bluuebunny/crossref_metadata_2025_split huggingface dataset:
Filling a blank in bivalve taxonomy: an integrative analysis of Cyamioidea (Mollusca: Bivalvia)
Authors: Zelaya Diego G , Güller Marina , Ituarte Cristián 
Published: October 2019

AbstractThis contribution provides the first integrative study of Cyamioidea, a group of bivalves largely neglected in the past. By combining information obtained from shell morphology, gross anatomy, histology, reproductive biology and DNA sequencing, the distinctive characters of Cyamioidea are determined, and the taxa belonging to this superfamily are revised. Gaimardioidea, previously considered as a distinct superfamily, is reduced to family level (Gaimardiidae), which, along with Cyamiidae, are assigned to Cyamioidea. All studied cyamioideans share a common reproductive character: the presence of a true follicular epithelium surrounding each developing oocyte, which persists after spawning, surrounding the developing embryos and participating in their anchorage to the gill filaments. Several morphological and anatomical characters support the distinction of Gaimardiidae and Cyamiidae. Based on that information, the placement of Gaimardia and Kidderia in Gaimardiidae, and that of Cyamiocardium, Cyamiomactra, Cyamium, Heteromactra, Pseudokelly, Ptychocardia and Reloncavia in Cyamiidae, is confirmed. Jukesena, historically placed in Veneroidea, is here allocated to Cyamiidae. Neoleptonidae, previously also attributed to Cyamioidea, are reallocated to Veneroidea.
In response to Luteijn et al.: Concerns regarding cGAMP uptake assay and evidence that SLC19A1 is not the major cGAMP importer in human PBMCs
Authors: Ritchie Christopher , Cordova Anthony F. , Li Lingyin 
Published: October 2019

AbstractWe previously reported that SLC19A1 is an importer of the immunotransmitter 2’3’-cyclic-GMP-AMP (cGAMP)1 by performing a genome wide screen in U937 cells. Soon after, Lutejin et al. reported similar findings by conducting a screen in THP-1 cells2. While the conclusions of these two studies largely overlap, we arrived at significantly different conclusions regarding how broadly SLC19A1 is used by different cell types. Our study suggests that in addition to SLC19A1, many cultured and primary cell types use alternative, unidentified transporters to import cGAMP and other cyclic dinucleotides (CDNs). This conclusion was based on our findings that inhibition of SLC19A1 did not significantly reduce extracellular cGAMP signaling in multiple cell types, including primary CD14+peripheral blood mononuclear cells (PBMCs) from most donors. In contrast, Luteijn et al. concluded that SLC19A1 is the major CDN importer in humans, largely based on their use of a radiolabeled [32P] cGAMP uptake assay. Using this assay, they showed that inhibition of SLC19A1 abolishes [32P] uptake in total PBMCs. However, they did not test whether inhibition of SLC19A1 affects extracellular cGAMP signaling in these cells. Here, we highlight an important issue with the [32P] cGAMP uptake assay used by Luteijn et al. and demonstrate that measuring extracellular cGAMP signaling through the STING pathway is currently the best method for evaluating cGAMP import. We also show that inhibition of SLC19A1 has no effect on extracellular cGAMP signaling in total PBMCs, confirming that this cell type relies on other transport mechanisms for cGAMP import.
Erosion of the Epigenetic Landscape and Loss of Cellular Identity as a Cause of Aging in Mammals
Authors: Yang Jae-Hyun , Griffin Patrick T. , Vera Daniel L. , Apostolides John K. , Hayano Motoshi , Meer Margarita V. , Salfati Elias L. , Su Qiao , Munding Elizabeth M. , Blanchette Marco , Bhakta Mital , Dou Zhixun , Xu Caiyue , Pippin Jeffrey W. , Creswell Michael L. , O’Connell Brendan L. , Green Richard E. , Garcia Benjamin A. , Berger Shelley L. , Oberdoerffer Philipp , Shankland Stuart J. , Gladyshev Vadim N. , Rajman Luis A. , Pfenning Andreas R. , Sinclair David A. 
Published: October 2019

