cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.5121160.v1
title: Supplementary Material for: Evidence for Hermaphroditism in the <i>Squalius alburnoides</i> Allopolyploid Fish Complex

description: Fish show an amazing variety of mechanisms of sex determination and modes of reproduction. Of these, simultaneous hermaphroditism has rarely been described. Here, we report a novel case of this phenomenon in adults of the <i>Squalius alburnoides</i> allopolyploid cyprinid complex. We found evidence for the simultaneous presence of mature male and female gonads on the basis of gonad gross morphology and histological analyses. Different stages of male and female germ cell maturation were identified, including motile spermatocytes. We hypothesize on the genetic and/or environmental causes of this phenomenon.
DOI: 10.6084/m9.figshare.5121163.v1
title: Supplementary Material for: Alterations in Lipid and Carbohydrate Metabolism in Patients with Classic Congenital Adrenal Hyperplasia due to 21-Hydroxylase Deficiency

description: <i>Background:</i> Classic 21-hydroxylase deficiency (21HD) presents some traits of the metabolic syndrome. <i>Aim:</i> To characterize discrete alterations of lipid and carbohydrate metabolism in children and young adults with classic 21HD, which could predict early atherogenesis. <i>Patients and Methods:</i> Twenty-seven Caucasian patients with classic 21HD (4–31 years); 27 sex-, age- and BMI-matched controls. Clinical parameters, hormonal status and genotype were assessed in all patients. Lipid parameters, including relative (%) and absolute (mg/dl) small-dense low-density lipoproteins subfractions (sd-LDL) were measured in patients and controls. Oral glucose tolerance tests were performed in both groups. <i>Results:</i> sd-LDL (%) was significantly higher in patients than controls (39.7 ± 5.9 vs. 35.5 ± 5.7%; p = 0.008). The same applies for absolute sd-LDL (mg/dl) (42.6 ± 11.9 vs. 36.4 ± 7.5; p = 0.029). HDL-cholesterol was lower in patients (p = 0.032). Fasting glucose and insulin were significantly higher in patients. Similar differences were noticed for HOMA-IR (p = 0.001), IRI (p = 0.001) and HOMA-B (p = 0.002). IRI correlated directly and significantly with the total hydrocortisone dose and the duration of treatment. Fasting glucose correlated with absolute sd-LDL. No obvious differences were seen between clinical forms or genotype groups. <i>Conclusions:</i> Substitution therapy should be adapted particularly at young ages to prevent early atherogenesis and cardiovascular risk in later life.
DOI: 10.6084/m9.figshare.5121151
title: Supplementary Material for: Recombinant Fusion Proteins Assembling Der p 1 and Der p 2 Allergens from <i>Dermatophagoides pteronyssinus</i>

description: <i>Background:</i> Fusion proteins assembling multiple allergens can be engineered by recombinant DNA technologies in order to produce tools for diagnostic and immunotherapeutic purposes. Herein, we developed and characterized chimeras assembling Der p 1 and Der p 2 allergens as potential candidate vaccines against house dust mite allergy. <i>Methods:</i> Fusion proteins encompassing Der p 2 with either mature or proDer p 1 were expressed in <i>Escherichia coli</i> or <i>Pichia pastoris</i>. Forms with mutation in Der p 1 catalytic site were also engineered. Purified chimeras were characterized by immunoblotting, circular dichroism, disulfide bond mapping, basophil and T lymphocyte stimulation assays. <i>Results:</i> Four fusion proteins were expressed in <i>E. coli </i>as inclusion bodies, whereas only chimeras comprising proDer p 1 were obtained in yeast. All such hybrids formed polymers and aggregates, and yeast-expressed chimeras were unstable. Circular dichroism analysis performed after refolding of bacteria expressed chimeras encompassing mature Der p 1 confirmed partial folding, consistent with the occurrence of both correct and inappropriate intramolecular disulfide bonds. All fusion molecules were recognized by Der p 1- and Der p 2-specific human IgEs, monoclonal and polyclonal antibodies. Fusion proteins activate basophils from mite-allergic patients and trigger the proliferation of specific CD4+ T cells, albeit to a lower level when compared to individual allergens. <i>Conclusions:</i> Production of multiple Der p 1-Der p 2 fusion proteins exhibiting partial folding and proper antigenic properties has been achieved. Nonetheless, significant solubility and stability issues currently limit the application of such chimeras for immunotherapy or diagnostic.
DOI: 10.6084/m9.figshare.5121148
title: Supplementary Material for: Association of <i>AHSG</i> Gene Polymorphisms and Aortic Stiffness in Peritoneal Dialysis Patients

