bluuebunny/crossref_metadata_2025_split huggingface dataset:
RPW8 promoter is involved in pathogen‐And stress‐inducible expression from Vitis pseudoreticulata
Authors: Lai Gongti , Song Shiren , Liu Yunxiao , Fu Peining , Xiang Jiang , Lu Jiang 
Published: December 2018

AbstractBased on previous cloning of VpRPW8‐e, we obtained a 1,126 bp VpRPW8‐e promoter sequence in this study. A large number of TATA‐boxes, CAAT‐boxes, and other cis‐acting elements were predicted including light‐responsive elements, hormone‐responsive elements, stress‐responsive elements, and growth‐ and development‐associated elements within the promoter sequence. To further investigate the function of this promoter, we examined its activity in response to biotic and abiotic stress. The VpRPW8‐e promoter was strongly activated by Plasmopara viticola infection, and activation also occurred when the orientation of the promoter was reversed, although to a lesser extent. Deletion analysis showed that the −1,126 to −475 bp region of VpRPW8‐e promoter had high activity. A promoter fragment 5′ deleted to −475 bp (P−475) was activated in response to heat and cold stress, and even more strongly in response to Phytophthora capsici and salicylic acid (SA). Furthermore, Transgenic Nicotiana benthamiana were generated, VpRPW8‐e driven by P−475 enhanced resistance to Ph. capsici in N. benthamiana. Based on these results, the −475 bp region was deduced to be an indispensable part of the VpRPW8‐e promoter. VpRPW8‐e promoter is involved in pathogen‐ and stress‐inducible expression.
Genomic variability of within‐host hepatitis C variants in acute infection
Authors: Rodrigo Chaturaka , Leung Preston , Lloyd Andrew R. , Bull Rowena A. , Luciani Fabio , Grebely Jason , Dore Gregory J. , Applegate Tanya , Page Kimberly , Bruneau Julie , Cox Andrea L. , Osburn William , Kim Arthur Y. , Shoukry Naglaa H. , Lauer Georg M. , Maher Lisa , Schinkel Janke , Prins Maria , Hellard Margaret , Eltahla Auda A. ,   the InC Collaborative
Published: December 2018

SummaryInteractions between the host immune system and the viral variants determine persistence of hepatitis C virus (HCV) infection after the acute phase of infection. This study describes the genetic variability of within‐host HCV viral variants in acute infection and correlates it with host‐ and virus‐related traits and infection outcome. Next generation sequence data (Illumina, MiSeq platform) of viral genomes from 116 incident acute infections (within 180 days of infection) were analysed to determine all the single nucleotide polymorphism (SNP) frequencies above a threshold of 0.1%. The variability of the SNPs for the full open reading frame of the genome as well as for each protein coding region were compared using mean standardized Shannon entropy (SE) values calculated separately for synonymous and nonsynonymous mutations. The envelope glycoproteins regions (E1 and E2) had the highest SE values (indicating greater variability) followed by the NS5B region. Nonsynonymous mutations rather than synonymous mutations were the main contributors to genomic variability in acute infection. The mean difference of Shannon entropy was also compared between subjects after categorizing the samples according to host and virus‐related traits. Host IFNL3 allele CC polymorphism at rs12979860 (vs others) and viral genotype 1a (vs 3a) were associated with higher genomic variability across the viral open reading frame. Time since infection, host gender or continent of origin was not associated with the viral genomic variability. Viral genomic variability did not predict spontaneous clearance.
A quantitative method to assess the role of indoor air decontamination to simultaneously reduce contamination of environmental surfaces: testing with vegetative and spore-forming bacteria
Authors: Zargar B. , Sattar S.A. , Rubino J.R. , Ijaz M.K. 
Published: December 2018

Abstract
Indoor air can spread pathogens, which can be removed/inactivated by a variety of means in healthcare and other settings. We quantitatively assessed if air decontamination could also simultaneously reduce environmental surface contamination in the same setting. Two types of vegetative bacteria (Staphylococcus aureus and Acinetobacter baumannii), and a bacterial spore-former (Geobacillus stearothermophilus) were tested as representative airborne bacteria. They were separately aerosolized with a Collison nebulizer into a 24-m3 aerobiology chamber and air samples collected with a programmable slit-to-agar sampler. Settling airborne particles were collected on culture plates placed at, and collected from, five different locations on the floor of the chamber with a custom-built remote plate-placement and -retriever system. Experimentally contaminated air in the chamber was decontaminated for 45 min with a device based on HEPA filtration and UV light. The plates were incubated and CFU counted. The device reduced the viability levels of all tested bacteria in the air by &gt;3 log10 (&gt;99·9%) in 45 min. Based on two separate tests, the average reductions in surface contamination for S. aureus, A. baumannii and G. stearothermophilus were respectively, 97, 87 and 97%. We thus showed that air decontamination could substantially and simultaneously reduce the levels of surface contamination in the same setting irrespective of the type of pathogen present.

