bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of divergent selection for residual feed intake on nitrogen metabolism and lysine utilization in growing pigs
Authors: Hewitt Deltora J , Dekkers Jack C M , Antonick Treyson , Gheisari Abbasali , Rakhshandeh Amanda R , Rakhshandeh Anoosh 
Published: May 2020

Abstract
A study was conducted to evaluate the effects of divergent genetic selection for residual feed intake (RFI) on nitrogen (N) metabolism and lysine utilization in growing pigs. Twenty-four gilts (body weight [BW] 66 ± 5 kg) were selected from generation nine of the low RFI (LRFI; n = 12) and high RFI (HRFI; n = 12) Iowa State University Yorkshire RFI selection lines. Six pigs from each genetic line were assigned to each of two levels of lysine intake: 70% and 100% of estimated requirements based on the potential of each genetic line for protein deposition (PD) and feed intake. For all diets, lysine was first limiting among amino acids. Using isotope tracer, N-balance, and nutrient digestibility evaluation approaches, whole-body N metabolism and the efficiency of lysine utilization were determined for each treatment group. No significant interaction effects of line and diet on dietary N or gross energy digestibility, PD, and the efficiency of lysine utilization for PD were observed. The line did not have a significant effect on PD and digestibility of dietary N and GE. An increase in lysine intake improved N retention in both lines (from 15.0 to 19.6 g/d, SE 1.44, in LRFI pigs; and from 16.9 to 19.8 g/d, SE 1.67, in HRFI pigs; P &lt; 0.01). At the low lysine intakes and when lysine clearly limited PD, the efficiency of using available lysine intake (above maintenance requirements) for PD was 80% and 91% (SE 4.6) for the LRFI and HRFI pigs, respectively (P = 0.006). There were no significant effects of line or of the line by diet interaction on N flux, protein synthesis, and protein degradation. Lysine intake significantly increased (P &lt; 0.05) N flux (from 119 to 150, SE 8.7 g/d), protein synthesis (from 99 to 117, SE 10.6 g of N/d), and protein degradation (from 85 to 100, SE 6.6 g of N/d). The protein synthesis-to-retention ratio tended to be higher in the LRFI line compared with the HRFI line (6.5 vs. 5.8 SE 0.62; P = 0.06), indicating a tendency for the lower efficiency of PD in this group. Collectively, these results indicate that genetic selection for low RFI is not associated with improvements in lysine utilization efficiency, protein turnover, and nutrient digestibility.
Taxonomic revision of Aegla lata Bond-Buckup & Buckup, 1994 (Decapoda: Anomura: Aeglidae), with the description of a new species of Aegla Leach, 1820 from the Upper Paraná Ecoregion, Brazil
Authors: Marçal Ingrid C , Páez Fernanda P , Souza-Shibatta Lenice , Sofia Silvia H , Teixeira Gustavo M 
Published: May 2020

Abstract
Aegla lata Bond-Buckup & Buckup, 1994 is considered extinct in the type locality. New populations of this species, however, have been found in northern Paraná state, Brazil. We revised the taxonomy of A. lata based on morphological data obtained from the type material and specimens recently obtained from streams of the Tibagi River sub-basin, Paranapanema River basin, Upper Paraná Ecoregion. Moreover, Aegla jacutingan. sp. is described and illustrated. The new species resembles A. lata in the shapes of the body and chelipeds. Both species are nevertheless separated by particular morphological characters of the carapace, chelipeds, and epimeron as well as by molecular (COI mtDNA) differences. Both species can be distinguished from their congeners based on morphological and molecular evidence.
Host Suitability and Fitness-Related Parameters in Coptera haywardi (Hymenoptera: Diapriidae) Reared on Irradiated Ceratitis capitata (Diptera: Tephritidae) Pupae Stemming From the tsl Vienna-8 Genetic Sexing Strain
Authors: Núñez-Campero Segundo R , Suárez Lorena , Buonocore Biancheri María Josefina , Cancino Jorge , Murúa Fernando , Molina Diego , Laría Osvaldo , Aluja Martín , Ovruski Sergio M 
Published: May 2020

