cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.3984534
title: Conformational changes associated with L16P and T118M mutations in the membrane-embedded PMP22 protein, consequential in CMT-1A

description: Peripheral myelin protein 22 (PMP22) resides in the plasma membrane and is required for myelin formation in the peripheral nervous system. Excess PMP22 mutants accumulate in the endoplasmic reticulum (ER) resulting in the inherited neuropathies of Charcot–Marie–Tooth disease. However, there was no evidence of the structure of PMP22 or how mutations affect its folding. Therefore, in this study, we combined bioinformatics and homology modeling approaches to obtain three-dimensional native and mutated PMP22 models and its anchoring to a POPC membrane, submitted to .5-μs MD simulations, to determine how the L16P and T118M mutations affect the conformational behavior of PMP22. In addition, we investigated the ability of the native and mutated species to accumulate in the ER, via interaction with RER1, by combining protein–protein docking and MD simulations, taking the conformations that were most representative of the native and mutated PMP22 systems and RER1 conformations. Principal component analysis over MD simulations revealed that L16P and T118M mutations resulted in increased structural instability compared to the native form, which is consistent with previous experimental findings of increased structural fluctuations along a loop connecting transmembrane α-helix1 and α-helix2. Docking and MD simulations coupled with the MMGBSA approach allowed the identification that the binding interface for the PMP22-RER1 complex takes place through transmembrane α-helix1 and α-helix2, with higher effective binding free energy values between the mutated PMP22 systems and RER1 than for the native PMP22, mainly through van der Waals interactions.
DOI: 10.6084/m9.figshare.3984520
title: Role of the sulfur to α-carbon thioether bridges in thurincin H

description: Thurincin H is a small protein produced by <i>Bacillus thuringiensis</i> SF361 with gram-positive antimicrobial properties. The toxins produced by <i>B. thuringiensis</i> are widely used in the agriculture as, e.g. natural preservatives in dairy products. The structure of thurincin H possesses four covalent sulfur to -carbon bonds that involve the cysteine side-chains; these bonds are probably responsible for the shape and stability of the protein and, thereby, for its antimicrobial properties. To examine the influence of the formation of the sulfur-carbon bonds on the folding pathways and stability of the protein, a series of canonical and multiplexed replica-exchange simulations with the coarse-grained UNRES force field was carried out without and with distance restraints imposed on selected S-C atom pairs. It was found that the order of the formation and breaking of the S-C thioether bonds significantly impacts on the foldability and stability of the thurincin H. It was also observed that thioether bridges play a major role in stabilizing the global fold of the protein, although it significantly diminishes the entropy of the system. The maximum foldability of thurincin H was observed in the presence of the optimal set of three out of four thioether bridges. Thus, the results suggest that the presence of ThnB enzyme and other agents that catalyze the formation of thioether bridges can be essential for correct folding of thurincin H and that the formation of the fourth bridge does not seem to facilitate folding; instead, it seems to rigidify the loop and prevent proteolysis.
DOI: 10.7910/dvn/v1rjpf/zcpvyl
title: snk20151104_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984520.v1
title: Role of the sulfur to α-carbon thioether bridges in thurincin H