SUMMARYAll living things experience entropy, manifested as a loss of inherited genetic and epigenetic information over time. As budding yeast cells age, epigenetic changes result in a loss of cell identity and sterility, both hallmarks of yeast aging. In mammals, epigenetic information is also lost over time, but what causes it to be lost and whether it is a cause or a consequence of aging is not known. Here we show that the transient induction of genomic instability, in the form of a low number of non-mutagenic DNA breaks, accelerates many of the chromatin and tissue changes seen during aging, including the erosion of the epigenetic landscape, a loss of cellular identity, advancement of the DNA methylation clock and cellular senescence. These data support a model in which a loss of epigenetic information is a cause of aging in mammals.One Sentence SummaryThe act of repairing DNA breaks induces chromatin reorganization and a loss of cell identity that may contribute to mammalian aging
Correlation between Serum Kisspeptin and Spermatogenic Function in Men
Authors: Yu Hongling , Liu Jin , Han Yilong , Chen Chao , Meng Fanwei 
Published: October 2019

AbstractKisspeptin along with its receptor GPR54 or KISS1R regulates the secretion of hormones involved in the hypothalamic-pituitary-testicular axis, which is one of the contributing factors of adolescent spermatogenesis. This study aimed to investigate the correlation between serum kisspeptin concentration and spermatogenic function, and its predictive value in azoospermia. We retrospectively analyzed data of 196 males who visited the Reproductive Medicine Center of Qilu Hospital of Shandong University from June–November 2018; 20 were fertile and 176 were infertile. The following semen tests were performed: serum kisspeptin level by enzyme immunoassay; and levels of follicle-stimulating and luteinizing hormones, and testosterone by chemiluminescence assay. Percutaneous testicular sperm aspiration was performed on males with azoospermia. Subjects were divided into 5 groups: azoospermia (group A: 22 men with obstructive azoospermia; group B: 54 men with non-obstructive azoospermia), oligospermia (group C: 56 men), infertility with normal semen concentration (group D: 44 men), and fertility with normal semen concentration (group E: 20 men). Kisspeptin levels in the fertile group were higher than those in the infertile group. Levels of serum hormones, testosterone, and kisspeptin correlated with sperm concentration, with the strongest correlation between kisspeptin and sperm concentration (correlation coefficient=0.692). Levels of kisspeptin in obstructive and non-obstructive azoospermia groups were analyzed using Receiver-Operating-Curve analysis. A serum kisspeptin level ≥80.655 was classified as obstructive azoospermia; otherwise, the classification was non-obstructive azoospermia. Serum kisspeptin levels in the fertility group were significantly higher than that in the infertility group; this suggests kisspeptin may be associated with male fertility. Moreover, kisspeptin had a stronger correlation with sperm concentration than the hormones. A serum kisspeptin level of 80.655 can be used to differentiate obstructive and non-obstructive azoospermia.
Genome-wide variations analysis of special waxy sorghum cultivar Hongyingzi for brewing Moutai liquor
Authors: Wang Can , Zhou Lingbo , Gao Xu , Ding Yanqing , Cheng Bin , Zhang Guobing , Cao Ning , Xu Yan , Shao Mingbo , Zhang Liyi 
Published: October 2019

AbstractsHongyingzi is a special waxy sorghum (Sorghum bicolorL. Moench) cultivar for brewing Moutai liquor. For an overall understanding of the whole genome of Hongyingzi, we performed whole-genome resequencing technology with 56.10 X depth to reveal its comprehensive variations. Compared with the BTx623 reference genome, 2.48% of genome sequences were altered in the Hongyingzi genome. Among these alterations, there were 1885774 single nucleotide polymorphisms (SNPs), 309381 small fragments insertions and deletions (Indels), 31966 structural variations (SVs), and 217273 copy number variations (CNVs). These alterations conferred 29614 genes variations. It was also predicted that 35 genes variations were related to the multidrug and toxic efflux (MATE) transporter, chalcone synthase (CHS), ATPase isoform 10 (AHA10) transporter, dihydroflavonol-4-reductase (DFR), the laccase 15 (LAC15), flavonol 3′-hydroxylase (F3′H), flavanone 3-hydroxylase (F3H),O-methyltransferase (OMT), flavonoid 3′5′ hydroxylase (F3′5′H), UDP-glucose:sterol-glucosyltransferase (SGT), flavonol synthase (FLS), and chalcone isomerase (CHI) involved in the tannin synthesis. These results would provide theoretical supports for the molecular markers developments and gene function studies related to the liquor-making traits, and the genetic improvement of waxy sorghum based on the genome editing technology.
Optimal fertigation for high yield and fruit quality of greenhouse strawberry
Authors: Yong Wu , Li Li , Minzan Li , Man Zhang , Hong Sun , Sygrimis Nikolaos 
Published: October 2019

