Semaphorin-Plexin Signaling Guides Patterning of the Developing Vasculature

AbstractMajor vessels of the vertebrate circulatory system display evolutionarily conserved and reproducible anatomy, but the cues guiding this stereotypic patterning remain obscure. In the nervous system, axonal pathways are shaped by repulsive cues provided by ligands of the semaphorin family that are sensed by migrating neuronal growth cones through plexin receptors. We show that proper blood vessel pathfinding requires the endothelial receptor PlexinD1 and semaphorin signals, and we identify mutations in plexinD1 in the zebrafish vascular patterning mutant out of bounds. These results reveal the fundamental conservation of repulsive patterning mechanisms between axonal migration in the central nervous system and vascular endothelium during angiogenesis

Use of sonic tomography to detect and quantify wood decay in living trees.

Premise of the studyField methodology and image analysis protocols using acoustic tomography were developed and evaluated as a tool to estimate the amount of internal decay and damage of living trees, with special attention to tropical rainforest trees with irregular trunk shapes.Methods and resultsLiving trunks of a diversity of tree species in tropical rainforests in the Republic of Panama were scanned using an Argus Electronic PiCUS 3 Sonic Tomograph and evaluated for the amount and patterns of internal decay. A protocol using ImageJ analysis software was used to quantify the proportions of intact and compromised wood. The protocols provide replicable estimates of internal decay and cavities for trees of varying shapes, wood density, and bark thickness.ConclusionsSonic tomography, coupled with image analysis, provides an efficient, noninvasive approach to evaluate decay patterns and structural integrity of even irregularly shaped living trees

Can current national surveillance systems in England and Wales monitor sexual transmission of hepatitis C among HIV-infected men who have sex with men?

BACKGROUND: Recent reports suggest an increase in sexually-transmitted hepatitis C infection among HIV-infected men who have sex with men (MSM) in European cities. We investigated whether current national surveillance systems in England and Wales (E&W) are able to monitor sexual transmission of hepatitis C infection among HIV-infected MSM. METHODS: Routine laboratory reports of hepatitis C diagnoses and data from sentinel hepatitis C testing surveillance were matched to HIV diagnosis reports to determine: (i) the number of MSM diagnosed with HIV and hepatitis C (1996–2003); (ii) the number of HIV-diagnosed MSM tested for hepatitis C and found to be positive at sentinel sites (2003). RESULTS: (i) Between 1996–2003, 38,027 hepatitis C diagnoses were reported; 25,938 (68%) were eligible for matching with HIV diagnoses. Thirty-one men (four in London) had both a HIV and hepatitis C diagnosis where the only risk was sex with another man. Numbers of "co-diagnosed" MSM increased from 0 in 1996 to 14 in 2003. The majority of MSM (22/31) tested hepatitis C positive after HIV diagnosis. (ii) Of 78,058 test results from sentinel hepatitis C testing sites in 2003, 67,712 (87%) were eligible for matching with HIV diagnoses. We identified 242 HIV-diagnosed MSM who did not inject drugs who tested for hepatitis C in 2003; 11 (4.5%) tested hepatitis C positive (95%CI: 2.3%–8.0%). Applying this percentage to all MSM seen for HIV-related care in E&W in 2003, an estimated 680 MSM living with diagnosed HIV would have tested positive for sexually-transmitted hepatitis C (95%CI: 346–1208). CONCLUSION: Matching routine laboratory reports of hepatitis C diagnoses with HIV diagnoses only identified 31 HIV infected MSM with sexually-transmitted hepatitis C infection. Clinical studies suggest that this is an underestimate. On the other hand, matching sentinel surveillance reports with HIV diagnoses revealed that in E&W in 2003 nearly 5% of HIV-diagnosed MSM tested hepatitis C positive where the only risk was sex with another man. Reports of sexually-transmitted hepatitis C infection were not confined to London. Enhanced surveillance is needed to monitor sexually-transmitted hepatitis C among HIV-infected MSM in E&W

Gymnastic-Based Movement Therapy for Children With Neurodevelopmental Disabilities: Results From a Pilot Feasibility Study