Abstract
Coptera haywardi (Ogloblin) is a pupal endoparasitoid of tephritid flies with great potential as a biological control agent worldwide as it does not attack other Diptera. To reach its full potential, its mass rearing needs to be enhanced lowering costs. Here, we focused on the use of irradiated pupae of Ceratitis capitata (Wiedemann) stemming from the temperature-sensitive lethal (tsl) Vienna-8 genetic sexing strain (= CcVienna-8), which is mass-produced in the San Juan Medfly and Parasitoid Mass Rearing Facility in Argentina. Exposure of 1- to 2-d-old CcVienna-8 pupae irradiated at 90 Gy to 6- to 8-d-old C. haywardi females at a 10:1 host/parasitoid ratio for 24 h turned out to be highly successful for the rearing of this parasitoid. High radiation doses (90–100 Gy) did not adversely influence fitness parameters of C. haywardi offspring F1, namely lifetime reproductive rates, adult life expectancy, and survival time. Demographic parameters in C. haywardi F1 from irradiated CcVienna-8 young pupae were improved compared to those values recorded from parasitoid originated from nonirradiated CcVienna-8 pupae. These findings will help to enhance parasitoid mass rearing for augmentative releases against medfly in Argentinean fruit-producing regions.
Growth Performance and Enzymatic Response of the Grasshopper, Calliptamus abbreviatus (Orthoptera: Acrididae), to Six Plant-Derived Compounds
Authors: Wang Yueyue , Huang Xunbing , Chang Babar Hussain , Zhang Zehua 
Published: May 2020

Abstract
Plant-derived compounds are sources of biopesticides for the control of insect pests. We compared the growth performance and enzymatic response of the grasshopper Calliptamus abbreviatus Ikonn to six plant-derived compounds (rutin, quercetin, nicotine, matrine, azadirachtin, and rotenone) in laboratory and field trials. When exposed to the six compounds, C. abbreviatus had significantly reduced growth and survival. All the compounds significantly induced an elevated level of reactive oxygen species, indicating oxidative damage. The activity of detoxifying enzymes, including cytochrome P450s, carboxylesterase, glutathione-S-transferase, and UDP-glucuronosyltransferase, and the antioxidant enzymes, including superoxide dismutase, catalase, and peroxidase, all significantly increased after exposure to the six compounds. These data suggest that the six plant-derived compounds had negative effects on C. abbreviatus. Of the six compounds, matrine, azadirachtin, and rotenone were more toxic to C. abbreviatus, followed by nicotine, quercetin, and rutin. These results show the potential of these compounds as botanical pesticides, which can be applied for the biological control of the grasshopper C. abbreviatus.
Prognostic significance of non-urothelial carcinoma of bladder: analysis of nationwide hospital-based cancer registry data in Japan
Authors: Nagumo Yoshiyuki , Kawai Koji , Kojima Takahiro , Shiga Masanobu , Kojo Kosuke , Tanaka Ken , Kandori Shuya , Kimura Tomokazu , Kawahara Takashi , Okuyama Ayako , Higashi Takahiro , Nishiyama Hiroyuki 
Published: May 2020

Abstract

Objectives
To identify the prognosis of pure non-urothelial carcinoma (non-UC) of bladder and to compare them with those of pure urothelial carcinoma (UC).

Methods
We used Japan’s nationwide hospital-based cancer registry data to extract histologically confirmed pure non-UC and UC cases of bladder diagnosed in 2008–2009. We estimated the 5-year overall survival (OS) by a Kaplan–Meier analysis.

Results
A total of 8094 patients with confirmed histological subtypes of bladder cancer were identified. The most common pure non-UC was squamous cell carcinoma (SQ, n = 192, 2.4%) followed by adenocarcinoma (AC, n = 138, 1.7%) and small cell neuroendocrine carcinoma (SmC, n = 54, 0.7%). The proportion of female patients (48%) was significantly higher in the SQ group compared with the pure UC group (P &lt; 0.001). The 5-year OS rate of the non-UC patients was significantly worse than that of the UC patients (40 vs. 61%, P &lt; 0.001). According to stages, the 5-year OS rates of the stage I and III non-UC patients were significantly worse than those of the UC patients (P = 0.001). Considering histologic subtypes and stages, the 5-year OS rates of the stage I SQ patients were worse than those of the AC and SmC patients (46, 68 and 64%, respectively).

