New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA

An innovative single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers, especially after reports of endogenous DNA content increases &gt;20-fold in some samples. To investigate the behavior of this method, we generated ssDNA and conventional double-stranded DNA (dsDNA) libraries from 23 ancient and historic plant and animal specimens. We found ssDNA library preparation substantially increased endogenous content when dsDNA libraries contained &lt;3% endogenous DNA, but this enrichment is less pronounced when dsDNA preparations successfully recover short endogenous DNA fragments (mean size &lt; 70 bp). Our findings can help researchers determine when to utilize the time- and resource-intensive ssDNA library preparation method. </jats:p

Ecological Niche Dimensionality and the Evolutionary Diversification of Stick Insects

The degree of phenotypic divergence and reproductive isolation between taxon pairs can vary quantitatively, and often increases as evolutionary divergence proceeds through various stages, from polymorphism to population differentiation, ecotype and race formation, speciation, and post-speciational divergence. Although divergent natural selection promotes divergence, it does not always result in strong differentiation. For example, divergent selection can fail to complete speciation, and distinct species pairs sometimes collapse (‘speciation in reverse’). Widely-discussed explanations for this variability concern genetic architecture, and the geographic arrangement of populations. A less-explored possibility is that the degree of phenotypic and reproductive divergence between taxon pairs is positively related to the number of ecological niche dimensions (i.e., traits) subject to divergent selection. Some data supporting this idea stem from laboratory experimental evolution studies using Drosophila, but tests from nature are lacking. Here we report results from manipulative field experiments in natural populations of herbivorous Timema stick insects that are consistent with this ‘niche dimensionality’ hypothesis. In such insects, divergent selection between host plants might occur for cryptic colouration (camouflage to evade visual predation), physiology (to detoxify plant chemicals), or both of these niche dimensions. We show that divergent selection on the single niche dimension of cryptic colouration can result in ecotype formation and intermediate levels of phenotypic and reproductive divergence between populations feeding on different hosts. However, greater divergence between a species pair involved divergent selection on both niche dimensions. Although further replication of the trends reported here is required, the results suggest that dimensionality of selection may complement genetic and geographic explanations for the degree of diversification in nature

IND-Enabling Studies for a Clinical Trial to Genetically Program a Persistent Cancer-Targeted Immune System

PURPOSE: To improve persistence of adoptively transferred T-cell receptor (TCR)-engineered T cells and durable clinical responses, we designed a clinical trial to transplant genetically-modified hematopoietic stem cells (HSCs) together with adoptive cell transfer of T cells both engineered to express an NY-ESO-1 TCR. Here, we report the preclinical studies performed to enable an investigational new drug (IND) application. EXPERIMENTAL DESIGN: HSCs transduced with a lentiviral vector expressing NY-ESO-1 TCR and the PET reporter/suicide gene HSV1-sr39TK and T cells transduced with a retroviral vector expressing NY-ESO-1 TCR were coadministered to myelodepleted HLA-A2/Kb mice within a formal Good Laboratory Practice (GLP)-compliant study to demonstrate safety, persistence, and HSC differentiation into all blood lineages. Non-GLP experiments included assessment of transgene immunogenicity and in vitro viral insertion safety studies. Furthermore, Good Manufacturing Practice (GMP)-compliant cell production qualification runs were performed to establish the manufacturing protocols for clinical use. RESULTS: TCR genetically modified and ex vivo-cultured HSCs differentiated into all blood subsets in vivo after HSC transplantation, and coadministration of TCR-transduced T cells did not result in increased toxicity. The expression of NY-ESO-1 TCR and sr39TK transgenes did not have a detrimental effect on gene-modified HSC's differentiation to all blood cell lineages. There was no evidence of genotoxicity induced by the lentiviral vector. GMP batches of clinical-grade transgenic cells produced during qualification runs had adequate stability and functionality. CONCLUSIONS: Coadministration of HSCs and T cells expressing an NY-ESO-1 TCR is safe in preclinical models. The results presented in this article led to the FDA approval of IND 17471

Coccolithophore calcification is independent of carbonate chemistry in the tropical ocean

