Extensive population genetic structure in the giraffe

<p>Abstract</p> <p>Background</p> <p>A central question in the evolutionary diversification of large, widespread, mobile mammals is how substantial differentiation can arise, particularly in the absence of topographic or habitat barriers to dispersal. All extant giraffes (<it>Giraffa camelopardalis</it>) are currently considered to represent a single species classified into multiple subspecies. However, geographic variation in traits such as pelage pattern is clearly evident across the range in sub-Saharan Africa and abrupt transition zones between different pelage types are typically not associated with extrinsic barriers to gene flow, suggesting reproductive isolation.</p> <p>Results</p> <p>By analyzing mitochondrial DNA sequences and nuclear microsatellite loci, we show that there are at least six genealogically distinct lineages of giraffe in Africa, with little evidence of interbreeding between them. Some of these lineages appear to be maintained in the absence of contemporary barriers to gene flow, possibly by differences in reproductive timing or pelage-based assortative mating, suggesting that populations usually recognized as subspecies have a long history of reproductive isolation. Further, five of the six putative lineages also contain genetically discrete populations, yielding at least 11 genetically distinct populations.</p> <p>Conclusion</p> <p>Such extreme genetic subdivision within a large vertebrate with high dispersal capabilities is unprecedented and exceeds that of any other large African mammal. Our results have significant implications for giraffe conservation, and imply separate <it>in situ </it>and <it>ex situ </it>management, not only of pelage morphs, but also of local populations.</p

A subset of platinum-containing chemotherapeutic agents kills cells by inducing ribosome biogenesis stress

Cisplatin and its platinum analogs, carboplatin and oxaliplatin, are some of the most widely used cancer chemotherapeutics. Although cisplatin and carboplatin are used primarily in germ cell, breast and lung malignancies, oxaliplatin is instead used almost exclusively to treat colorectal and other gastrointestinal cancers. Here we utilize a unique, multi-platform genetic approach to study the mechanism of action of these clinically established platinum anti-cancer agents, as well as more recently developed cisplatin analogs. We show that oxaliplatin, unlike cisplatin and carboplatin, does not kill cells through the DNA-damage response. Rather, oxaliplatin kills cells by inducing ribosome biogenesis stress. This difference in drug mechanism explains the distinct clinical implementation of oxaliplatin relative to cisplatin, and it might enable mechanistically informed selection of distinct platinum drugs for distinct malignancies. These data highlight the functional diversity of core components of front-line cancer therapy and the potential benefits of applying a mechanism-based rationale to the use of our current arsenal of anti-cancer drugs

Multi-messenger observations of a binary neutron star merger

On 2017 August 17 a binary neutron star coalescence candidate (later designated GW170817) with merger time 12:41:04 UTC was observed through gravitational waves by the Advanced LIGO and Advanced Virgo detectors. The Fermi Gamma-ray Burst Monitor independently detected a gamma-ray burst (GRB 170817A) with a time delay of ~1.7 s with respect to the merger time. From the gravitational-wave signal, the source was initially localized to a sky region of 31 deg2 at a luminosity distance of 40+8-8 Mpc and with component masses consistent with neutron stars. The component masses were later measured to be in the range 0.86 to 2.26 Mo. An extensive observing campaign was launched across the electromagnetic spectrum leading to the discovery of a bright optical transient (SSS17a, now with the IAU identification of AT 2017gfo) in NGC 4993 (at ~40 Mpc) less than 11 hours after the merger by the One- Meter, Two Hemisphere (1M2H) team using the 1 m Swope Telescope. The optical transient was independently detected by multiple teams within an hour. Subsequent observations targeted the object and its environment. Early ultraviolet observations revealed a blue transient that faded within 48 hours. Optical and infrared observations showed a redward evolution over ~10 days. Following early non-detections, X-ray and radio emission were discovered at the transient’s position ~9 and ~16 days, respectively, after the merger. Both the X-ray and radio emission likely arise from a physical process that is distinct from the one that generates the UV/optical/near-infrared emission. No ultra-high-energy gamma-rays and no neutrino candidates consistent with the source were found in follow-up searches. These observations support the hypothesis that GW170817 was produced by the merger of two neutron stars in NGC4993 followed by a short gamma-ray burst (GRB 170817A) and a kilonova/macronova powered by the radioactive decay of r-process nuclei synthesized in the ejecta

