bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wing phosphorylation is a major functional determinant of the Lrs14‐type biofilm and motility regulator AbfR1 in Sulfolobus acidocaldarius
Authors: Li Lingling , Banerjee Ankan , Bischof Lisa Franziska , Maklad Hassan Ramadan , Hoffmann Lena , Henche Anna‐Lena , Veliz Fabian , Bildl Wolfgang , Schulte Uwe , Orell Alvaro , Essen Lars‐Oliver , Peeters Eveline , Albers Sonja‐Verena 
Published: June 2017

SummaryIn response to a variety of environmental cues, prokaryotes can switch between a motile and a sessile, biofilm‐forming mode of growth. The regulatory mechanisms and signaling pathways underlying this switch are largely unknown in archaea but involve small winged helix‐turn‐helix DNA‐binding proteins of the archaea‐specific Lrs14 family. Here, we study the Lrs14 member AbfR1 of Sulfolobus acidocaldarius. Small‐angle X‐ray scattering data are presented, which are consistent with a model of dimeric AbfR1 in which dimerization occurs via an antiparallel coiled coil as suggested by homology modeling. Furthermore, solution structure data of AbfR1‐DNA complexes suggest that upon binding DNA, AbfR1 induces deformations in the DNA. The wing residues tyrosine 84 and serine 87, which are phosphorylated in vivo, are crucial to establish stable protein‐DNA contacts and their substitution with a negatively charged glutamate or aspartate residue inhibits formation of a nucleoprotein complex. Furthermore, mutation abrogates the cellular abundance and transcription regulatory function of AbfR1 and thus affects the resulting biofilm and motility phenotype of S. acidocaldarius. This work establishes a novel wHTH DNA‐binding mode for Lrs14‐like proteins and hints at an important role for protein phosphorylation as a signal transduction mechanism for the control of biofilm formation and motility in archaea.
Analytical approaches to subspecies delimitation with genetic data
Authors: Martien Karen K. , Leslie Matthew S. , Taylor Barbara L. , Morin Phillip A. , Archer Frederick I. , Hancock‐Hanser Brittany L. , Rosel Patricia E. , Vollmer Nicole L. , Viricel Amélia , Cipriano Frank 
Published: June 2017

AbstractThe vast and remote distributions and large body size of most cetaceans make it difficult to obtain and maintain morphological collections adequate for advancing sound taxonomic arguments. Consequently, genetic data are playing an increasingly important role in cetacean species and subspecies delimitation. We review seven categories of analytical methods useful in delimiting subspecies based on genetic data. For each category, we summarize its utility in evaluating putative subspecies, the types of markers to which it can be applied, and potential challenges in interpreting results in a taxonomic context. We focus on the utility of each type of method to evaluate the critical features distinguishing subspecies from populations and species: the degree of diagnosability between putative taxa and the extent to which the putative taxa have diverged along separate evolutionary pathways. We conclude that diagnosability is best estimated with either assignment tests or multivariate methods, while evaluating the degree of divergence requires a synthesis of multiple lines of evidence derived from different analytical methods and different data types, including nongenetic data.
A review of molecular genetic markers and analytical approaches that have been used for delimiting marine mammal subspecies and species
Authors: Rosel Patricia E. , Taylor Barbara L. , Hancock‐Hanser Brittany L. , Morin Phillip A. , Archer Frederick I. , Lang Aimee R. , Mesnick Sarah L. , Pease Victoria L. , Perrin William F. , Robertson Kelly M. , Leslie Matthew S. , Berta Annalisa , Cipriano Frank , Parsons Kim M. , Viricel Amélia , Vollmer Nicole L. , Martien Karen K. 
Published: June 2017

