Site structure analysis and optimization

The article contains information about current situation of site development, reasons why sites are so essential for activity of organizations and why researches of their structure improvement are so important. Short analysis of previous researches is provided, with their negative features and ways for further researches being exposed. Several ways to formulate recommendations and requirements for site structure are suggested, as well as methods for its optimization. A method for implementation of research results as software product is proposed. The information about an example of such software which performs analysis of sites of educational institution is provided too

Comparative performance of the 16S rRNA gene in DNA barcoding of amphibians

BACKGROUND: Identifying species of organisms by short sequences of DNA has been in the center of ongoing discussions under the terms DNA barcoding or DNA taxonomy. A C-terminal fragment of the mitochondrial gene for cytochrome oxidase subunit I (COI) has been proposed as universal marker for this purpose among animals. RESULTS: Herein we present experimental evidence that the mitochondrial 16S rRNA gene fulfills the requirements for a universal DNA barcoding marker in amphibians. In terms of universality of priming sites and identification of major vertebrate clades the studied 16S fragment is superior to COI. Amplification success was 100% for 16S in a subset of fresh and well-preserved samples of Madagascan frogs, while various combination of COI primers had lower success rates.COI priming sites showed high variability among amphibians both at the level of groups and closely related species, whereas 16S priming sites were highly conserved among vertebrates. Interspecific pairwise 16S divergences in a test group of Madagascan frogs were at a level suitable for assignment of larval stages to species (1–17%), with low degrees of pairwise haplotype divergence within populations (0–1%). CONCLUSION: We strongly advocate the use of 16S rRNA as standard DNA barcoding marker for vertebrates to complement COI, especially if samples a priori could belong to various phylogenetically distant taxa and false negatives would constitute a major problem

A molecular survey across Madagascar does not yield positive records of the amphibian chytrid fungus Batrachochytrium dendrobatidis.

Madagascar harbors a rich and diverse amphibian fauna, with over 280 nominal species of native frogs, all of which are endemic to the island. Although many species are threatened predominantly by habitat destruction, so far this fauna has not experienced any enigmatic declines as amphibians have in other parts of the globe. The amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd), associated with mass amphibian die offs in Europe, the Americas and Australia has so far not been detected in Madagascar, but surveys so far were based mainly on histological examination of frog samples, with molecular data from only a single site. Here, we present results from a molecular screening of altogether 300 frog specimens belonging to 53 species in 13 genera, from 12 sites throughout Madagascar spanning all of Madagascar`s major bioclimatic regions and an array of different elevations from 20 to 2400 m above sea level. All samples were analyzed using a standard quantitative real time polymerase chain reaction (qPCR) assay and yielded only negative results, suggesting the widespread absence or very localized and low prevalence of the amphibian chytrid fungus across Madagascar during the sampling years 2006 and 2007.This research was supported by Conservation International, by the Spanish Ministry of Science, by the Volkswagen Foundation, and by The US National Science Foundation (EF-0723563 and 1120283)Peer Reviewe

The importance of comparative phylogeography in diagnosing introduced species: a lesson from the seal salamander, Desmognathus monticola

<p>Abstract</p> <p>Background</p> <p>In most regions of the world human influences on the distribution of flora and fauna predate complete biotic surveys. In some cases this challenges our ability to discriminate native from introduced species. This distinction is particularly critical for isolated populations, because relicts of native species may need to be conserved, whereas introduced species may require immediate eradication. Recently an isolated population of seal salamanders, <it>Desmognathus monticola</it>, was discovered on the Ozark Plateau, ~700 km west of its broad continuous distribution in the Appalachian Mountains of eastern North America. Using Nested Clade Analysis (NCA) we test whether the Ozark isolate results from population fragmentation (a natural relict) or long distance dispersal (a human-mediated introduction).</p> <p>Results</p> <p>Despite its broad distribution in the Appalachian Mountains, the primary haplotype diversity of <it>D. monticola </it>is restricted to less than 2.5% of the distribution in the extreme southern Appalachians, where genetic diversity is high for other co-distributed species. By intensively sampling this genetically diverse region we located haplotypes identical to the Ozark isolate. Nested Clade Analysis supports the hypothesis that the Ozark population was introduced, but it was necessary to include haplotypes that are less than or equal to 0.733% divergent from the Ozark population in order to arrive at this conclusion. These critical haplotypes only occur in < 1.2% of the native distribution and NCA excluding them suggest that the Ozark population is a natural relict.</p> <p>Conclusion</p> <p>Our analyses suggest that the isolated population of <it>D. monticola </it>from the Ozarks is not native to the region and may need to be extirpated rather than conserved, particularly because of its potential negative impacts on endemic Ozark stream salamander communities. Diagnosing a species as introduced may require locating nearly identical haplotypes in the known native distribution, which may be a major undertaking. Our study demonstrates the importance of considering comparative phylogeographic information for locating critical haplotypes when distinguishing native from introduced species.</p

Functional colour genes and signals of selection in colour polymorphic salamanders

