bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dynamics in Natural and Designed Elastins and Their Relation to Elastic Fiber Structure and Recoil
Authors: Carvajal Ma. Faye Charmagne A. , Preston Jonathan M. , Jamhawi Nour M. , Sabo T. Michael , Bhattacharya Shibani , Aramini James M. , Wittebort Richard J. , Koder Ronald L. 
Published: July 2020

ABSTRACTElastin fibers assemble in the extracellular matrix from the precursor protein tropoelastin and provide the flexibility and spontaneous recoil required for arterial function. Unlike many proteins, a structure-function mechanism for elastin has been elusive. We have performed detailed NMR relaxation studies of the dynamics of the minielastins24x′and20x′using solution NMR, and of purified bovine elastin fibers in the presence and absence of mechanical stress using solid state NMR. The low sequence complexity of the minielastins enables us to determine dynamical timescales and degrees of local ordering with residue-specific resolution in the cross-link and hydrophobic modules using NMR relaxation. We find an extremely high degree of disorder, with order parameters for the entirety of the hydrophobic domains near zero, resembling that of simple chemical polymers and less than the order parameters that have been observed in other intrinsically disordered proteins. We find that backbone order parameters in natural, purified elastin fibers are comparable to those found in24x′and20x′in solution. The difference in dynamics, compared to the minielastins, is that backbone correlation times are significantly slowed in purified elastin. Moreover, when elastin is mechanically stretched, the high chain disorder in purified elastin is retained - showing that any change in local ordering is below that detectable in our experiment. Combined with our previous finding of a 10-fold increase in the ordering of water when fully hydrated elastin fibers are stretched by 50%, these results support the hypothesis that stretch induced solvent ordering, i.e., the hydrophobic effect, is a key player in the elastic recoil of elastin as opposed to configurational entropy loss.SIGNIFICANCEElastin is responsible for the spontaneous recoil of arterial walls that is necessary for cardiovascular function. Despite this critical role, the mechanism driving entropic recoil has remained unclear. Elastin is unusual in that it is intrinsically disordered in both soluble and fibrous forms. Using NMR, we have determined the timescales and amplitudes of dynamics in two soluble elastin mimetics and in relaxed and stretched states of purified bovine elastin fibers. Although dynamical timescales are different, both the soluble elastin mimetic and fibrillar elastin display an exceptionally high degree of disorder. No detectable increase in protein ordering was observed upon stretching, suggesting that entropic recoil is primarily driven by the hydrophobic effect and not configurational entropy loss.
Genome analyses reveal the hybrid origin of the staple food crop white Guinea yam
Authors: Sugihara Yu , Darkwa Kwabena , Yaegashi Hiroki , Natsume Satoshi , Shimizu Motoki , Abe Akira , Hirabuchi Akiko , Ito Kazue , Oikawa Kaori , Tamiru-Oli Muluneh , Ohta Atsushi , Matsumoto Ryo , Paterne Agre , De Koeyer David , Pachakkil Babil , Yamanaka Shinsuke , Muranaka Satoru , Takagi Hiroko , White Ben , Asiedu Robert , Innan Hideki , Asfaw Asrat , Adebola Patrick , Terauchi Ryohei 
Published: July 2020

AbstractWhite Guinea yam (Dioscorea rotundata) is an important staple tuber crop of West Africa. However, its origin remains unclear. In this study, we re-sequenced 336 accessions of white Guinea yam and compared them with the sequences of the wildDioscoreaspecies using an improved reference genome sequence ofD. rotundata. Our results suggest a hybrid origin of white Guinea yam from crosses between the rainforest wild speciesD. praehensilisand the savannah-adaptedD. abyssinica. We identified a higher genomic contribution fromD. abyssinicain the sex chromosome of Guinea yam and an extensive introgression around theSWEETIEgene. Our findings point to a complex domestication scenario for Guinea yam and highlight the importance of wild species as gene donors for improvement of this crop through molecular breeding.
Bioinformatic Analysis of Structure and Function of LIM Domains of Human Zyxin Family Proteins
Authors: Siddiqui Mohammad Quadir , Badmalia Maulik D. , Patel Trushar R. 
Published: July 2020

