Search

A research study on Bacillus subtilis 271 kb chromosomal region between gerBC (311 degrees) and licR (334 degrees) was conducted to describe the region's features. The two regions were cloned through DNA manipulations. Findings revealed that the genes within the region are responsible for growth conditions. There were also 273 putative sequences identified in the DNA sequencing of the B. subtilus. Furthermore, the study of genetic content and gene function analysis was promoted by the sequencing analysis of the licR-gerBC regions.

Vine-plot mapping and monitoring are crucial issues in land management, particularly for areas where vineyards are dominant like in some French regions. In this context, the availability of an automatic tool for vineyard detection and characterization would be very useful. The objective of the study is to compare two different approaches to meet this need. The first one uses directional variations of the contrast feature computed from Haralick's co-occurrence matrices and the second one is based on a local Fourier transform. For each pixel, a 'vine index' is computed on a sliding window. To foster large-scale applications, test and validation were carried out on standard very high spatial resolution remote sensing data. 70.8% and 86% of the 271 plots of the study area were correctly classified using the co-occurrence and the frequency method, respectively. Moreover, the latter enabled an accurate determination (less than 3% error) of inter-row width and row orientation. [ABSTRACT FROM AUTHOR]

Abstract: The transforming growth factor β (TGFβ) superfamily includes bone morphogenetic proteins, activins and TGF-βsensu stricto (s.s.). These ligands have been shown to play a key role in numerous biological processes including early embryonic development and immune regulation. They transduce their signal through a hetromeric complex of type I and type II receptors. Such receptors have been identified in ecdysozoans but none have been found as yet in the other major protostomal clade, the lophotrochozoans. Here, we report the identification of the first lophotrochozoan TGFβs.s. type I receptor (Cg-TGFβRI) from the mollusk Crassostrea gigas. The phylogenetic and structural analyses as well as the expression pattern during early development suggest Cg-TGFβRI to belong to the TGFβs.s./activin type I receptor clade and functional studies corroborate these deductions. The use of the zebrafish embryo as a reporter organism reveals that either Cg-TGFβRI or its dominant negative acting truncated form, when overexpressed during gastrulation, resulted in a range of phenotypes displaying severe disturbance of anterioposterior patterning due to a strong modulation of ventrolateral mesoderm patterning. Finally, a Cg-TGFβRI cytokine activity during immune regulation in C. gigas has been investigated by real-time PCR in haemocytes and mantle edge during an in vivo bacterial LPS challenge. One piece of evidence from this study suggests that the molecular mechanisms controlling mesodermal patterning and some immune regulations across all bilateria could be conserved through a functional TGF-β s.s. pathway in lophotrochozoans. [Copyright &y& Elsevier]

Abstract Background Research using the Pacific oyster Crassostrea gigas as a model organism has experienced rapid growth in recent years due to the development of high-throughput molecular technologies. As many as 56,268 EST sequences have been sequenced to date, representing a genome-wide resource that can be used for transcriptomic investigations. Results In this paper, we developed a Pacific oyster microarray containing oligonucleotides representing 31,918 transcribed sequences selected from the publicly accessible GigasDatabase. This newly designed microarray was used to study the transcriptome of male and female gonads, mantle, gills, posterior adductor muscle, visceral ganglia, hemocytes, labial palps and digestive gland. Statistical analyses identified genes differentially expressed among tissues and clusters of tissue-enriched genes. These genes reflect major tissue-specific functions at the molecular level, such as tissue formation in the mantle, filtering in the gills and labial palps, and reproduction in the gonads. Hierarchical clustering predicted the involvement of unannotated genes in specific functional pathways such as the insulin/NPY pathway, an important pathway under study in our model species. Microarray data also accurately identified reference genes whose mRNA level appeared stable across all the analyzed tissues. Adp-ribosylation factor 1 (arf1) appeared to be the most robust reference for normalizing gene expression data across different tissues and is therefore proposed as a relevant reference gene for further gene expression analysis in the Pacific oyster. Conclusions This study provides a new transcriptomic tool for studies of oyster biology, which will help in the annotation of its genome and which identifies candidate reference genes for gene expression analysis.