Marañón, Emilio ... et al.-- 13 pages, 7 figures, 1 table, supporting information https://dx.doi.org/10.1002/lno.10295Short-term experiments indicate that seawater acidification can cause a decrease in the rate of calcification by coccolithophores, but the relationship between carbonate chemistry and coccolithophore calcification rate in natural assemblages is still unclear. During the Malaspina 2010 circumnavigation, we measured primary production, calcification, coccolithophore abundance, particulate inorganic carbon (PIC) concentration, and the parameters of the carbonate system, along basin-scale transects in the tropical Atlantic, Indian and Pacific oceans. Euphotic layer-integrated calcification and mean cell-specific calcification in the euphotic layer ranged between 2–10 mgC m−2 d−1 and 5–20 pgC cell−1 d−1, respectively. We found a significant relationship between primary production and calcification, such that the calcification to primary production (CP/PP) ratio was relatively invariant among ocean basins, with an overall mean value of 0.05 ± 0.04. Extrapolating this value to the entire ocean would result in a global pelagic calcification rate of 2.4 PtC yr−1. The mean PIC concentration in surface waters was 1.8 ± 1.6 mgC m−3 and its turnover time averaged 20 d. We combined our data of calcification, primary production, and carbonate chemistry from Malaspina 2010 with those obtained during two previous cruises in the northern Arabian Sea. Both the CP/PP ratio and cell-specific calcification were largely constant across a wide range of calcite saturation state (1.5–6.5), [ inline image]/[H+] (0.08–0.24; mol: μmol), and pH (7.6–8.1), which indicates that calcification by natural coccolithophore assemblages was independent of carbonate chemistry. Our results suggest that coccolithophore calcification, at least in tropical regions, may not be decreasing in the currently acidifying oceanFunding for this study was provided by the Spanish Ministry of Science and Innovation through research projects Malaspina 2010 (grant no. CSD2008-00077), PERSEO (CTM2007-28925-E/MAR), MANIFEST (CTM2012-32017) and TERRIFIC (CTM2014-53582-R). Funding for W.M.B. came from the NSF (OCE-0961660; OCE1220068), NASA (NNX11AO72G; NNX11AL93G; NNX14AQ41G; NNX14AQ43A; NNX14AL92G; NNX14AM77G) and NOAA (NA11OAR4310055).Peer Reviewe

Permanent Genetic Resources added to Molecular Ecology Resources Database 1 February 2013-31 March 2013

This article documents the addition of 142 microsatellite marker loci to the Molecular Ecology Resources database. Loci were developed for the following species: Agriophyllum squarrosum, Amazilia cyanocephala, Batillaria attramentaria, Fungal strain CTeY1 (Ascomycota), Gadopsis marmoratus, Juniperus phoenicea subsp. turbinata, Liriomyza sativae, Lupinus polyphyllus, Metschnikowia reukaufii, Puccinia striiformis and Xylocopa grisescens. These loci were cross-tested on the following species: Amazilia beryllina, Amazilia candida, Amazilia rutila, Amazilia tzacatl, Amazilia violiceps, Amazilia yucatanensis, Campylopterus curvipennis, Cynanthus sordidus, Hylocharis leucotis, Juniperus brevifolia, Juniperus cedrus, Juniperus osteosperma, Juniperus oxycedrus, Juniperus thurifera, Liriomyza bryoniae, Liriomyza chinensis, Liriomyza huidobrensis and Liriomyza trifolii. © 2013 John Wiley & Sons Ltd.Peer Reviewe

