cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.1284396.v2
title: The E3 ligase APC/C-Cdh1 regulates MEF2A-dependent transcription by targeting SUMO-specific protease 2 for ubiquitination and degradation

description: Activity-dependent stimuli induced a calcineurin-mediated dephosphorylation of the transcriptional factor MEF2A at serine408 and promoted a switch from SUMOylation to acetylation at lysine403 which led to MEF2A transcriptional activation. We previously identified SENP2 is the de-SUMOylation enzyme for MEF2A and promotes MEF2A-dependent transcription. We report here a requirement for APC<sup>Cdh1</sup>-SENP2-MEF2A axis in the regulation of MEF2A transcriptional activation. APC<sup>Cdh1</sup> interacts with and targets SENP2 for ubiquitination and destruction in the cytoplasm by recognizing a conserved canonical D-box motif in SENP2. Moreover, Cdh1 regulates the transcriptional activity of MEF2A in a SENP2 dependent manner. Activity-dependent stimuli prevented APC<sup>Cdh1</sup>-induced SENP2 ubiquitination, promoted SENP2 nuclear accumulations, and caused MEF2A de-SUMOylation and MEF2A acetylation, leading to MEF2A transcriptional activation. Thus, our findings defined a post-transcriptional mechanism underlying activity-dependent stimuli-induced MEF2A transcriptional activation.
DOI: 10.7284/135963
title: GNSS (Global Navigation Satellite System) data collected during research cruise AT42-16 using a Furuno GP-90D instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.1284391
title: Bioacoustics of the Neotropical Eneopterinae (Orthoptera, Grylloidea, Gryllidae)

description: In members of the cricket subfamily Eneopterinae (Orthoptera, Grylloidea), songs with powerful high-frequency (HF) harmonics have evolved, which likely represents a distinctive acoustic adaptation. In this study, we analysed or reanalysed the songs of the three eneopterine genera present in the Neotropics to evaluate whether they also possess high-amplitude HF components. We present new data and combine several lines of evidence to interpret or reinterpret the calling signals of a representative species for each genus. We used new recordings in order to detect and analyse potential HF components of the songs. Stridulatory files were measured, and stridulation was studied using high-speed video recordings. The results suggest that all eneopterine genera from the Neotropics use HFs to communicate, based on the rich harmonic content of their songs. Strikingly, the Neotropical eneopterines possess high dominant frequencies, recalling the patterns observed in the tribe Lebinthini, the most speciose tribe of the subfamily distributed in the Western Pacific region and in Southeast Asia: <i>Ligypterus</i> and <i>Ponca</i> show dominant harmonic peaks, whereas <i>Eneoptera</i> possesses unique features. The three species under study, however, deal differently with HFs.
DOI: 10.6084/m9.figshare.1284387
title: The chromodomain-containing histone acetyltransferase TIP60 acts as a code reader, recognizing the epigenetic codes for initiating transcription

description: TIP60 can act as a transcriptional activator or a repressor depending on the cellular context. However, little is known about the role of the chromodomain in the functional regulation of TIP60. In this study, we found that TIP60 interacted with H3K4me3 in response to TNF-α signaling. TIP60 bound to H3K4me3 at the promoters of the NF-κB target genes <i>IL6</i> and <i>IL8</i>. Unlike the wild-type protein, a TIP60 chromodomain mutant did not localize to chromatin regions. Because TIP60 binds to histones with specific modifications and transcriptional regulators, we used a histone peptide assay to identify histone codes recognized by TIP60. TIP60 preferentially interacted with methylated or acetylated histone H3 and H4 peptides. Phosphorylation near a lysine residue significantly reduced the affinity of TIP60 for the modified histone peptides. Our findings suggest that TIP60 acts as a functional link between the histone code and transcriptional regulators.
DOI: 10.7284/135964
title: Gyrocompass data collected during research cruise AT42-16 using a Sperry MK-37 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.1284391.v2
title: Bioacoustics of the Neotropical Eneopterinae (Orthoptera, Grylloidea, Gryllidae)