Conclusion
The prognosis of pure non-UC was worse than that of pure UC, especially in the stage I and III non-UC patients. To improve these patients’ oncologic outcomes, a more aggressive surgical approach may be necessary in stage I patients with non-UC, especially in pure SQ.
Correlation between optical and UV variability of a large sample of quasars
Authors: Xin Chengcheng , Charisi Maria , Haiman Zoltán , Schiminovich David 
Published: May 2020

ABSTRACT
The variability of quasars across multiple wavelengths is a useful probe of physical conditions in active galactic nuclei. In particular, variable accretion rates, instabilities, and reverberation effects in the accretion disc of a supermassive black hole are expected to produce correlated flux variations in ultraviolet (UV) and optical bands. Recent work has further argued that binary quasars should exhibit strongly correlated UV and optical periodicities. Strong UV–optical correlations have indeed been established in small samples of (N ≲ 30) quasars with well-sampled light curves, and have extended the ‘bluer-when-brighter’ trend previously found within the optical bands. Here, we further test the nature of quasar variability by examining the observed-frame UV–optical correlations among bright quasars extracted from the Half Million Quasars (HMQ) catalogue. We identified a large sample of 1315 quasars in HMQ with overlapping UV and optical light curves from the Galaxy Evolution Explorer and the Catalina Real-time Transient Survey, respectively. We find that strong correlations exist in this much larger sample, but we rule out, at ∼95 per cent confidence, the simple hypothesis that the intrinsic UV and optical variations of all quasars are fully correlated. Our results therefore imply the existence of physical mechanism(s) that can generate uncorrelated optical and UV flux variations.
The SEPT12 complex is required for the establishment of a functional sperm head–tail junction
Authors: Shen Yi-Ru , Wang Han-Yu , Tsai Yung-Chieh , Kuo Yung-Che , Wu Shang-Rung , Wang Chia-Yih , Kuo Pao-Lin 
Published: May 2020

Abstract
The connecting pieces of the sperm neck link the flagellum and the sperm head, and they are important for initiating flagellar beating. The connecting pieces are important building blocks for the sperm neck; however, the mechanism of connecting piece assembly is poorly understood. In the present study, we explored the role of septins in sperm motility and found that Sept12D197N knock-in (KI) mice produce acephalic and immotile spermatozoa. Electron microscopy analysis showed defective connecting pieces in sperm from KI mice, indicating that SEPT12 is required for the establishment of connecting pieces. We also found that SEPT12 formed a complex with SEPT1, SEPT2, SEPT10 and SEPT11 at the sperm neck and that the D197N mutation disrupted the complex, suggesting that the SEPT12 complex is involved in the assembly of connecting pieces. Additionally, we found that SEPT12 interacted and colocalized with γ-tubulin in elongating spermatids, implying that SEPT12 and pericentriolar materials jointly contribute to the formation of connecting pieces. Collectively, our findings suggest that SEPT12 is required for the formation of striated columns, and the capitulum and for maintaining the stability of the sperm head–tail junction.
The human telomeric nucleosome displays distinct structural and dynamic properties
Authors: Soman Aghil , Liew Chong Wai , Teo Hsiang Ling , Berezhnoy Nikolay V , Olieric Vincent , Korolev Nikolay , Rhodes Daniela , Nordenskiöld Lars 
Published: May 2020

Abstract
Telomeres protect the ends of our chromosomes and are key to maintaining genomic integrity during cell division and differentiation. However, our knowledge of telomeric chromatin and nucleosome structure at the molecular level is limited. Here, we aimed to define the structure, dynamics as well as properties in solution of the human telomeric nucleosome. We first determined the 2.2 Å crystal structure of a human telomeric nucleosome core particle (NCP) containing 145 bp DNA, which revealed the same helical path for the DNA as well as symmetric stretching in both halves of the NCP as that of the 145 bp ‘601’ NCP. In solution, the telomeric nucleosome exhibited a less stable and a markedly more dynamic structure compared to NCPs containing DNA positioning sequences. These observations provide molecular insights into how telomeric DNA forms nucleosomes and chromatin and advance our understanding of the unique biological role of telomeres.
InteractomeSeq: a web server for the identification and profiling of domains and epitopes from phage display and next generation sequencing data
Authors: Puccio Simone , Grillo Giorgio , Consiglio Arianna , Soluri Maria Felicia , Sblattero Daniele , Cotella Diego , Santoro Claudio , Liuni Sabino , Bellis Gianluca De , Lugli Enrico , Peano Clelia , Licciulli Flavio 
Published: May 2020