AbstractUncertainty in marine mammal taxonomy is increasingly being addressed using molecular genetic data. We examined 32 peer‐reviewed articles published between 1994 and 2011to review methodological practices, consistency of markers and analytical methods, and overall quality of arguments used when genetic data have been employed to delimit new species and subspecies of marine mammals. The mitochondrial DNA (mtDNA) control region was the primary genetic marker used in these studies, but analytical methods varied greatly across studies. Diagnosability, a common metric for delimiting subspecies with morphological data, was only used through citing of fixed differences in mtDNA sequences. Assignment tests based on microsatellite data were less common but were applied at both taxonomic levels. Nuclear DNA sequence data were rarely used. Basic background material needed to evaluate the strength of arguments, such as distribution and sampling maps, were often missing. For most studies, sample sizes were good, but adequate geographic sampling for broadly distributed taxa was often lacking, diminishing the strength of evidence for taxonomic distinctness. Examining these empirical cases revealed a mixture of sound and inadequate practices for genetic studies of cetacean taxonomy and suggested that improvements could be made to the field by developing standard guidelines.
Marinesco bodies and substantia nigra neuron density in Parkinson's disease
Authors: Abbott R. D. , Nelson J. S. , Ross G.W. , Uyehara‐Lock J. H. , Tanner C. M. , Masaki K. H. , Launer L. J. , White L. R. , Petrovitch H. 
Published: June 2017

AimMarinesco bodies (MB) are intranuclear inclusions in pigmented neurons of the substantia nigra (SN). While rare in children, frequency increases with normal ageing and is high in Alzheimer's disease, dementia with Lewy bodies and other neurodegenerative disorders. Coinciding with the age‐related rise in MB frequency is initiation of cell death among SN neurons. Whether MB have a role in this process is unknown. Our aim is to examine the association of MB with SN neuron density in Parkinson's disease (PD) in the Honolulu‐Asia Aging Study.MethodsData on MB and neuron density were measured in SN transverse sections in 131 autopsied men aged 73–99 years at the time of death from 1992 to 2007.ResultsMarinesco body frequency was low in the presence vs. absence of PD (2.3% vs. 6.6%, P < 0.001). After PD onset, MB frequency declined as duration of PD increased (P = 0.006). Similar patterns were observed for SN neuron density. When MB frequency was low, neuron density was noticeably reduced in the SN ventrolateral quadrant, the region most vulnerable to PD neurodegeneration. Low MB frequency was unique to PD as its high frequency in non‐PD cases was unrelated to parkinsonian signs and incidental Lewy bodies. Frequency was high in the presence of Alzheimer's disease and apolipoprotein ε4 alleles.ConclusionsWhile findings confirm that MB frequency is low in PD, declines in MB frequency continue with PD duration. The extent to which MB have a distinct relationship with PD warrants clarification. Further studies of MB could be important in understanding PD processes.
Identification of differentially regulated maize proteins conditioning Sugarcane mosaic virus systemic infection
Authors: Chen Hui , Cao Yanyong , Li Yiqing , Xia Zihao , Xie Jipeng , Carr John P. , Wu Boming , Fan Zaifeng , Zhou Tao 
Published: June 2017

Summary

Sugarcane mosaic virus (SCMV) is the most important cause of maize dwarf mosaic disease. To identify maize genes responsive to SCMV infection and that may be involved in pathogenesis, a comparative proteomic analysis was performed using the first and second systemically infected leaves (termed 1 SL and 2 SL, respectively).

Seventy‐one differentially expressed proteins were identified in 1 SL and 2 SL upon SCMV infection. Among them, eight proteins showed the same changing patterns in both 1 SL and 2 SL. Functional annotations of regulated proteins and measurement of photosynthetic activity revealed that photosynthesis was more inhibited and defensive gene expression more pronounced in 1 SL than in 2 SL.

Knockdown of regulated proteins in both 1 SL and 2 SL by a brome mosaic virus‐based gene silencing vector in maize indicated that protein disulfide isomerase‐like and phosphoglycerate kinase were required for optimal SCMV replication. By contrast, knockdown of polyamine oxidase (ZmPAO) significantly increased SCMV accumulation, implying that ZmPAO activity might contribute to resistance or tolerance.

The results suggest that combining comparative proteomic analyses of different tissues and virus‐induced gene silencing is an efficient way to identify host proteins supporting virus replication or enhancing resistance to virus infection.
Considering the unintentional consequences of pollinator gardens for urban native plants: is the road to extinction paved with good intentions?
Authors: Johnson Anna L. , Fetters Andrea M. , Ashman Tia‐Lynn 
Published: June 2017

