cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1409398.v239
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which, based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation in the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leukospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins promoting anti-self-reactive cellular cytotoxicity in male gamete performance.
DOI: 10.6084/m9.figshare.1399111.v1
title: Effects of solar radiation on pigmentation and induction of a mycosporine-like amino acid in two cyanobacteria, <i>Anabaena</i> sp. and <i>Nostoc</i> sp. ISC26

description: The effect of filtered natural solar radiation, including photosynthetically active radiation (PAR) and PAR+ultraviolet radiation (UVR), on pigmentation and synthesis of a UV absorbing ‘mycosporine-like amino acid’ (MAA) in two filamentous and heterocystous cyanobacteria, <i>Anabaena</i> sp. and <i>Nostoc</i> sp. ISC26 was studied over 3 days. In <i>Anabaena</i> sp. and <i>Nostoc</i> sp. ISC26, chlorophyll <i>a</i> (chl <i>a</i>) content decreased after 72 h to 5.45 ± 0.09 and 7.01 ± 0.54 μg mg<sup>−</sup><sup>1</sup> DW respectively under PAR treatments; and to 4.33 ± 0.22, 6.12 ± 0.04 μg mg<sup>−</sup><sup>1</sup> DW in PAR+UV treatments, as did carotenoids (Car) (2.68 ± 0.01, 2.93 ± 0.01 μg mg<sup>−</sup><sup>1</sup> DW) (PAR), (2.53 ± 0.01, 2.57 ± 0.05 μg mg<sup>−</sup><sup>1</sup> DW) (PAR+UV). A considerable increase was observed in the carotenoid:chlorophyll <i>a</i> (Car/Chl <i>a</i>) ratio as a result of carotenoid accumulation in the first 24 h and reduction of chlorophyll in the following days. A single MAA was isolated, purified by high performance liquid chromatography (HPLC) and identified as shinorine. Shinorine concentration increased significantly during 72 h specifically under PAR+UV (1270.8 ± 50.42, 2208.09 ± 73.04 nmol g<sup>−</sup><sup>1</sup> DW) in <i>Anabaena</i> sp. and <i>Nostoc</i> sp. ISC26, respectively, indicating an adaptation strategy of cyanobacteria against harmful solar short wavelength radiation especially in natural habitats.
DOI: 10.6084/m9.figshare.1409398.v240
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which, based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation in the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leukospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins promoting anti-self-reactive cellular cytotoxicity in male gamete performance.
DOI: 10.6084/m9.figshare.1399102.v1
title: Raw Data (Anonymised)

description: The data pertaines to the article "The Intra- and Inter-Rater Reliability of an Instrumented Spasticity Assessment in Children with Cerebral Palsy". The values were used to calculate the various components of reliability.
DOI: 10.6084/m9.figshare.1409398.v241
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which, based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation in the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leukospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins promoting anti-self-reactive cellular cytotoxicity in male gamete performance.
DOI: 10.6084/m9.figshare.1397546
title: Genome partition data for mouse genome build 9, HindIII and NcoI

description: Genome partition data for mouse genome build 9, HindIII and NcoI
DOI: 10.6084/m9.figshare.1397547
title: Genome parition data for human genome build 19, HindIII and MboI

description: Genome parition data for human genome build 19, HindIII and MboI
DOI: 10.6084/m9.figshare.1397547.v1
title: Genome parition data for human genome build 19, HindIII and MboI

description: Genome parition data for human genome build 19, HindIII and MboI
DOI: 10.6084/m9.figshare.1397544
title: VRK1 chromatin kinase phosphorylates H2AX and is required for foci formation induced by DNA damage

description: All types of DNA damage cause a local alteration and relaxation of chromatin structure. Sensing and reacting to this initial chromatin alteration is a necessary trigger for any type of DNA damage response (DDR). In this context, chromatin kinases are likely candidates to participate in detection and reaction to a locally altered chromatin as a consequence of DNA damage and, thus, initiate the appropriate cellular response. In this work, we demonstrate that VRK1 is a nucleosomal chromatin kinase and that its depletion causes loss of histones H3 and H4 acetylation, which are required for chromatin relaxation, both in basal conditions and after DNA damage, independently of ATM. Moreover, VRK1 directly and stably interacts with histones H2AX and H3 in basal conditions. In response to DNA damage induced by ionizing radiation, histone H2AX is phosphorylated in Ser139 by VRK1. The phosphorylation of H2AX and the formation of γH2AX foci induced by ionizing radiation (IR), are prevented by VRK1 depletion and are rescued by kinase-active, but not kinase-dead, VRK1. In conclusion, we found that VRK1 is a novel chromatin component that reacts to its alterations and participates very early in DDR, functioning by itself or in cooperation with ATM.
DOI: 10.6084/m9.figshare.1409398.v242
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which, based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation in the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leukospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins promoting anti-self-reactive cellular cytotoxicity in male gamete performance.
DOI: 10.6084/m9.figshare.1397542
title: Differential DNA methylation in umbilical cord blood of infants exposed to mercury and arsenic <i>in utero</i>

