Systematic human/zebrafish comparative identification of cis-regulatory activity around vertebrate developmental transcription factor genes

AbstractPan-vertebrate developmental cis-regulatory elements are discernible as highly conserved noncoding elements (HCNEs) and are often dispersed over large areas around the pleiotropic genes whose expression they control. On the loci of two developmental transcription factor genes, SOX3 and PAX6, we demonstrate that HCNEs conserved between human and zebrafish can be systematically and reliably tested for their regulatory function in multiple stable transgenes in zebrafish, and their genomic reach estimated with confidence using synteny conservation and HCNE density along these loci. HCNEs of both human and zebrafish function as specific developmental enhancers in zebrafish. We show that human HCNEs result in expression patterns in zebrafish equivalent to those in mouse, establishing zebrafish as a suitable model for large-scale testing of human developmental enhancers. Orthologous human and zebrafish enhancers underwent functional evolution within their sequence and often directed related but non-identical expression patterns. Despite an evolutionary distance of 450 million years, one pax6 HCNE drove expression in identical areas when comparing zebrafish vs. human HCNEs. HCNEs from the same area often drive overlapping patterns, suggesting that multiple regulatory inputs are required to achieve robust and precise complex expression patterns exhibited by developmental genes

Penerapan Community-Based Tourism di Desa Budo, Kabupaten Minahasa Utara

Budo Tourism Village is located in North Minahasa Regency, North Sulawesi. This tourist village which is included in the top 50 at the 2022 Indonesian Tourism Village Award (ADWI) has tourism potential in the form of natural and cultural attractions. The Budo Tourism Village was initiated by the village community by working with the government and academics to develop their tourism potential into tourist attractions and encourage the formation of tourist destinations which then gave birth to tourism activities whose management is carried out by the community (community-based tourism). The research was conducted to determine how far the implementation of Community-Based Tourism was carried out in the Budo Tourism Village based on the 10 stages of Community-Based Tourism Development.Desa Wisata Budo terletak di Kabupaten Minahasa Utara, Sulawesi Utara. Desa wisata yang masuk dalam 50 besar pada ajang Anugerah Desa Wisata Indonesia (ADWI) 2022 ini memiliki potensi pariwisata berupa daya tarik alam dan budaya. Desa Wisata Budo diinisiasi oleh masyarakat desa dengan cara berupaya menggandeng pemerintah dan akademisi untuk mengembangkan potensi wisata yang dimiliki menjadi atraksi wisata dan mendorong pembentukan destinasi wisata yang kemudian melahirkan aktivitas pariwisata yang pengelolaannya dilakukan oleh masyarakat (community-based tourism). Penelitian dilakukan dengan tujuan untuk mengetahui sejauh mana penerapan Community-Based Tourism dilaksanakan di Desa Wisata Budo berdasarkan 10 tahapan Community-Based Tourism Development

Circulating Concentrations of Vitamin B6 and Kidney Cancer Prognosis: A Prospective Case-Cohort Study

Prospective cohort studies have found that prediagnostic circulating vitamin B6 is inversely associated with both risk of kidney cancer and kidney cancer prognosis. We investigated whether circulating concentrations of vitamin B6 at kidney cancer diagnosis are associated with risk of death using a case-cohort study of 630 renal cell carcinoma (RCC) patients. Blood was collected at the time of diagnosis, and vitamin B6 concentrations were quantified using LC-MS/MS. Hazard ratios (HR) and 95% confidence intervals (CI) were calculated using Cox regression models. After adjusting for stage, age, and sex, the hazard was 3 times lower among those in the highest compared to the lowest fourth of B6 concentration (HR4vs1 0.33, 95% CI [0.18, 0.60]). This inverse association was solely driven by death from RCC (HR4vs1 0.22, 95% CI [0.11, 0.46]), and not death from other causes (HR4vs1 0.89, 95% CI [0.35, 2.28], p-interaction = 0.008). These results suggest that circulating vitamin B6 could provide additional prognostic information for kidney cancer patients beyond that afforded by tumour stage