description: Thurincin H is a small protein produced by <i>Bacillus thuringiensis</i> SF361 with gram-positive antimicrobial properties. The toxins produced by <i>B. thuringiensis</i> are widely used in the agriculture as, e.g. natural preservatives in dairy products. The structure of thurincin H possesses four covalent sulfur to -carbon bonds that involve the cysteine side-chains; these bonds are probably responsible for the shape and stability of the protein and, thereby, for its antimicrobial properties. To examine the influence of the formation of the sulfur-carbon bonds on the folding pathways and stability of the protein, a series of canonical and multiplexed replica-exchange simulations with the coarse-grained UNRES force field was carried out without and with distance restraints imposed on selected S-C atom pairs. It was found that the order of the formation and breaking of the S-C thioether bonds significantly impacts on the foldability and stability of the thurincin H. It was also observed that thioether bridges play a major role in stabilizing the global fold of the protein, although it significantly diminishes the entropy of the system. The maximum foldability of thurincin H was observed in the presence of the optimal set of three out of four thioether bridges. Thus, the results suggest that the presence of ThnB enzyme and other agents that catalyze the formation of thioether bridges can be essential for correct folding of thurincin H and that the formation of the fourth bridge does not seem to facilitate folding; instead, it seems to rigidify the loop and prevent proteolysis.
DOI: 10.6084/m9.figshare.3984534.v1
title: Conformational changes associated with L16P and T118M mutations in the membrane-embedded PMP22 protein, consequential in CMT-1A

description: Peripheral myelin protein 22 (PMP22) resides in the plasma membrane and is required for myelin formation in the peripheral nervous system. Excess PMP22 mutants accumulate in the endoplasmic reticulum (ER) resulting in the inherited neuropathies of Charcot–Marie–Tooth disease. However, there was no evidence of the structure of PMP22 or how mutations affect its folding. Therefore, in this study, we combined bioinformatics and homology modeling approaches to obtain three-dimensional native and mutated PMP22 models and its anchoring to a POPC membrane, submitted to .5-μs MD simulations, to determine how the L16P and T118M mutations affect the conformational behavior of PMP22. In addition, we investigated the ability of the native and mutated species to accumulate in the ER, via interaction with RER1, by combining protein–protein docking and MD simulations, taking the conformations that were most representative of the native and mutated PMP22 systems and RER1 conformations. Principal component analysis over MD simulations revealed that L16P and T118M mutations resulted in increased structural instability compared to the native form, which is consistent with previous experimental findings of increased structural fluctuations along a loop connecting transmembrane α-helix1 and α-helix2. Docking and MD simulations coupled with the MMGBSA approach allowed the identification that the binding interface for the PMP22-RER1 complex takes place through transmembrane α-helix1 and α-helix2, with higher effective binding free energy values between the mutated PMP22 systems and RER1 than for the native PMP22, mainly through van der Waals interactions.
DOI: 10.7910/dvn/v1rjpf/kvrrtr
title: snk20160901_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/jiqvo9
title: snk20160314_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/u9onl3
title: snk20160410_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/nagofb
title: snk20150223_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/kfcpgf
title: snk20150305_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984502
title: Dataset for: A novel diet-induced murine model of steatohepatitis with fibrosis for screening and evaluation of drug candidates for non-alcoholic steatohepatitis

description: Many animal models of non-alcoholic steatohepatitis have been reported. While these models exhibit mild onset of hepatitis and fibrosis, induction is often slow. For faster screening of drug candidates, there is a compelling need for convenient animal models of steatohepatitis and non-alcoholic steatohepatitis in which fatty liver and hepatitis are stably induced within a short period. Here, we analyzed the hepatic lipid composition in non-alcoholic steatohepatitis, and used this information to successfully establish a murine model where steatohepatitis is induced within only 1 week using a novel diet (steatohepatitis-inducing high-fat diet, STHD-01) high in saturated fatty acids and cholesterol. After receiving STHD-01 for 1 week, normal mice (C57BL/6J) showed elevated markers of fatty liver and hepatitis, including hepatic triglycerides and plasma alanine aminotransferase; the administration of angiotensin receptor blockers reduced these symptoms. Furthermore, we confirmed that STHD-01 administration for 36 weeks induced not only sustained elevation of hepatic triglyceride and plasma alanine aminotransferase levels, but also fibrosis and tumor formation. Pretreatment with the carcinogen diethylnitrosamine accelerated tumor formation, and hepatic lesions were observed within 30 weeks of STHD-01 feeding following diethylnitrosamine pretreatment. Finally, branched-chain amino acids, known to reduce the risk for hepatocellular carcinoma in preclinical models, were effective in reducing the progression of liver fibrosis induced by STHD-01 feeding after diethylnitrosamine pretreatment. We concluded that STHD-01 administration successfully induces steatohepatitis within a short period of time. The proposed murine model is suitable for studying the long-term effects of pharmaceutical agents targeting steatohepatitis, fibrosis, and tumor formation.
DOI: 10.6084/m9.figshare.3984502.v1
title: Dataset for: A novel diet-induced murine model of steatohepatitis with fibrosis for screening and evaluation of drug candidates for non-alcoholic steatohepatitis