AbstractNitrogen (N), phosphorus (P), potassium (K), and water are four crucial factors that have significant effects on strawberry yield and fruit quality. A quadratic regression orthogonal rotation combination experiment that involved 36 treatments with five levels of the four variables (N, P, and K fertilizers and water) was executed to optimize the fertilization and water combination for high yield and quality. SSC/TA ratio (the ratio of soluble solid content to titratable acid) was selected as the index of quality. Results showed that the N fertilizer was the most important factor, followed by water and P fertilizer, and the N fertilizer had a significant effect on yield and SSC/TA ratio. By contrast, the K fertilizer had a significant effect only on yield. N×K fertilizer interaction had a significant effect on yield, whereas the other interactions among the four factors had no significant effects on yield and SSC/TA ratio. The effects of the four factors on the yield and SSC/TA ratio were ranked as N fertilizer > water > K fertilizer > P fertilizer and N fertilizer > P fertilizer > water > K fertilizer, respectively. The yield and SSC/TA ratio increased and then decreased when NPK fertilizer and water increased. The optimal fertilizer and water combination was 22.28–24.61 g/plant Ca (NO3)2⋅4H2O, 1.75–2.03 g/plant NaH2PO4, 12.41–13.91 g/plant K2SO4, and 12.00– 13.05 L/plant water for yields of more than 110 g/plant and optimal SSC/TA ratio of 8.5–14.
Activation of phospholipase C β by Gβγ and Gαqinvolves C-terminal rearrangement to release auto-inhibition
Authors: Fisher Isaac , Jenkins Meredith , Tall Greg , Burke John E , Smrcka Alan V. 
Published: October 2019

AbstractPhospholipase C (PLC) enzymes hydrolyse phosphoinositide lipids to inositol phosphates and diacylglycerol. Direct activation of PLCβ by Gαqand/or Gβγ subunits mediates signalling by Gq and some Gi coupled G protein-coupled receptors (GPCRs), respectively. PLCβ isoforms contain a unique C-terminal extension, consisting of proximal and distal C-terminal domains (CTD) separated by a flexible linker. The structure of PLCβ3 bound to Gαqis known, however, for both Gαqand Gβγ, the mechanism for PLCβ activation on membranes is unknown. We examined PLCβ2 dynamics on membranes using hydrogen deuterium exchange mass spectrometry (HDX-MS). Gβγ caused a robust increase in dynamics of the distal C-terminal domain (CTD). Gαqshowed decreased deuterium incorporation at the Gαqbinding site on PLCβ.In vitroGβγ-dependent activation of PLC is inhibited by the distal CTD. The results suggest that disruption of auto-inhibitory interactions with the CTD, respectively, leads to increased PLCβ hydrolase activity.
Elevated Expression of a Functional Suf Pathway in theE.coliBL21(DE3) Cell Line Enhances Recombinant Production of an Iron-Sulfur Cluster Containing Protein
Authors: Corless Elliot I. , Mettert Erin L. , Kiley Patricia J. , Antony Edwin 
Published: October 2019

ABSTRACTStructural and spectroscopic analysis of iron-sulfur [Fe-S] cluster-containing proteins is often limited by the occupancy and yield of recombinantly produced proteins. Here we report thatEscherichia coliBL21(DE3), a strain routinely used to overexpress [Fe-S] cluster-containing proteins, has a nonfunctional Suf pathway, one of twoE. coli[Fe-S] cluster biogenesis pathways. We confirmed that BL21(DE3) and commercially available derivatives carry a deletion that results in an inframe fusion ofsufAandsufBgenes within thesufABCDSEoperon. We show that this fusion protein accumulates in cells but is - inactive in [Fe-S] biogenesis. Restoration of an intact Suf pathway combined with enhanced suf operon expression led to a remarkable (~3-fold) increase in the production of the [4Fe-4S] cluster-containing BchL protein, a key component of the dark-operative protochlorophyllide oxido-reductase complex. These results show that this engineered ‘SufFeScient’ derivative of BL21(DE3) is suitable for enhanced large-scale synthesis of an [Fe-S] cluster-containing protein.IMPORTANCELarge quantities of recombinantly overexpressed iron-sulfur cluster-containing proteins are necessary for their in-depth biochemical characterization. Commercially availableE. colistrain BL21(DE3) and its derivatives have a mutation that inactivates the function of one of the two native pathways (Suf pathway) responsible for cluster biogenesis. Correction of the mutation, combined with sequence changes that increase Suf expression can increase yield and cluster occupancy of [Fe-S] cluster-containing enzymes, facilitating the biochemical analysis of this fascinating group of proteins.
Development of flight and foraging behaviour in a juvenile seabird with extreme soaring capacities
Authors: Corbeau Alexandre , Prudor Aurélien , Kato Akiko , Weimerskirch Henri 
Published: October 2019