Background: Developmental and behavioral issues often limit the participation of children with neurodevelopmental disabilities (NDD) in community-based activities with their peers, which decreases opportunities for their social learning and development. Parents of children with NDD seek out programs that address physical and psychosocial development. Several studies already support the positive effects for the child to attend physical activity programs (PAPs). However, these studies are highly prone to biases and Hawthorne effect. In the planning stage of a large prospective study to assess the effectiveness of PAPs we reviewed the records of children who participated in a gymnastic-based program, the Empowering Steps Movement Therapy (ESMT). Besides generating useful data for developing the prospective study we thought these data reflect the rate of changes in context of normal practice in a naturalistic environment; therefore protected from Hawthorne effect and other biases.Design: This is a historical cohort: the files of 67 children with NDD were examined across a 2-year period (Jan 2011 to Jan 2013). As part of standard practice, the ESMT therapists document changes in motor function every 6 months, using the ESMT's proprietary motor scale. Parents also completed a parental questionnaire in June 2011 regarding their perceptions of changes in their child's physical and psychosocial function, as well as family functioning since their child started the program.Results: Linear Mixed Effects Model clearly identified three groups according to changes in motor function: the ones with rapid changes (mostly functional children with autism spectrum disorder: n = 13), the ones with moderate changes (different types of NDD diagnoses: n = 41) and the ones that did not change or even decreased motor skills over the follow-up (children with complex diseases or uncontrolled epilepsy despite treatment: n = 13). Parental questionnaires (n = 39) reported improvement in most of the children's physical and psychosocial abilities; they also indicated improvement in some of the family parameters. There was no association between the changes in children's motor functions and parents' responses to the questionnaire.Conclusion: Despite limitations due to the retrospective nature of the study, the absence of a control group and the absence of validated measurement tools, the observed positive effects of attending movement therapy center on motor performance and psychosocial development confirm in a naturalistic environment what has been shown in context of clinical trials or quasi-experimental studies. These results are not conclusive. They warrant further, rigorous investigation using validated instruments, independent assessors, and control groups

Methods for specifying the target difference in a randomised controlled trial : the Difference ELicitation in TriAls (DELTA) systematic review

Peer reviewedPublisher PD

Simple PCR Assays Improve the Sensitivity of HIV-1 Subtype B Drug Resistance Testing and Allow Linking of Resistance Mutations

The success of antiretroviral therapy is known to be compromised by drug-resistant HIV-1 at frequencies detectable by conventional bulk sequencing. Currently, there is a need to assess the clinical consequences of low-frequency drug resistant variants occurring below the detection limit of conventional genotyping. Sensitive detection of drug-resistant subpopulations, however, requires simple and practical methods for routine testing.We developed highly-sensitive and simple real-time PCR assays for nine key drug resistance mutations and show that these tests overcome substantial sequence heterogeneity in HIV-1 clinical specimens. We specifically used early wildtype virus samples from the pre-antiretroviral drug era to measure background reactivity and were able to define highly-specific screening cut-offs that are up to 67-fold more sensitive than conventional genotyping. We also demonstrate that sequencing the mutation-specific PCR products provided a direct and novel strategy to further detect and link associated resistance mutations, allowing easy identification of multi-drug-resistant variants. Resistance mutation associations revealed in mutation-specific amplicon sequences were verified by clonal sequencing.Combined, sensitive real-time PCR testing and mutation-specific amplicon sequencing provides a powerful and simple approach that allows for improved detection and evaluation of HIV-1 drug resistance mutations

A pleiotropic missense variant in SLC39A8 is associated with Crohn's disease and human gut microbiome composition

Genome-wide association studies have identified 200 inflammatory bowel disease (IBD) loci, but the genetic architecture of Crohn's disease (CD) and ulcerative colitis remain incompletely defined. Here, we aimed to identify novel associations between IBD and functional genetic variants using the Illumina ExomeChip (San Diego, CA)

A spatially resolved analysis of star-formation burstiness by comparing UV and Hα\alpha in galaxies at z∼\sim1 with UVCANDELS