Abstract Background Although bivalves are among the most-studied marine organisms because of their ecological role and economic importance, very little information is available on the genome sequences of oyster species. This report documents three large-scale cDNA sequencing projects for the Pacific oyster Crassostrea gigas initiated to provide a large number of expressed sequence tags that were subsequently compiled in a publicly accessible database. This resource allowed for the identification of a large number of transcripts and provides valuable information for ongoing investigations of tissue-specific and stimulus-dependant gene expression patterns. These data are crucial for constructing comprehensive DNA microarrays, identifying single nucleotide polymorphisms and microsatellites in coding regions, and for identifying genes when the entire genome sequence of C. gigas becomes available. Description In the present paper, we report the production of 40,845 high-quality ESTs that identify 29,745 unique transcribed sequences consisting of 7,940 contigs and 21,805 singletons. All of these new sequences, together with existing public sequence data, have been compiled into a publicly-available Website http://public-contigbrowser.sigenae.org:9090/Crassostrea_gigas/index.html. Approximately 43% of the unique ESTs had significant matches against the SwissProt database and 27% were annotated using Gene Ontology terms. In addition, we identified a total of 208 in silico microsatellites from the ESTs, with 173 having sufficient flanking sequence for primer design. We also identified a total of 7,530 putative in silico, single-nucleotide polymorphisms using existing and newly-generated EST resources for the Pacific oyster. Conclusion A publicly-available database has been populated with 29,745 unique sequences for the Pacific oyster Crassostrea gigas. The database provides many tools to search cleaned and assembled ESTs. The user may input and submit several filters, such as protein or nucleotide hits, to select and download relevant elements. This database constitutes one of the most developed genomic resources accessible among Lophotrochozoans, an orphan clade of bilateral animals. These data will accelerate the development of both genomics and genetics in a commercially-important species with the highest annual, commercial production of any aquatic organism.

An abstract of the article "A Taxonomical Reassessment of Pavlovophyceae," by E.M. Bendif and colleagues is presented.

Hereby presented data consists of a land use / land cover map of an 84 km 2 part of the Vavatenina district, in the Analanjirofo Region of the east coast of Madagascar, where the landscape is dominated by woody vegetation. This map was obtained by processing very high spatial resolution multispectral images acquired by the Pleiades satellite sensor in 2018. Pleiades data were produced by Airbus defence & Space (France), and distributed by the French National Space Agency (CNES, France). An object-based approach was chosen to exploit the advantages of such images, allowing the use of various texture indices derived from the image to discriminate between different surfaces sharing similar radiometric properties while being structurally different. The object-based image analysis consists of iterative segmentations of the image into homogeneous regions, called objects, which can afterwards be classified using radiometric and textural variables. The reference database, computed out of field knowledge and used to train the mapping methodology, is also described here. It includes 2105 georeferenced points labelled with one of the 9 following classes: Built up/road/bare areas, Annual crops/pasture/short vegetation, Clove dominated park, Clove monoculture, Diversified agroforest, Diversified park, Plantation of woody species, Shrubby fallow, Woody fallow. It is formatted as a geographical information system, accessible for any other purpose like further methodology development. These ground-truth data also helped to the definition of the 13 thematic land use / land cover types to be distinguished in the area. Multiple segmentation levels were thus necessary to gradually derive these classes, with different classification algorithms depending on the level. The final map provides an exhaustive description of the area with a good overall accuracy, reaching 80%. It is openly available as an ESRI shapefile to allow quantitative spatial analysis in key applications such as agriculture, environment, or food security., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2022 The Author(s). Published by Elsevier Inc.)