Significance and Impact of the Study
The innovative and generic test protocol described can quantitatively assess the reduction in environmental surface contamination from microbial decontamination of indoor air in the same setting. This added advantage from air decontamination has implications for infection prevention and control in healthcare and other settings without the need for additional expense or effort. Continuous operation of an air decontamination device, such as the one tested here, can lead to ongoing reductions in pathogens in air and on environmental surfaces.
Information transfer about food as a reason for sociality in bats
Authors: Gager Yann 
Published: December 2018

AbstractInformation transfer about food is a potential reason for sociality in many animals. If an animal is better informed, it should then be better able to adjust its behaviour and reduce the uncertainty of finding food in a variable world.Given the remarkable range of social systems and ecological niches of bats throughout the world, bats are well‐suited as a model to review mechanisms and fitness consequences of information transfer about food. The aim of this manuscript was to conduct a systematic literature review for mechanisms for information transfer and their potential fitness consequences for bats.Information transfer behaviour is found in bats under various ecological conditions, including in groups of males in temperate regions, in groups of males or females in subtropical regions, and in mixed groups in tropical regions. Bats can learn about food indirectly, for example via chemical cues carried by the breath and body of frugivorous bats, or via acoustic cues from feeding buzzes from insectivorous bats. The majority of playback studies in captivity and in the wild showed stronger intra‐specific and inter‐specific attraction of bats to feeding buzzes than to silence controls or to search phase calls. Bats can also transfer information directly, via signals intended to attract, to repel or even to jam the echolocation of conspecifics.Social foraging in bats can be categorised as local enhancement, information‐centre hypothesis, group foraging or food sharing, depending on the type of information transfer and the food sources used. Fitness consequences of information transfer from the actor's and the recipient's perspective remain poorly investigated to date. Recent studies in insectivorous bats suggest a balance of benefits from prey searching and costs of acoustic interference that may condition group size.The future use of a wide array of methods promises to reveal exciting insights about mechanisms and fitness consequences of information transfer by bats about food.
Formation of a recent hybrid zone offers insight into the geographic puzzle and maintenance of species boundaries in musk turtles
Authors: Scott Peter A. , Glenn Travis C. , Rissler Leslie J. 
Published: December 2018

AbstractSpeciation is the result of an accumulation of reproductive barriers between populations, but pinpointing the factors involved is often difficult. However, hybrid zones can form when these barriers are not complete, especially when lineages come into contact in intermediate or modified habitats. We examine a hybrid zone between two closely related riverine turtle species, Sternotherus depressus and S. peltifer, and use dual‐digest RAD sequencing to understand how this hybrid zone formed and elucidate genomic patterns of reproductive isolation. First, the geographical extent and timing of formation of the hybrid zone is established to provide context for understanding the role of extrinsic and intrinsic reproductive isolating mechanisms in this system. The strength of selection on taxon‐specific contributions to maintenance of the hybrid zone is then inferred using a Bayesian genomic cline model. These analyses identify a role for selection inhibiting introgression in some genomic regions at one end of the hybrid zone and promoting introgression in many loci at the other. When selective pressures necessary to generate outliers to the genomic cline are considered with the geographical and temporal context of this hybrid zone, we conclude that habitat‐specific selection probably limits introgression from S. depressus to S. peltifer in the direction of river flow. However, selection is mediating rapid, unidirectional introgression from S. peltifer to S. depressus, which is probably facilitated by anthropogenic habitat alteration. These findings indicate a potentially imminent threat of population‐level genomic extinction for an already imperiled species due to ongoing human‐caused habitat alteration.
Using multirate rapid A/Ci curves as a tool to explore new questions in the photosynthetic physiology of plants
Authors: Stinziano Joseph R. , Adamson Rachael K. , Hanson David T. 
Published: December 2018

Summary

Steady‐state photosynthetic CO2 responses (A/Ci curves) are used to assess environmental responses of photosynthetic traits and to predict future vegetative carbon uptake through modeling. The recent development of rapid A/Ci curves (RACiRs) permits faster assessment of these traits by continuously changing [CO2] around the leaf, and may reveal additional photosynthetic properties beyond what is practical or possible with steady‐state methods.

