cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.14320375
title: Identification of soybean trans-factors associated with plastid RNA editing sites

description: Abstract RNA editing is a posttranscriptional process that changes nucleotide sequences, among which cytosine-to-uracil by a deamination reaction can revert non-neutral codon mutations. Pentatricopeptide repeat (PPR) proteins comprise a family of RNA-binding proteins, with members acting as editing trans-factors that recognize specific RNA cis-elements and perform the deamination reaction. PPR proteins are classified into P and PLS subfamilies. In this work, we have designed RNA biotinylated probes based in soybean plastid RNA editing sites to perform trans-factor specific protein isolation. Soybean cis-elements from these three different RNA probes show differences in respect to other species. Pulldown samples were submitted to mass spectrometry for protein identification. Among detected proteins, five corresponded to PPR proteins. More than one PPR protein, with distinct functional domains, was pulled down with each one of the RNA probes. Comparison of the soybean PPR proteins to Arabidopsis allowed identification of the closest homologous. Differential gene expression analysis demonstrated that the PPR locus Glyma.02G174500 doubled its expression under salt stress, which correlates with the increase of its potential rps14 editing. The present study represents the first identification of RNA editing trans-factors in soybean. Data also indicated that potential multiple trans-factors should interact with RNA cis-elements to perform the RNA editing.
DOI: 10.6084/m9.figshare.14320378.v1
title: Screening of BRCA1 variants c.190T&gt;C, 1307delT, g.5331G&gt;A and c.2612C&gt;T in breast cancer patients from North India

description: Abstract The polymorphic variants of BRCA1, which lead to amino acid substitutions, have a known pathogenic role in breast cancer. The present study investigated in North Indian breast cancer patients the association of risk with four reported pathogenic variants of BRCA1: c.190T&gt;C (p.Cys64Arg), 1307delT, g.5331G&gt;A (p.G1738R) and c.2612C&gt;T (p.Pro871Leu). Genotyping was done by PCR-RFLP method in 255 clinically confirmed breast cancer patients and 255 age and gender matched healthy individuals. For c.190T&gt;C, 1307delT and g.5331G&gt;A, all the patients and controls had the wild-type genotype indicating no association with breast cancer risk. For c.2612C&gt;T polymorphism, the frequency of the CC, CT, and TT genotypes was 14.5 vs 15.7%, 59.6 vs 53.7% and 25.9 vs 30.6% in breast cancer patients and controls respectively. The frequency of heterozygotes (CT genotype) was higher in cases than controls but the difference was not statistically significant. Genetic model analysis showed no association of the four analyzed BRCA1 variants with breast cancer risk with any model. The studied variants were not associated with the risk of breast cancer in Punjab, North west India, suggesting a need for further screening of other BRCA1 variants. It is the first reported study on these 4 variants from India.
DOI: 10.6084/m9.figshare.14320378
title: Screening of BRCA1 variants c.190T&gt;C, 1307delT, g.5331G&gt;A and c.2612C&gt;T in breast cancer patients from North India

description: Abstract The polymorphic variants of BRCA1, which lead to amino acid substitutions, have a known pathogenic role in breast cancer. The present study investigated in North Indian breast cancer patients the association of risk with four reported pathogenic variants of BRCA1: c.190T&gt;C (p.Cys64Arg), 1307delT, g.5331G&gt;A (p.G1738R) and c.2612C&gt;T (p.Pro871Leu). Genotyping was done by PCR-RFLP method in 255 clinically confirmed breast cancer patients and 255 age and gender matched healthy individuals. For c.190T&gt;C, 1307delT and g.5331G&gt;A, all the patients and controls had the wild-type genotype indicating no association with breast cancer risk. For c.2612C&gt;T polymorphism, the frequency of the CC, CT, and TT genotypes was 14.5 vs 15.7%, 59.6 vs 53.7% and 25.9 vs 30.6% in breast cancer patients and controls respectively. The frequency of heterozygotes (CT genotype) was higher in cases than controls but the difference was not statistically significant. Genetic model analysis showed no association of the four analyzed BRCA1 variants with breast cancer risk with any model. The studied variants were not associated with the risk of breast cancer in Punjab, North west India, suggesting a need for further screening of other BRCA1 variants. It is the first reported study on these 4 variants from India.
DOI: 10.6084/m9.figshare.14320380
title: Making a bat: The developmental basis of bat evolution