description: <i>Background/Aims:</i> Fetuin-A is a negative acute-phase reactant and extraosseous calcification inhibitor. Decreased serum concentration of fetuin-A is independently related to all-cause and cardiovascular mortality in dialysis patients. Our aim is to investigate the association between the genetic polymorphism of α<sub>2</sub>-Heremans-Schmid-glycoprotein <i>(AHSG)</i> encoding fetuin-A and its serum concentration, vascular calcification, and aortic stiffness in peritoneal dialysis (PD) patients. <i>Method:</i> A total of six single nucleotide polymorphisms (SNPs) in the <i>AHSG</i> gene were genotyped and evaluated for association with serum fetuin-A level, quantitative measures of vascular calcification and aortic stiffness represented by heart-to-femoral pulse wave velocity (hfPWV). <i>Results:</i> Five SNPs in the <i>AHSG</i> gene were nominally associated with the serum fetuin-A level in our PD patients. In haplotype analyses, there were haplotypes positively (H1; AGCA, H2; CC) and inversely (H1; TTCG, H2; TT) related with the serum fetuin-A level. The serum fetuin-A level inversely and independently correlated with hfPWV. Moreover, the serum fetuin-A concentration was a determinant for the simple vascular calcification score (SVCS), which subsequently was associated with hfPWV. <i>Conclusions:</i> Our study showed an association between <i>AHSG</i> polymorphism and its serum concentration, and also revealed an association of the serum fetuin-A level with SVCS and aortic stiffness in PD patients.
DOI: 10.6084/m9.figshare.5121157.v1
title: Supplementary Material for: Progressive Sensorineural Hearing Loss and Normal Vestibular Function in a Dutch DFNB7/11 Family with a Novel Mutation in <i>TMC1</i>

description: In a Dutch family with autosomal recessive hearing loss, genome-wide single-nucleotide polymorphism analysis mapped the genetic defect to the DFNB7/11 locus. A novel homozygous A-to-G change in the TMC1 gene was detected near the splice donor site of intron 19 (c.1763+3A→G) segregating with the hearing loss in this family. One of the 6 transmembrane domains and the actual TMC channel domain are predicted to be absent in the mutant protein. The sensorineural hearing impairment in this DFNB7/11 family has a postlingual onset. Audiometric analysis initially showed a steeply downward-sloping threshold configuration. The progressive phenotype in this family resembles the phenotype previously described for families with dominant TMC1 mutations (DFNA36) rather than that of families with recessive TMC1 mutations (DFNB7/11) which invariably cause severe-to-profound prelingual hearing impairment.
DOI: 10.6084/m9.figshare.5121139
title: Supplementary Material for: Polyunsaturated Fatty Acids, DNA Repair Single Nucleotide Polymorphisms and Colorectal Cancer in the Singapore Chinese Health Study

description: Animal and in vitrostudies support a role for polyunsaturated fatty acids (PUFAs) in colon carcinogenesis; however, the epidemiological evidence is inconclusive. Recently, we investigated their role within the Singapore Chinese Health Study, a population-based cohort of Singapore Chinese men and women. We reported that a high intake of marine n–3 PUFAs was associated with an increased risk of colorectal cancer (CRC). Oxidation of PUFAs incorporated into cell membranes generates lipid hydroperoxides, which can be mutagenic. In this report, we investigated whether single nucleotide polymorphisms (SNPs) in DNA repair genes modified the effect of PUFAs on CRC risk using a nested case-control study within the Singapore Chinese Health Study. We genotyped 1,181 controls and 311 cases (180 colon and 131 rectal cancer) for SNPs in the <i>XRCC1</i> (Arg194Trp, Arg399Gln), <i>OGG1 </i>(Ser326Cys), <i>PARP </i>(Val762Ala, Lys940Arg), and <i>XPD</i> (Asp312Asn, Lys751Gln) genes. We observed that the <i>PARP</i> Val762Ala SNP modified the association between marine n–3 PUFA and rectal cancer risk, with no evidence of interaction among colon cancer (heterogeneity test p = 0.003). Our results suggest a positive association between high intake of marine n–3 PUFA and rectal cancer risk among carriers of at least one <i>PARP </i>codon 762 Ala allele (odds ratio = 1.7, 95% confidence interval = 1.1–2.7).
DOI: 10.6084/m9.figshare.5121136
title: Supplementary Material for: An 8-Week High-Fat Diet Induces Obesity and Insulin Resistance with Small Changes in the Muscle Transcriptome of C57BL/6J Mice

