cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.4781059
title: Supplementary Material for: Adaptive Alternative Splicing Correlates with Less Environmental Risk of Parkinsonism

description: <em>Background/Objective:</em> Environmental exposure to anti-acetylcholinesterases (AChEs) aggravates the risk of Parkinsonism due to currently unclear mechanism(s). We explored the possibility that the brain’s capacity to induce a widespread adaptive alternative splicing response to such exposure may be involved. <i>Methods:</i> Following exposure to the dopaminergic neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), brain region transcriptome profiles were tested. <i>Results:</i> Changes in transcript profiles, alternative splicing patterns and splicing-related gene categories were identified. Engineered mice over-expressing the protective AChE-R splice variant showed less total changes but more splicing-related ones than hypersensitive AChE-S over-expressors with similarly increased hydrolytic activities. Following MPTP exposure, the substantia nigra and prefrontal cortex (PFC) of both strains showed a nuclear increase in the splicing factor ASF/SF2 protein. Furthermore, intravenous injection with highly purified recombinant human AChE-R changed transcript profiles in the striatum. <i>Conclusions:</i> Our findings are compatible with the working hypothesis that inherited or acquired alternative splicing deficits may promote parkinsonism, and we propose adaptive alternative splicing as a strategy for attenuating its progression.
DOI: 10.6084/m9.figshare.4781053
title: Supplementary Material for: The Forkhead Gene Family in Medaka: Expression Patterns and Gene Evolution

description: Using the genome sequence of the medaka, <i>Oryzias latipes</i>, we examined the genomic complement of Fox genes in this organism to gain insight into the evolutionary relationships and expression patterns of this gene family. We identified 31 Fox genes by searching for Forkhead domains in the medaka genome and by polymerase chain reaction (PCR) using primers designed from protein alignments. All the medaka Fox genes are encoded in 18 subclasses as follows: 5 Fox genes in subclass D; 3 Fox genes in subclass O; 2 Fox genes in each of subclass A, B, E, F, G, I, P, and Q, respectively; 1 Fox gene in each of subclass C, H, J, K, M, N, and R. The gene structures and general features are also discussed. In addition, we examined the expression patterns of some of these genes in different adult tissues and during embryonic development in medaka using quantitative PCR and in situ hybridization. The present study shows that Forkhead transcription factors play an important role during early embryonic development in medaka, and the results will enhance our knowledge in terms of Fox family evolution in different taxa.
DOI: 10.6084/m9.figshare.4781059.v1
title: Supplementary Material for: Adaptive Alternative Splicing Correlates with Less Environmental Risk of Parkinsonism

description: <em>Background/Objective:</em> Environmental exposure to anti-acetylcholinesterases (AChEs) aggravates the risk of Parkinsonism due to currently unclear mechanism(s). We explored the possibility that the brain’s capacity to induce a widespread adaptive alternative splicing response to such exposure may be involved. <i>Methods:</i> Following exposure to the dopaminergic neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), brain region transcriptome profiles were tested. <i>Results:</i> Changes in transcript profiles, alternative splicing patterns and splicing-related gene categories were identified. Engineered mice over-expressing the protective AChE-R splice variant showed less total changes but more splicing-related ones than hypersensitive AChE-S over-expressors with similarly increased hydrolytic activities. Following MPTP exposure, the substantia nigra and prefrontal cortex (PFC) of both strains showed a nuclear increase in the splicing factor ASF/SF2 protein. Furthermore, intravenous injection with highly purified recombinant human AChE-R changed transcript profiles in the striatum. <i>Conclusions:</i> Our findings are compatible with the working hypothesis that inherited or acquired alternative splicing deficits may promote parkinsonism, and we propose adaptive alternative splicing as a strategy for attenuating its progression.
DOI: 10.6084/m9.figshare.4781053.v1
title: Supplementary Material for: The Forkhead Gene Family in Medaka: Expression Patterns and Gene Evolution

