bluuebunny/crossref_metadata_2025_split huggingface dataset:
Not the time or the place: the missing spatio‐temporal link in publicly available genetic data
Authors: Pope Lisa C. , Liggins Libby , Keyse Jude , Carvalho Silvia B , Riginos Cynthia 
Published: May 2015

AbstractGenetic data are being generated at unprecedented rates. Policies of many journals, institutions and funding bodies aim to ensure that these data are publicly archived so that published results are reproducible. Additionally, publicly archived data can be ‘repurposed’ to address new questions in the future. In 2011, along with other leading journals in ecology and evolution, Molecular Ecology implemented mandatory public data archiving (the Joint Data Archiving Policy). To evaluate the effect of this policy, we assessed the genetic, spatial and temporal data archived for 419 data sets from 289 articles in Molecular Ecology from 2009 to 2013. We then determined whether archived data could be used to reproduce analyses as presented in the manuscript. We found that the journal's mandatory archiving policy has had a substantial positive impact, increasing genetic data archiving from 49 (pre‐2011) to 98% (2011–present). However, 31% of publicly archived genetic data sets could not be recreated based on information supplied in either the manuscript or public archives, with incomplete data or inconsistent codes linking genetic data and metadata as the primary reasons. While the majority of articles did provide some geographic information, 40% did not provide this information as geographic coordinates. Furthermore, a large proportion of articles did not contain any information regarding date of sampling (40%). Although the inclusion of spatio‐temporal data does require an increase in effort, we argue that the enduring value of publicly accessible genetic data to the molecular ecology field is greatly compromised when such metadata are not archived alongside genetic data.
Citrus psorosis virus 24K protein interacts with citrus miRNA precursors, affects their processing and subsequent miRNA accumulation and target expression
Authors: Reyes Carina A. , Ocolotobiche Eliana E. , Marmisollé Facundo E. , Robles Luna Gabriel , Borniego María B. , Bazzini Ariel A. , Asurmendi Sebastian , García María L. 
Published: May 2015

SummarySweet orange (Citrus sinensis), one of the most important fruit crops worldwide, may suffer from disease symptoms induced by virus infections, thus resulting in dramatic economic losses. Here, we show that the infection of sweet orange plants with two isolates of Citrus psorosis virus (CPsV) expressing different symptomatology alters the accumulation of a set of endogenous microRNAs (miRNAs). Within these miRNAs, miR156, miR167 and miR171 were the most down‐regulated, with almost a three‐fold reduction in infected samples. This down‐regulation led to a concomitant up‐regulation of some of their targets, such as Squamosa promoter‐binding protein‐like 9 and 13, as well as Scarecrow‐like 6. The processing of miRNA precursors, pre‐miR156 and pre‐miR171, in sweet orange seems to be affected by the virus. For instance, virus infection increases the level of unprocessed precursors, which is accompanied by a concomitant decrease in mature species accumulation. miR156a primary transcript accumulation remained unaltered, thus strongly suggesting a processing deregulation for this transcript. The co‐immunoprecipitation of viral 24K protein with pre‐miR156a or pre‐miR171a suggests that the alteration in the processing of these precursors might be caused by a direct or indirect interaction with this particular viral protein. This result is also consistent with the nuclear localization of both miRNA precursors and the CPsV 24K protein. This study contributes to the understanding of the manner in which a virus can alter host regulatory mechanisms, particularly miRNA biogenesis and target expression.
Improved photosynthetic performance during severe drought in Nicotiana tabacum overexpressing a nonenergy conserving respiratory electron sink
Authors: Dahal Keshav , Martyn Greg D. , Vanlerberghe Greg C. 
Published: May 2015

Summary

Chloroplasts have means to manage excess reducing power but these mechanisms may become restricted by rates of ATP turnover. Alternative oxidase (AOX) is a mitochondrial terminal oxidase that uncouples the consumption of reducing power from ATP synthesis.

Physiological and biochemical analyses were used to compare respiration and photosynthesis of Nicotiana tabacum wild‐type (WT) plants with that of transgenic lines overexpressing AOX, under both well‐watered and drought stress conditions.

With increasing drought severity, AOX overexpression acted to increase respiration in the light (RL) relative to WT. CO2 and light response curves indicated that overexpression also improved photosynthetic performance relative to WT, as drought severity increased. This was not due to an effect of AOX amount on leaf water status or the development of the diffusive limitations that occur due to drought. Rather, AOX overexpression dampened photosystem stoichiometry adjustments and losses of key photosynthetic components that occurred in WT.