description: In members of the cricket subfamily Eneopterinae (Orthoptera, Grylloidea), songs with powerful high-frequency (HF) harmonics have evolved, which likely represents a distinctive acoustic adaptation. In this study, we analysed or reanalysed the songs of the three eneopterine genera present in the Neotropics to evaluate whether they also possess high-amplitude HF components. We present new data and combine several lines of evidence to interpret or reinterpret the calling signals of a representative species for each genus. We used new recordings in order to detect and analyse potential HF components of the songs. Stridulatory files were measured, and stridulation was studied using high-speed video recordings. The results suggest that all eneopterine genera from the Neotropics use HFs to communicate, based on the rich harmonic content of their songs. Strikingly, the Neotropical eneopterines possess high dominant frequencies, recalling the patterns observed in the tribe Lebinthini, the most speciose tribe of the subfamily distributed in the Western Pacific region and in Southeast Asia: <i>Ligypterus</i> and <i>Ponca</i> show dominant harmonic peaks, whereas <i>Eneoptera</i> possesses unique features. The three species under study, however, deal differently with HFs.
DOI: 10.6084/m9.figshare.1284391.v1
title: Bioacoustics of the Neotropical Eneopterinae (Orthoptera, Grylloidea, Gryllidae)

description: In members of the cricket subfamily Eneopterinae (Orthoptera, Grylloidea), songs with powerful high-frequency (HF) harmonics have evolved, which likely represents a distinctive acoustic adaptation. In this study, we analysed or reanalysed the songs of the three eneopterine genera present in the Neotropics to evaluate whether they also possess high-amplitude HF components. We present new data and combine several lines of evidence to interpret or reinterpret the calling signals of a representative species for each genus. We used new recordings in order to detect and analyse potential HF components of the songs. Stridulatory files were measured, and stridulation was studied using high-speed video recordings. The results suggest that all eneopterine genera from the Neotropics use HFs to communicate, based on the rich harmonic content of their songs. Strikingly, the Neotropical eneopterines possess high dominant frequencies, recalling the patterns observed in the tribe Lebinthini, the most speciose tribe of the subfamily distributed in the Western Pacific region and in Southeast Asia: <i>Ligypterus</i> and <i>Ponca</i> show dominant harmonic peaks, whereas <i>Eneoptera</i> possesses unique features. The three species under study, however, deal differently with HFs.
DOI: 10.7284/135970
title: Meteorological Station data collected during research cruise AT42-16 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.1284387.v2
title: The chromodomain-containing histone acetyltransferase TIP60 acts as a code reader, recognizing the epigenetic codes for initiating transcription

description: TIP60 can act as a transcriptional activator or a repressor depending on the cellular context. However, little is known about the role of the chromodomain in the functional regulation of TIP60. In this study, we found that TIP60 interacted with H3K4me3 in response to TNF-α signaling. TIP60 bound to H3K4me3 at the promoters of the NF-κB target genes <i>IL6</i> and <i>IL8</i>. Unlike the wild-type protein, a TIP60 chromodomain mutant did not localize to chromatin regions. Because TIP60 binds to histones with specific modifications and transcriptional regulators, we used a histone peptide assay to identify histone codes recognized by TIP60. TIP60 preferentially interacted with methylated or acetylated histone H3 and H4 peptides. Phosphorylation near a lysine residue significantly reduced the affinity of TIP60 for the modified histone peptides. Our findings suggest that TIP60 acts as a functional link between the histone code and transcriptional regulators.
DOI: 10.6084/m9.figshare.1284386
title: Structure-based design and synthesis of a bivalent iminobiotin analog showing strong affinity toward a low immunogenic streptavidin mutant

description: The streptavidin/biotin interaction has been widely used as a useful tool in research fields. For application to a pre-targeting system, we previously developed a streptavidin mutant that binds to an iminobiotin analog while abolishing affinity for natural biocytin. Here, we design a bivalent iminobiotin analog that shows 1000-fold higher affinity than before, and determine its crystal structure complexed with the mutant protein.
DOI: 10.6084/m9.figshare.1284387.v1
title: The chromodomain-containing histone acetyltransferase TIP60 acts as a code reader, recognizing the epigenetic codes for initiating transcription

description: TIP60 can act as a transcriptional activator or a repressor depending on the cellular context. However, little is known about the role of the chromodomain in the functional regulation of TIP60. In this study, we found that TIP60 interacted with H3K4me3 in response to TNF-α signaling. TIP60 bound to H3K4me3 at the promoters of the NF-κB target genes <i>IL6</i> and <i>IL8</i>. Unlike the wild-type protein, a TIP60 chromodomain mutant did not localize to chromatin regions. Because TIP60 binds to histones with specific modifications and transcriptional regulators, we used a histone peptide assay to identify histone codes recognized by TIP60. TIP60 preferentially interacted with methylated or acetylated histone H3 and H4 peptides. Phosphorylation near a lysine residue significantly reduced the affinity of TIP60 for the modified histone peptides. Our findings suggest that TIP60 acts as a functional link between the histone code and transcriptional regulators.
DOI: 10.6084/m9.figshare.1284384
title: Using Technology to Expand The Classroom in Time, Space and Diversity