description: Many animal models of non-alcoholic steatohepatitis have been reported. While these models exhibit mild onset of hepatitis and fibrosis, induction is often slow. For faster screening of drug candidates, there is a compelling need for convenient animal models of steatohepatitis and non-alcoholic steatohepatitis in which fatty liver and hepatitis are stably induced within a short period. Here, we analyzed the hepatic lipid composition in non-alcoholic steatohepatitis, and used this information to successfully establish a murine model where steatohepatitis is induced within only 1 week using a novel diet (steatohepatitis-inducing high-fat diet, STHD-01) high in saturated fatty acids and cholesterol. After receiving STHD-01 for 1 week, normal mice (C57BL/6J) showed elevated markers of fatty liver and hepatitis, including hepatic triglycerides and plasma alanine aminotransferase; the administration of angiotensin receptor blockers reduced these symptoms. Furthermore, we confirmed that STHD-01 administration for 36 weeks induced not only sustained elevation of hepatic triglyceride and plasma alanine aminotransferase levels, but also fibrosis and tumor formation. Pretreatment with the carcinogen diethylnitrosamine accelerated tumor formation, and hepatic lesions were observed within 30 weeks of STHD-01 feeding following diethylnitrosamine pretreatment. Finally, branched-chain amino acids, known to reduce the risk for hepatocellular carcinoma in preclinical models, were effective in reducing the progression of liver fibrosis induced by STHD-01 feeding after diethylnitrosamine pretreatment. We concluded that STHD-01 administration successfully induces steatohepatitis within a short period of time. The proposed murine model is suitable for studying the long-term effects of pharmaceutical agents targeting steatohepatitis, fibrosis, and tumor formation.
DOI: 10.7910/dvn/v1rjpf/tys9ej
title: snk20150424_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/1222rs
title: snk20160730_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984488
title: Glasgow Orthopaedic Research Initiative Conference Report 2015

description: Conference Report on the Glasgow Orthopaedic Research Initiative (GLORI). GLORI aims to bring clinicians and academics together to discuss the field of orthopaedic technologies. The Keynote speaker was Professor Jason Burdick from the University of Pennsylvania who discussed designing materials for chondrogenesis as a result of damaged cartilage from diseases such as osteoarthritis.
DOI: 10.6084/m9.figshare.3984488.v1
title: Glasgow Orthopaedic Research Initiative Conference Report 2015

description: Conference Report on the Glasgow Orthopaedic Research Initiative (GLORI). GLORI aims to bring clinicians and academics together to discuss the field of orthopaedic technologies. The Keynote speaker was Professor Jason Burdick from the University of Pennsylvania who discussed designing materials for chondrogenesis as a result of damaged cartilage from diseases such as osteoarthritis.
DOI: 10.7910/dvn/v1rjpf/hvuzrn
title: snk20150511_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/seouh1
title: snk20150515_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984482
title: GOrizaola_JAE-2016-00305.xlsx

description: Dataset for the paper "Intra-specific priority effects modify compensatory responses to changes in hatching phenology in an amphibian" by Andrea Murillo, Nora Kolter, Anssi Laurila and Germán Orizaola, published in Journal of Animal Ecology MS JAE-2016-00305R1.
DOI: 10.7910/dvn/v1rjpf/ckynus
title: snk20150709_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984482.v1
title: GOrizaola_JAE-2016-00305.xlsx