AbstractMembers of the human Zyxin family are LIM domain-containing proteins that perform critical cellular functions and are indispensable for cellular integrity. Despite their importance, not much is known about their structure, functions, interactions and dynamics. To provide insights into these, we used a set of in-silico tools and databases and analyzed their amino acid sequence, phylogeny, post-translational modifications, structure-dynamics, molecular interactions, and functions. Our analysis revealed that zyxin members are ohnologs. Presence of a conserved nuclear export signal composed of LxxLxL/LxxxLxL consensus sequence, as well as a possible nuclear localization signal, suggesting that Zyxin family members may have nuclear and cytoplasmic roles. The molecular modeling and structural analysis indicated that Zyxin family LIM domains share similarities with transcriptional regulators and have positively charged electrostatic patches, which may indicate that they have previously unanticipated nucleic acid binding properties. Intrinsic dynamics analysis of Lim domains suggest that only Lim1 has similar internal dynamics properties, unlike Lim2/3. Furthermore, we analyzed protein expression and mutational frequency in various malignancies, as well as mapped protein-protein interaction networks they are involved in. Overall, our comprehensive bioinformatic analysis suggests that these proteins may play important roles in mediating protein-protein and protein-nucleic acid interactions.
Development of a genetically-encoded oxytocin sensor
Authors: Mignocchi Neymi , Krüssel Sarah , Jung Kanghoon , Lee Dongmin , Kwon Hyung-Bae 
Published: July 2020

AbstractOxytocin (OXT) is a neuropeptide originating in the paraventricular nucleus (PVN) of the hypothalamus, with a role in influencing various social behaviors. However, pinpointing its actions only during the time animals are performing specific behaviors has been difficult to study. Here we developed an optogenetic gene expression system designed to selectively label neuronal populations activated by OXT in the presence of blue-light, named “OXTR-iTango2”. The OXTR-iTango2 was capable of inducing gene expression of a reporter gene in both human embryonic kidney (HEK) cells and neurons in a quantitative manner.In vivoexpression of OXTR-iTango2 selectively labeled OXT-sensitive neurons in a blue-light dependent manner. Furthermore, we were able to detect a subset of dopamine (DA) neurons in the ventral tegmental area (VTA) that receive OXT activation during social interaction. Thus, we provide a genetically-encoded, scalable optogenetic toolset to target neural circuits activated by OXT in behaving animals with a high temporal resolution.
Are single peripheral measurements of baseline oxytocin in saliva and plasma reliable biomarkers of the physiology of the oxytocin system in humans?
Authors: Martins Daniel , Gabay Anthony , Mehta Mitul A. , Paloyelis Yannis 
Published: July 2020

AbstractBackgroundSingle measurements of salivary and plasmatic oxytocin are used as indicators of the physiology of the oxytocin system. However, questions remain about whether they are sufficiently stable to provide valid biomarkers of the physiology of the oxytocin system, and whether salivary oxytocin can accurately index its plasmatic concentrations.MethodsUsing radioimmunoassay, we measured baseline plasmatic and/or salivary oxytocin from two independent datasets. Dataset A comprised 17 healthy men sampled on four occasions approximately at weekly intervals. We administered exogenous oxytocin intravenously and intranasally in a triple dummy, within-subject, placebo-controlled design and compared baseline levels and the effects of routes of administration. Dataset B comprised baseline plasmatic oxytocin measurements from 20 healthy men sampled on two separate occasions. Additionally, in dataset A, we tested whether salivary oxytocin can predict plasmatic oxytocin at baseline and after intranasal and intravenous oxytocin administration.ResultsSingle measurements of plasmatic and salivary oxytocin showed poor reliability across visits in both datasets. Intranasal administration of exogenous oxytocin increases salivary oxytocin, but intravenous administration of a considerable dose does not produce any changes. Saliva and plasma oxytocin did not correlate at baseline or after administration of exogenous oxytocin.ConclusionsOur findings question the use of single measurements of baseline oxytocin concentrations in saliva and plasma as valid biomarkers of the physiology of the oxytocin system in humans. Salivary oxytocin is a weak surrogate for plasmatic oxytocin. The increases in salivary oxytocin observed after intranasal oxytocin most likely reflect unabsorbed peptide and should not be used to predict treatment effects.
Cortical Presynaptic Boutons Progressively Engulf Spinules As They Mature
Authors: Campbell Charles , Lindhartsen Sarah , Knyaz Adam , Erisir Alev , Nahmani Marc 
Published: July 2020

