The Endosymbiotic Coral Algae Symbiodiniaceae Are Sensitive to a Sensory Pollutant: Artificial Light at Night, ALAN

Artificial Light at Night, ALAN, is a major emerging issue in biodiversity conservation, which can negatively impact both terrestrial and marine environments. Therefore, it should be taken into serious consideration in strategic planning for urban development. While the lion’s share of research has dealt with terrestrial organisms, only a handful of studies have focused on the marine milieu. To determine if ALAN impacts the coral reef symbiotic algae, that are fundamental for sustainable coral reefs, we conducted a short experiment over a period of one-month by illuminating isolated Symbiodiniaceae cell cultures from the genera Cladocopium (formerly Clade C) and Durusdinium (formerly Clade D) with LED light. Cell cultures were exposed nightly to ALAN levels of 0.15 μmol quanta m–2 s–1 (∼4–5 lux) with three light spectra: blue, yellow and white. Our findings showed that even in very low levels of light at night, the photo-physiology of the algae’s Electron Transport Rate (ETR), Non-Photochemical Quenching, (NPQ), total chlorophyll, and meiotic index presented significantly lower values under ALAN, primarily, but not exclusively, in Cladocopium cell cultures. The findings also showed that diverse Symbiodiniaceae types have different photo-physiology and photosynthesis performances under ALAN. We believe that our results sound an alarm for the probable detrimental effects of an increasing sensory pollutant, ALAN, on the eco-physiology of symbiotic corals. The results of this study point to the potential effects of ALAN on other organisms in marine ecosystem such as fish, zooplankton, and phytoplankton in which their biorhythms is entrained by natural light and dark cycles

Evidence for Shaping of Light Chain Repertoire by Structural Selection

International audienceThe naïve immunoglobulin (IG) repertoire in the blood differs from the direct output of the rearrangement process. These differences stem from selection that affects the ger-mline gene usage and the junctional nucleotides. A major complication obscuring the details of the selection mechanism in the heavy chain is the failure to properly identify the D germline and determine the nucleotide addition and deletion in the junction region. The selection affecting junctional diversity can, however, be studied in the light chain that has no D gene. We use probabilistic and deterministic models to infer and disentangle gene ration and selection of the light chain, using large samples of light chains sequenced from healthy donors and transgenic mice. We have previously used similar models for the beta chain of T-cell receptors and the heavy chain of IGs. Selection is observed mainly in the CDR3. The CDR3 length and mass distributions are narrower after selection than before, indicating stabilizing selection for mid-range values. Within the CDR3, proline and cysteine undergo negative selection, while glycine undergoes positive selection. The results presented here suggest structural selection maintaining the size of the CDR3 within a limited range, and preventing turns in the CDR3 region

Converging evolution leads to near maximal junction diversity through parallel mechanisms in B and T cell receptors

T and B cell receptor (TCR and BCR) complementarity determining region 3 (CDR3) genetic diversity is produced through multiple diversification and selection stages. Potential holes in the CDR3 repertoire were argued to be linked to immunodeficiencies and diseases. In contrast with BCRs, TCRs have practically no Dβ germline genetic diversity, and the question emerges as to whether they can produce a diverse CDR3 repertoire. In order to address the genetic diversity of the adaptive immune system, appropriate quantitative measures for diversity and large-scale sequencing are required. Such a diversity method should incorporate the complex diversification mechanisms of the adaptive immune response and the BCR and TCR loci structure. We combined large-scale sequencing and diversity measures to show that TCRs have a near maximal CDR3 genetic diversity. Specifically, TCR have a larger junctional and V germline diversity, which starts more 5' in Vβ than BCRs. Selection decreases the TCR repertoire diversity, but does not affect BCR repertoire. As a result, TCR is as diverse as BCR repertoire, with a biased CDR3 length toward short TCRs and long BCRs. These differences suggest parallel converging evolutionary tracks to reach the required diversity to avoid holes in the CDR3 repertoir

Landraces of snake melon, an ancient Middle Eastern crop, reveal extensive morphological and DNA diversity for potential genetic improvement