Evidence for rangewide panmixia despite multiple barriers to dispersal in a marine mussel

Oceanographic features shape the distributional and genetic patterns of marine species by interrupting or promoting connections among populations. Although general patterns commonly arise, distributional ranges and genetic structure are species-specific and do not always comply with the expected trends. By applying a multimarker genetic approach combined with Lagrangian particle simulations (LPS) we tested the hypothesis that oceanographic features along northeastern Atlantic and Mediterranean shores influence dispersal potential and genetic structure of the intertidal mussel Perna perna. Additionally, by performing environmental niche modelling we assessed the potential and realized niche of P. perna along its entire native distributional range and the environmental factors that best explain its realized distribution. Perna perna showed evidence of panmixia across > 4,000 km despite several oceanographic breaking points detected by LPS. This is probably the result of a combination of life history traits, continuous habitat availability and stepping-stone dynamics. Moreover, the niche modelling framework depicted minimum sea surface temperatures (SST) as the major factor shaping P. perna distributional range limits along its native areas. Forthcoming warming SST is expected to further change these limits and allow the species to expand its range polewards though this may be accompanied by retreat from warmer areas.Fundacao para a Ciencia e Tecnologia (FCT-MEC, Portugal) [UID/Multi/04326/2013, IF/01413/2014/CP1217/CT0004]; South African Research Chairs Initiative (SARChI) of the Department of Science and Technology; National Research Foundation; South African National Research Foundation (NRF); Portuguese Fundacao para a Ciencia e Tecnologia (FCT) [SFRH/BPD/85040/2012, SFRH/BPD/111003/2015]info:eu-repo/semantics/publishedVersio

Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (Senecio carniolicus, Asteraceae)

Recent evidence suggests that survival of arctic-alpine organisms in peripheral or interior glacial refugia are not mutually exclusive and may both be involved in shaping an organism’s Pleistocene history, yet potentially at different time levels. Here, we test this hypothesis in a high-mountain plant (diploid lineage of Senecio carniolicus, Asteraceae) from the Eastern European Alps, in which patterns of morphological variation and current habitat requirements suggest survival in both types of refugia. To this end, we used AFLPs, nuclear and plastid DNA sequences and analysed them, among others, within a graph theoretic framework and using novel Bayesian methods of phylogeographic inference. On the basis of patterns of genetic diversity, occurrence of rare markers, distribution of distinct genetic lineages and patterns of range connectivity both interior refugia in the formerly strongly glaciated central Alps and peripheral refugia along the southern margin of the Alps were identified. The presence of refugia congruently inferred by markers resolving at different time levels suggests that these refugia acted as such throughout several glacial cycles. The high degree of range persistence together with gradual range expansion, which contrasts with the extent of range shifts implied for other Alpine species, is likely responsible for incipient lineage differentiation evident from the genetic data. Replacing a simplistic peripheral vs. interior refugia dualism by more complex models involving both types of refugia and considering different time levels will help identifying common phylogeographic patterns with respect to, for instance, location of refugia and colonization routes and elucidating their underlying genetic and/or ecological causes

Inpatient use and area-level socio-environmental factors in people with psychosis