Abstract

The early life of animals is a period of high mortality, when foraging capacities are assumed to be improved progressively. In birds, this critical period involves the improvement of the flight. How do young birds gain these capacities has rarely been studied in natural conditions especially in seabirds that spend most of their life at sea.

We used detailed GPS and body acceleration data on 37 great frigatebirds (Fregata minor), to test the hypothesis that juveniles starting their first flights have lower flying capacities than adults, but that these capacities will improve during a long learning period, before independence from parents, specific to this seabird that can spend months on the wing at sea.

We found that most flight components improved over time to tend towards those of adults, especially the travel speed, range, duration and maximum altitude of trips. However, unexpectedly, juveniles had higher ascent rates, soaring and gliding capacities above the sea than adults. Moreover, energy expenditure of juveniles was similar to adults during low cost travelling movements and during active foraging, but juveniles spent more time foraging actively than adults.

Our results suggest that flight tactics based on long‐distance effortless movements specific to this family are acquired during a long period, but soaring and gliding capacities are already inherited by juveniles and possibly favoured by morphological adaptations specific to juveniles. These adaptations might explain the extreme dispersive capacities of juveniles.
Fungal connections between plants and biocrusts facilitate plants but have little effect on biocrusts
Authors: Dettweiler‐Robinson Eva , Sinsabaugh Robert L. , Rudgers Jennifer A. 
Published: October 2019

AbstractSpecies interactions may couple the resource dynamics of different primary producers and may enhance productivity by reducing loss from the system. In low‐resource systems, this biotic control may be especially important for maintaining productivity. In drylands, the activities of vascular plants and biological soil crusts can be decoupled in space because biocrusts grow on the soil surface but plant roots are underground, and decoupled in time due to biocrusts activating with smaller precipitation events than plants. Soil fungi are hypothesized to functionally couple the plants and biocrusts by transporting nutrients. We studied whether disrupting fungi between biocrusts and plants reduces nitrogen transfer and retention and decreases primary production as predicted by the fungal loop hypothesis. Additionally, we compared varying precipitation regimes that can drive different timing and depth of biological activities.We used field mesocosms in which the potential for fungal connections between biocrusts and roots remained intact or were impeded by mesh. We imposed a precipitation regime of small, frequent or large, infrequent rain events. We used15N to track fungal‐mediated nitrogen (N) transfer. We quantified microbial carbon use efficiency and plant and biocrust production and N content.Fungal connections with biocrusts benefitted plant biomass and nutrient retention under favourable (large, infrequent) precipitation regimes but not under stressful (small, frequent) regimes, demonstrating context dependency in the fungal loop. Translocation of a15N tracer from biocrusts to roots was marginally lower when fungal connections were impeded than intact. Under large, infrequent rains, when fungal connections were intact, the C:N of leaves converged towards the C:N of biocrusts, suggesting higher N retention in the plant, and plant above‐ground biomass was greater relative to the fungal connections‐impeded treatment. Carbon use efficiency in both biocrust and rooting zone soil was less C‐limited when connections were intact than impeded, again only in the large, infrequent precipitation regime.Synthesis. Although we did not find evidence of a reciprocal transfer of C and N between plants and biocrusts, plant production was benefited by fungal connections with biocrusts under favourable conditions.
Propagule composition regulates the success of an invasive seaweed across a heterogeneous seascape
Authors: Bulleri Fabio , Marzinelli Ezequiel M. , Voerman Sofie E. , Gribben Paul E. 
Published: October 2019

Abstract

Propagule pressure is acknowledged as a key determinant of invasion success. Nonetheless, the role of morphological or physiological attributes of propagules (i.e. their quality) in regulating invader establishment has been little explored. In particular, no study has investigated how the presence of propagules differing in quality within an inoculum influences establishment across heterogeneous landscapes.