description: Using the genome sequence of the medaka, <i>Oryzias latipes</i>, we examined the genomic complement of Fox genes in this organism to gain insight into the evolutionary relationships and expression patterns of this gene family. We identified 31 Fox genes by searching for Forkhead domains in the medaka genome and by polymerase chain reaction (PCR) using primers designed from protein alignments. All the medaka Fox genes are encoded in 18 subclasses as follows: 5 Fox genes in subclass D; 3 Fox genes in subclass O; 2 Fox genes in each of subclass A, B, E, F, G, I, P, and Q, respectively; 1 Fox gene in each of subclass C, H, J, K, M, N, and R. The gene structures and general features are also discussed. In addition, we examined the expression patterns of some of these genes in different adult tissues and during embryonic development in medaka using quantitative PCR and in situ hybridization. The present study shows that Forkhead transcription factors play an important role during early embryonic development in medaka, and the results will enhance our knowledge in terms of Fox family evolution in different taxa.
DOI: 10.6084/m9.figshare.4781002
title: Supplementary Material for: Revealing the Latent Mobilization Capability of the Staphylococcal Bacteriocinogenic Plasmid pRJ9

description: Plasmid pRJ9 is a non-self-mobilizable bacteriocinogenic plasmid from <i>Staphylococcus aureus</i>. Despite this feature, DNA sequencing and RT-PCR experiments showed that it presents a Mob region with three genes <i>(mobCAB)</i>, transcribed as an operon. In silico analysis of the Mob proteins encoded by pRJ9 showed that they present all the conserved functional features reported until present as being essential for plasmid mobilization. Moreover, they showed a high identity to Mob proteins encoded by mobilizable plasmids from <i>Staphylococcus</i> spp., especially to those encoded by plasmid pRJ6, which presents four <i>mob</i> genes <i>(mobCDAB)</i>. A putative <i>oriT </i>region was also found upstream of the pRJ9 <i>mob</i> operon. pRJ9 could only be successfully mobilized by pGO1 when pRJ6 was present in the same strain. Further experiments showed that the pRJ9 <i>oriT</i> can be recognized by the pRJ6 Mob proteins, confirming its functionality. As pRJ9 does not possess a <i>mobD </i>gene while pRJ6 does, the absence of this gene was believed to be responsible for its lack of mobilization. However, conjugation experiments with a donor strain carrying also <i>mobD</i> cloned into an <i>S. aureus </i>vector showed that pRJ9 does not become mobilized even in the presence of the protein MobD encoded by pRJ6. Therefore, the reasons for pRJ9 failure to be mobilized are presently unknown.
DOI: 10.6084/m9.figshare.4781002.v1
title: Supplementary Material for: Revealing the Latent Mobilization Capability of the Staphylococcal Bacteriocinogenic Plasmid pRJ9

description: Plasmid pRJ9 is a non-self-mobilizable bacteriocinogenic plasmid from <i>Staphylococcus aureus</i>. Despite this feature, DNA sequencing and RT-PCR experiments showed that it presents a Mob region with three genes <i>(mobCAB)</i>, transcribed as an operon. In silico analysis of the Mob proteins encoded by pRJ9 showed that they present all the conserved functional features reported until present as being essential for plasmid mobilization. Moreover, they showed a high identity to Mob proteins encoded by mobilizable plasmids from <i>Staphylococcus</i> spp., especially to those encoded by plasmid pRJ6, which presents four <i>mob</i> genes <i>(mobCDAB)</i>. A putative <i>oriT </i>region was also found upstream of the pRJ9 <i>mob</i> operon. pRJ9 could only be successfully mobilized by pGO1 when pRJ6 was present in the same strain. Further experiments showed that the pRJ9 <i>oriT</i> can be recognized by the pRJ6 Mob proteins, confirming its functionality. As pRJ9 does not possess a <i>mobD </i>gene while pRJ6 does, the absence of this gene was believed to be responsible for its lack of mobilization. However, conjugation experiments with a donor strain carrying also <i>mobD</i> cloned into an <i>S. aureus </i>vector showed that pRJ9 does not become mobilized even in the presence of the protein MobD encoded by pRJ6. Therefore, the reasons for pRJ9 failure to be mobilized are presently unknown.
DOI: 10.6084/m9.figshare.4780984
title: Tautomeric equilibria of isoguanine and related purine analogs