The UltraViolet imaging of the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey Fields (UVCANDELS) program provides HST/UVIS F275W imaging for four CANDELS fields. We combine this UV imaging with existing HST/near-IR grism spectroscopy from 3D-HST+AGHAST to directly compare the resolved rest-frame UV and H$\alpha$ emission for a sample of 979 galaxies at $0.7<z<1.5$ spanning a range in stellar mass of $10^{8-11.5}~M_\odot$. Since both rest-UV and H$\alpha$ are sensitive to on-going star-formation but over different timescales, their resolved comparison allows us to infer the burstiness in star-formation as a function of galaxy structural parameters. We generate homogenized maps of rest-UV and H$\alpha$ emission for all galaxies in our sample and stack them to compute the average UV-to-H$\alpha$ luminosity ratio as a function of galactocentric radius. We find that galaxies below stellar mass of $\sim10^{9.5}~M_\odot$, at all radii, have a UV-to-H$\alpha$ ratio higher than the equilibrium value expected from constant star-formation, indicating a significant contribution from bursty star-formation. Even for galaxies with stellar mass $\gtrsim10^{9.5} M_\odot$, the UV-to-H$\alpha$ ratio is elevated towards in their outskirts ($R/R_{eff}>1.5$), suggesting that bursty star-formation is likely prevalent in the outskirts of even the most massive galaxies but is likely over-shadowed by their brighter cores. Furthermore, we present the UV-to-H$\alpha$ ratio as a function of galaxy surface brightness, a proxy for stellar mass surface density, and find that regions below $\sim10^8~M_\odot~kpc^{-2}$ are consistent with bursty star-formation, regardless of their galaxy stellar mass, potentially suggesting that local star-formation is independent of global galaxy properties at the smallest scales.Comment: 19 pages, 8 figures; submitted to Ap

Developing a community-based genetic nomenclature for anole lizards

Background: Comparative studies of amniotes have been hindered by a dearth of reptilian molecular sequences. With the genomic assembly of the green anole, Anolis carolinensis available, non-avian reptilian genes can now be compared to mammalian, avian, and amphibian homologs. Furthermore, with more than 350 extant species in the genus Anolis, anoles are an unparalleled example of tetrapod genetic diversity and divergence. As an important ecological, genetic and now genomic reference, it is imperative to develop a standardized Anolis gene nomenclature alongside associated vocabularies and other useful metrics. Results: Here we report the formation of the Anolis Gene Nomenclature Committee (AGNC) and propose a standardized evolutionary characterization code that will help researchers to define gene orthology and paralogy with tetrapod homologs, provide a system for naming novel genes in Anolis and other reptiles, furnish abbreviations to facilitate comparative studies among the Anolis species and related iguanid squamates, and classify the geographical origins of Anolis subpopulations. Conclusions: This report has been generated in close consultation with members of the Anolis and genomic research communities, and using public database resources including NCBI and Ensembl. Updates will continue to be regularly posted to new research community websites such as lizardbase. We anticipate that this standardized gene nomenclature will facilitate the accessibility of reptilian sequences for comparative studies among tetrapods and will further serve as a template for other communities in their sequencing and annotation initiatives.Organismic and Evolutionary BiologyOther Research Uni

The Lyman Continuum Escape Fraction of Star-forming Galaxies at 2.4≲z≲3.72.4\lesssim z\lesssim3.7 from UVCANDELS

The UltraViolet Imaging of the Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey Fields (UVCANDELS) survey is a Hubble Space Telescope (HST) Cycle-26 Treasury Program, allocated in total 164 orbits of primary Wide-Field Camera 3 Ultraviolet and Visible light F275W imaging with coordinated parallel Advanced Camera for Surveys F435W imaging, on four of the five premier extragalactic survey fields: GOODS-N, GOODS-S, EGS, and COSMOS. We introduce this survey by presenting a thorough search for galaxies at $z\gtrsim2.4$ that leak significant Lyman continuum (LyC) radiation, as well as a stringent constraint on the LyC escape fraction ($f_{\rm esc}$) from stacking the UV images of a population of star-forming galaxies with secure redshifts. Our extensive search for LyC emission and stacking analysis benefit from the catalogs of high-quality spectroscopic redshifts compiled from archival ground-based data and HST slitless spectroscopy, carefully vetted by dedicated visual inspection efforts. We report a sample of five galaxies as individual LyC leaker candidates, showing $f_{\rm esc}^{\rm rel}\gtrsim60\%$ estimated using detailed Monte Carlo analysis of intergalactic medium attenuation. We develop a robust stacking method to apply to five samples of in total 85 non-detection galaxies in the redshift range of $z\in[2.4,3.7]$. Most stacks give tight 2-$\sigma$ upper limits below $f_{\rm esc}^{\rm rel}<6\%$. A stack for a subset of 32 emission-line galaxies shows tentative LyC leakage detected at 2.9-$\sigma$, indicating $f_{\rm esc}^{\rm rel}=5.7\%$ at $z\sim2.65$, supporting the key role of such galaxies in contributing to the cosmic reionization and maintaining the UV ionization background. These new F275W and F435W imaging mosaics from UVCANDELS have been made publicly available on the Barbara A. Mikulski Archive for Space Telescopes.Comment: 33 pages, 21 figures, and 5 tables. Resubmitted after addressing the referee repor