Gas exchange necessarily incorporates photosynthesis and (photo)respiration. Each process was expected to respond on different timescales due to differences in metabolite compartmentation, biochemistry and diffusive pathways. We hypothesized that metabolic lags in photorespiration relative to photosynthesis/respiration and CO2 diffusional limitations can be detected by varying the rate of change in [CO2] during RACiR assays. We tested these hypotheses through modeling and experiments at ambient and 2% oxygen.

Our data show that photorespiratory delays cause offsets in predicted CO2 compensation points that are dependent on the rate of change in [CO2]. Diffusional limitations may reduce the rate of change in chloroplastic [CO2], causing a reduction in apparent RACiR slopes under high CO2 ramp rates.

Multirate RACiRs may prove useful in assessing diffusional limitations to gas exchange and photorespiratory rates.
Auxin‐mediated Aux/IAA‐ARF‐HB signaling cascade regulates secondary xylem development in Populus
Authors: Xu Changzheng , Shen Yun , He Fu , Fu Xiaokang , Yu Hong , Lu Wanxiang , Li Yongli , Li Chaofeng , Fan Di , Wang Hua Cassan , Luo Keming 
Published: December 2018

Summary

Wood development is strictly regulated by various phytohormones and auxin plays a central regulatory role in this process. However, how the auxin signaling is transducted in developing secondary xylem during wood formation in tree species remains unclear.

Here, we identified an Aux/INDOLE‐3‐ACETIC ACID 9 (IAA9)‐AUXIN RESPONSE FACTOR 5 (ARF5) module in Populus tomentosa as a key mediator of auxin signaling to control early developing xylem development.

PtoIAA9, a canonical Aux/IAA gene, is predominantly expressed in vascular cambium and developing secondary xylem and induced by exogenous auxin. Overexpression of PtoIAA9m encoding a stabilized IAA9 protein significantly represses secondary xylem development in transgenic poplar. We further showed that PtoIAA9 interacts with PtoARF5 homologs via the C‐terminal III/IV domains. The truncated PtoARF5.1 protein without the III/IV domains rescued defective phenotypes caused by PtoIAA9m. Expression analysis showed that the PtoIAA9‐PtoARF5 module regulated the expression of genes associated with secondary vascular development in PtoIAA9m‐ and PtoARF5.1‐overexpressing plants. Furthermore, PtoARF5.1 could bind to the promoters of two Class III homeodomain‐leucine zipper (HD‐ZIP III) genes, PtoHB7 and PtoHB8, to modulate secondary xylem formation.

Taken together, our results suggest that the Aux/IAA9‐ARF5 module is required for auxin signaling to regulate wood formation via orchestrating the expression of HD‐ZIP III transcription factors in poplar.
Non‐syndromic cleft lip with or without palate susceptible loci is associated with tooth agenesis
Authors: Fan Liwen , Kan Shiyi , Yang Fan , Xu Hai , Li Hu , Zhu Guirong , Ma Lan , Zhang Chi , Lou Shu , Li Dandan , Wang Hua , Zhang Weibing , Pan Yongchu 
Published: December 2018