description: Nucleobase pairs in DNA match hydrogen-bond donor and acceptor groups on the nucleobases. However, these can adopt more than one tautomeric form, and can consequently pair with nucleobases other than their canonical complements, possibly a source of natural mutation. These issues are now being re-visited by synthetic biologists increasing the number of replicable pairs in DNA by exploiting unnatural hydrogen bonding patterns, where tautomerism can also create mutation. Here, we combine spectroscopic measurements on methylated analogs of isoguanine tautomers and tautomeric mixtures with statistical analyses to a set of isoguanine analogs, the complement of isocytosine, the 5th and 6th “letters” in DNA.
DOI: 10.6084/m9.figshare.4780984.v2
title: Tautomeric equilibria of isoguanine and related purine analogs

description: Nucleobase pairs in DNA match hydrogen-bond donor and acceptor groups on the nucleobases. However, these can adopt more than one tautomeric form, and can consequently pair with nucleobases other than their canonical complements, possibly a source of natural mutation. These issues are now being re-visited by synthetic biologists increasing the number of replicable pairs in DNA by exploiting unnatural hydrogen bonding patterns, where tautomerism can also create mutation. Here, we combine spectroscopic measurements on methylated analogs of isoguanine tautomers and tautomeric mixtures with statistical analyses to a set of isoguanine analogs, the complement of isocytosine, the 5th and 6th “letters” in DNA.
DOI: 10.6084/m9.figshare.4780984.v1
title: Tautomeric equilibria of iso-guanine and related purine analogs

description: Nucleobase pairs in DNA match hydrogen-bond donor and acceptor groups on the nucleobases. However, these can adopt more than one tautomeric form, and can consequently pair with nucleobases other than their canonical complements, possibly a source of natural mutation. These issues are now being re-visited by synthetic biologists increasing the number of replicable pairs in DNA by exploiting unnatural hydrogen bonding patterns, where tautomerism can also create mutation. Here, we combine spectroscopic measurements on methylated analogs of isoguanine tautomers and tautomeric mixtures with statistical analyses to a set of isoguanine analogs, the complement of isocytosine, the 5th and 6th “letters” in DNA.
DOI: 10.6084/m9.figshare.4780939
title: Supplementary Material for: Uromodulin and α1-Antitrypsin Urinary Peptide Analysis to Differentiate Glomerular Kidney Diseases

description: <em>Background/Aims:</em> Glomerular kidney disease (GKD) is suspected in patients based on proteinuria, but its diagnosis relies primarily on renal biopsy. We used urine peptide profiling as a noninvasive means to link GKD-associated changes to each glomerular entity. <i>Methods:</i> Urinary peptide profiles of 60 biopsy-proven glomerular patients and 14 controls were analyzed by combining magnetic bead peptide enrichment, MALDI-TOF MS analysis, and ClinProTools v2.0 to select differential peptides. Tentative identification of the differential peptides was carried out by HPLC-MS/MS. <i>Results:</i> The HPLC-MS/MS results suggest that uromodulin (UMOD; m/z: 1682, 1898 and 1913) and α<sub>1</sub>-antitrypsin (A1AT; m/z: 1945, 2392 and 2505) are differentially expressed urinary peptides that distinguish between GKD patients and healthy subjects. Low UMOD and high A1AT peptide abundance was observed in 80–92% of patients with GKD. Proliferative forms of GKD were distinguished from nonproliferative forms, based on a combination of UMOD and A1AT peptides. Nonproliferative forms correlated with higher A1AT peptide levels – focal segmental glomerulosclerosis was linked more closely to high levels of the m/z 1945 peptide than minimal change disease. <i>Conclusion:</i> We describe a workflow – urinary peptide profiling coupled with histological findings – that can be used to distinguish GKD accurately and noninvasively, particularly its nonproliferative forms.
DOI: 10.6084/m9.figshare.4780939.v1
title: Supplementary Material for: Uromodulin and α1-Antitrypsin Urinary Peptide Analysis to Differentiate Glomerular Kidney Diseases