description: My talk at the 2015 Society for Integrative and Comparative Biology
DOI: 10.7284/135971
title: Meteorological Station data collected during research cruise AT42-16 using a Vaisala WXT520 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.1284381
title: Extra tyrosine in the carbohydrate-binding module of <i>Irpex lacteus</i> Xyn10B enhances its cellulose-binding ability

description: The xylanase (Xyn10B) that strongly adsorbs on microcrystalline cellulose was isolated from Driselase. The Xyn10B contains a Carbohydrate-binding module family 1 (CBM1) (<i>Irp</i>CBM<sub>Xyn10B</sub>) at N-terminus. The canonical essential aromatic residues required for cellulose binding were conserved in <i>Irp</i>CBM<sub>Xyn10B</sub>; however, its adsorption ability was markedly higher than that typically observed for the CBM1 of an endoglucanase from <i>Trametes hirsuta</i> (<i>Th</i>CBM<sub>EG1</sub>). An analysis of the CBM-GFP fusion proteins revealed that the binding capacity to cellulose (7.8 μmol/g) and distribution coefficient (2.0 L/μmol) of <i>Irp</i>CBM<sub>Xyn10B</sub>-GFP were twofold higher than those of <i>Th</i>CBM<sub>EG1</sub>-GFP (3.4 μmol/g and 1.2 L/μmol, respectively), used as a reference structure. Besides the canonical aromatic residues (W24-Y50-Y51) of typical CBM1-containing proteins, <i>Irp</i>CBM<sub>Xyn10B</sub> had an additional aromatic residue (Y52). The mutation of Y52 to Ser (<i>Irp</i>CBM<sub>Y52S</sub>-GFP) reduced these adsorption parameters to 4.4 μmol/g and 1.5 L/μmol, which were similar to those of <i>Th</i>CBM<sub>EG1</sub>-GFP. These results indicate that Y52 plays a crucial role in strong cellulose binding.
DOI: 10.6084/m9.figshare.1284386.v2
title: Structure-based design and synthesis of a bivalent iminobiotin analog showing strong affinity toward a low immunogenic streptavidin mutant

description: The streptavidin/biotin interaction has been widely used as a useful tool in research fields. For application to a pre-targeting system, we previously developed a streptavidin mutant that binds to an iminobiotin analog while abolishing affinity for natural biocytin. Here, we design a bivalent iminobiotin analog that shows 1000-fold higher affinity than before, and determine its crystal structure complexed with the mutant protein.
DOI: 10.6084/m9.figshare.1284358
title: LTSTM data from December 2004

description: This is low temperature STM data from December 2004.
DOI: 10.6084/m9.figshare.1284384.v2
title: Using Technology to Expand The Classroom in Time, Space and Diversity

description: My talk at the 2015 Society for Integrative and Comparative Biology
DOI: 10.6084/m9.figshare.1284386.v1
title: Structure-based design and synthesis of a bivalent iminobiotin analog showing strong affinity toward a low immunogenic streptavidin mutant

description: The streptavidin/biotin interaction has been widely used as a useful tool in research fields. For application to a pre-targeting system, we previously developed a streptavidin mutant that binds to an iminobiotin analog while abolishing affinity for natural biocytin. Here, we design a bivalent iminobiotin analog that shows 1000-fold higher affinity than before, and determine its crystal structure complexed with the mutant protein.
DOI: 10.7284/135968
title: Multibeam Echosounder data collected during research cruise AT42-16 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.1284358.v1
title: LTSTM data from December 2004

description: This is low temperature STM data from December 2004.
DOI: 10.6084/m9.figshare.1284381.v2
title: Extra tyrosine in the carbohydrate-binding module of <i>Irpex lacteus</i> Xyn10B enhances its cellulose-binding ability

