The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity

Genome size varies 2400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants' environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat "communities" are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors. We show that palm genome size and repeat "community" composition are best explained by aridity. Specifically, Ty3-gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1-copia and LINE elements were more abundant in drier environments. Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress-response genes (e.g. Ty1-copia) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat "communities".JP was supported by a Ramón y Cajal Fellowship (RYC-2017-2274) funded by MCIN/AEI/10.13039/501100011033 and by ‘ESF Investing in your future’. SB was funded by a Garfield Weston Foundation postdoctoral fellowship. PN and JM were supported by the ELIXIR CZ Research Infrastructure Project (Czech Ministry of Education, Youth and Sports; grant no. LM2018131).IntroductionMaterials and Methods Plant material collection and genome size measurement Phylogenetic, environmental and genomic data collection Modelling relationships between genome size and environmental variables DNA repeat profiling Assessing repeat dynamics in palm genomesResults Palm genome size variation Aridity preferences of palm species help explain genome size variation Ecological metrics of palm repeat ‘communities’ vary with genome size Repeat abundances correlate with genome size Aridity preferences of palm species explain abundances of certain repeat lineagesDiscussion Palm genome size variation Aridity thresholds best explain palm genome size diversity The ‘community ecology’ of repeats correlates with genome size Repeat dynamics may be modulated by aridityConclusionsAcknowledgementsAuthor contributionsPeer reviewe

Identification of a novel CHEK2 variant and assessment of its contribution to the risk of breast cancer in French Canadian women

<p>Abstract</p> <p>Background</p> <p><it>BRCA1 </it>and <it>BRCA2 </it>account for the majority of the known familial breast cancer risk, however, the impact of other cancer susceptibility genes largely remains to be elucidated. Checkpoint Kinase 2 (<it>CHEK2</it>) is an important signal transducer of cellular responses to DNA damage, whose defects have been associated with an increase in breast cancer risk. Previous studies have identified low penetrance <it>CHEK2 </it>alleles such as 1100delC and I157T, as well as variants such as S428F in the Ashkenazi Jewish population and IVS2 + 1G>A in the Polish population. No founder allele has been specifically identified in the French Canadian population.</p> <p>Methods</p> <p>The 14 coding exons of <it>CHEK2 </it>were fully sequenced for variant alleles in a panel of 25 affected French Canadian women and 25 healthy controls. Two variants were identified of which one novel variant was further screened for in an additional panel of 667 breast cancer patients and 6548 healthy controls. Additional genotyping was conducted using allele specific PCR and a restriction digest assay. Significance of amino acid substitutions were deduced by employing comparative analysis techniques.</p> <p>Results</p> <p>Two variants were identified: the previously reported silent substitution 252A>G (E84E) and the novel missense variant, 1217G>A (R406H). No significant difference in allele distribution between French Canadian women with breast cancer and healthy controls was observed (3/692, 0.43% vs. 22/6573, 0.33%, respectively, P = 0.73).</p> <p>Conclusion</p> <p>The novel CHEK2 missense variant identified in this study, R406H, is unlikely to contribute to breast cancer risk in French Canadian women.</p

The balloon-borne large-aperture submillimeter telescope for polarimetry: BLAST-Pol

The Balloon-borne Large Aperture Submillimeter Telescope for Polarimetry (BLAST-Pol) is a suborbital mapping experiment designed to study the role played by magnetic fields in the star formation process. BLAST-Pol is the reconstructed BLAST telescope, with the addition of linear polarization capability. Using a 1.8 m Cassegrain telescope, BLAST-Pol images the sky onto a focal plane that consists of 280 bolometric detectors in three arrays, observing simultaneously at 250, 350, and 500 um. The diffraction-limited optical system provides a resolution of 30'' at 250 um. The polarimeter consists of photolithographic polarizing grids mounted in front of each bolometer/detector array. A rotating 4 K achromatic half-wave plate provides additional polarization modulation. With its unprecedented mapping speed and resolution, BLAST-Pol will produce three-color polarization maps for a large number of molecular clouds. The instrument provides a much needed bridge in spatial coverage between larger-scale, coarse resolution surveys and narrow field of view, and high resolution observations of substructure within molecular cloud cores. The first science flight will be from McMurdo Station, Antarctica in December 2010.Comment: 14 pages, 9 figures Submitted to SPIE Astronomical Telescopes and Instrumentation Conference 201