description: <em>Background/Aims:</em> Glomerular kidney disease (GKD) is suspected in patients based on proteinuria, but its diagnosis relies primarily on renal biopsy. We used urine peptide profiling as a noninvasive means to link GKD-associated changes to each glomerular entity. <i>Methods:</i> Urinary peptide profiles of 60 biopsy-proven glomerular patients and 14 controls were analyzed by combining magnetic bead peptide enrichment, MALDI-TOF MS analysis, and ClinProTools v2.0 to select differential peptides. Tentative identification of the differential peptides was carried out by HPLC-MS/MS. <i>Results:</i> The HPLC-MS/MS results suggest that uromodulin (UMOD; m/z: 1682, 1898 and 1913) and α<sub>1</sub>-antitrypsin (A1AT; m/z: 1945, 2392 and 2505) are differentially expressed urinary peptides that distinguish between GKD patients and healthy subjects. Low UMOD and high A1AT peptide abundance was observed in 80–92% of patients with GKD. Proliferative forms of GKD were distinguished from nonproliferative forms, based on a combination of UMOD and A1AT peptides. Nonproliferative forms correlated with higher A1AT peptide levels – focal segmental glomerulosclerosis was linked more closely to high levels of the m/z 1945 peptide than minimal change disease. <i>Conclusion:</i> We describe a workflow – urinary peptide profiling coupled with histological findings – that can be used to distinguish GKD accurately and noninvasively, particularly its nonproliferative forms.
DOI: 10.6084/m9.figshare.4780777
title: Supplementary Material for: Three-Dimensional Arrangement of Genes Involved in Lipid Metabolism in Nuclei of Porcine Adipocytes and Fibroblasts in Relation to Their Transcription Level

description: The 3-dimensional arrangement of chromosomes and genes within a nuclear space is considered to represent the level of transcriptional regulation. Understanding how the nuclear architecture of adipocyte cells contributes to gene expression has become the subject of great<b> </b>interest in the context of obesity research. In this study we investigated nuclear positioning of 3 gene loci involved in lipid metabolism in the pig (<i>Sus scrofa</i>, SSC) which is considered as an important animal model for obesity in humans. We found that the position of the <i>SCD</i> gene in the 3-dimensional space of the cell nucleus is not correlated with transcriptional activity. The gene locus as well as chromosome territory SSC14 occupied the same peripheral location in adipocyte and fibroblast cells, in spite of the fact that their transcription level differs significantly between both cell types. For the 2 other investigated genes, i.e. <i>ACACA</i> and <i>SREBF1 </i>and their chromosome territory (SSC12), slightly different nuclear locations were found. They occupied intermediate nuclear positions in fibroblast nuclei, while in adipocytes they were positioned in the nuclear interior. The more internal location of these genes corresponds to increased transcription levels in fat cells. Our results confirm the non-random position of genes and chromosome territories in nuclei of adult porcine cells and indicate that relationship between transcription activity and gene positioning exists only for some but not all genes.
DOI: 10.6084/m9.figshare.4780777.v1
title: Supplementary Material for: Three-Dimensional Arrangement of Genes Involved in Lipid Metabolism in Nuclei of Porcine Adipocytes and Fibroblasts in Relation to Their Transcription Level

description: The 3-dimensional arrangement of chromosomes and genes within a nuclear space is considered to represent the level of transcriptional regulation. Understanding how the nuclear architecture of adipocyte cells contributes to gene expression has become the subject of great<b> </b>interest in the context of obesity research. In this study we investigated nuclear positioning of 3 gene loci involved in lipid metabolism in the pig (<i>Sus scrofa</i>, SSC) which is considered as an important animal model for obesity in humans. We found that the position of the <i>SCD</i> gene in the 3-dimensional space of the cell nucleus is not correlated with transcriptional activity. The gene locus as well as chromosome territory SSC14 occupied the same peripheral location in adipocyte and fibroblast cells, in spite of the fact that their transcription level differs significantly between both cell types. For the 2 other investigated genes, i.e. <i>ACACA</i> and <i>SREBF1 </i>and their chromosome territory (SSC12), slightly different nuclear locations were found. They occupied intermediate nuclear positions in fibroblast nuclei, while in adipocytes they were positioned in the nuclear interior. The more internal location of these genes corresponds to increased transcription levels in fat cells. Our results confirm the non-random position of genes and chromosome territories in nuclei of adult porcine cells and indicate that relationship between transcription activity and gene positioning exists only for some but not all genes.
DOI: 10.6084/m9.figshare.4780693
title: Supplementary Material for: Citrus Limonin Lacks the Antichemotherapeutic Effect in Human Models of Breast Cancer