AbstractObjectiveNon‐syndromic tooth agenesis (NSTA) may share common genetic factors with non‐syndromic cleft lip with or without cleft palate (NSCL/P). Single‐nucleotide polymorphisms (SNPs) were associated with individual's susceptibility to these anomalies. We selected five NSCL/P‐associated SNPs from our previous genome‐wide association study (GWAS) to test for the associations with NSTA.Materials and methodsA total of 677 NSTA cases and 1,144 healthy controls were recruited in this case–control study. Five genome‐wide NSCL/P‐associated SNPs (rs2235371, rs7078160, rs8049367, rs4791774, and rs13041247) were genotyped by TaqMan platform and evaluated for the associations with NSTA using plink software.ResultsNo significant associations between these SNPs and risk of NSTA were observed in the overall analysis and subgroup analysis with the number of missing teeth. However, in the subgroup analysis by tooth position, rs8049367 was nominally associated with mandibular premolar agenesis (Dominant model: ORdom = 0.66, 95% CIdom = 0.47–0.93, pdom = 0.016; Heterozygote model: ORhet = 0.60, 95% CIhet = 0.41–0.88, Phet = 0.008). Rs4791774 showed a nominal association with congenitally missing maxillary canine (Dominant model: ORdom = 0.53, 95% CIdom = 0.28–0.98, pdom = 0.041; Heterozygote model: ORhet = 0.50, 95% CIhet = 0.26–0.97, Phet = 0.041) and premolar (Additive model: OR = 0.59, 95% CI = 0.36–0.96, p = 0.035).ConclusionThis study showed that NSCL/P susceptible loci rs8049367 and rs4791774 were probably associated with the risk of NSTA.
Functional reclassification of variants of uncertain significance in the HCN4 gene identified in sudden unexpected death
Authors: Dong Jingyun , Subbotina Ekaterina , Williams Nori , Sampson Barbara A. , Tang Yingying , Coetzee William A. 
Published: December 2018

AbstractThe HCN4 gene encodes a subunit of the hyperpolarization‐activated cyclic nucleotide‐gated channel, type 4 that is essential for the proper generation of pacemaker potentials in the sinoatrial node. The HCN4 gene is often present in targeted genetic testing panels for various cardiac conduction system disorders and there are several reports of HCN4 variants associated with conduction disorders. Here, we report the in vitro functional characterization of four rare variants of uncertain significance (VUS) in HCN4, identified through testing a cohort of 296 sudden unexpected natural deaths. The variants are all missense alterations, leading to single amino acid changes: p.E66Q in the N‐terminus, p.D546N in the C‐linker domain, and both p.S935Y and p.R1044Q in the C‐terminus distal to the CNBD. We also identified a likely benign variant, p. P1063T, which has a high minor allele frequency in the gnomAD, which is utilized here as a negative control. Three of the HCN4 VUS (p.E66Q, p.S935Y, and p.R1044Q) had electrophysiological characteristics similar to the wild‐type channel, suggesting that these variants are benign. In contrast, the p.D546N variant in the C‐linker domain exhibited a larger current density, slower activation, and was unresponsive to cyclic adenosine monophosphate (cAMP) compared to wild‐type. With functional assays, we reclassified three rare HCN4 VUS to likely benign variants, eliminating the necessity for costly and time‐consuming further study. Our studies also provide a new lead to investigate how a VUS located in the C‐linker connecting the pore to the cAMP binding domain may affect the channel open state probability and cAMP response.
Production of tetravalent dengue virus envelope protein domain III based antigens in lettuce chloroplasts and immunologic analysis for future oral vaccine development
Authors: van Eerde André , Gottschamel Johanna , Bock Ralph , Hansen Kristine Eraker Aasland , Munang'andu Hetron Mweemba , Daniell Henry , Liu Clarke Jihong 
Published: December 2018

SummaryDengue fever is a mosquito (Aedes aegypti) ‐transmitted viral disease that is endemic in more than 125 countries around the world. There are four serotypes of the dengue virus (DENV 1‐4) and a safe and effective dengue vaccine must provide protection against all four serotypes. To date, the first vaccine, Dengvaxia (CYD‐TDV), is available after many decades’ efforts, but only has moderate efficacy. More effective and affordable vaccines are hence required. Plants offer promising vaccine production platforms and food crops offer additional advantages for the production of edible human and animal vaccines, thus eliminating the need for expensive fermentation, purification, cold storage and sterile delivery. Oral vaccines can elicit humoural and cellular immunity via both the mucosal and humoral immune systems. Here, we report the production of tetravalent EDIII antigen (EDIII‐1‐4) in stably transformed lettuce chloroplasts. Transplastomic EDIII‐1‐4‐expressing lettuce lines were obtained and homoplasmy was verified by Southern blot analysis. Expression of EDIII‐1‐4 antigens was demonstrated by immunoblotting, with the EDIII‐1‐4 antigen accumulating to 3.45% of the total protein content. Immunological assays in rabbits showed immunogenicity of EDIII‐1‐4. Our in vitro gastrointestinal digestion analysis revealed that EDIII‐1‐4 antigens are well protected when passing through the oral and gastric digestion phases but underwent degradation during the intestinal phase. Our results demonstrate that lettuce chloroplast engineering is a promising approach for future production of an affordable oral dengue vaccine.
Maize Sep15‐like functions in endoplasmic reticulum and reactive oxygen species homeostasis to promote salt and osmotic stress resistance
Authors: Zhu Jiantang , Wang Guangling , Li Cuiling , Li Qingqing , Gao Yankun , Chen Fanguo , Xia Guangmin 
Published: December 2018