description: Abstract Bats are incredibly diverse, both morphologically and taxonomically. Bats are the only mammalian group to have achieved powered flight, an adaptation that is hypothesized to have allowed them to colonize various and diverse ecological niches. However, the lack of fossils capturing the transition from terrestrial mammal to volant chiropteran has obscured much of our understanding of bat evolution. Over the last 20 years, the emergence of evo-devo in non-model species has started to fill this gap by uncovering some developmental mechanisms at the origin of bat diversification. In this review, we highlight key aspects of studies that have used bats as a model for morphological adaptations, diversification during adaptive radiations, and morphological novelty. To do so, we review current and ongoing studies on bat evolution. We first investigate morphological specialization by reviewing current knowledge about wing and face evolution. Then, we explore the mechanisms behind adaptive diversification in various ecological contexts using vision and dentition. Finally, we highlight the emerging work into morphological novelties using bat wing membranes.
DOI: 10.6084/m9.figshare.14320380.v1
title: Making a bat: The developmental basis of bat evolution

description: Abstract Bats are incredibly diverse, both morphologically and taxonomically. Bats are the only mammalian group to have achieved powered flight, an adaptation that is hypothesized to have allowed them to colonize various and diverse ecological niches. However, the lack of fossils capturing the transition from terrestrial mammal to volant chiropteran has obscured much of our understanding of bat evolution. Over the last 20 years, the emergence of evo-devo in non-model species has started to fill this gap by uncovering some developmental mechanisms at the origin of bat diversification. In this review, we highlight key aspects of studies that have used bats as a model for morphological adaptations, diversification during adaptive radiations, and morphological novelty. To do so, we review current and ongoing studies on bat evolution. We first investigate morphological specialization by reviewing current knowledge about wing and face evolution. Then, we explore the mechanisms behind adaptive diversification in various ecological contexts using vision and dentition. Finally, we highlight the emerging work into morphological novelties using bat wing membranes.
DOI: 10.6084/m9.figshare.14320386.v1
title: Haplotypic characterization of BRCA1 c.5266dupC, the prevailing mutation in Brazilian hereditary breast/ovarian cancer

description: Abstract Specific pathogenic mutations associated with breast cancer development can vary between ethnical groups. One example is BRCA1 c.5266dupC that was first described as a founder mutation in the Ashkenazi Jewish population, but was later also found in other populations. In Brazil, this mutation corresponds to 20% of pathogenic BRCA1 variants reported. Our objective was to investigate the haplotype component of a group of Brazilian families who inherited c.5266dupC in the BRCA1 gene and to verify the ancestry contribution from European, African, and Amerindian origins. Fourteen probands carrying c.5266dupC and 16 relatives (carriers and non-carriers) were investigated. The same haplotype was observed segregating within all the families analyzed, revealing no recombinants in a region of 0.68 Mb. Ancestry analysis demonstrated that the European component was predominant among probands. The BRCA1 c.5266dupC analysis indicates that there was a founder effect in the Brazilian population.
DOI: 10.6084/m9.figshare.14320381
title: Newborn screening for lysosomal disorders in Brazil: A pilot study using customized fluorimetric assays

description: Abstract Lysosomal storage disorders (LSDs) are a group of genetic disorders characterized by deficiency of specific lysosomal enzymes. In general, patients are clinically normal at birth, and progressively develop severe signs and symptoms. Diagnosis is usually made several years after onset of manifestations, preventing patients to have the benefits of the early treatment. Newborn screening programs are being considered for LSDs to allow early diagnosis and treatment. The present study evaluated the feasibility of a customized screening approach based on modified fluorometric assays with reduced amounts of reagents, substrates and samples for: mucopolysaccharidosis (MPS) type I (MPS I), MPS VI, Fabry, Gaucher, and Pompe diseases. We also evaluated the advantages of including blood chitotriosidase and urinary glycosaminoglycans in the protocol. By the measurement of the specific disease-associated enzymes (plus blood chitotriosidase and urinary glycosaminoglycans) we analyzed 834 de-identified DBS of unselected newborns. No positive case was detected, and the false-positive rates were low. Taking into consideration the limitations of this methodology, we believe that, after defining proper cutoffs, it could be a viable alternative to provide NBS for LSDs by laboratories that may not be able to afford the commercial methods available.
DOI: 10.6084/m9.figshare.14320381.v1
title: Newborn screening for lysosomal disorders in Brazil: A pilot study using customized fluorimetric assays