description: <strong><em>Background/Aims:</em></strong> Chemicals that interfere with reactive oxygen species metabolism can act as potential candidates for the treatment of cancer. Some of the glucosides of citrus limonin inhibit the endogenously generated reactive oxygen species. The aim is to study the interactions of limonin with chemotherapy. <b><i>Methods:</i></b> Breast cancer cell lines MCF-7 (p53 wild type) and MDA-MB-231 (p53 mutant) as well as the nontumorigenic epithelial cell line MCF-10 were used to screen the effect of limonin at 1-, 5- and 10-µ<i>M</i> concentrations with camptothecin for apoptosis and NFĸB, p38 and ERK-MAPK signaling kinase assays. The effect of cyclophosphamide and limonin on MDA MB 231 xenografts was also studied. <b><i>Results:</i></b> Our results indicate that limonin did not inhibit camptothecin-induced apoptosis in human breast cancer cells in vitro through noninterference of camptothecin-induced phosphorylation of p38 MAPK and ERK-MAPK. Using an in vivo model of human breast cancer, limonin in combination with cyclophosphamide was not found to inhibit the cyclophosphamide-induced tumor regression through a reduced mitotic index of tumor xenograft cells when compared to treatment with cyclophosphamide alone. <b><i>Conclusion:</i></b> Both in vitro and in vivo results suggest that limonin could be beneficial for breast cancer patients undergoing chemotherapy.
DOI: 10.6084/m9.figshare.4780684
title: Processing of Illumina MiSeq-generated nifH amplicons from boreal forest moss samples - output after FunGene, CART models and chimera removal

description: A portion of the nifH (nitrogenase) gene was amplified from twelve samples of boreal forest moss stems (Pleurozium schreberi) from Sweden, using degenerate primers IGK3 and DVV. Sequencing was carried out using the Illumina MiSeq platform, paired-end 300 bp kit. Bioinformatic processing included the RDP FunGene pipeline and a classification and regressions trees (CART) model (Frank et al. 2016, Environ Microbiol Rep 8:905-916). Output from key steps is available here. Raw data are available on NCBI's SRA, accession numbers SRR5366534-SRR5366545.
DOI: 10.6084/m9.figshare.4780690
title: Annual anomalies and trends for TOMS reflectivities (1978–2005) in the Southern Hemisphere

description: Annual anomalies of Lambertian equivalent reflectivity (LER) retrieved from the total ozone mapping spectrometer spanning the period November 1978–November 2005 were studied in the Southern Hemisphere, in a region bounded by 0° S and 60° S, and their trends were estimated. With the exception of few regions where the variable may represent the contribution of both cloudiness and snow, trends in LER anomalies provided an evolution of total cloudiness. On average, the study region experienced a net increase in LER values of 0.78 reflectivity units (RU) decade<b><sup>−1</sup></b>; if only significant trend values are considered this figure increased to 1.18 RU decade<b><sup>−1</sup></b>. The region that showed the largest upward trend, up to 4 RU decade<b><sup>−1</sup></b>, was located over the eastern Pacific, off the coasts of Chile and Peru, where the presence of marine stratocumulus is frequent. Despite the overall positive trend there were regions that yielded a negative one, most notably the tropical latitudes of South America and Africa. The yearly zonal means also showed a positive trend at all latitudes, but significance occurred beyond 20° S only. Correlation maps between LER anomalies and five different circulation indices were also introduced. The indices with the highest and lowest number of significant correlation values were the Madden–Julian oscillation at 70° E and the quasi-biennial Oscillation, respectively.
DOI: 10.6084/m9.figshare.4780684.v1
title: Processing of Illumina MiSeq-generated nifH amplicons from boreal forest moss samples - output after FunGene, CART models and chimera removal

description: A portion of the nifH (nitrogenase) gene was amplified from twelve samples of boreal forest moss stems (Pleurozium schreberi) from Sweden, using degenerate primers IGK3 and DVV. Sequencing was carried out using the Illumina MiSeq platform, paired-end 300 bp kit. Bioinformatic processing included the RDP FunGene pipeline and a classification and regressions trees (CART) model (Frank et al. 2016, Environ Microbiol Rep 8:905-916). Output from key steps is available here. Raw data are available on NCBI's SRA, accession numbers SRR5366534-SRR5366545.
DOI: 10.6084/m9.figshare.4780636
title: Data_BritoB_UpcomingForestTradingMechanism.xlsx

description: Dataset related to the paper Potential Trajectories of the Upcoming Forest Trading Mechanism in Pará State, Brazilian Amazon.