Practical guidance for clinical microbiology laboratories: Viruses causing acute respiratory tract infections

Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens

Comparison of prestellar core elongations and large-scale molecular cloud structures in the Lupus 1 region

Turbulence and magnetic fields are expected to be important for regulating molecular cloud formation and evolution. However, their effects on sub-parsec to 100 parsec scales, leading to the formation of starless cores, are not well understood. We investigate the prestellar core structure morphologies obtained from analysis of the Herschel-SPIRE 350 mum maps of the Lupus I cloud. This distribution is first compared on a statistical basis to the large-scale shape of the main filament. We find the distribution of the elongation position angle of the cores to be consistent with a random distribution, which means no specific orientation of the morphology of the cores is observed with respect to the mean orientation of the large-scale filament in Lupus I, nor relative to a large-scale bent filament model. This distribution is also compared to the mean orientation of the large-scale magnetic fields probed at 350 mum with the Balloon-borne Large Aperture Telescope for Polarimetry during its 2010 campaign. Here again we do not find any correlation between the core morphology distribution and the average orientation of the magnetic fields on parsec scales. Our main conclusion is that the local filament dynamics---including secondary filaments that often run orthogonally to the primary filament---and possibly small-scale variations in the local magnetic field direction, could be the dominant factors for explaining the final orientation of each core

A BAFF-R mutation associated with non-Hodgkin lymphoma alters TRAF recruitment and reveals new insights into BAFF-R signaling

A BAFF receptor mutation associated with non-Hodgkin lymphoma provides new insight into the proximal players of normal BAFF-R signaling

Multiple syndemic psychosocial factors are associated with reduced engagement in HIV care among a multinational, online sample of HIV-infected MSM in Latin America

ABSTRACT Latin America has some of the highest levels of antiretroviral therapy (ART) coverage of any developing region in the world. Early initiation and optimal adherence to ART are necessary for improved health outcomes and reduction in onward transmission. Previous work has demonstrated the role of psychosocial problems as barriers to uptake and adherence to ART, and recently, a syndemic framework has been applied to the role of multiple psychosocial syndemic factors and adherence to ART, in the USA. However, to our knowledge, these associations have not been investigated outside of the USA, nor in a multi-country context. To address these gaps, we assessed the association between multiple co-occurring psychosocial factors and engagement in HIV-related medical care and adherence to ART among a large, multinational sample of sexually-active HIV-infected men who have sex with men in Latin America. Among the 2020 respondents, 80.7% reported currently receiving HIV-related medical care, 72.3% reported currently receiving ART; among those, 62.5% reported 100% adherence. Compared with experiencing no psychosocial health problems, experiencing five or more psychosocial health problems is associated with 42% lower odds of currently receiving HIV-related medical care (adjusted odds ratio, aOR = 0.58, 95% CI 0.36, 0.95) and of currently receiving ART (aOR = 0.58, 95% CI 0.38, 0.91). The number of psychosocial health problems experienced was associated with self-reported ART adherence in a dose–response relationship; compared to those with none of the factors, individuals with one syndemic factor had 23% lower odds (aOR = 0.77, 95% CI 0.60, 0.97) and individuals with five or more syndemic factors had 72% lower odds (aOR = 0.28, 95% CI 0.14, 0.55) of reporting being 100% adherent to ART. Addressing co-occurring psychosocial problems as potential barriers to uptake and adherence of ART in Latin America may improve the effectiveness of secondary prevention interventions