibited significantly greater head movements and significantly lower localization scores when using the nonretinotopic electrode mapping. There was no significant difference in localization performance or head movement for the remaining two subjects when comparing retinotopic to nonretinotopic electrode mapping.
Successful discrimination of retinotopic information is possible with a suprachoroidal retinal prosthesis. Head movement behavior during a localization task can be modified using a nonretinotopic mapping. Behavioral comparisons using retinotopic and nonretinotopic electrode mapping may be able to highlight deficiencies in retinotopic discrimination, with a view to address these deficiencies in a rehabilitation environment. (ClinicalTrials.gov number, NCT01603576).
Translational research in vision prosthetics, gene therapy, optogenetics, stem cell and other forms of transplantation, and sensory substitution is creating new therapeutic options for patients with ...neural forms of blindness. The technical challenges faced by each of these disciplines differ considerably, but they all face the same challenge of how to assess vision in patients with ultra-low vision (ULV), who will be the earliest subjects to receive new therapies. Historically, there were few tests to assess vision in ULV patients. In the 1990s, the field of visual prosthetics expanded rapidly, and this activity led to a heightened need to develop better tests to quantify end points for clinical studies. Each group tended to develop novel tests, which made it difficult to compare outcomes across groups. The common lack of validation of the tests and the variable use of controls added to the challenge of interpreting the outcomes of these clinical studies. In 2014, at the bi-annual International "Eye and the Chip" meeting of experts in the field of visual prosthetics, a group of interested leaders agreed to work cooperatively to develop the International Harmonization of Outcomes and Vision Endpoints in Vision Restoration Trials (HOVER) Taskforce. Under this banner, more than 80 specialists across seven topic areas joined an effort to formulate guidelines for performing and reporting psychophysical tests in humans who participate in clinical trials for visual restoration. This document provides the complete version of the consensus opinions from the HOVER taskforce, which, together with its rules of governance, will be posted on the website of the Henry Ford Department of Ophthalmology (www.artificialvision.org). Research groups or companies that choose to follow these guidelines are encouraged to include a specific statement to that effect in their communications to the public. The Executive Committee of the HOVER Taskforce will maintain a list of all human psychophysical research in the relevant fields of research on the same website to provide an overview of methods and outcomes of all clinical work being performed in an attempt to restore vision to the blind. This website will also specify which scientific publications contain the statement of certification. The website will be updated every 2 years and continue to exist as a living document of worldwide efforts to restore vision to the blind. The HOVER consensus document has been written by over 80 of the world's experts in vision restoration and low vision and provides recommendations on the measurement and reporting of patient outcomes in vision restoration trials.
ABSTRACT
Background
Diploid genome assembly is typically impeded by heterozygosity because it introduces errors when haplotypes are collapsed into a consensus sequence. Trio binning offers an ...innovative solution that exploits heterozygosity for assembly. Short, parental reads are used to assign parental origin to long reads from their F1 offspring before assembly, enabling complete haplotype resolution. Trio binning could therefore provide an effective strategy for assembling highly heterozygous genomes, which are traditionally problematic, such as insect genomes. This includes the wood tiger moth (Arctia plantaginis), which is an evolutionary study system for warning colour polymorphism.
Findings
We produced a high-quality, haplotype-resolved assembly for Arctia plantaginis through trio binning. We sequenced a same-species family (F1 heterozygosity ∼1.9%) and used parental Illumina reads to bin 99.98% of offspring Pacific Biosciences reads by parental origin, before assembling each haplotype separately and scaffolding with 10X linked reads. Both assemblies are contiguous (mean scaffold N50: 8.2 Mb) and complete (mean BUSCO completeness: 97.3%), with annotations and 31 chromosomes identified through karyotyping. We used the assembly to analyse genome-wide population structure and relationships between 40 wild resequenced individuals from 5 populations across Europe, revealing the Georgian population as the most genetically differentiated with the lowest genetic diversity.
Conclusions
We present the first invertebrate genome to be assembled via trio binning. This assembly is one of the highest quality genomes available for Lepidoptera, supporting trio binning as a potent strategy for assembling heterozygous genomes. Using our assembly, we provide genomic insights into the geographic population structure of A. plantaginis.
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