SummaryUrban centers are important foci for plant biodiversity and yet widespread planting of wildflower gardens in cities to sustain pollinator biodiversity is on the rise, without full consideration of potential ecological consequences. The impact of intentional wildflower plantings on remnant native plant diversity in urban and peri‐urban settings has not received attention, although shared pollinators are likely to mediate several types of biotic interactions between human‐introduced plants and remnant native ones. Additionally, if wildflower species escape gardens these indirect effects may be compounded with direct ones. We review the potential positive and negative impacts of wildflower gardens on urban native flowering plants, and we reveal substantial gaps in our knowledge. We present a roadmap for research to address whether wildflower gardens, while benefiting pollinators, could also hasten the extinction of native remnant plants in urban settings, or whether they could have other effects that enrich urban biodiversity. Goals of future wildflower mixes should consider the totality of potential interactions.
Increased Sympathetic Outflow Induces Adaptation to Acute Experimental Pain
Authors: Dayan Lior , Hochberg Uri , Nahman‐Averbuch Hadas , Brill Silviu , Ablin Jacob N. , Jacob Giris 
Published: June 2017

AbstractBackgroundThere are interrelationships between the autonomic nervous system and pain. This study aims to explore the effect of different autonomic manipulations on pain perception and modulation.MethodsTwenty healthy subjects (10 men and 10 women, mean age 25 ± 3 years) participated in this single‐blinded, semi‐randomized, controlled study, which included 2 study visits. Warm detection thresholds, heat pain thresholds, conditioned pain modulation (CPM), and pain adaptation were tested before and after administration of phenylephrine, clonidine, yohimbine, and saline.ResultsChanges in heart rate and blood pressure were found after all the pharmacological interventions. The only effect on pain measures was that yohimbine enhanced pain adaptation capacity while phenylephrine reduced it (P = 0.032). Several significant correlations were found between autonomic and pain parameters; greater decreases in heart rate after phenylephrine were associated with reduced pain ratings (r2 = 0.288, P = 0.018). In addition, enhanced pain adaptation was associated with higher total vascular resistance (r2 = 0.442, P = 0.01).ConclusionsDifferent effects of acute autonomic manipulations on experimental pain were found: an increase in sympathetic tone induced by yohimbine led to reduced pain sensitivity; a decrease in sympathetic tone with no effect on vagal‐parasympathetic tone induced by phenylephrine led to reduction in pain adaptation capacity; and a decrease in sympathetic tone and increase in vagal parasympathetic tone by clonidine led to no change in pain adaptation capacity. While increased sympathetic outflow does facilitate pain adaptation, activation of either the sympathetic or parasympathetic limbs of the autonomic nervous system does not affect pain thresholds or CPM. Finally, a correlation exists between nociception and cardiovascular parameters only due to baroreflex activation.
Two NHX‐type transporters from Helianthus tuberosus improve the tolerance of rice to salinity and nutrient deficiency stress
Authors: Zeng Yang , Li Qing , Wang Haiya , Zhang Jianliang , Du Jia , Feng Huimin , Blumwald Eduardo , Yu Ling , Xu Guohua 
Published: June 2017

SummaryThe NHX‐type cation/H+ transporters in plants have been shown to mediate Na+(K+)/H+ exchange for salinity tolerance and K+ homoeostasis. In this study, we identified and characterized two NHX homologues, HtNHX1 and HtNHX2 from an infertile and salinity tolerant species Helianthus tuberosus (cv. Nanyu No. 1). HtNHX1 and HtNHX2 share identical 5′‐ and 3′‐UTR and coding regions, except for a 342‐bp segment encoding 114 amino acids (L272 to Q385) which is absent in HtNHX2. Both hydroponics and soil culture experiments showed that the expression of HtNHX1 or HtNHX2 improved the rice tolerance to salinity. Expression of HtNHX2, but not HtNHX1, increased rice grain yield, harvest index, total nutrient uptake under K+‐limited salt‐stress or general nutrient deficiency conditions. The results provide a novel insight into NHX function in plant mineral nutrition.
Overexpression of Hevea brasiliensis ethylene response factor HbERF‐IXc5 enhances growth and tolerance to abiotic stress and affects laticifer differentiation
Authors: Lestari Retno , Rio Maryannick , Martin Florence , Leclercq Julie , Woraathasin Natthakorn , Roques Sandrine , Dessailly Florence , Clément‐Vidal Anne , Sanier Christine , Fabre Denis , Melliti Sémi , Suharsono Sony , Montoro Pascal 
Published: June 2017