description: Mercury and arsenic are known developmental toxicants. Prenatal exposures are associated with adverse childhood health outcomes that could be in part mediated by epigenetic alterations that may also contribute to altered immune profiles. In this study, we examined the association between prenatal mercury exposure on both DNA methylation and white blood cell composition of cord blood, and evaluated the interaction with prenatal arsenic exposure. A total of 138 mother-infant pairs with postpartum maternal toenail mercury, prenatal urinary arsenic concentrations, and newborn cord blood were assessed using the Illumina Infinium Methylation450 array. White blood cell composition was inferred from DNA methylation measurements. A doubling in toenail mercury concentration was associated with a 2.5% decrease (95% CI: 5.0%, 1.0%) in the estimated monocyte proportion. An increase of 3.5% (95% CI: 1.0, 7.0) in B-cell proportion was observed for females only. Among the top 100 CpGs associated with toenail mercury levels (ranked on <i>P-value</i>), there was a significant enrichment of loci located in North shore regions of CpG islands (<i>P</i> = 0.049), and the majority of these loci were hypermethylated (85%). Among the top 100 CpGs for the interaction between arsenic and mercury, there was a greater than expected proportion of loci located in CpG islands (<i>P</i> = 0.045) and in South shore regions (<i>P</i> = 0.009) and all of these loci were hypermethylated. This work supports the hypothesis that mercury may be contributing to epigenetic variability and immune cell proportion changes, and suggests that <i>in utero</i> exposure to mercury and arsenic, even at low levels, may interact to impact the epigenome.
DOI: 10.6084/m9.figshare.1397543
title: An aromatic cage is required but not sufficient for binding of Tudor domains of the Polycomblike protein family to H3K36me3

description: Polycomblike (Pcl) proteins are important transcriptional regulators and components of the Polycomb Repressive Complex 2 (PRC2). The Tudor domains of human homologs PHF1 and PHF19 have been found to recognize trimethylated lysine 36 of histone H3 (H3K36me3); however, the biological role of Tudor domains of other Pcl proteins remains poorly understood. Here, we characterize the molecular basis underlying histone binding activities of the Tudor domains of the Pcl family. In contrast to a predominant view, we found that the methyl lysine-binding aromatic cage is necessary but not sufficient for recognition of H3K36me3 by these Tudor domains and that a hydrophobic patch, adjacent to the aromatic cage, is also required.
DOI: 10.6084/m9.figshare.1397544.v1
title: VRK1 chromatin kinase phosphorylates H2AX and is required for foci formation induced by DNA damage

description: All types of DNA damage cause a local alteration and relaxation of chromatin structure. Sensing and reacting to this initial chromatin alteration is a necessary trigger for any type of DNA damage response (DDR). In this context, chromatin kinases are likely candidates to participate in detection and reaction to a locally altered chromatin as a consequence of DNA damage and, thus, initiate the appropriate cellular response. In this work, we demonstrate that VRK1 is a nucleosomal chromatin kinase and that its depletion causes loss of histones H3 and H4 acetylation, which are required for chromatin relaxation, both in basal conditions and after DNA damage, independently of ATM. Moreover, VRK1 directly and stably interacts with histones H2AX and H3 in basal conditions. In response to DNA damage induced by ionizing radiation, histone H2AX is phosphorylated in Ser139 by VRK1. The phosphorylation of H2AX and the formation of γH2AX foci induced by ionizing radiation (IR), are prevented by VRK1 depletion and are rescued by kinase-active, but not kinase-dead, VRK1. In conclusion, we found that VRK1 is a novel chromatin component that reacts to its alterations and participates very early in DDR, functioning by itself or in cooperation with ATM.
DOI: 10.6084/m9.figshare.1409398.v243
title: ABO phenotype protected reproduction as it is based on fucosylations.