description: Abstract Lysosomal storage disorders (LSDs) are a group of genetic disorders characterized by deficiency of specific lysosomal enzymes. In general, patients are clinically normal at birth, and progressively develop severe signs and symptoms. Diagnosis is usually made several years after onset of manifestations, preventing patients to have the benefits of the early treatment. Newborn screening programs are being considered for LSDs to allow early diagnosis and treatment. The present study evaluated the feasibility of a customized screening approach based on modified fluorometric assays with reduced amounts of reagents, substrates and samples for: mucopolysaccharidosis (MPS) type I (MPS I), MPS VI, Fabry, Gaucher, and Pompe diseases. We also evaluated the advantages of including blood chitotriosidase and urinary glycosaminoglycans in the protocol. By the measurement of the specific disease-associated enzymes (plus blood chitotriosidase and urinary glycosaminoglycans) we analyzed 834 de-identified DBS of unselected newborns. No positive case was detected, and the false-positive rates were low. Taking into consideration the limitations of this methodology, we believe that, after defining proper cutoffs, it could be a viable alternative to provide NBS for LSDs by laboratories that may not be able to afford the commercial methods available.
DOI: 10.6084/m9.figshare.14320386
title: Haplotypic characterization of BRCA1 c.5266dupC, the prevailing mutation in Brazilian hereditary breast/ovarian cancer

description: Abstract Specific pathogenic mutations associated with breast cancer development can vary between ethnical groups. One example is BRCA1 c.5266dupC that was first described as a founder mutation in the Ashkenazi Jewish population, but was later also found in other populations. In Brazil, this mutation corresponds to 20% of pathogenic BRCA1 variants reported. Our objective was to investigate the haplotype component of a group of Brazilian families who inherited c.5266dupC in the BRCA1 gene and to verify the ancestry contribution from European, African, and Amerindian origins. Fourteen probands carrying c.5266dupC and 16 relatives (carriers and non-carriers) were investigated. The same haplotype was observed segregating within all the families analyzed, revealing no recombinants in a region of 0.68 Mb. Ancestry analysis demonstrated that the European component was predominant among probands. The BRCA1 c.5266dupC analysis indicates that there was a founder effect in the Brazilian population.
DOI: 10.6084/m9.figshare.14320387
title: Leigh syndrome in a patient with a novel C12orf65 pathogenic variant: case report and literature review

description: Abstract Leigh syndrome is an early onset progressive disorder caused by defects in mitochondrial oxidative phosphorylation. Pathogenic variants in nuclear and mitochondrial genes are associated with the syndrome. Homozygous pathogenic variants in the C12orf65 gene impair the mitochondrial oxidative phosphorylation system. We describe a new case of Leigh syndrome caused by a novel pathogenic variant of the C12orf65 gene resulting in the lack of the Gly-Gly-Gln (GGQ) domain in the predicted protein, and review clinical and molecular data from previously reported patients. Our study supports that the phenotype caused by C12orf65 gene variants is heterogeneous and varies from spastic paraparesis to Leigh syndrome. Loss-of-function variants are more likely to cause the disease, and variants affecting the GGQ domain tend to be associated with more severe phenotypes, reinforcing a possible genotype-phenotype correlation.
DOI: 10.6084/m9.figshare.14320387.v1
title: Leigh syndrome in a patient with a novel C12orf65 pathogenic variant: case report and literature review

description: Abstract Leigh syndrome is an early onset progressive disorder caused by defects in mitochondrial oxidative phosphorylation. Pathogenic variants in nuclear and mitochondrial genes are associated with the syndrome. Homozygous pathogenic variants in the C12orf65 gene impair the mitochondrial oxidative phosphorylation system. We describe a new case of Leigh syndrome caused by a novel pathogenic variant of the C12orf65 gene resulting in the lack of the Gly-Gly-Gln (GGQ) domain in the predicted protein, and review clinical and molecular data from previously reported patients. Our study supports that the phenotype caused by C12orf65 gene variants is heterogeneous and varies from spastic paraparesis to Leigh syndrome. Loss-of-function variants are more likely to cause the disease, and variants affecting the GGQ domain tend to be associated with more severe phenotypes, reinforcing a possible genotype-phenotype correlation.
DOI: 10.5281/zenodo.4639759
title: SciExpeM - 10.5281/zenodo.4639759