Abstract
High-Throughput Sequencing technologies are transforming many research fields, including the analysis of phage display libraries. The phage display technology coupled with deep sequencing was introduced more than a decade ago and holds the potential to circumvent the traditional laborious picking and testing of individual phage rescued clones. However, from a bioinformatics point of view, the analysis of this kind of data was always performed by adapting tools designed for other purposes, thus not considering the noise background typical of the ‘interactome sequencing’ approach and the heterogeneity of the data. InteractomeSeq is a web server allowing data analysis of protein domains (‘domainome’) or epitopes (‘epitome’) from either Eukaryotic or Prokaryotic genomic phage libraries generated and selected by following an Interactome sequencing approach. InteractomeSeq allows users to upload raw sequencing data and to obtain an accurate characterization of domainome/epitome profiles after setting the parameters required to tune the analysis. The release of this tool is relevant for the scientific and clinical community, because InteractomeSeq will fill an existing gap in the field of large-scale biomarkers profiling, reverse vaccinology, and structural/functional studies, thus contributing essential information for gene annotation or antigen identification. InteractomeSeq is freely available at https://InteractomeSeq.ba.itb.cnr.it/
3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome
Authors: Wlasnowolski Michal , Sadowski Michal , Czarnota Tymon , Jodkowska Karolina , Szalaj Przemyslaw , Tang Zhonghui , Ruan Yijun , Plewczynski Dariusz 
Published: May 2020

Abstract
Structural variants (SVs) that alter DNA sequence emerge as a driving force involved in the reorganisation of DNA spatial folding, thus affecting gene transcription. In this work, we describe an improved version of our integrated web service for structural modeling of three-dimensional genome (3D-GNOME), which now incorporates all types of SVs to model changes to the reference 3D conformation of chromatin. In 3D-GNOME 2.0, the default reference 3D genome structure is generated using ChIA-PET data from the GM12878 cell line and SVs data are sourced from the population-scale catalogue of SVs identified by the 1000 Genomes Consortium. However, users may also submit their own structural data to set a customized reference genome structure, and/or a custom input list of SVs. 3D-GNOME 2.0 provides novel tools to inspect, visualize and compare 3D models for regions that differ in terms of their linear genomic sequence. Contact diagrams are displayed to compare the reference 3D structure with the one altered by SVs. In our opinion, 3D-GNOME 2.0 is a unique online tool for modeling and analyzing conformational changes to the human genome induced by SVs across populations. It can be freely accessed at https://3dgnome.cent.uw.edu.pl/.
DNA damage invokes mitophagy through a pathway involving Spata18
Authors: Dan Xiuli , Babbar Mansi , Moore Anthony , Wechter Noah , Tian Jingyan , Mohanty Joy G , Croteau Deborah L , Bohr Vilhelm A 
Published: May 2020

Abstract
Mitochondria are vital for cellular energy supply and intracellular signaling after stress. Here, we aimed to investigate how mitochondria respond to acute DNA damage with respect to mitophagy, which is an important mitochondrial quality control process. Our results show that mitophagy increases after DNA damage in primary fibroblasts, murine neurons and Caenorhabditis elegans neurons. Our results indicate that modulation of mitophagy after DNA damage is independent of the type of DNA damage stimuli used and that the protein Spata18 is an important player in this process. Knockdown of Spata18 suppresses mitophagy, disturbs mitochondrial Ca2+ homeostasis, affects ATP production, and attenuates DNA repair. Importantly, mitophagy after DNA damage is a vital cellular response to maintain mitochondrial functions and DNA repair.
Deep sequencing of non-enzymatic RNA primer extension
Authors: Duzdevich Daniel , Carr Christopher E , Szostak Jack W 
Published: May 2020

Abstract
Life emerging in an RNA world is expected to propagate RNA as hereditary information, requiring some form of primitive replication without enzymes. Non-enzymatic template-directed RNA primer extension is a model of the copying step in this posited form of replication. The sequence space accessed by primer extension dictates potential pathways to self-replication and, eventually, ribozymes. Which sequences can be accessed? What is the fidelity of the reaction? Does the recently illuminated mechanism of primer extension affect the distribution of sequences that can be copied? How do sequence features respond to experimental conditions and prebiotically relevant contexts? To help answer these and related questions, we here introduce a deep-sequencing methodology for studying RNA primer extension. We have designed and vetted special RNA constructs for this purpose, honed a protocol for sample preparation and developed custom software that analyzes sequencing data. We apply this new methodology to proof-of-concept controls, and demonstrate that it works as expected and reports on key features of the sequences accessed by primer extension.
Mammalian Nudix proteins cleave nucleotide metabolite caps on RNAs
Authors: Sharma Sunny , Grudzien-Nogalska Ewa , Hamilton Keith , Jiao Xinfu , Yang Jun , Tong Liang , Kiledjian Megerditch 
Published: May 2020