Anotacijska shema i njezina evaluacija: primjer uvredljivoga jezika

The present paper focuses on the presentation and discussion of aspects of OFFENSIVE LANGUAGE linguistic annotation, including the creation, annotation practice, curation, and evaluation of an OFFENSIVE LANGUAGE annotation taxonomy scheme, that was first proposed in Lewandowska-Tomaszczyk et al. (2021). An extended offensive language ontology comprising 17 categories, structured in terms of 4 hierarchical levels, has been shown to represent the encoding of the defined offensive language schema, trained in terms of non-contextual word embeddings – i.e., Word2Vec and Fast Text, and eventually juxtaposed to the data acquired by using a pair wise training and testing analysis for existing categories in the HateBERT model (Lewandowska-Tomaszczyk et al. submitted). The study reports on the annotation practice in WG 4.1.1. Incivility in media and social media in the context of COST Action CA 18209 European network for Web-centred linguistic data science (Nexus Linguarum) with the INCEpTION tool (https://github.com/inception-project/inception) – a semantic annotation platform offering assistance in the annotation. The results partly support the proposed ontology of explicit offense and positive implicitness types to provide more variance among widely recognized types of figurative language (e.g., metaphorical, metonymic, ironic, etc.). The use of the annotation system and the representation of linguistic data were also evaluated in a series of the annotators’ comments, by means of a questionnaire and an open discussion. The annotation results and the questionnaire showed that for some of the categories there was low or medium inter-annotator agreement, and it was more challenging for annotators to distinguish between category items than between aspect items, with the category items offensive, insulting and abusive being the most difficult in this respect. The need for taxonomic simplification measures on the basis of these results has been recognized for further annotation practices.U ovome je radu predstavljen proces označavanja uvredljivoga jezika koji uključuje izradu klasifikacije toga jezika, označivačku praksu, vođenje procesa i evaluaciju. Klasifikacijska je shema prvi put predložena u Lewandowska-Tomaszczyk i dr. (2021). Proširena ontologija uvredljivoga jezika sadrži 17 kategorija posloženih u četiri hijerarhijske razine te tako predstavlja shemu uvredljivoga jezika koja je trenirana u okviru nekontekstualiziranih vektorskih prikaza riječi (engl. word embeddings) poput Word2Vec i Fast Text koji su naposljetku supostavljeni podatcima prikupljenima korištenjem analize parova i analize testiranja za postojeće kategorije u modelu HateBERT (Lewandowska-Tomaszczyk i dr., u postupku recenzije). U radu se izvještava o označivačkoj praksi u okviru radne grupe WG 4.1.1. Incivility in media and social media COST-ove akcije CA 18209 European network for Web-centred linguistic data science (Nexus Linguarum). Označavanje je provedeno u alatu INCEpTION (https://github.com/inception-project/inception) – platformi za semantičko označavanje koja ima ugrađene alate za takvu obradu podataka. Dobiveni rezultati podupiru predloženu ontologiju eksplicitnoga i implicitnoga uvredljivog jezika koja omogućuje veću raznovrsnost među već prepoznatim tipovima figurativnoga jezika (primjerice metafora, metonimija, ironija itd.). Upotreba sustava za označavanje i prikazivanje jezičnih podataka također je procijenjena u povratnim komentarima koje su pružili označivači. Komentari označivača prikupljeni su metodom upitnika te otvorenom raspravom. Na kraju je usustavljen niz preporuka za buduće označivačke prakse

Loss of chromosome Y leads to down regulation of KDM5D and KDM6C epigenetic modifiers in clear cell renal cell carcinoma

Recent genomic studies of sporadic clear cell renal cell carcinoma (ccRCC) have uncovered novel driver genes and pathways. Given the unequal incidence rates among men and women (male:female incidence ratio approaches 2:1), we compared the genome-wide distribution of the chromosomal abnormalities in both sexes. We observed a higher frequency for the somatic recurrent chromosomal copy number variations (CNVs) of autosomes in male subjects, whereas somatic loss of chromosome X was detected exclusively in female patients (17.1%). Furthermore, somatic loss of chromosome Y (LOY) was detected in about 40% of male subjects, while mosaic LOY was detected in DNA isolated from peripheral blood in 9.6% of them, and was the only recurrent CNV in constitutional DNA samples. LOY in constitutional DNA, but not in tumor DNA was associated with older age. Amongst Y-linked genes that were downregulated due to LOY, KDM5D and KDM6C epigenetic modifiers have functionally-similar X-linked homologs whose deficiency is involved in ccRCC progression. Our findings establish somatic LOY as a highly recurrent genetic defect in ccRCC that leads to downregulation of hitherto unsuspected epigenetic factors, and suggest that different mechanisms may underlie the somatic and mosaic LOY observed in tumors and peripheral blood, respectively

Dissecting the Transcriptional Regulatory Properties of Human Chromosome 16 Highly Conserved Non-Coding Regions

Non-coding DNA conservation across species has been often used as a predictor for transcriptional enhancer activity. However, only a few systematic analyses of the function of these highly conserved non-coding regions (HCNRs) have been performed. Here we use zebrafish transgenic assays to perform a systematic study of 113 HCNRs from human chromosome 16. By comparing transient and stable transgenesis, we show that the first method is highly inefficient, leading to 40% of false positives and 20% of false negatives. When analyzed in stable transgenic lines, a great majority of HCNRs were active in the central nervous system, although some of them drove expression in other organs such as the eye and the excretory system. Finally, by testing a fraction of the HCNRs lacking enhancer activity for in vivo insulator activity, we find that 20% of them may contain enhancer-blocking function. Altogether our data indicate that HCNRs may contain different types of cis-regulatory activity, including enhancer, insulators as well as other not yet discovered functions

Monocytes Contribute to Differential Immune Pressure on R5 versus X4 HIV through the Adipocytokine Visfatin/NAMPT