description: "Further study on the ignition delay times of propane–hydrogen–oxygen– argon mixtures: Effect of equivalence ratio" Chenglong Tang, Xingjia Man, Liangjie Wei, Lun Pan, Zuohua Huang
DOI: 10.6084/m9.figshare.14320389
title: Genetic variability of blood groups in southern Brazil

description: Abstract We evaluated genetic variability among the blood groups Kell (c.578C &gt; T and c.1790T &gt; C), Kidd (c.838A &gt; G), Duffy (c.125A &gt; G, c.265C &gt; T and c.1-67T &gt; C), Diego (c.2561C &gt; T), MNS (c.143T &gt; C) and Rh (c.676G &gt; C) in Rio Grande do Sul in southern Brazil. Genetic profiling from 382 volunteer blood donors was performed through allelic discrimination assays using a hydrolysis probe (TaqMan®) with a real-time PCR system. The sample was divided into two groups: Euro-Brazilian and Afro-Brazilian. A comparison with studies from other regions of Brazil and the 1000 Genomes Database showed significant differences for almost all polymorphisms evaluated in our population. Population differentiation between the Euro- and Afro-Brazilian groups was low (FST value 0.055). However, when each locus was evaluated individually, KEL*06 and FY*02N.01 allele frequencies were significantly higher in the Afro-Brazilian group than in the Euro-Brazilian group. Ethnic classification that uses phenotypic criteria to find blood units with rare antigens may be important when there is a need to detect blood units with an absence of Duffy antigens. There is also a greater probability of finding donors in the Afro-Brazilian group. Taken together, the data indicate strong European and African contributions to the gene pool, with intense admixture.
DOI: 10.6084/m9.figshare.14320389.v1
title: Genetic variability of blood groups in southern Brazil

description: Abstract We evaluated genetic variability among the blood groups Kell (c.578C &gt; T and c.1790T &gt; C), Kidd (c.838A &gt; G), Duffy (c.125A &gt; G, c.265C &gt; T and c.1-67T &gt; C), Diego (c.2561C &gt; T), MNS (c.143T &gt; C) and Rh (c.676G &gt; C) in Rio Grande do Sul in southern Brazil. Genetic profiling from 382 volunteer blood donors was performed through allelic discrimination assays using a hydrolysis probe (TaqMan®) with a real-time PCR system. The sample was divided into two groups: Euro-Brazilian and Afro-Brazilian. A comparison with studies from other regions of Brazil and the 1000 Genomes Database showed significant differences for almost all polymorphisms evaluated in our population. Population differentiation between the Euro- and Afro-Brazilian groups was low (FST value 0.055). However, when each locus was evaluated individually, KEL*06 and FY*02N.01 allele frequencies were significantly higher in the Afro-Brazilian group than in the Euro-Brazilian group. Ethnic classification that uses phenotypic criteria to find blood units with rare antigens may be important when there is a need to detect blood units with an absence of Duffy antigens. There is also a greater probability of finding donors in the Afro-Brazilian group. Taken together, the data indicate strong European and African contributions to the gene pool, with intense admixture.
DOI: 10.5281/zenodo.4639758
title: SciExpeM - 10.5281/zenodo.4639759

description: "Further study on the ignition delay times of propane–hydrogen–oxygen– argon mixtures: Effect of equivalence ratio" Chenglong Tang, Xingjia Man, Liangjie Wei, Lun Pan, Zuohua Huang
DOI: 10.6084/m9.figshare.14320390
title: DNA damage, oxidative stress, and inflammation in children with celiac disease