AbstractWe recently reported the presence of nicotinamide adenine dinucleotide (NAD)-capped RNAs in mammalian cells and a role for DXO and the Nudix hydrolase Nudt12 in decapping NAD-capped RNAs (deNADding) in cells. Analysis of 5′caps has revealed that in addition to NAD, mammalian RNAs also contain other metabolite caps including flavin adenine dinucleotide (FAD) and dephosphoCoA (dpCoA). In the present study we systematically screened all mammalian Nudix proteins for their potential deNADing, FAD cap decapping (deFADding) and dpCoA cap decapping (deCoAping) activity. We demonstrate that Nudt16 is a novel deNADding enzyme in mammalian cells. Additionally, we identified seven Nudix proteins—Nudt2, Nudt7, Nudt8, Nudt12, Nudt15, Nudt16 and Nudt19, to possess deCoAping activity in vitro. Moreover, our screening revealed that both mammalian Nudt2 and Nudt16 hydrolyze FAD-capped RNAs in vitro with Nudt16 regulating levels of FAD-capped RNAs in cells. All decapping activities identified hydrolyze the metabolite cap substrate within the diphosphate linkage. Crystal structure of human Nudt16 in complex with FAD at 2.7 Å resolution provide molecular insights into the binding and metal-coordinated hydrolysis of FAD by Nudt16. In summary, our study identifies novel cellular deNADding and deFADding enzymes and establishes a foundation for the selective functionality of the Nudix decapping enzymes on non-canonical metabolite caps.
Noncoding Y RNAs regulate the levels, subcellular distribution and protein interactions of their Ro60 autoantigen partner
Authors: Leng Yuanyuan , Sim Soyeong , Magidson Valentin , Wolin Sandra L 
Published: May 2020

AbstractNoncoding Y RNAs are abundant in animal cells and present in many bacteria. These RNAs are bound and stabilized by Ro60, a ring-shaped protein that is a target of autoantibodies in patients with systemic lupus erythematosus. Studies in bacteria revealed that Y RNA tethers Ro60 to a ring-shaped exoribonuclease, forming a double-ringed RNP machine specialized for structured RNA degradation. In addition to functioning as a tether, the bacterial RNA gates access of substrates to the Ro60 cavity. To identify roles for Y RNAs in mammals, we used CRISPR to generate mouse embryonic stem cells lacking one or both of the two murine Y RNAs. Despite reports that animal cell Y RNAs are essential for DNA replication, cells lacking these RNAs divide normally. However, Ro60 levels are reduced, revealing that Y RNA binding is required for Ro60 to accumulate to wild-type levels. Y RNAs regulate the subcellular location of Ro60, since Ro60 is reduced in the cytoplasm and increased in nucleoli when Y RNAs are absent. Last, we show that Y RNAs tether Ro60 to diverse effector proteins to generate specialized RNPs. Together, our data demonstrate that the roles of Y RNAs are intimately connected to that of their Ro60 partner.
Identifying key predictors of mortality in young patients on chronic haemodialysis—a machine learning approach
Authors: Gotta Verena , Tancev Georgi , Marsenic Olivera , Vogt Julia E , Pfister Marc 
Published: May 2020

Abstract

Background
The mortality risk remains significant in paediatric and adult patients on chronic haemodialysis (HD) treatment. We aimed to identify factors associated with mortality in patients who started HD as children and continued HD as adults.

Methods
The data originated from a cohort of patients &lt;30 years of age who started HD in childhood (≤19 years) on thrice-weekly HD in outpatient DaVita dialysis centres between 2004 and 2016. Patients with at least 5 years of follow-up since the initiation of HD or death within 5 years were included; 105 variables relating to demographics, HD treatment and laboratory measurements were evaluated as predictors of 5-year mortality utilizing a machine learning approach (random forest).

Results
A total of 363 patients were included in the analysis, with 84 patients having started HD at &lt;12 years of age. Low albumin and elevated lactate dehydrogenase (LDH) were the two most important predictors of 5-year mortality. Other predictors included elevated red blood cell distribution width or blood pressure and decreased red blood cell count, haemoglobin, albumin:globulin ratio, ultrafiltration rate, z-score weight for age or single-pool Kt/V (below target). Mortality was predicted with an accuracy of 81%.

Conclusions
Mortality in paediatric and young adult patients on chronic HD is associated with multifactorial markers of nutrition, inflammation, anaemia and dialysis dose. This highlights the importance of multimodal intervention strategies besides adequate HD treatment as determined by Kt/V alone. The association with elevated LDH was not previously reported and may indicate the relevance of blood–membrane interactions, organ malperfusion or haematologic and metabolic changes during maintenance HD in this population.