The results indicate that AOX amount influences RL, particularly during severe drought, when cytochrome pathway respiration may become increasingly restricted. This impacts the chloroplast redox state, influencing how the photosynthetic apparatus responds to increasing drought severity. In particular, the development of biochemical limitations to photosynthesis are dampened in plants with increased nonenergy conserving RL.
Effects of fire and CO2 on biogeography and primary production in glacial and modern climates
Authors: Martin Calvo Maria , Prentice Iain Colin 
Published: May 2015

Summary

Dynamic global vegetation models (DGVMs) can disentangle causes and effects in the control of vegetation and fire. We used a DGVM to analyse climate, CO2 and fire influences on biome distribution and net primary production (NPP) in last glacial maximum (LGM) and pre‐industrial (PI) times.

The Land surface Processes and eXchanges (LPX) DGVM was run in a factorial design with fire ‘off’ or ‘on’, CO2 at LGM (185 ppm) or PI (280 ppm) concentrations, and LGM (modelled) or recent climates. Results were analysed by Stein–Alpert decomposition to separate primary effects from synergies.

Fire removal causes forests to expand and global NPP to increase slightly. Low CO2 greatly reduces forest area (dramatically in a PI climate; realistically under an LGM climate) and global NPP. NPP under an LGM climate was reduced by a quarter as a result of low CO2. The reduction in global NPP was smaller at low temperatures, but greater in the presence of fire.

Global NPP is controlled by climate and CO2 directly through photosynthesis, but also through biome distribution, which is strongly influenced by fire. Future vegetation simulations will need to consider the coupled responses of vegetation and fire to CO2 and climate.
Multiple functions of fire ant Solenopsis invicta mandibular gland products
Authors: Choi Man‐Yeon , Vander Meer Robert K. 
Published: May 2015

AbstractAlarm pheromones of social insects are best known for their role in the defence and maintenance of colony integrity. Previous studies with the fire ant Solenopsis invicta Buren (Hymenoptera: Formicidae) demonstrate that the mandibular glands of workers (sterile females) and male and female sexuals produce an alarm pheromone, 2‐ethyl‐3,6‐dimethylpyrazine. The function of alarm pheromones in worker ants is well understood and divergent from the function of these compounds in the winged sexual forms. The present study quantifies the amount of pyrazine in the mandibular glands from male and female alate sexuals, as well as queens. Pyrazine production in female alates starts in the late pupal stage and increases until they reach mating flight‐ready maturity; however, after mating flight participation, the pyrazine level declines by >50%. Interestingly, mature male alates lose >85% of their mandibular gland pyrazine during mating flight activity. The results of the present study indicate that male and female sexuals use mandibular gland secretions for mating flight initiation and during mating flights. Furthermore, the ontogeny of mandibular gland products (pyrazine as the marker) from newly‐mated queens to mature colony queens shows a more than two‐fold increase in the amount of pyrazine by 6 months after mating. However, this is followed by a decline to trace amounts in mature colony queens (>2 years old), suggesting a function for mandibular gland products during colony development. Multifunctional use of social insect pheromones is well documented and data are reported in the present study suggesting new roles for mandibular gland products in fire ants.
The effectiveness and safety of tranexamic acid in total hip or knee arthroplasty: a meta‐analysis of 2720 cases
Authors: Wei Z. , Liu M. 
Published: May 2015

SUMMARYAimsTo evaluate the safety and efficacy of tranexamic acid (TXA) in total knee arthroplasty (TKA) and total hip arthroplasty (THA). The specific endpoints assessed in this meta‐analysis include the total blood loss, the incidence rate of deep vein thrombosis (DVT) and pulmonary embolisms (PE), the number of patients requiring at least 1 U of red blood cell following surgery.BackgroundThe prevalence of THA and TKA is increasing and both are usually accompanied by considerable blood loss. TXA has been reported to reduce total blood loss in many orthopaedic surgeries. TXA administration continues to be a controversial topic in the literature about joint arthroplasty, and many studies have reported substantial doubt with respect to its benefits and safety.Methods/materialsWe conducted a meta‐analysis that combined all data from available randomised controlled trials, regardless the methods of TXA administration, which included administrated intravenously, intra‐articularly, topically or orally. Finally, available data from the 39 included trials were pooled for analysis. Then, mean differences with 95% confidence intervals (CIs) was calculated for continuous outcomes and relative risks with 95% CIs for dichotomous outcomes.ResultsThis meta‐analysis suggests that the administration of TXA significantly reduced blood loss and the need for allogeneic blood transfusion, without apparent increased risk of DVT or PE thromboembolic complications.ConclusionTo our knowledge, this meta‐analysis is more powerful and persuasive than any other published before. It suggests that the use of TXA reduced the risk of blood loss and the need for allogeneic blood transfusion significantly, without apparent increased risk of DVT or PE complications.
Roles and responsibilities in newborn care in four African sites
Authors: Iganus R. , Hill Z. , Manzi F. , Bee M. , Amare Y. , Shamba D. , Odebiyi A. , Adejuyigbe E. , Omotara B. , Skordis‐Worrall J. 
Published: May 2015