PURPOSE: There is consistent evidence that socio-environmental factors measured at an area-level, such as ethnic density, urban environment and deprivation are associated with psychosis risk. However, whether area-level socio-environmental factors are associated with outcomes following psychosis onset is less clear. This study aimed to examine whether the number of inpatient days used by people presenting to mental health services for psychosis was associated with five key area-level socio-environmental factors: deprivation, ethnic density, social capital, population density and social fragmentation. METHODS: Using a historical cohort design based on electronic health records from the South London and Maudsley NHS Trust Foundation electronic Patient Journey System, people who presented for the first time to SLAM between 2007 and 2010 with psychosis were included. Structured data were extracted on age at presentation, gender, ethnicity, residential area at first presentation and number of inpatient days over 5 years of follow-up. Data on area-level socio-environmental factors taken from published sources were linked to participants’ residential addresses. The relationship between the number of inpatient days and each socio-environmental factor was investigated in univariate negative binomial regression models with time in contact with services treated as an offset variable. RESULTS: A total of 2147 people had full data on area level outcomes and baseline demographics, thus, could be included in the full analysis. No area-level socio-environmental factors were associated with inpatient days. CONCLUSION: Although a robust association exists between socio-environmental factors and psychosis risk, in this study we found no evidence that neighbourhood deprivation was linked to future inpatient admissions following the onset of psychosis. Future work on the influence of area-level socio-environmental factors on outcome should examine more nuanced outcomes, e.g. recovery, symptom trajectory, and should account for key methodological challenges, e.g. accounting for changes in address

Population Genetics of GYPB and Association Study between GYPB*S/s Polymorphism and Susceptibility to P. falciparum Infection in the Brazilian Amazon

Merozoites of Plasmodium falciparum invade through several pathways using different RBC receptors. Field isolates appear to use a greater variability of these receptors than laboratory isolates. Brazilian field isolates were shown to mostly utilize glycophorin A-independent invasion pathways via glycophorin B (GPB) and/or other receptors. The Brazilian population exhibits extensive polymorphism in blood group antigens, however, no studies have been done to relate the prevalence of the antigens that function as receptors for P. falciparum and the ability of the parasite to invade. Our study aimed to establish whether variation in the GYPB*S/s alleles influences susceptibility to infection with P. falciparum in the admixed population of Brazil.Two groups of Brazilian Amazonians from Porto Velho were studied: P. falciparum infected individuals (cases); and uninfected individuals who were born and/or have lived in the same endemic region for over ten years, were exposed to infection but have not had malaria over the study period (controls). The GPB Ss phenotype and GYPB*S/s alleles were determined by standard methods. Sixty two Ancestry Informative Markers were genotyped on each individual to estimate admixture and control its potential effect on the association between frequency of GYPB*S and malaria infection.GYPB*S is associated with host susceptibility to infection with P. falciparum; GYPB*S/GYPB*S and GYPB*S/GYPB*s were significantly more prevalent in the in the P. falciparum infected individuals than in the controls (69.87% vs. 49.75%; P<0.02). Moreover, population genetics tests applied on the GYPB exon sequencing data suggest that natural selection shaped the observed pattern of nucleotide diversity.Epidemiological and evolutionary approaches suggest an important role for the GPB receptor in RBC invasion by P. falciparum in Brazilian Amazons. Moreover, an increased susceptibility to infection by this parasite is associated with the GPB S+ variant in this population

Watch me grow integrated (WMG-I): protocol for a cluster randomised controlled trial of a web-based surveillance approach for developmental screening in primary care settings

Introduction The increasing prevalence of developmental disorders in early childhood poses a significant global health burden. Early detection of developmental problems is vital to ensure timely access to early intervention, and universal developmental surveillance is recommended best practice for identifying issues. Despite this, there is currently considerable variation in developmental surveillance and screening between Australian states and territories and low rates of developmental screening uptake by parents. This study aims to evaluate an innovative web-based developmental surveillance programme and a sustainable approach to referral and care pathways, linking primary care general practice (GP) services that fall under federal policy responsibility and state government-funded child health services. Methods and analysis The proposed study describes a longitudinal cluster randomised controlled trial (c-RCT) comparing a â € Watch Me Grow Integrated' (WMG-I) approach for developmental screening, to Surveillance as Usual (SaU) in GPs. Forty practices will be recruited across New South Wales and Queensland, and randomly allocated into either the (1) WMG-I or (2) SaU group. A cohort of 2000 children will be recruited during their 18-month vaccination visit or opportunistic visit to GP. At the end of the c-RCT, a qualitative study using focus groups/interviews will evaluate parent and practitioner views of the WMG-I programme and inform national and state policy recommendations. Ethics and dissemination The South Western Sydney Local Health District (2020/ETH01625), UNSW Sydney (2020/ETH01625) and University of Queensland (2021/HE000667) Human Research Ethics Committees independently reviewed and approved this study. Findings will be reported to the funding bodies, study institutes and partners; families and peer-reviewed conferences/publications