description: <i>Background:</i> Skeletal muscle is responsible for most of the insulin-stimulated glucose uptake and metabolism. Therefore, it plays an important role in the development of insulin resistance, one of the characteristics of the metabolic syndrome (MS). As the prevalence of the MS is increasing, there is an urgent need for more effective intervention strategies. <i>Methods:</i> C57BL/6J mice were fed an 8-week low-fat diet (10 kcal%; LFD) or high-fat diet (45 kcal%; HFD). Microarray analysis was performed by using two comparisons: (1) 8-week HFD transcriptome versus 8-week LFD transcriptome and (2) transcriptome of mice sacrificed at the start of the intervention versus 8-week LFD transcriptome and 8-week HFD transcriptome, respectively. <i>Results:</i> Although an 8-week HFD induced obesity and impaired insulin sensitivity, HFD-responsive changes in the muscle transcriptome were relatively small (&lt;1.3-fold). In fact, 8-weeks of aging induced more pronounced changes than an HFD. One comparison revealed the transcriptional downregulation of the mito- gen-activated protein kinase cascade, whereas both comparisons showed the upregulation of fatty acid oxidation, demonstrating that the two comparison strategies are confirmative as well as complementary. <i>Conclusion:</i> We suggest using complementary analysis strategies in the genome-wide search for gene expression changes induced by mild interventions, such as an HFD.
DOI: 10.6084/m9.figshare.5121142
title: Supplementary Material for: Dendritic Spine Alterations in Neocortical Pyramidal Neurons following Postnatal Neuronal Nogo-A Knockdown

description: The myelin-associated protein Nogo-A is a well-known inhibitor of axonal regeneration and compensatory plasticity, yet functions of neuronal Nogo-A are not as clear. The present study examined the effects of decreased levels of neuronal Nogo-A on dendritic spines of developing neocortical neurons. Decreased Nogo-A levels in these neurons resulted in lowered spine density and an increase in filopodial type protrusions. These results suggest a role for neuronal Nogo-A in maintaining a spine phenotype in neocortical pyramidal cells.
DOI: 10.6084/m9.figshare.5121130
title: Supplementary Material for: Analysis of Segmental Duplications, Mouse Genome Synteny and Recurrent Cancer-Associated Amplicons in Human Chromosome 6p21–p12

description: It has been proposed that regions of microhomology in the human genome could facilitate genomic rearrangements, copy number transitions, and rapid genomic change during tumor progression. To investigate this idea, this study examines the role of repetitive sequence elements, and corresponding syntenic mouse genomic features, in targeting cancer-associated genomic instability of specific regions of the human genome. Automated database-mining algorithms designed to search for frequent copy number transitions and genomic breakpoints were applied to 2 publicly-available online databases and revealed that 6p21–p12 is one of the regions of the human genome most frequently involved in tumor-specific alterations. In these analyses, 6p21–p12 exhibited the highest frequency of genomic amplification in osteosarcomas. Analysis of repetitive elements in regions of homology between human chromosome 6p and the syntenic regions of the mouse genome revealed a strong association between the location of segmental duplications greater than 5 kilobase-pairs and the position of discontinuities at the end of the syntenic region. The presence of clusters of segmental duplications flanking these syntenic regions also correlated with a high frequency of amplification and genomic alteration. Collectively, the experimental findings, in silico analyses, and comparative genomic studies presented here suggest that segmental duplications may facilitate cancer-associated copy number transitions and rearrangements at chromosome 6p21–p12. This process may involve homology-dependent DNA recombination and/or repair, which may also contribute towards the overall plasticity of the human genome.
DOI: 10.6084/m9.figshare.5121133
title: Supplementary Material for: Genomic Characterization and Chromosomal Mapping of 5 River Buffalo Skeletal Muscle Differentiation Master Genes