description: Dataset for the paper "Intra-specific priority effects modify compensatory responses to changes in hatching phenology in an amphibian" by Andrea Murillo, Nora Kolter, Anssi Laurila and Germán Orizaola, published in Journal of Animal Ecology MS JAE-2016-00305R1.
DOI: 10.6084/m9.figshare.3984474
title: An Interview with Manuel Salmeron-Sanchez

description: Blog article featured on Centre for Cell Engineering's Website (www.cceuog.co.uk) concerning an interview with Manuel Salmeron-Sanchez, professor at the University of Glasgow. Our interview concerns bone engineering using growth factors for which Manuel recently received a £2.8M grant from the charity Find a Better Way.
DOI: 10.6084/m9.figshare.3984480
title: Dynamic microRNAome profiles in the developing porcine liver

description: Increasing evidence suggests that micro (mi)RNAs play important roles in various biological process. To evaluate the roles of miRNA in the porcine liver, we investigated the dynamic profiles of microRNAomes using liver tissue from pigs during the embryonic period (embryonic day 90), weaning stage (postnatal day 30), and adult stage (7 years old). A total of 186 unique miRNAs were differentially expressed during liver development. We also identified that 17, 13, and 6 miRNAs were specifically abundant at embryonic day 90, postnatal day 30, and at 7 years, respectively. Besides regulating basic cellular roles in development, miRNAs expressed at the three developmental stages also participated in regulating “embryonic liver development,” “early hepatic growth and generating a functioning liver,” and “energy metabolic processes,” respectively. Our study indicates that miRNAs are extensively involved in liver development, and provides a valuable resource for the further elucidation of miRNA regulatory roles during liver development. miRNAs are extensively involved in liver development, especially for these stage-enriched miRNAs.
DOI: 10.7910/dvn/v1rjpf/wgnpak
title: snk20160315_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/vfnhhq
title: snk20160617_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/o4xttk
title: snk20160819_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984474.v1
title: An Interview with Manuel Salmeron-Sanchez

description: Blog article featured on Centre for Cell Engineering's Website (www.cceuog.co.uk) concerning an interview with Manuel Salmeron-Sanchez, professor at the University of Glasgow. Our interview concerns bone engineering using growth factors for which Manuel recently received a £2.8M grant from the charity Find a Better Way.
DOI: 10.7910/dvn/v1rjpf/cgkvp9
title: snk20151221_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984466
title: Database_14860R3.xlsx

description: Data base for Diaz-Gutierrez J, et al. Plos One 2016. Please, before use the data base contact to Maira Bes-Rastrollo (mbas@unav.es).
DOI: 10.7910/dvn/v1rjpf/25ootr
title: snk20150926_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/kztqoi
title: snk20150524_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984429
title: Supplementary 6 from Foot pressure distributions during walking in African elephants (<i>Loxodonta africana</i>)

description: Elephants, the largest living land mammals, have evolved a specialized foot morphology to help reduce locomotor pressures while supporting their large body mass. Peak pressures that could cause tissue damage are mitigated passively by the anatomy of elephants' feet, yet this mechanism does not seem to work well for some captive animals. This study tests how foot pressures vary among African and Asian elephants from habitats where natural substrates predominate but where foot care protocols differ. Variations in pressure patterns might be related to differences in husbandry, including but not limited to trimming and the substrates that elephants typically stand and move on. Both species' samples exhibited the highest concentration of peak pressures on the lateral digits of their feet (which tend to develop more disease in elephants) and lower pressures around the heel. The trajectories of the foot's centre of pressure were also similar, confirming that when walking at similar speeds, both species load their feet laterally at impact and then shift their weight medially throughout the step until toe-off. Overall, we found evidence of variations in foot pressure patterns that might be attributable to husbandry and other causes, deserving further examination using broader, more comparable samples.
DOI: 10.7910/dvn/v1rjpf/65r7s4
title: snk20160311_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984429.v1
title: Supplementary 6 from Foot pressure distributions during walking in African elephants (<i>Loxodonta africana</i>)