A global compilation of coccolithophore calcification rates

The biological production of calcium carbonate (CaCO3), a process termed calcification, is a key term in the marine carbon cycle. A major planktonic group responsible for such pelagic CaCO3 production (CP) is the coccolithophores, single-celled haptophytes that inhabit the euphotic zone of the ocean. Satellite-based estimates of areal CP are limited to surface waters and open-ocean areas, with current algorithms utilising the unique optical properties of the cosmopolitan bloom-forming species Emiliania huxleyi, whereas little understanding of deep-water ecology, optical properties or environmental responses by species other than E. huxleyi is currently available to parameterise algorithms or models. To aid future areal estimations and validate future modelling efforts we have constructed a database of 2765 CP measurements, the majority of which were measured using 12 to 24 h incorporation of radioactive carbon (14C) into acid-labile inorganic carbon (CaCO3). We present data collated from over 30 studies covering the period from 1991 to 2015, sampling the Atlantic, Pacific, Indian, Arctic and Southern oceans. Globally, CP in surface waters ( < 20 m) ranged from 0.01 to 8398 µmol C m−3 d−1 (with a geometric mean of 16.1 µmol C m−3 d−1). An integral value for the upper euphotic zone (herein surface to the depth of 1 % surface irradiance) ranged from  < 0.1 to 6 mmol C m−2 d−1 (geometric mean 1.19 mmol C m−2 d−1). The full database is available for download from PANGAEA at https://doi.org/10.1594/PANGAEA.888182

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Export and turnover of transparent exopolymer particles into the deep ocean

2nd Meeting of the Iberian Ecological Society (SIBECOL), XXI conference of the Iberian Association of Limnology (AIL) and 21st National Congress of the Portuguese Ecological Society (SPECO), 3-8 July 2022, AveiroAcidic polysaccharides released by phytoplankton and prokaryotic heterotrophs promote the formation of gel-like transparent exopolymer particles (TEPs). TEPs play a key role in the biological carbon pump due to their carbon-rich composition and their ability to coagulate and sink towards the deep ocean. Yet, very little is known about TEP distribution, export, and turnover at a global scale, particularly at deep ocean depths. We provide the first inventory of TEP from the surface up to 4000 m depth in the Atlantic, Indian, and Pacific Oceans and have assessed their contribution to carbon export into the deep ocean. Primary production determines TEP concentration above the deep chlorophyll maximum, and prokaryotic biomass also contributes in deeper waters. In the deep ocean waters, TEP concentrations are lower and mirror the concentrations in the surface, evidencing the importance of TEP sinking both at the export depth (200 m) with a global value of 2.9 Pg C year-1 and at the sequestration depth (1000 m) of 0.9 Pg C year-1 of particulate carbon. However, incubation experiments across ocean basins depicted rapid TEP turnover rates of 71 and 333 days (on average) within the export and sequestration depths, respectively. These findings reveal that the export of carbon by TEP sinking towards deep oceans escapes from long-term paths of the global carbon cycleN

Memorias del Séptimo Foro de la Enseñanza de las Matemáticas

En el Séptimo Foro de Enseñanza de las Matemática Ibero 2017 se abordaron temas relacionados con el uso de la historia de las matemáticas en el aula, las transformaciones en las habilidades, destrezas y conocimientos en los alumnos universitarios en la primera década del 2000, el uso de plataformas digitales en la enseñanza de las matemáticas; se expuso sobre situaciones problema en la vida cotidiana relacionados con las matemáticas escolares y la modelación matemática, sobre la historia de la enseñanza de las matermáticas, entre otros temas.ITESO, A.C.Universidad Iberoamericana, Campus Santa F

Exome-Derived Adiponectin-Associated Variants Implicate Obesity and Lipid Biology

Circulating levels of adiponectin, an adipocyte-secreted protein associated with cardiovascular and metabolic risk, are highly heritable. To gain insights into the biology that regulates adiponectin levels, we performed an exome array meta-analysis of 265,780 genetic variants in 67,739 individuals of European, Hispanic, African American, and East Asian ancestry. We identified 20 loci associated with adiponectin, including 11 that had been reported previously (p .60) spanning as much as 900 kb. To identify potential genes and mechanisms through which the previously unreported association signals act to affect adiponectin levels, we assessed cross-trait associations, expression quantitative trait loci in subcutaneous adipose, and biological pathways of nearby genes. Eight of the nine loci were also associated (p <1 x 10(-4)) with at least one obesity or lipid trait. Candidate genes include PRKAR2A, PTH1R, and HDAC9, which have been suggested to play roles in adipocyte differentiation or bone marrow adipose tissue. Taken together, these findings provide further insights into the processes that influence circulating adiponectin levels.Peer reviewe