Abstract Background Snake melon (Cucumis melo var. flexuosus, “Faqqous”) is a traditional and ancient vegetable in the Mediterranean area. A collection of landraces from 42 grower fields in Israel and Palestinian territories was grown and characterized in a “Common Garden” rain-fed experiment, at the morphological-horticultural and molecular level using seq-DArT markers. Results The different landraces (“populations”) showed extensive variation in morphology and quantitative traits such as yield and femaleness, and clustered into four horticultural varieties. Yield was assessed by five harvests along the season, with middle harvests producing the highest yields. Yield correlated with early vigor, and with femaleness, but not with late vigor. At the molecular level, 2784 SNP were produced and > 90% were mapped to the melon genome. Populations were very polymorphic (46–72% of the markers biallelic in a 4 individuals sample), and observed heterozygosity was higher than the expected, suggesting gene flow among populations and extensive cross pollination among individuals in the field. Genetic distances between landraces were significantly correlated with the geographical distance between collecting sites, and with long term March precipitation average; variation in yield correlated with April temperature maxima. Conclusions The extensive variation suggests that selection of local snake melon could result in yield improvement. Correlations between traits and climatic variables could suggest local adaptation of landraces to the diverse environment in which they evolved. This study stresses the importance of preserving this germplasm, and its potential for breeding better snake melons as an heirloom crop in our region

Correction to: Landraces of snake melon, an ancient Middle Eastern crop, reveal extensive morphological and DNA diversity for potential genetic improvement

Following publication of the original article [1], the authors reported the need for a more detailed acknowledgement of the source of the samples that were analyzed and their coordinates, which are discussed in the ‘Methods’ section of the article. This Correction provides an addition to the ‘Methods’ section, and a subsequently revised ‘Acknowledgements’ and ‘Availability of data and materials’ section

Regulatory chromatin landscape in Arabidopsis thaliana roots uncovered by coupling INTACT and ATAC-seq

Abstract Background There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever-growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors (TFs) to specific DNA sequence motifs across the genome. However, these sequences are hindered by the packaging of DNA to chromatin. Thus, the accessibility of these loci for TF binding is highly regulated and determines where and when TFs bind. We present a workflow for measuring chromatin accessibility in Arabidopsis thaliana and define organ-specific regulatory sites and binding motifs of TFs at these sites. Results We coupled the recently described isolation of nuclei tagged in specific cell types (INTACT) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) as a genome-wide strategy to uncover accessible regulatory sites in Arabidopsis based on their accessibility to nuclease digestion. By applying this pipeline in Arabidopsis roots, we revealed 41,419 accessible sites, of which approximately half are found in gene promoters and contain the H3K4me3 active histone mark. The root-unique accessible sites from this group are enriched for root processes. Interestingly, most of the root-unique accessible sites are found in nongenic regions but are correlated with root-specific expression of distant genes. Importantly, these gene-distant sites are enriched for binding motifs of TFs important for root development as well as motifs for TFs that may play a role as novel transcriptional regulators in roots, suggesting that these accessible loci are functional novel gene-distant regulatory elements. Conclusions By coupling INTACT with ATAC-seq methods, we present a feasible pipeline to profile accessible chromatin in plants. We also introduce a rapid measure of the experiment quality. We find that chromatin accessibility at promoter regions is strongly associated with transcription and active histone marks. However, root-specific chromatin accessibility is primarily found at intergenic regions, suggesting their predominance in defining organ identity possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions

Additional file 1: of Landraces of snake melon, an ancient Middle Eastern crop, reveal extensive morphological and DNA diversity for potential genetic improvement

Omari et al. Table S1. Data on landraces used in this study and their respective collection sites. Table provides, for each population (collection site), the full set of geographic and climatic variables, morphological scores, and genetic diversity parameters that were calculated from the molecular data. (XLS 103 kb

Surgical Determinants of Post Operative Pain in Patients Undergoing Laparoscopic Adnexectomy

Objective The objective of our study was to determine the main surgical factors associated with postoperative pains in patients undergoing adnexectomy. Material and Methods Patients that underwent adnexectomy in two French Gynecological centers between July, 2018 and March, 2020 were prospectively included and retrospectively analyzed. The main pre and per operative surgical factors were analyzed to assess their impact on immediate postoperative pain. Analgesic consumption was recorded for each patient and pain was evaluated using the validated numeric rating scale (ranging between 0 and 10). Results One hundred and seventeen patients underwent laparoscopic adnexectomy. Eighty-four patients (72%) experienced either no or minor postoperative pain (NRS ≤ 2). Seventeen patients (14.5%) required strong opioids (subcutaneous morphine injection) in the immediate postoperative period. The only two parameters that had a significant impact on immediate postoperative pain were the realization of a fascia closure and the duration of pneumoperitoneum longer than 60 minutes. Pneumoperitoneum pressure and size of ports were not significantly correlated with postoperative pain. Conclusion Fascia closure and increased surgical time were significantly associated with immediate postoperative pain and the need for strong opioids consumption. Surgical training to limit prolonged surgeries should be strongly emphasized to lower postoperative pain and limit opioids consumption