description: Elephants, the largest living land mammals, have evolved a specialized foot morphology to help reduce locomotor pressures while supporting their large body mass. Peak pressures that could cause tissue damage are mitigated passively by the anatomy of elephants' feet, yet this mechanism does not seem to work well for some captive animals. This study tests how foot pressures vary among African and Asian elephants from habitats where natural substrates predominate but where foot care protocols differ. Variations in pressure patterns might be related to differences in husbandry, including but not limited to trimming and the substrates that elephants typically stand and move on. Both species' samples exhibited the highest concentration of peak pressures on the lateral digits of their feet (which tend to develop more disease in elephants) and lower pressures around the heel. The trajectories of the foot's centre of pressure were also similar, confirming that when walking at similar speeds, both species load their feet laterally at impact and then shift their weight medially throughout the step until toe-off. Overall, we found evidence of variations in foot pressure patterns that might be attributable to husbandry and other causes, deserving further examination using broader, more comparable samples.
DOI: 10.7910/dvn/v1rjpf/z70ffc
title: snk20151228_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/iht4k2
title: snk20160820_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984240
title: Musical Correlates of Group Synchrony in a Real-World Club Environment

description: Data from the dance club acquisition and the reliability test session<br>
DOI: 10.7910/dvn/v1rjpf/0cz9ca
title: snk20160728_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984240.v1
title: Musical Correlates of Group Synchrony in a Real-World Club Environment

description: Data from the dance club acquisition and the reliability test session<br>
DOI: 10.7910/dvn/v1rjpf/wb71dr
title: snk20150517_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/hibx9i
title: snk20161102_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/rcy7hf
title: snk20150502_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/7vrhol
title: snk20150617_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/nbncwo
title: snk20161129_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/tkoefu
title: snk20160211_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/2e3jqo
title: snk20150206_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/87eub3
title: snk20150430_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/y1nkni
title: snk20150604_03.txt.gz

description: :unav
DOI: 10.7910/dvn/v1rjpf/gs2cl6
title: snk20151017_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984117
title: Identifying the morphological phenotypes of MDA-MB-231 cells in a DIGME

description: we use this date set to identifying the morphological phenotypes of MDA-MB-231 cells in a DIGME.<br><br>
DOI: 10.7910/dvn/v1rjpf/torplc
title: snk20150827_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984117.v1
title: 3D Cell Morphological Phenotypes

description: The collective migration of MDA-MB-231 cells in a DIGME device.<b></b><i></i><sub></sub><sup></sup><br>
DOI: 10.6084/m9.figshare.3984117.v2
title: Identifying the morphological phenotypes of MDA-MB-231 cells in a DIGME

description: we use this date set to identifying the morphological phenotypes of MDA-MB-231 cells in a DIGME.<br><br>
DOI: 10.7910/dvn/v1rjpf/u3giyk
title: snk20160301_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984111
title: Data Repository for "Does social environment influence learning ability in a family-living lizard?"

description: This dataset is from a study that compared spatial learning ability between Tree Skinks (<i>Egernia striolata</i>) that were raised in either an isolated or social environment for 1 year before we quantified their individual learning ability.
DOI: 10.7910/dvn/v1rjpf/0svpmr
title: snk20160117_03.txt.gz

description: :unav
DOI: 10.6084/m9.figshare.3984111.v1
title: Data Repository for "Does social environment influence learning ability in a family-living lizard?"

description: This dataset is from a study that compared spatial learning ability between Tree Skinks (<i>Egernia striolata</i>) that were raised in either an isolated or social environment for 1 year before we quantified their individual learning ability.
DOI: 10.7910/dvn/v1rjpf/psarqj
title: snk20150211_03.txt.gz

description: :unav