description: The molecular biological relationship between human fertility and ABO(H) blood group phenotype formation becomes evident with the rare (Oh) or <i>Bombay</i> blood type, which, based on the history of his own family, Charles Darwin would have interpreted as resulting from reduced fertility in consanguinities. In its native form, the <i>Bombay</i> type occurs in individuals with an extremely rare genotype (h/h;se/se), by which the fucosyltransferases FUT1 and FUT2 are not produced due to point mutations. These enzymes, encoded on chromosome 19, are epistatically connected with the A and B allelic glycotransferase functions encoded on chromosome 9, while the fucosyl residues provide the functional-structural basis for the formation of any ABO(H) phenotype on the cell surface or in secretions and plasma proteins. Immunoglobulins are also heavily fucosylated, and via developmental variation in the positions between the cell surfaces and the heavy chains of immunoglobulins, fucosyl residues appear to augment or reduce antibody-mediated cellular cytotoxicity involving physiological anti-self-reactivity; moreover, by regulating the assembly and intracellular signaling of precursor B cell receptors, the core fucosylation of immunoglobulin heavy chains represents a key mechanism in clonal selection. In fact, the seminal plasma of leukospermic infertile men has been reported to exert high levels of poorly core-fucosylated IgG. Consequently, in <i>Bombay </i>type individuals, non-somatic glycosylation processes of embryogenic stem cell-to-germ cell transformation, which involve the modification and <i>O</i>-fucosylation of epidermal growth factor (EGF), are most likely exposed to metabolic competition with multiple glycosidic sites of poorly fucosylated, glycan-depleted immunoglobulins promoting anti-self-reactive cellular cytotoxicity in male gamete performance.
DOI: 10.6084/m9.figshare.1397535
title: Biochemical fractionation of soil organic matter after incorporation of organic residues

description: Description will come when the associated paper will be published.
DOI: 10.6084/m9.figshare.1397543.v1
title: An aromatic cage is required but not sufficient for binding of Tudor domains of the Polycomblike protein family to H3K36me3

description: Polycomblike (Pcl) proteins are important transcriptional regulators and components of the Polycomb Repressive Complex 2 (PRC2). The Tudor domains of human homologs PHF1 and PHF19 have been found to recognize trimethylated lysine 36 of histone H3 (H3K36me3), however the biological role of Tudor domains of other Pcl proteins remains poorly understood. Here, we characterize the molecular basis underlying histone binding activities of the Tudor domains of the Pcl family. In contrast to a predominant view, we found that the methyllysine-binding aromatic cage is necessary but not sufficient for recognition of H3K36me3 by these Tudor domains and that a hydrophobic patch, adjacent to the aromatic cage, is also required.
DOI: 10.6084/m9.figshare.1397542.v1
title: Differential DNA Methylation in Umbilical Cord Blood of Infants Exposed to Mercury and Arsenic <i>in utero</i>

description: ABSTRACTMercury and arsenic are known developmental toxicants. Prenatal exposures are associated with adverse childhood health outcomes that could be in part mediated by epigenetic alterations that may also contribute to altered immune profiles. In this study, we examined the association between prenatal mercury exposure on both DNA methylation and white blood cell composition of cord blood, and evaluated the interaction with prenatal arsenic exposure. A total of 138 mother-infant pairs with postpartum maternal toenail mercury, prenatal urinary arsenic concentrations, and newborn cord blood were assessed using the Illumina Infinium Methylation450 array. White blood cell composition was inferred from DNA methylation measurements. A doubling in toenail mercury concentration was associated with a 2.5% decrease (95% CI: 5.0%, 1.0%) in the estimated monocyte proportion. An increase of 3.5% (95% CI: 1.0, 7.0) in B-cell proportion was observed for females only. Among the top 100 CpGs associated with toenail mercury levels (ranked on <i>P</i>-value), there was a significant enrichment of loci located in North shore regions of CpG islands (<i>P</i>=0.049), and the majority of these loci were hypermethylated (85%). Among the top 100 CpGs for the interaction between arsenic and mercury, there was a greater than expected proportion of loci located in CpG islands (<i>P</i>=0.045) and in South shore regions (<i>P</i>=0.009) and all of these loci were hypermethylated. This work supports the hypothesis that mercury may be contributing to epigenetic variability and immune cell proportion changes, and suggests that <i>in utero</i> exposure to mercury and arsenic, even at low levels, may interact to impact the epigenome.
DOI: 10.6084/m9.figshare.1397544.v2
title: VRK1 chromatin kinase phosphorylates H2AX and is required for foci formation induced by DNA damage

description: All types of DNA damage cause a local alteration and relaxation of chromatin structure. Sensing and reacting to this initial chromatin alteration is a necessary trigger for any type of DNA damage response (DDR). In this context, chromatin kinases are likely candidates to participate in detection and reaction to a locally altered chromatin as a consequence of DNA damage and, thus, initiate the appropriate cellular response. In this work, we demonstrate that VRK1 is a nucleosomal chromatin kinase and that its depletion causes loss of histones H3 and H4 acetylation, which are required for chromatin relaxation, both in basal conditions and after DNA damage, independently of ATM. Moreover, VRK1 directly and stably interacts with histones H2AX and H3 in basal conditions. In response to DNA damage induced by ionizing radiation, histone H2AX is phosphorylated in Ser139 by VRK1. The phosphorylation of H2AX and the formation of γH2AX foci induced by ionizing radiation (IR), are prevented by VRK1 depletion and are rescued by kinase-active, but not kinase-dead, VRK1. In conclusion, we found that VRK1 is a novel chromatin component that reacts to its alterations and participates very early in DDR, functioning by itself or in cooperation with ATM.