Background: The immune system exerts a diversifying selection pressure on HIV through cellular, humoral and innate mechanisms. This pressure drives viral evolution throughout infection. A better understanding of the natural immune pressure on the virus during infection is warranted, given the clinical interest in eliciting and sustaining an immune response to HIV which can help to control the infection. We undertook to evaluate the potential of the novel HIV-induced, monocyte-derived factor visfatin to modulate viral infection, as part of the innate immune pressure on viral populations. Results: We show that visfatin is capable of selectively inhibiting infection by R5 HIV strains in macrophages and resting PBMC in vitro, while at the same time remaining indifferent to or even favouring infection by X4 strains. Furthermore, visfatin exerts a direct effect on the relative fitness of R5 versus X4 infections in a viral competition setup. Direct interaction of visfatin with the CCR5 receptor is proposed as a putative mechanism for this differential effect. Possible in vivo relevance of visfatin induction is illustrated by its association with the dominance of CXCR4-using HIV in the plasma. Conclusions: As an innate factor produced by monocytes, visfatin is capable of inhibiting infections by R5 but not X4 strains, reflecting a potential selective pressure against R5 viruses. © 2012 Van den Bergh et al.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Exploring the Dynamic Range of the Kinetic Exclusion Assay in Characterizing Antigen-Antibody Interactions

Therapeutic antibodies are often engineered or selected to have high on-target binding affinities that can be challenging to determine precisely by most biophysical methods. Here, we explore the dynamic range of the kinetic exclusion assay (KinExA) by exploiting the interactions of an anti-DKK antibody with a panel of DKK antigens as a model system. By tailoring the KinExA to each studied antigen, we obtained apparent equilibrium dissociation constants (KD values) spanning six orders of magnitude, from approximately 100 fM to 100 nM. Using a previously calibrated antibody concentration and working in a suitable concentration range, we show that a single experiment can yield accurate and precise values for both the apparent KD and the apparent active concentration of the antigen, thereby increasing the information content of an assay and decreasing sample consumption. Orthogonal measurements obtained on Biacore and Octet label-free biosensor platforms further validated our KinExA-derived affinity and active concentration determinations. We obtained excellent agreement in the apparent affinities obtained across platforms and within the KinExA method irrespective of the assay orientation employed or the purity of the recombinant or native antigens

Spectrum and characterisation of BRCA1 and BRCA2 deleterious mutations in high-risk Czech patients with breast and/or ovarian cancer

<p>Abstract</p> <p>Background</p> <p>The incidence of breast cancer has doubled over the past 20 years in the Czech Republic. Hereditary factors may be a cause of young onset, bilateral breast or ovarian cancer, and familial accumulation of the disease. <it>BRCA1 </it>and <it>BRCA2 </it>mutations account for an important fraction of hereditary breast and ovarian cancer cases. One thousand and ten unrelated high-risk probands with breast and/or ovarian cancer were analysed for the presence of a <it>BRCA1 </it>or <it>BRCA2 </it>gene mutation at the Masaryk Memorial Cancer Institute (Czech Republic) during 1999–2006.</p> <p>Methods</p> <p>The complete coding sequences and splice sites of both genes were screened, and the presence of large intragenic rearrangements in <it>BRCA1 </it>was verified. Putative splice-site variants were analysed at the cDNA level for their potential to alter mRNA splicing.</p> <p>Results</p> <p>In 294 unrelated families (29.1% of the 1,010 probands) pathogenic mutations were identified, with 44 different <it>BRCA1 </it>mutations and 41 different <it>BRCA2 </it>mutations being detected in 204 and 90 unrelated families, respectively. In total, three <it>BRCA1 </it>founder mutations (c.5266dupC; c.3700_3704del5; p.Cys61Gly) and two <it>BRCA2 </it>founder mutations (c.7913_7917del5; c.8537_8538del2) represent 52% of all detected mutations in Czech high-risk probands. Nine putative splice-site variants were evaluated at the cDNA level. Three splice-site variants in <it>BRCA1 </it>(c.302-3C>G; c.4185G>A and c.4675+1G>A) and six splice-site variants in <it>BRCA2 </it>(c.475G>A; c.476-2>G; c.7007G>A; c.8755-1G>A; c.9117+2T>A and c.9118-2A>G) were demonstrated to result in aberrant transcripts and are considered as deleterious mutations.</p> <p>Conclusion</p> <p>This study represents an evaluation of deleterious genetic variants in the <it>BRCA1 </it>and <it>2 </it>genes in the Czech population. The classification of several splice-site variants as true pathogenic mutations may prove useful for genetic counselling of families with high risk of breast and ovarian cancer.</p

Transcriptome map of mouse isochores

<p>Abstract</p> <p>Background</p> <p>The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we investigate how base composition affects mammalian gene expression, an issue of prime practical and evolutionary interest.</p> <p>Results</p> <p>We present the transcriptome map of the mouse isochores (DNA segments with a fairly homogeneous base composition) for the three different tissues and the effects of isochores' base composition on their expression activity. Our analyses also cover the relations between the genes' expression activity and their localization in the isochore families.</p> <p>Conclusions</p> <p>This study is the first where next-generation sequencing data are used to associate the effects of both genomic and genic compositional properties to their corresponding expression activity. Our findings confirm previous results, and further support the existence of a relationship between isochores and gene expression. This relationship corroborates that isochores are primarily a product of evolutionary adaptation rather than a simple by-product of neutral evolutionary processes.</p