Coloration has been associated with multiple biologically relevant traits that drive adaptation and diversification in many taxa. However, despite the great diversity of colour patterns present in amphibians the underlying molecular basis is largely unknown. Here, we use insight from a highly colour-variable lineage of the European fire salamander (Salamandra salamandra bernardezi) to identify functional associations with striking variation in colour morph and pattern. The three focal colour morphs—ancestral black-yellow striped, fully yellow and fully brown—differed in pattern, visible coloration and cellular composition. From population genomic analyses of up to 4,702 loci, we found no correlations of neutral population genetic structure with colour morph. However, we identified 21 loci with genotype–phenotype associations, several of which relate to known colour genes. Furthermore, we inferred response to selection at up to 142 loci between the colour morphs, again including several that relate to coloration genes. By transcriptomic analysis across all different combinations, we found 196 differentially expressed genes between yellow, brown and black skin, 63 of which are candidate genes involved in animal coloration. The concordance across different statistical approaches and ‘omic data sets provide several lines of evidence for loci linked to functional differences between colour morphs, including TYR, CAMK1 and PMEL. We found little association between colour morph and the metabolomic profile of its toxic compounds from the skin secretions. Our research suggests that current ecological and evolutionary hypotheses for the origins and maintenance of these striking colour morphs may need to be revisited.This research was supported by a Natural Environment Research Council; a Royal Society Research Grant; a Glasgow Natural History Society grant; a Wellcome Trust ISSF Catalyst Grant and a Spanish Ministry of Science Grant

Impact of the COVID-19 Lockdown on a Long-Term Care Facility: The Role of Social Contact

(1) Background: Long-term care facilities (LTCFs) have been harmed by the coronavirus, and older adults have remained isolated for a long time with many restrictions. The aim of this study was to measure the decline in cognitive, functional, and affective status in a care facility after the lockdown in the first wave of the COVID-19 pandemic and to compare it with previous measures in order to determine if this decline was accelerated. (2) Methods: Ninety-eight participants were recruited. Data from three retrospective pre-lockdown assessments and an additional post-lockdown assessment were analyzed. Mixed ANOVA analyses were performed according to the Clinical Dementia Rating levels, considering social-contact frequency during the lockdown as a covariate. (3) Results: The cognitive and functional scores were lower and depression scores were higher after the strict lockdown, accelerating a general pattern of decline that was already present in LTCF residents. The frequency of social contact eliminated the measurement differences in the cognitive and functional scores and the group differences in depression scores. (4) Conclusions: The effects of the SARS-CoV-2 lockdown in an LTCF were mediated by the frequency of contact. Clinical implications: Preventive measures must be taken to ensure social contact with relatives and friends and reduce the negative consequences of social isolation in LTCFsS

Does empirically derived classification of individuals with subjective cognitive complaints predict dementia?

Background: Early identification of mild cognitive impairment (MCI) in people reporting subjective cognitive complaints (SCC) and the study of progression of cognitive decline are important issues in dementia research. This paper examines whether empirically derived procedures predict progression from MCI to dementia. (2) Methods: At baseline, 192 participants with SCC were diagnosed according to clinical criteria as cognitively unimpaired (70), single-domain amnestic MCI (65), multiple-domain amnestic MCI (33) and multiple-domain non-amnestic MCI (24). A two-stage hierarchical cluster analysis was performed for empirical classification. Categorical regression analysis was then used to assess the predictive value of the clusters obtained. Participants were re-assessed after 36 months. (3) Results: Participants were grouped into four empirically derived clusters: Cluster 1, similar to multiple-domain amnestic MCI; Cluster 2, characterized by subjective cognitive decline (SCD) but with low scores in language and working memory; Cluster 3, with specific deterioration in episodic memory, similar to single-domain amnestic MCI; and Cluster 4, with SCD but with scores above the mean in all domains. The majority of participants who progressed to dementia were included in Cluster 1. (4) Conclusions: Cluster analysis differentiated between MCI and SCD in a sample of people with SCC and empirical criteria were more closely associated with progression to dementia than standard criteria.This work was financially supported by the Spanish Directorate General of Scientific and Technical Research (Project PSI2014- 55316-C3-1-R) and by the Galician Government (Consellería de Cultura, Educación e Ordenación Universitaria; axudas para a consolidación e Estruturación de unidades de investigación competitivas do Sistema universitario de Galicia; GRC (GI-1807-USC); Ref: ED431-2017/27) through FEDER fundsS