The Pacific oyster, Crassostrea gigas, is a successive irregular hermaphrodite mollusk which has an annual breeding cycle. Oysters are naturally diploid organisms, but triploid oysters have been developed for use in shellfish aquaculture, with the aim of obtaining sterile animals with commercial value. However, studies have shown that some triploid oysters are partially able to undergo gametogenesis, with numerous proliferating cells closed to diploids (3n alpha) or a partial one with an accumulation of locked germ cells (3n beta). The aim of our study therefore was to understand the regulation of spermatogenesis in both groups of triploid oysters (alpha and beta) from the beginning of spermatogenesis, during mitosis and meiosis events. Our results demonstrate that the reduced spermatogenesis in triploids results from a deregulation of the development of the germinal lineage and the establishment of the gonadal tract led by a lower number of tubules. Morphological cellular investigation also revealed an abnormal condensation of germ cell nuclei and the presence of clear patches in the nucleoplasm of triploid cells, which were more pronounced in beta oysters. Furthermore, studies of molecular and cellular regulation showed a downregulation of mitotic spindle checkpoint in beta oysters, resulting in disturbance of chromosomal segregation, notably on spindle assembly checkpoint involved in the binding of microtubules to chromosomes. Taken together, our results suggest that the lower reproductive ability of triploid oysters may be due to cellular and molecular events such as impairment of spermatogenesis and disruptions of mitosis and meiosis, occurring early and at various stages of the gametogenetic cycle., (© 2021 The Authors. FEBS Open Bio published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.)

Salvia miltiorrhiza Bunge, commonly called danshen, is widely used in traditional Chinese medicine for its cardiovascular and neuroprotective effects, which include antioxidative, anti-inflammatory, and antifibrotic properties. The purpose of this study was to evaluate the preclinical potential of S. miltiorrhiza extracts for the treatment of COVID-19. First, the impact of the extract on the binding between SARS-CoV-2 and the cellular ACE2 receptors was assessed using atomic force microscopy (AFM), showing a significant reduction in binding by the extract at concentrations in the µg/mL range. Second, the interference of this extract with the inflammatory response of blood mononuclear cells (PBMCs) was determined, demonstrating potent inhibitory properties in the same concentration range on pro-inflammatory cytokine release and interference with the activation of NFκB signaling. Together, these in vitro data demonstrate the potential of S. miltiorrhiza against COVID-19, consisting first of the blockade of the binding of SARS-CoV-2 to the ACE2 receptor and the mitigation of the inflammatory response from leukocytes by interfering with NFκB signaling. This dataset prompts the launch of a clinical trial to address in vivo the clinical benefits of this promising agent.

Among Pseudo-nitzschia species, some produce the neurotoxin domoic acid (DA), a source of serious health problems for marine organisms. Filter-feeding organisms-e.g., bivalves feeding on toxigenic Pseudo-nitzschia spp.-are the main vector of DA in humans. However, little is known about the interactions between bivalves and Pseudo-nitzschia . In this study, we examined the interactions between two juvenile bivalve species-oyster ( Crassostrea gigas ) and scallop ( Pecten maximus )-and two toxic Pseudo-nitzschia species- P. australis and P. fraudulenta. We characterized the influence of (1) diet composition and the Pseudo-nitzschia DA content on the feeding rates of oysters and scallops, and (2) the presence of bivalves on Pseudo-nitzschia toxin production. Both bivalve species fed on P. australis and P. fraudulenta . However, they preferentially filtered the non-toxic Isochrysis galbana compared to Pseudo-nitzschia . The presence of the most toxic P. australis species resulted in a decreased clearance rate in C. gigas . The two bivalve species accumulated DA in their tissues (up to 0.35 × 10 -3 and 5.1 × 10 -3 µg g -1 for C. gigas and P. maximus , respectively). Most importantly, the presence of bivalves induced an increase in the cellular DA contents of both Pseudo-nitzschia species (up to 58-fold in P. fraudulenta in the presence of C. gigas ). This is the first evidence of DA production by Pseudo-nitzschia species stimulated in the presence of filter-feeding bivalves. The results of this study highlight complex interactions that can influence toxin production by Pseudo-nitzschia and accumulation in bivalves. These results will help to better understand the biotic factors that drive DA production by Pseudo-nitzschia and bivalve contamination during Pseudo-nitzschia blooms.