We experimentally tested the hypothesis that the quality (+Fronds+Rhizoids; +Fronds−Rhizoids; −Fronds+Rhizoids) and the diversity (1, 2 and 3 fragment types) of vegetative fragments of the seaweed Caulerpa taxifolia determine their establishment success across seascapes consisting of bare sediments and patches of the seagrass Zostera muelleri exposed to different disturbance intensities (control, seagrass canopy clipping and total removal).

After 6 weeks, seaweed biomass, stolon and frond length, frond and rhizoid number were generally greater in unvegetated habitats (bare sediments and total seagrass removal) than full or reduced seagrass canopies. The type and the diversity of types of fragments inoculated had significant effects on the final biomass and morphological features of C. taxifolia only in vegetated habitats. In control plots, inocula of fragments retaining both fronds and rhizoids achieved higher biomass, developed longer stolons and more fronds. In canopy clipping plots, mixed inocula of +Fronds+Rhizoids and −Fronds+Rhizoids fragments had the greatest biomass and stolon length.

Synthesis. Assessing how propagules differing in quality perform in different habitats might be not sufficient to draw a comprehensive picture of invasion risk, as their establishment can be modulated by both negative and positive interactions among them. Propagule composition should be, therefore, considered as a further dimension of propagule pressure. Our results also suggest that the relevance of specific propagule traits for invader establishment decreases from intact to degraded habitats. Considering propagule size in terms of amount of competent propagules, rather than an absolute measure, would refine our ability of predicting invasion risk across habitats differing in biotic or abiotic conditions.
Suppletive Stem Distribution: A Diachronic Perspective
Authors: Kim Ronald I. 
Published: October 2019

AbstractSuppletion is typically conceived of in diachronic terms as a discontinuous phenomenon, by which two or more originally distinct lexical items come to share slots in a single paradigm. However, it has long been known that regular sound change acting undisturbed over long periods of time can in fact give rise to what in synchronic terms must be considered suppletive stem relationships. It is proposed, on the basis of examples from ancient and modern Indo‐European languages, that instances of suppletion with a morphosyntactically unmotivated distribution are more likely to have arisen by the accretion of sound change than those which neatly contrast morphosyntactic categories such as singular vs. plural, which typically result from merger of two or more lexemes. Supporting this view is the phonological origin of several well‐known cases of morphomic alternations, which can serve as a gateway for the introduction of suppletive stems. However, this hypothesis is to be understood only as a general tendency, since the distribution of stems in phonological suppletion may be altered by irregular morphological developments.
EnTAP: Bringing faster and smarter functional annotation to non‐model eukaryotic transcriptomes
Authors: Hart Alexander J. , Ginzburg Samuel , Xu Muyang (Sam) , Fisher Cera R. , Rahmatpour Nasim , Mitton Jeffry B. , Paul Robin , Wegrzyn Jill L. 
Published: October 2019

AbstractEnTAP (Eukaryotic Non‐Model Transcriptome Annotation Pipeline) was designed to improve the accuracy, speed, and flexibility of functional gene annotation for de novo assembled transcriptomes in non‐model eukaryotes. This software package addresses the fragmentation and related assembly issues that result in inflated transcript estimates and poor annotation rates of protein‐coding transcripts. Following filters applied through assessment of true expression and frame selection, open‐source tools are leveraged to functionally annotate the reduced set of translated proteins. Downstream features include fast similarity search across five repositories, protein domain assignment, orthologous gene family assessment, and Gene Ontology (GO) term assignment. The final annotation integrates across multiple databases and selects an optimal assignment from a combination of weighted metrics describing similarity search score, taxonomic relationship, and informativeness. Researchers have the option to include additional filters to identify and remove contaminants, identify associated pathways, and prepare the transcripts for enrichment analysis. This fully featured pipeline is easy to install, configure, and runs significantly faster than comparable annotation packages. EnTAP is optimized to generate extensive functional information for the gene space of organisms with limited or poorly characterized genomic resources.