AbstractDespite decades of discussion in the neuroanatomical literature, the role of the synaptic ‘spinule’ in synaptic development and function remains elusive. Canonically, spinules are finger-like projections that emerge from postsynaptic spines and can become enveloped by presynaptic boutons. When a presynaptic bouton encapsulates a spinule in this manner, the membrane apposition between the spinule and surrounding bouton can be significantly larger than the membrane interface at the synaptic active zone. Hence, spinules may represent a mechanism for extrasynaptic neuronal communication, and/or may function as structural ‘anchors’ that increase the stability of cortical synapses. Yet despite their potential to impact synaptic function, we have little information on the percentages of developing and adult cortical bouton populations that contain spinules, the percentages of these cortical spinule-bearing boutons (SBBs) that contain spinules from distinct neuronal/glial origins, or whether the onset of activity or cortical plasticity are correlated with increased prevalence of cortical SBBs. Here, we employed 2D and 3D electron microscopy to determine the prevalence of spinules in excitatory presynaptic boutons at key developmental time points in the primary visual cortex (V1) of female and male ferrets. We find that the prevalence of SBBs in V1 increases across postnatal development, such that ~25% of excitatory boutons in late adolescent ferret V1 contain spinules. In addition, we find that a majority of spinules within SBBs at later developmental time points emerge from postsynaptic spines and adjacent boutons/axons, suggesting that synaptic spinules may enhance synaptic stability and allow for axo-axonal communication in mature sensory cortex.Significance StatementSynaptic spinules are finger-like projections from neurites that can become completely embedded within presynaptic boutons, potentially enhancing synaptic communication and stability. Yet while their existence has been discussed for decades, spinule prevalence, projection origins, and relationship to neocortical sensory activity remain unknown. In this study, we employed 2D and 3D electron microscopy techniques to characterize the development of excitatory cortical spinule-bearing boutons (SBBs) and their relationship to sensory activity and plasticity. Our results demonstrate that neocortical presynaptic SBB prevalence is not correlated with the onset of sensory activity or heightened cortical plasticity, and that by late adolescence nearly one-quarter of presynaptic boutons contain a spinule. Hence, synaptic spinules may play progressively important roles in cortical function as these synapses mature.
Transcription factor recruitment by parallel G-quadruplexes to promote transcription: the case of herpes simplex virus-1 ICP4
Authors: Frasson Ilaria , Soldà Paola , Nadai Matteo , Lago Sara , Richter Sara N. 
Published: July 2020

SUMMARYG-quadruplexes (G4s), four-stranded nucleic acid structures that adopt several distinctive conformations, are abundant at gene promoters and have been proposed as transcription regulatory elements. G4s form in the herpes simplex virus-1 (HSV-1) genome during its viral cycle. Here by cross-linking/pull-down assay we identified ICP4 as the protein that most interacts with viral G4s during infection. In vitro and in infected cells, ICP4 specifically and directly bound and unfolded parallel G4s, including those present in HSV-1 immediate early gene promoters, and consequently induced transcription. This mechanism was also exploited by ICP4 to promote its own transcription. By proximity ligation assay we visualized ICP4 interaction at the single G4 in cells. G4 ligands inhibited ICP4 binding to G4s. Our results indicate the existence of a well-defined G4-viral protein network that regulates the productive HSV-1 cycle. They also point to G4s as elements that recruit transcription factors to activate transcription in cells.
A standardized broad host range inverter package for genetic circuitry design in Gram-negative bacteria
Authors: Tas Huseyin , Goñi-Moreno Ángel , de Lorenzo Víctor 
Published: July 2020

ABSTRACTGenetically encoded logic gates, especially inverters—NOT gates—are the building blocks for designing circuits, engineering biosensors or decision-making devices in synthetic biology. However, the repertoire of inverters readily available for different species is rather limited. In this work, a large whole of NOT gates that was shown to function previously in a specific strain ofEscherichia coli, was recreated as broad host range (BHR) collection of constructs assembled in low, medium and high copy number plasmid backbones of the SEVA (Standard European Vector Architecture) collection. The input/output function of each of the gates was characterized and parameterized in the environmental bacterium and metabolic engineering chassisPseudomonas putida. Comparisons of the resulting fluorescence cytometry data with those published for the same gates inEscherichia coliprovided useful hints on the portability of the corresponding gates. The hereby described BHR inverter package (20 different versions of 12 distinct gates) thus becomes a toolbox of choice for designing genetic circuitries in a variety of Gram-negative species other thanE. coli.
The Nesprin-1/-2 ortholog ANC-1 regulates organelle positioning inC. eleganswithout its KASH or actin-binding domains
Authors: Hao Hongyan , Kalra Shilpi , Jameson Laura E. , Guerrero Leslie A. , Cain Natalie E. , Bolivar Jessica , Starr Daniel A. 
Published: July 2020