SummaryEthylene response factor 1 (ERF1) is an essential integrator of the jasmonate and ethylene signalling pathways coordinating a large number of genes involved in plant defences. Its orthologue in Hevea brasiliensis, HbERF‐IXc5, has been assumed to play a major role in laticifer metabolism and tolerance to harvesting stress for better latex production. This study sets out to establish and characterize rubber transgenic lines overexpressing HbERF‐IXc5. Overexpression of HbERF‐IXc5 dramatically enhanced plant growth and enabled plants to maintain some ecophysiological parameters in response to abiotic stress such as water deficit, cold and salt treatments. This study revealed that HbERF‐IXc5 has rubber‐specific functions compared to Arabidopsis ERF1 as transgenic plants overexpressing HbERF‐IXc5 accumulated more starch and differentiated more latex cells at the histological level. The role of HbERF‐IXc5 in driving the expression of some target genes involved in laticifer differentiation is discussed.
Photosynthate partitioning to starch in Arabidopsis thaliana is insensitive to light intensity but sensitive to photoperiod due to a restriction on growth in the light in short photoperiods
Authors: Mengin Virginie , Pyl Eva‐Theresa , Alexandre Moraes Thiago , Sulpice Ronan , Krohn Nicole , Encke Beatrice , Stitt Mark 
Published: June 2017

AbstractPhotoperiod duration can be predicted from previous days, but irradiance fluctuates in an unpredictable manner. To investigate how allocation to starch responds to changes in these two environmental variables, Arabidopsis Col‐0 was grown in a 6 h and a 12 h photoperiod at three different irradiances. The absolute rate of starch accumulation increased when photoperiod duration was shortened and when irradiance was increased. The proportion of photosynthate allocated to starch increased strongly when photoperiod duration was decreased but only slightly when irradiance was decreased. There was a small increase in the daytime level of sucrose and twofold increases in glucose, fructose and glucose 6‐phosphate at a given irradiance in short photoperiods compared to long photoperiods. The rate of starch accumulation correlated strongly with sucrose and glucose levels in the light, irrespective of whether these sugars were responding to a change in photoperiod or irradiance. Whole plant carbon budget modelling revealed a selective restriction of growth in the light period in short photoperiods. It is proposed that photoperiod sensing, possibly related to the duration of the night, restricts growth in the light period in short photoperiods, increasing allocation to starch and providing more carbon reserves to support metabolism and growth in the long night.
Using numerical plant models and phenotypic correlation space to design achievable ideotypes
Authors: Picheny Victor , Casadebaig Pierre , Trépos Ronan , Faivre Robert , Da Silva David , Vincourt Patrick , Costes Evelyne 
Published: June 2017

AbstractNumerical plant models can predict the outcome of plant traits modifications resulting from genetic variations, on plant performance, by simulating physiological processes and their interaction with the environment. Optimization methods complement those models to design ideotypes, that is, ideal values of a set of plant traits, resulting in optimal adaptation for given combinations of environment and management, mainly through the maximization of performance criteria (e.g. yield and light interception). As use of simulation models gains momentum in plant breeding, numerical experiments must be carefully engineered to provide accurate and attainable results, rooting them in biological reality. Here, we propose a multi‐objective optimization formulation that includes a metric of performance, returned by the numerical model, and a metric of feasibility, accounting for correlations between traits based on field observations. We applied this approach to two contrasting models: a process‐based crop model of sunflower and a functional–structural plant model of apple trees. In both cases, the method successfully characterized key plant traits and identified a continuum of optimal solutions, ranging from the most feasible to the most efficient. The present study thus provides successful proof of concept for this enhanced modelling approach, which identified paths for desirable trait modification, including direction and intensity.
Arginase‐2, a miR‐1299 target, enhances pigmentation in melasma by reducing melanosome degradation via senescence‐induced autophagy inhibition
Authors: Kim Nan‐Hyung , Choi Soo‐Hyun , Yi Nayoung , Lee Tae Ryong , Lee Ai‐Young 
Published: June 2017