description: The xylanase (Xyn10B) that strongly adsorbs on microcrystalline cellulose was isolated from Driselase. The Xyn10B contains a Carbohydrate-binding module family 1 (CBM1) (<i>Irp</i>CBM<sub>Xyn10B</sub>) at N-terminus. The canonical essential aromatic residues required for cellulose binding were conserved in <i>Irp</i>CBM<sub>Xyn10B</sub>; however, its adsorption ability was markedly higher than that typically observed for the CBM1 of an endoglucanase from <i>Trametes hirsuta</i> (<i>Th</i>CBM<sub>EG1</sub>). An analysis of the CBM-GFP fusion proteins revealed that the binding capacity to cellulose (7.8 μmol/g) and distribution coefficient (2.0 L/μmol) of <i>Irp</i>CBM<sub>Xyn10B</sub>-GFP were twofold higher than those of <i>Th</i>CBM<sub>EG1</sub>-GFP (3.4 μmol/g and 1.2 L/μmol, respectively), used as a reference structure. Besides the canonical aromatic residues (W24-Y50-Y51) of typical CBM1-containing proteins, <i>Irp</i>CBM<sub>Xyn10B</sub> had an additional aromatic residue (Y52). The mutation of Y52 to Ser (<i>Irp</i>CBM<sub>Y52S</sub>-GFP) reduced these adsorption parameters to 4.4 μmol/g and 1.5 L/μmol, which were similar to those of <i>Th</i>CBM<sub>EG1</sub>-GFP. These results indicate that Y52 plays a crucial role in strong cellulose binding.
DOI: 10.6084/m9.figshare.1284356
title: Dark Research - supplementary materials

description: This is the supplementary materials for a preprint I'm uploading to PeerJ Preprints
DOI: 10.6084/m9.figshare.1284384.v1
title: Using Technology to Expand The Classroom in Time, Space and Diversity

description: My talk at the 2015 Society for Integrative and Comparative Biology
DOI: 10.6084/m9.figshare.1284350
title: Cloning and tissue expression profiling of the <i>GnRHR</i> gene of the Muscovy duck (<i>Cairina moschata</i>): polymorphism and association with egg-laying performance

description: 1. cDNA sequence of gonadotropin-releasing-hormone receptor (<i>GnRHR</i>) gene was cloned and an association analysis between mutations and laying performance was conducted.2. A 1680-bp cDNA sequence of Muscovy duck <i>GnRHR</i>, which encodes 415 amino acids, was obtained and characterised. Phylogenetic analysis revealed that Muscovy duck <i>GnRHR</i> has a close relationship with <i>Gallus gallus GnRHR</i>.3. There were significantly different expression profiles between 4 age periods in the hypothalamus, pituitary, and ovary. The expression of <i>GnRHR</i> at the age of 36 weeks (laying period) was higher than other time points in the three tissues. <i>GnRHR</i> was expressed in 12 different tissues. The highest expression levels were observed in hypothalamus, pituitary and gonads.4. A single nucleotide polymorphism detected in the second intron was associated with egg-laying performance. Individuals with genotype TT had better egg-laying performance from individuals with genotypes CC or TC. Therefore, <i>GnRHR</i> could be used as a marker gene for laying performance in Muscovy duck.
DOI: 10.6084/m9.figshare.1284381.v1
title: Extra tyrosine in the carbohydrate-binding module of <i>Irpex lacteus</i> Xyn10B enhances its cellulose-binding ability

description: The xylanase (Xyn10B) that strongly adsorbs on microcrystalline cellulose was isolated from Driselase. The Xyn10B contains a Carbohydrate-binding module family 1 (CBM1) (<i>Irp</i>CBM<sub>Xyn10B</sub>) at N-terminus. The canonical essential aromatic residues required for cellulose binding were conserved in <i>Irp</i>CBM<sub>Xyn10B</sub>; however, its adsorption ability was markedly higher than that typically observed for the CBM1 of an endoglucanase from <i>Trametes hirsuta</i> (<i>Th</i>CBM<sub>EG1</sub>). An analysis of the CBM-GFP fusion proteins revealed that the binding capacity to cellulose (7.8 μmol/g) and distribution coefficient (2.0 L/μmol) of <i>Irp</i>CBM<sub>Xyn10B</sub>-GFP were twofold higher than those of <i>Th</i>CBM<sub>EG1</sub>-GFP (3.4 μmol/g and 1.2 L/μmol, respectively), used as a reference structure. Besides the canonical aromatic residues (W24-Y50-Y51) of typical CBM1-containing proteins, <i>Irp</i>CBM<sub>Xyn10B</sub> had an additional aromatic residue (Y52). The mutation of Y52 to Ser (<i>Irp</i>CBM<sub>Y52S</sub>-GFP) reduced these adsorption parameters to 4.4 μmol/g and 1.5 L/μmol, which were similar to those of <i>Th</i>CBM<sub>EG1</sub>-GFP. These results indicate that Y52 plays a crucial role in strong cellulose binding.
DOI: 10.7284/135972
title: Multibeam Echosounder data collected during research cruise AT42-16 using a Kongsberg EM122 instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.1284347
title: Primary Bone Marrow Endothelial Cell from patient #2