description: River buffalo (<i>Bubalus bubalis</i>, 2n = 50, BBU) is a species of economic relevance in a number of countries. This species shows a very peculiar biology and a great capacity for environmental adaptation. There has been an increasing economic interest as well as a growing demand for a more detailed knowledge of molecular features in this species. From this perspective we report a genomic, transcriptional and cytogenetic analysis of 5 master genes involved in skeletal muscle development. Of these 5 genes, <i>MYOD1</i>, <i>MYF5</i>, <i>MYF6</i> and <i>MYOG</i> belong to the basic helix-loop helix protein family while <i>MSTN</i> belongs to the TNF-B protein family. In mammals, these genes are involved in the early stages of skeletal muscle differentiation, development and regeneration. These pivotal biological functions are finely regulated in a tissue- and temporal-specific manner. We used a comparative genomic approach to obtain the buffalo specific sequences of <i>MYOD1</i> and <i>MYF6</i>. The nucleotide sequence similarity and the protein domain conservation of the newly obtained sequences are analysed with respect to bovine and other mammalian species showing sequence similarity. The presence of a polymorphism in <i>MYOD1</i> coding sequence is described and its possible effect discussed. Using a quantitative PCR approach, we compared the level of the 5 transcripts in adult and fetal muscle. These genes were physically localised on river buffalo R-banded chromosomes by FISH using bovine genomic BAC-clones. Here, we present a genomic and cytogenetic analysis which could offer a background to better characterise the buffalo genes involved in muscle function and which may be responsible for buffalo-specific meat features.
DOI: 10.6084/m9.figshare.5121136.v1
title: Supplementary Material for: An 8-Week High-Fat Diet Induces Obesity and Insulin Resistance with Small Changes in the Muscle Transcriptome of C57BL/6J Mice

description: <i>Background:</i> Skeletal muscle is responsible for most of the insulin-stimulated glucose uptake and metabolism. Therefore, it plays an important role in the development of insulin resistance, one of the characteristics of the metabolic syndrome (MS). As the prevalence of the MS is increasing, there is an urgent need for more effective intervention strategies. <i>Methods:</i> C57BL/6J mice were fed an 8-week low-fat diet (10 kcal%; LFD) or high-fat diet (45 kcal%; HFD). Microarray analysis was performed by using two comparisons: (1) 8-week HFD transcriptome versus 8-week LFD transcriptome and (2) transcriptome of mice sacrificed at the start of the intervention versus 8-week LFD transcriptome and 8-week HFD transcriptome, respectively. <i>Results:</i> Although an 8-week HFD induced obesity and impaired insulin sensitivity, HFD-responsive changes in the muscle transcriptome were relatively small (&lt;1.3-fold). In fact, 8-weeks of aging induced more pronounced changes than an HFD. One comparison revealed the transcriptional downregulation of the mito- gen-activated protein kinase cascade, whereas both comparisons showed the upregulation of fatty acid oxidation, demonstrating that the two comparison strategies are confirmative as well as complementary. <i>Conclusion:</i> We suggest using complementary analysis strategies in the genome-wide search for gene expression changes induced by mild interventions, such as an HFD.
DOI: 10.6084/m9.figshare.5121121
title: Supplementary Material for: Cytogenetic Characterization and Fluorescence in situ Hybridization of (GATA)<sub>10</sub> Repeats on Established Primary Cell Cultures from Indian Water Snake <i>(Natrix piscator)</i> and Indian Mugger <i>(Crocodylus palustris)</i> Embryos

description: Sex determination among reptiles has continued to draw the attention of geneticists and the mechanisms involved have been extensively studied and documented in the past 3 decades. The setting up of primary cell lines of reptilian tissues is an important tool in the present study which is a unique aspect not applied in earlier studies. Establishing the cell lines from various species of reptiles would help in our understanding of the mechanisms of evolution and differentiation of sex chromosomes. Therefore, in the present study, we have established for the first time primary cell cultures from Indian water snake <i>(Natrix piscator)</i> and Indian mugger <i>(Crocodylus palustris)</i> embryos. In the preliminary growth stage, 2 types of cells, fibroblast- and epithelial-like, were found to be attached and proliferating in vitro. These fibroblast-like cell cultures were later overtaken by epithelial cells. The cell lines were grown in minimal essential medium supplemented with fetal bovine serum and subcultured for a period of 8–10 months. The morphology of cell types was kept under constant observation microscopically. Interestingly, at a subsequent passage of the cells sporadically scattered neuronal-like and beating cells were observed. The suitable temperature for growth of these cell cultures was 28–30°C. Chromosome analysis was performed from the actively proliferating cells, which revealed 5 pairs of macrochromosomes and 15 pairs of microchromosomes in <i>Natrix piscator,</i> and 15 pairs of only macrochromosomes in <i>Crocodylus palustris</i>. (GATA)<sub>n</sub> repeats are well known to be associated with sex chromosomes. Fluorescence in situ hybridization performed with (GATA)<sub>10</sub> repeats delineated the W chromosome in the cells of <i>Natrix piscator</i> which has so far not been reported. This cell culture method has presently only been applied to water snakes and crocodile embryos in the current study, but it will be employed in other reptilian species and could go a long way to being a sustainable source of primary cells. This would eventually serve as an important tool for molecular studies in reptiles and other species in the future.
DOI: 10.6084/m9.figshare.5121130.v1
title: Supplementary Material for: Analysis of Segmental Duplications, Mouse Genome Synteny and Recurrent Cancer-Associated Amplicons in Human Chromosome 6p21–p12