SummaryExpression profiles revealed miR‐1299 downregulation concomitant with arginase‐2 (ARG2) upregulation in hyperpigmented skin of melasma patients. Opposite regulation of tyrosinase and PMEL17 by miR‐1299 and inverse relationship between miR‐1299 and ARG2 expression denoted a role of miR‐1299 in pigmentation with ARG2 as a miR‐1299 target. ARG2 overexpression or knock‐down in keratinocytes, the main source of ARG2 in epidermis, positively regulated tyrosinase and PMEL17 protein levels, but not mRNA levels or melanosome transfer. ARG2 overexpression in keratinocytes reduced autophagy equivalent to 3‐MA, an autophagy inhibitor which also increased tyrosinase and PMEL17 protein levels, whereas ARG2 knock‐down induced opposite results. Autophagy inducer rapamycin reduced ARG2‐increased tyrosinase and PMEL17 protein levels. Also, autophagy was reduced in late passage‐induced senescent keratinocytes showing ARG2 upregulation. ARG2, but not 3‐MA, stimulated keratinocyte senescence. These results suggest that ARG2 reduces autophagy in keratinocytes by stimulating cellular senescence, resulting in skin pigmentation by reducing degradation of transferred melanosomes.
16‐Year follow‐up of an avulsed maxillary central incisor after replantation following 10‐h storage: An unusual case
Authors: Kırzıoğlu Zuhal , Erken Güngör Özge , Erdoğan Yıldırım 
Published: June 2017

ABSTRACTTooth avulsion is a type of dental injury defined as the complete displacement of a tooth out of the alveolar socket, and the lack of prompt treatment measures can result in the loss of function, poor quality of life, and psychological and social problems. However, several factors may not permit the immediate replantation of an avulsed tooth; therefore, delayed replantation has emerged as an alternative to meet the esthetic, functional, and psychological demands of patients. Here it was described that the successful replantation of an avulsed maxillary central incisor in a 9‐year‐old boy who presented at the clinic with the tooth stored in unfavorable conditions as dry and then in olive oil‐milk mixture almost 10 h after the event. The tooth has remained in its socket healthy for 16 years after treatment. The patient was satisfied with both esthetics and function.
Adjunct Extraposition: Base Generation or Movement?
Authors: Reeve Matthew , Hicks Glyn 
Published: June 2017

AbstractIt has been argued that extraposition fromDPis derived differently according to whether a complement or an adjunct is extraposed, with complement extraposition being derived by movement and adjunct extraposition being derived via covert Quantifier Raising (QR) of the hostDPplus Late Merge of the adjunct (Fox & Nissenbaum 1999). We argue that adjunct extraposition is itself derivationally ambiguous and may be derived either by movement of the adjunct or by base generation of the adjunct in extraposed position. Accordingly, we argue for a relaxation of the strictly compositional view that nominal modification is always mediated by syntactic sisterhood. We argue that whereas base‐generated extraposition is possible with quantificational hostDPs, adjunct extraposition from definites must be derived by movement. This accounts for a number of asymmetries between extraposition from definites and from other types ofDP, concerning reconstruction for condition C, scope reconstruction, and information‐structural restrictions on extraposition.
A genome‐wide association study of 23 agronomic traits in Chinese wheat landraces
Authors: Liu Yaxi , Lin Yu , Gao Shang , Li Zhanyi , Ma Jian , Deng Mei , Chen Guoyue , Wei Yuming , Zheng Youliang 
Published: June 2017

SummaryUncovering the genetic basis of agronomic traits in wheat landraces is important for ensuring global food security via the development of improved varieties. Here, 723 wheat landraces from 10 Chinese agro‐ecological zones were evaluated for 23 agronomic traits in six environments. All accessions could be clustered into five subgroups based on phenotypic data via discriminant function analysis, which was highly consistent with genotypic classification. A genome‐wide association study was conducted for these traits using 52 303 DArT‐seq markers to identify marker‐trait associations and candidate genes. Using both the general linear model and the mixed linear model, 149 significant markers were identified for 21 agronomic traits based on best linear unbiased prediction values. Considering the linkage disequilibrium decay distance in this study, significant markers within 10 cM were combined as a quantitative trait locus (QTL), with a total of 29 QTL identified for 15 traits. Of these, five QTL for heading date, flag leaf width, peduncle length, and thousand kernel weight had been reported previously. Twenty‐five candidate genes associated with significant markers were identified. These included the known vernalization genes VRN‐B1 and vrn‐B3 and the photoperiod response genes Ppd and PRR. Overall, this study should be helpful in elucidating the underlying genetic mechanisms of complex agronomic traits and performing marker‐assisted selection in wheat.