description: Mass Spec analysis of secreted proteins from Primary Bone Marrow Endothelial Cell
DOI: 10.6084/m9.figshare.1284348
title: Primary Bone Marrow Endothelial Cell from patient #1

description: Mass Spec analysis of secreted proteins from Primary Bone Marrow Endothelial Cell
DOI: 10.6084/m9.figshare.1284356.v2
title: Dark Research - supplementary materials

description: This is the supplementary materials for a preprint I'm uploading to PeerJ Preprints
DOI: 10.6084/m9.figshare.1284348.v1
title: Primary Bone Marrow Endothelial Cell from patient #1

description: Mass Spec analysis of secreted proteins from Primary Bone Marrow Endothelial Cell
DOI: 10.6084/m9.figshare.1284335
title: Part 2 of November 2004 LTSTM data set

description: This is the second part of a low temperature STM data set from November 2004.
DOI: 10.6084/m9.figshare.1284347.v1
title: Primary Bone Marrow Endothelial Cell from patient #2

description: Mass Spec analysis of secreted proteins from Primary Bone Marrow Endothelial Cell
DOI: 10.6084/m9.figshare.1284356.v1
title: Dark Research - supplementary materials

description: This is the supplementary materials for a preprint I'm uploading to PeerJ Preprints
DOI: 10.6084/m9.figshare.1284321
title: Part 2 of October 2004 LTSTM data set

description: This is the second part of an October 2004 low temperature STM data set.
DOI: 10.6084/m9.figshare.1284333
title: Part 1 of November 2004 LTSTM data set.

description: This is the first part of a November 2004 low temperature STM data set.
DOI: 10.6084/m9.figshare.1284335.v2
title: Part 2 of November 2004 LTSTM data set

description: This is the second part of a low temperature STM data set from November 2004.
DOI: 10.6084/m9.figshare.1284350.v1
title: Cloning and tissue expression profiling of the <i>GnRHR</i> gene of the Muscovy duck (<i>Cairina moschata</i>): Polymorphism and association with egg-laying performance

description: 1. The cDNA sequence of the <i>GnRHR</i> gene was cloned and an association analysis between mutations and laying performance was conducted.2. A 1680-bp cDNA sequence of Muscovy duck <i>GnRHR</i>, which encodes 415 amino acids, was obtained and characterised. Phylogenetic analysis revealed that Muscovy duck <i>GnRHR</i> has a close relationship with <i>Gallus gallus GnRHR</i>.3. There were significantly different expression profiles between 4 age periods in the hypothalamus, pituitary, and ovary. The expression of <i>GnRHR</i> at the age of 36 weeks (laying period) was higher than other time points in the three tissues. <i>GnRHR</i> was expressed in 12 different tissues. The highest expression levels were observed in the hypothalamus, pituitary and gonads.4. A single nucleotide polymorphism detected in the second intron was associated with egg-laying performance. Individuals with the genotype TT had better egg-laying performance from individuals with the genotypes CC or TC. Therefore, <i>GnRHR</i> could be used as a marker gene for laying performance in the Muscovy duck.
DOI: 10.7284/135975
title: Radiometer data collected during research cruise AT42-16 using a Eppley RAD instrument system onboard the platform RV Atlantis

description: Original (unprocessed) data collected during a Field_expedition
DOI: 10.6084/m9.figshare.1284333.v1
title: Part 1 of November 2004 LTSTM data set.

description: This is the first part of a November 2004 low temperature STM data set.
DOI: 10.6084/m9.figshare.1284306
title: Part 2 of LTSTM data set from Sept 2004

description: This is the second part of a data set from September 2004 of low temperature STM data.
DOI: 10.6084/m9.figshare.1284321.v1
title: Part 2 of October 2004 LTSTM data set

description: This is the second part of an October 2004 low temperature STM data set.
DOI: 10.6084/m9.figshare.1284335.v1
title: Part 2 of December 2004 LTSTM data set

description: This is the second part of a low temperature STM data set from November 2004.