AbstractKASH proteins in the outer nuclear membrane comprise the cytoplasmic half of LINC complexes that connect nuclei to the cytoskeleton.Caenorhabditis elegansANC-1, an ortholog of Nesprin-1/2, contains actin-binding and KASH domains at opposite ends of a long spectrin-like region. Deletion of either the KASH or calponin homology (CH) domains does not completely disrupt nuclear positioning, suggesting neither KASH nor CH domains are essential. Deletions in the spectrin-like region of ANC-1 led to significant defects, but only recapitulated the null phenotype in combination with mutations in the trans-membrane span. Inanc-1mutants, the ER was unanchored, moving throughout the cytoplasm, and often fragmented. The data presented here support a cytoplasmic integrity model where ANC-1 localizes to the ER membrane and extends into the cytoplasm to position nuclei, ER, mitochondria, and likely other organelles in place.
Glutathione S-transferase: A Candidate Gene for Berry Color in Muscadine Grapes (Vitis rotundifolia)
Authors: Varanasi Aruna , Worthington Margaret , Nelson Lacy , Brown Autumn , Threlfall Renee , Howard Luke , Clark John R. 
Published: July 2020

AbstractMuscadine grapes (Vitis rotundifoliaMichx.) are a specialty crop cultivated in the southern United States. Muscadines (2n=40) belong to theMuscadiniasubgenus ofVitis,while all other cultivated grape species belong to the subgenusEuvitis(2n=38). The berry color locus in muscadines has been mapped to a 0.8 Mbp region syntenic with chromosome 4 ofV. vinifera. In this study, we identified glutathione S-transferase4 (GST4) as a likely candidate gene for anthocyanin transport within the berry color locus. PCR and KASP genotyping identified a single intragenic SNP (C/T) marker corresponding to a proline to leucine mutation within the muscadineGST4(VrGST4) that differentiated black (CC and CT) from bronze (TT) muscadines in 65 breeding selections, 14 cultivars, and 320 progeny from two mapping populations. Anthocyanin profiling on a subset of the progeny indicated a dominantVrGST4action, with no allele dosage effect on total anthocyanin content or composition of individual anthocyanins. Proanthocyanidin content was similar in the seeds of both black and bronze genotypes, and seeds had much higherVrGST3expression and lowerVrGST4expression than skins.VrGST4expression was higher in post-veraison berries of black muscadines compared to pre-veraison berries, but no changes in gene expression in pre- and post-veraison berries were observed in the bronze muscadine cultivar.VrMybA1expression was higher in post-veraison berries of both black and bronze muscadines. These results suggest that berry pigmentation in muscadines is regulated by a mechanism distinct from theMybAgene cluster that is responsible for berry color variation inV. vinifera.
Bacterial quorum sensing signal arrests phytoplankton cell division and protects against virus-induced mortality
Authors: Pollara Scott B. , Becker Jamie W. , Nunn Brook L. , Boiteau Rene , Repeta Daniel , Mudge Miranda C. , Downing Grayton , Chase Davis , Harvey Elizabeth L. , Whalen Kristen E. 
Published: July 2020

ABSTRACTInteractions between phytoplankton and heterotrophic bacteria fundamentally shape marine ecosystems. These interactions are driven by the exchange of compounds, however, linking these chemical signals, their mechanisms of action, and resultant ecological consequences remains a fundamental challenge. The bacterial signal 2-heptyl-4-quinolone (HHQ), induces immediate cellular stasis in the coccolithophore,Emiliania huxleyi, however, the mechanism responsible remains unknown. Here, we show that HHQ exposure leads to the accumulation of DNA damage in phytoplankton and prevents its repair. While this effect is reversible, HHQ-exposed phytoplankton are also protected from viral mortality, ascribing a new role of quorum sensing signals in regulating multi-trophic interactions. Further results demonstrate global HHQ production potential and the firstin situmeasurements of HHQ which coincide with areas of enhanced micro- and nanoplankton biomass. Our results support bacterial communication signals as emerging players, providing a new mechanistic framework for how compounds may contribute to structure complex marine microbial communities.
MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments
Authors: Porter Teresita M. , Hajibabaei Mehrdad 
Published: July 2020