description: Abstract The objective of this study was to evaluate the level of genomic instability in patients with celiac disease and to establish a relationship between inflammation, oxidative stress, and DNA damage in these patients. Myeloperoxidase (MPO) activity, adenosine deaminase, nitric oxide (NOx), thiobarbituric acid, catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), and DNA damage were evaluated in peripheral blood samples from 47 celiac disease patients and 31 controls. Patients with celiac disease presented higher levels of DNA damage in comparison to controls (p=0.023). This difference was also observed for markers of oxidative stress, such as CAT (p=0.011) and SOD (p=0.013), and inflammatory markers such as MPO (p &lt; 0.001) and NOx (p=0.009). Positive correlations were found between DNA damage levels and the values of CAT (r=0.405; p=0.009) and SOD (r=0.516; p &lt; 0.001). Positive correlations were also found between GPx and NOx (r=0.349; p=0.030) and MPO and NOx (r=0.239; p=0.039). CAT and NOx showed a negative correlation (r= −0.315; p=0.042). In conclusion, intestinal inflammation can have systemic effects, causing an imbalance between oxidant and antioxidant markers, which may promote increased levels of DNA damage.
DOI: 10.6084/m9.figshare.14320390.v1
title: DNA damage, oxidative stress, and inflammation in children with celiac disease

description: Abstract The objective of this study was to evaluate the level of genomic instability in patients with celiac disease and to establish a relationship between inflammation, oxidative stress, and DNA damage in these patients. Myeloperoxidase (MPO) activity, adenosine deaminase, nitric oxide (NOx), thiobarbituric acid, catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GPx), and DNA damage were evaluated in peripheral blood samples from 47 celiac disease patients and 31 controls. Patients with celiac disease presented higher levels of DNA damage in comparison to controls (p=0.023). This difference was also observed for markers of oxidative stress, such as CAT (p=0.011) and SOD (p=0.013), and inflammatory markers such as MPO (p &lt; 0.001) and NOx (p=0.009). Positive correlations were found between DNA damage levels and the values of CAT (r=0.405; p=0.009) and SOD (r=0.516; p &lt; 0.001). Positive correlations were also found between GPx and NOx (r=0.349; p=0.030) and MPO and NOx (r=0.239; p=0.039). CAT and NOx showed a negative correlation (r= −0.315; p=0.042). In conclusion, intestinal inflammation can have systemic effects, causing an imbalance between oxidant and antioxidant markers, which may promote increased levels of DNA damage.
DOI: 10.6084/m9.figshare.14320392
title: Importance of naturalized breeds as a base for the formation of exotic sheep (Ovis aries) breeds in tropical altitude regions

description: Abstract Recent molecular tools and technologies have marked the discovery of the origin and domestication processes of a wide variety of species, using either genomic or mitochondrial molecular markers to provide input for selection programs, as well as the management and conservation of animal breeds. This study aimed to analyze genes of mitochondrial DNA of the following sheep (Ovis aries) breeds: Pantaneira, Bergamácia, Dorper, White Dorper, Ile de France and Hampshire Down, to obtain their population genetic parameters and investigate the origin of these sheep populations reared in the State of Mato Grosso do Sul. The analysis of mitochondrial DNA allowed to infer their phylogenetic relationships and revealed significant differences among them when compared with each other and with sequences obtained from GenBank. Through the formation of haplotypes, it was noted that the Pantaneira breed served as the maternal basis for the formation of the other breeds reared in the region, and it was possible to suggest a European origin for the sheep populations studied.
DOI: 10.6084/m9.figshare.12210347
title: Genetic diversity in populations of African mahogany (Khaya grandioliola C. DC.) introduced in Brazil

description: Abstract Given its high-valued wood, the African mahogany (Khaya grandifoliola) has been envisaged as a renewable source of tropical hardwoods in Brazil. However, there are concerns about the hypothesized low diversity among the few K. grandifoliola germplasm sources introduced in the country. Using eight microsatellite markers, we evaluated the genetic diversity and divergence among 53 superior trees selected from three provenances of K. grandifoliola located in the state of Para. These populations are among the oldest plantations (&gt;15 years) in Brazil and, therefore, the country's main seed sources. The average number of alleles per locus was 5.9, expected heterozygosity was moderate (^=0.56) and lower than the high observed heterozygosity (HO=0.74). Therefore, the intrapopulation fixation index was negative (f=-0.31) indicating the possibility that selection of superior trees might have favored heterozygous plants with heterosis. No genetic structure was observed between provenances. The genetic diversity observed within selected trees, with an effective population size (Ne) of 30.4, is comparable to that of natural populations of African and Brazilian mahoganies. Therefore, our results contradict the idea that the genetic diversity of K. grandifoliola introduced in Brazil is low and show that our germplasm can be exploited for breeding purposes.