AbstractIn animals, the Sep15 protein participates in disease resistance, growth, and development, but the function of its plant homologues remains unclear. Here, the function of maize Sep15 was analysed by characterization of two independent Sep15‐like loss‐of‐function mutants. In the absence of ZmSep15‐like, seedling tolerance to both water and salinity stress was compromised. The mutants experienced a heightened level of endoplasmic reticulum stress, and over‐accumulated reactive oxygen species, resulting in leaf necrosis. Characterization of Arabidopsis thaliana atsep15 mutant as well as like with ectopic expression of ZmSep15‐like indicated that ZmSep15‐like contributed to tolerance of both osmotic and salinity stress. ZmSep15‐like interacted physically with UDP‐glucose: glycoprotein glucosyltransferase1 (UGGT1). When the interaction was disrupted, the response to both osmotic and salinity stresses was impaired in maize or Arabidopsis. Co‐expressing ZmUGGT1 and ZmUGGT2 enhanced the tolerance of A. thaliana to both stressors, indicating a functional interaction between them. Together, the data indicated that plants Sep15‐like proteins promote osmotic and salinity stress resistance by influencing endoplasmic reticulum stress response and reactive oxygen species level.
Acanthamoeba proteases contribute to macrophage activation through PAR1, but not PAR2
Authors: Cano Antonella , Mattana Antonella , Henriquez Fiona L. , Alexander James , Roberts Craig W. 
Published: December 2018

SummaryAimAcanthamoeba infections are characterized by an intense localized innate immune response associated with an influx of macrophages. Acanthamoeba protease production is known to affect virulence. Herein, the ability of Acanthamoeba trophozoite proteases, of either the laboratory Neff strain or a recently isolated clinical strain, to stimulate IL‐12 and IL‐6 and to activate protease‐activated receptors, PAR1 and PAR2 expressed on murine macrophages, was investigated.Method and ResultsUsing selected protease inhibitors, leupeptin and E64, we showed that Acanthamoeba proteases can stimulate IL‐12 and IL‐6 by murine macrophages. Subsequently, using specific antagonists to inhibit PAR1, and bone marrow‐derived macrophages from PAR2 gene‐deficient mice, we demonstrate that PAR1, but not PAR2 contributes to macrophage IL‐12 production in response to Acanthamoeba. In contrast, Acanthamoeba‐induced IL‐6 production is PAR1 and PAR2 independent.ConclusionThis study shows for the first time the involvement of PARs, expressed on macrophages, in the response to Acanthamoeba trophozoites and might provide useful insight into Acanthamoeba infections and their future treatments.
The potential of quantitative models to improve microalgae photosynthetic efficiency
Authors: Perin Giorgio , Bellan Alessandra , Bernardi Andrea , Bezzo Fabrizio , Morosinotto Tomas 
Published: December 2018

The massive increase in carbon dioxide concentration in the atmosphere driven by human activities is causing huge negative consequences and new sustainable sources of energy, food and materials are highly needed. Algae are unicellular photosynthetic microorganisms that can provide a highly strategic contribution to this challenge as alternative source of biomass to complement crops cultivation. Algae industrial cultures are commonly limited by light availability, and biomass accumulation is strongly dependent on their photon‐to‐biomass conversion efficiency. Investigation of algae photosynthetic metabolism is thus strategic for the generation of more efficient strains with higher productivity.Algae are cultivated at industrial scale in conditions highly different from the natural niches they adapted to and strains development efforts must fully consider the seminal influence on productivity of regulatory mechanism of photosynthesis as well as of cultivation parameters like cells concentration, light distribution in the culture, mixing, nutrients and carbon dioxide availability. In this review we will focus in particular on how mathematical models can account for the complex influence of all environmental parameters and can be exploited for development of improved algae strains.