description: It has been proposed that regions of microhomology in the human genome could facilitate genomic rearrangements, copy number transitions, and rapid genomic change during tumor progression. To investigate this idea, this study examines the role of repetitive sequence elements, and corresponding syntenic mouse genomic features, in targeting cancer-associated genomic instability of specific regions of the human genome. Automated database-mining algorithms designed to search for frequent copy number transitions and genomic breakpoints were applied to 2 publicly-available online databases and revealed that 6p21–p12 is one of the regions of the human genome most frequently involved in tumor-specific alterations. In these analyses, 6p21–p12 exhibited the highest frequency of genomic amplification in osteosarcomas. Analysis of repetitive elements in regions of homology between human chromosome 6p and the syntenic regions of the mouse genome revealed a strong association between the location of segmental duplications greater than 5 kilobase-pairs and the position of discontinuities at the end of the syntenic region. The presence of clusters of segmental duplications flanking these syntenic regions also correlated with a high frequency of amplification and genomic alteration. Collectively, the experimental findings, in silico analyses, and comparative genomic studies presented here suggest that segmental duplications may facilitate cancer-associated copy number transitions and rearrangements at chromosome 6p21–p12. This process may involve homology-dependent DNA recombination and/or repair, which may also contribute towards the overall plasticity of the human genome.
DOI: 10.6084/m9.figshare.5121133.v1
title: Supplementary Material for: Genomic Characterization and Chromosomal Mapping of 5 River Buffalo Skeletal Muscle Differentiation Master Genes

description: River buffalo (<i>Bubalus bubalis</i>, 2n = 50, BBU) is a species of economic relevance in a number of countries. This species shows a very peculiar biology and a great capacity for environmental adaptation. There has been an increasing economic interest as well as a growing demand for a more detailed knowledge of molecular features in this species. From this perspective we report a genomic, transcriptional and cytogenetic analysis of 5 master genes involved in skeletal muscle development. Of these 5 genes, <i>MYOD1</i>, <i>MYF5</i>, <i>MYF6</i> and <i>MYOG</i> belong to the basic helix-loop helix protein family while <i>MSTN</i> belongs to the TNF-B protein family. In mammals, these genes are involved in the early stages of skeletal muscle differentiation, development and regeneration. These pivotal biological functions are finely regulated in a tissue- and temporal-specific manner. We used a comparative genomic approach to obtain the buffalo specific sequences of <i>MYOD1</i> and <i>MYF6</i>. The nucleotide sequence similarity and the protein domain conservation of the newly obtained sequences are analysed with respect to bovine and other mammalian species showing sequence similarity. The presence of a polymorphism in <i>MYOD1</i> coding sequence is described and its possible effect discussed. Using a quantitative PCR approach, we compared the level of the 5 transcripts in adult and fetal muscle. These genes were physically localised on river buffalo R-banded chromosomes by FISH using bovine genomic BAC-clones. Here, we present a genomic and cytogenetic analysis which could offer a background to better characterise the buffalo genes involved in muscle function and which may be responsible for buffalo-specific meat features.
DOI: 10.6084/m9.figshare.5121118
title: Supplementary Material for: Synaptonemal Complex Protein SYCP3 Exists in Two Isoforms Showing Different Conservation in Mammalian Evolution

description: Meiosis-specific protein SYCP3 is a major structural component of synaptonemal complex (SC) lateral elements. SYCP3 is rather well conserved in vertebrates. However, some differences in SYCP3 expression have been shown among mammals. To clarifiy these differences, we have investigated SYCP3 expression with the aid of bioinformatic, biochemical and cell biological methods. Here we show that, in contrast to other vertebrates, rat and mouse SYCP3 exist in 2 isoforms. The short isoform is conserved among vertebrates. However, the longer isoform, which represents an N-terminal extension of the shorter one, most likely appeared about 15 million years ago in a common ancestor of rat and mouse and after separation from the hamster branch.