AbstractMulti-marker metabarcoding is increasingly being used to generate biodiversity information across different domains of life from microbes to fungi to animals such as for molecular ecology and biomonitoring applications in different sectors from academic research to regulatory agencies and industry. Current popular bioinformatic pipelines support microbial and fungal marker analysis, while ad hoc methods are often used to process animal metabarcode markers from the same study. MetaWorks provides a harmonized processing environment, pipeline, and taxonomic assignment approach for demultiplexed Illumina reads for all biota using a wide range of metabarcoding markers such as 16S, ITS, and COI. A Conda environment is provided to quickly gather most of the programs and dependencies for the pipeline. Several workflows are provided such as: taxonomically assigning exact sequence variants, provides an option to generate operational taxonomic units, and facilitates single-read processing. Pipelines are automated using Snakemake to minimize user intervention and facilitate scalability. All pipelines use the RDP classifier to provide taxonomic assignments with confidence measures. We extend the functionality of the RDP classifier for taxonomically assigning 16S (bacteria), ITS (fungi), and 28S (fungi), to also support COI (animals), rbcL (eukaryotes, land plants, diatoms), 12S (fish), 18S (eukaryotes, diatoms) and ITS (fungi, plants). MetaWorks properly handles ITS by trimming flanking conserved rRNA gene regions as well as protein coding genes by providing two options for removing obvious pseudogenes. MetaWorks is available athttps://github.com/terrimporter/MetaWorksalong with quick-start instructions using test data, detailed workflow descriptions, and a tutorial for new users.
Mitogenome reconstruction of an endangered African seahorse from a Traditional Chinese Medicine market was based on a misidentification
Authors: Teske Peter R. 
Published: July 2020

AbstractThe recently published complete mitochondrial genome of the endangered Knysna seahorse,Hippocampus capensisBoulenger, 1900, was based on a specimen obtained from a Traditional Chinese Medicine market. AsH. capensisis endemic to temperate South Africa and exceptionally rare, illegal trade to supply Asian markets would constitute a considerable extinction risk. I investigated the phylogenetic placement of the Chinese specimen using mitochondrial DNA control region and cytochromebsequences from theH. capensismitogenome among corresponding published sequences ofH. capensisand a number of closely related seahorse species. The Chinese specimen was distinct fromH. capensisand instead clustered withH. casscsio, a seahorse that was recently described from the South China Sea. The sequences ofH. casscsioclustered randomly among those of specimens identified asH. fuscus, a species whose taxonomic validity is disputed, and which is considered to be a synonym of the widespread Indo-Pacific seahorseH. kuda. Given that the morphological identification of seahorses is difficult, it is recommended that the publication of new species descriptions and genomic resources be preceded by a comprehensive comparison with the available molecular data. The taxonomy of seahorses is far from resolved, and cutting-edge molecular studies will not improve this situation if they do not take existing information into consideration.
Repression of interrupted and intact rDNA by the SUMO pathway inDrosophila melanogaster
Authors: Luo Yicheng , Fefelova Elena , Ninova Maria , Chen Yung-Chia Ariel , Aravin Alexei A. 
Published: July 2020

AbstractRibosomal RNAs (rRNAs) are essential components of the ribosome and are among the most abundant macromolecules in the cell. To ensure high rRNA level, eukaryotic genomes contain dozens to hundreds of rDNA genes, however, only a fraction of the rRNA genes seems to be active, while others are transcriptionally silent. We found that individual rDNA genes have high level of cell-to-cell heterogeneity in their expression inDrosophila melanogaster. Insertion of heterologous sequences into rDNA leads to repression associated with reduced expression in individual cells and decreased number of cells expressing rDNA with insertions. We found that SUMO (Small Ubiquitin-like Modifier) and SUMO ligase Ubc9 are required for efficient repression of interrupted rDNA units and variable expression of intact rDNA. Disruption of the SUMO pathway abolishes discrimination of interrupted and intact rDNAs and removes cell-to-cell heterogeneity leading to uniformly high expression of individual rDNA in single cells. Our results suggest that the SUMO pathway is responsible for both repression of interrupted units and control of intact rDNA expression.