The Relationship between Population Structure and Aluminum Tolerance in Cultivated Sorghum

Background: Acid soils comprise up to 50% of the world's arable lands and in these areas aluminum (Al) toxicity impairs root growth, strongly limiting crop yield. Food security is thereby compromised in many developing countries located in tropical and subtropical regions worldwide. In sorghum, SbMATE, an Al-activated citrate transporter, underlies the Alt(SB) locus on chromosome 3 and confers Al tolerance via Al-activated root citrate release. Methodology: Population structure was studied in 254 sorghum accessions representative of the diversity present in cultivated sorghums. Al tolerance was assessed as the degree of root growth inhibition in nutrient solution containing Al. A genetic analysis based on markers flanking Alt(SB) and SbMATE expression was undertaken to assess a possible role for Alt(SB) in Al tolerant accessions. In addition, the mode of gene action was estimated concerning the Al tolerance trait. Comparisons between models that include population structure were applied to assess the importance of each subpopulation to Al tolerance. Conclusion/Significance: Six subpopulations were revealed featuring specific racial and geographic origins. Al tolerance was found to be rather rare and present primarily in guinea and to lesser extent in caudatum subpopulations. Alt(SB) was found to play a role in Al tolerance in most of the Al tolerant accessions. A striking variation was observed in the mode of gene action for the Al tolerance trait, which ranged from almost complete recessivity to near complete dominance, with a higher frequency of partially recessive sources of Al tolerance. A possible interpretation of our results concerning the origin and evolution of Al tolerance in cultivated sorghum is discussed. This study demonstrates the importance of deeply exploring the crop diversity reservoir both for a comprehensive view of the dynamics underlying the distribution and function of Al tolerance genes and to design efficient molecular breeding strategies aimed at enhancing Al tolerance.CGIAR[G3007.04]McKnight FoundationFundacao de Amparo a Pesquisa do Estado de Minas Gerais (FAPEMIG)National Council for Scientific and Technological Development (CNPq

Epidemiological and some clinical characteristics of neuroblastoma in Mexican children (1996–2005)

<p>Abstract</p> <p>Background</p> <p>Neuroblastoma (NB) is the principal tumor of the sympathetic nervous system in children under one year of age. The incidence in developed countries is greater than that in developing countries. The aim of this article is to present the epidemiological and some clinical characteristics of Mexican children with NB.</p> <p>Methods</p> <p>A population-based, prolective study, with data obtained from the Childhood Cancer Registry of the Instituto Mexicano de Seguro Social. Statistical analysis: The simple frequencies of the variables of the study and the annual average incidence (per 1,000,000 children/years) by age and sex were obtained. The trend was evaluated by calculating the annual percentage of change. The curves of Kaplan-Meyer were employed for the survival rate and the log-rank test was used to compare the curves.</p> <p>Results</p> <p>Of a total of 2,758 children with cancer registered during the period from 1996–2005, 72 (2.6%) were identified as having Group IV, defined according to the International Classification of Childhood Cancer. The incidence for NB was 3.8 per 1,000,000 children/year; NB was highest in the group of children under one year of age, followed by the group of children between the ages 1–4 years (18.5 and 5.4 per 1,000,000 children/years, respectively). The male/female ratio was 1.1 and there was no trend toward an increase. The time of diagnosis was 26 days (median), but varied according to the stage at diagnosis. Stages III and IV were presented in 88% of the cases. There was no association between the stage, the age at time of diagnosis, or the histological pattern. The overall five-year survival rate was 64%; the patients with stage I, II, III, or IVs did not die; and the five-year survival rate of cases in Stage IV was 40%.</p> <p>Conclusion</p> <p>It is possible that the low incidence of neuroblastoma in Mexican children is due to the difficulty in diagnosing the cases with the best prognosis, some of which could have had spontaneous regression. There was no trend to an increase; the majority of the cases were diagnosed in the advanced stages; and the overall five-years survival rate was similar to that for developed countries.</p