MicroRNA-200 Family Modulation in Distinct Breast Cancer Phenotypes

The epithelial to mesenchymal transition (EMT) contributes to tumor invasion and metastasis in a variety of cancer types. In human breast cancer, gene expression studies have determined that basal-B/claudin-low and metaplastic cancers exhibit EMT-related characteristics, but the molecular mechanisms underlying this observation are unknown. As the family of miR-200 microRNAs has been shown to regulate EMT in normal tissues and cancer, here we evaluated whether the expression of the miR-200 family (miR-200f) and their epigenetic state correlate with EMT features in human breast carcinomas. We analyzed by qRT-PCR the expression of miR-200f members and various EMT-transcriptional inducers in a series of 70 breast cancers comprising an array of phenotypic subtypes: estrogen receptor positive (ER+), HER2 positive (HER2+), and triple negative (TN), including a subset of metaplastic breast carcinomas (MBCs) with sarcomatous (homologous or heterologous) differentiation. No MBCs with squamous differentiation were included. The DNA methylation status of miR-200f loci in tumor samples were inspected using Sequenom MassArray® MALDI-TOF platform. We also used two non-tumorigenic breast basal cell lines that spontaneously undergo EMT to study the modulation of miR-200f expression during EMT in vitro. We demonstrate that miR-200f is strongly decreased in MBCs compared with other cancer types. TN and HER2+ breast cancers also exhibited lower miR-200f expression than ER+ tumors. Significantly, the decreased miR-200f expression found in MBCs is accompanied by an increase in the expression levels of EMT-transcriptional inducers, and hypermethylation of the miR-200c-141 locus. Similar to tumor samples, we demonstrated that downregulation of miR-200f and hypermethylation of the miR-200c-141 locus, together with upregulation of EMT-transcriptional inducers also occur in an in vitro cellular model of spontaneous EMT. Thus, the expression and methylation status of miR-200f could be used as hypothetical biomarkers to assess the occurrence of EMT in breast cancer. © 2012 Castilla et al.This work was supported by grants from: the Instituto de Salud Carlos III (ISCIII; Grant Nos PI07/90324 and PI080971) and the Ministerio de Ciencia e Innovación (MCINN), co-financed by the European Development Regional Fund, “A way to achieve Europe” EDRF (Grant No. RD06/0020/0013); the Junta de Andalucía (Consejería de Salud, Grant No.PI-0384/2007, PI0581/2009); the Consejería de Innovación (Proyecto de Excelencia, Grant No. P07-CVI-03100); and Sandra Ibarra Foundation (Grant No. 2011/088) to JP. MAC and JDM are PhD researchers funded by the ISCIII (Grant No. RD06/0020/0013) and the Consejería de Salud, Junta de Andalucía (PI0581/2009), respectively. DS was funded by an EU Marie Curie Intra-European Fellowship (PIEF-GA-2008-221083) and by Breakthrough Breast Cancer. LRP is a PhD student recipient of a PFIS fellowship (Grant No. F109/00193). MB is a researcher funded by the ISCIII-Red de Biobancos RD09/0076/00085. SR works as a lab technician supported by the ISCIII (PI080971). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer Reviewe

The prognostic significance of tumor-infiltrating lymphocytes, PD-L1, BRCA mutation status and tumor mutational burden in early-stage high-grade serous ovarian carcinoma. A study by the Spanish Group for Ovarian Cancer Research (GEICO)

Early stages are under-represented in studies on the molecular and immune features of high-grade serous ovarian carcinoma (HGSOC), and specific studies focused on early-stage HGSOC are required for a better prognostic stratification and to personalize chemotherapy. The aim of this study was to determine the prognostic significance of CD8+ and CD4+ tumor-infiltrating lymphocytes (TILs), tumoral cell PD-L1 expression, BRCA mutational status and tumor mutation burden (TMB) in early-stage HGSOC. A retrospective study was performed on stage I and II HGSOC from the Molecular Reclassification of Early Stages of Ovarian Cancer (RECLAMO) cohort from the Spanish Group of Ovarian Cancer Research (GEICO). Centralized histological typing was performed based on morphological and immunohistochemical features. Intraepithelial (i) and stromal (s) CD8+ and CD4+ T cells and PD-L1 were evaluated on tissue microarrays by immunohistochemistry. BRCA1 and BRCA2 mutation status and TMB were analyzed in tumor DNA using next-generation sequencing. The study included 124 tumors. High iCD8+ (>20 TILs/core), low/intermediate CD4+ (35/core) were associated with favorable outcomes. Tumor cell PD-L1 expression (TPS ≥ 1) was present in only 8% of tumors. In total, 11 (16%) and 6 (9%) out of 69 HGSOC tested carried pathogenic or likely pathogenic BRCA1 or BRCA2 mutations, respectively. Median TMB of 40 tumors analyzed was 5.04 mutations/Mb and only 6 tumors had 10 or more mutations/Mb. BRCA status and TMB were not associated with TILs or prognosis. When compared with studies on advanced HGSOC, our results suggested that prognostic variables differed according to stage and that more studies focused on early stages of HGSOC are needed to better stratify these tumors: This work was supported by Instituto de Salud Carlos III (ISCIII) (grants PI19/01331, PI22/01892 and PMP22/00054); CIBERONC (grant CB16/12/00316); European Development Re gional Fund ‘A way to achieve Europe’ (FEDER), Spanish Group of Research in Ovarian Cancer (GEICO group); and by the Spanish Association Against Cancer Scientific Foundation (AECC)