AbstractObjectivesTo explore roles and responsibilities in newborn care in the intra‐ and postpartum period in Nigeria, Tanzania and Ethiopia.MethodsQualitative data were collected using in‐depth interviews with mothers, grandmothers, fathers, health workers and birth attendants and were analysed through content and framework analyses.ResultsWe found that birth attendants were the main decision‐makers and care takers in the intrapartum period. Birth attendants varied across sites and included female relatives (Ethiopia and Nigeria), traditional birth attendants (Tanzania and Nigeria), spiritual birth attendants (Nigeria) and health workers (Tanzania and Nigeria). In the early newborn period, when the mother is deemed to be resting, female family members assumed this role. The mothers themselves only took full responsibility for newborn care after a few days or weeks. The early newborn period was protracted for first‐time mothers, who were perceived as needing training on caring for the baby. Clear gender roles were described, with newborn care being considered a woman's domain. Fathers had little physical contact with the newborn, but played an important role in financing newborn care, and were considered the ultimate decision‐maker in the family.ConclusionInterventions should move beyond a focus on the mother–child dyad, to include other carers who perform and decide on newborn care practices. Given this power dynamic, interventions that involve men have the potential to result in behaviour change.
Post‐translational mechanisms are associated with fertility restoration of cytoplasmic male sterility in sugar beet (Beta vulgaris)
Authors: Kitazaki Kazuyoshi , Arakawa Takumi , Matsunaga Muneyuki , Yui‐Kurino Rika , Matsuhira Hiroaki , Mikami Tetsuo , Kubo Tomohiko 
Published: May 2015

SummaryGenetic conflict between cytoplasmically inherited elements and nuclear genes arising from their different transmission patterns can be seen in cytoplasmic male sterility (CMS), the mitochondrion‐encoded inability to shed functional pollen. CMS is associated with a mitochondrial open reading frame (ORF) that is absent from non‐sterility inducing mitochondria (S‐orf). Nuclear genes that suppress CMS are called restorer‐of‐fertility (Rf) genes. Post‐transcriptional and translational repression of S‐orf mediates the molecular action of Rf that encodes a class of RNA‐binding proteins with pentatricopeptide repeat (PPR) motifs. Besides the PPR‐type of Rfs, there are also non‐PPR Rfs, but the molecular interactions between non‐PPR Rf and S‐orf have not been described. In this study, we investigated the interaction of bvORF20, a non‐PPR Rf from sugar beet (Beta vulgaris), with preSatp6, the S‐orf from sugar beet. Anthers expressing bvORF20 contained a protein that interacted with preSATP6 protein. Analysis of anthers and transgenic calli expressing a FLAG‐tagged bvORF20 suggested the binding of preSATP6 to bvORF20. To see the effect of bvORF20 on preSATP6, which exists as a 250‐kDa protein complex in CMS plants, signal bands of preSATP6 in bvORF20‐expressing and non‐expressing anthers were compared by immunoblotting combined with Blue Native polyacrylamide gel electrophoresis. The signal intensity of the 250‐kDa band decreased significantly, and 200‐ and 150‐kDa bands appeared in bvORF20‐expressing anthers. Transgenic callus expressing bvORF20 also generated the 200‐ and 150‐kDa bands. The 200‐kDa complex is likely to include both preSATP6 and bvORF20. Post‐translational interaction between preSATP6 and bvORF20 appears to alter the higher order structure of preSATP6 that may lead to fertility restoration in sugar beet.
Independent evaluation of tolerance of therapeutic plasma inactivated by amotosalen‐HCl–UVA (Intercept™) over a 5‐year period of extensive delivery
Authors: Bost V. , Chavarin P. , Boussoulade F. , Fabrigli P. , Chabre C. , Benamara H. , Odent‐Malaure H. , Legrand D. , Cognasse F. , Garraud O. 
Published: May 2015

Amotosalen‐HCl–UVA (AI) is a process to inactivate pathogens in therapeutic plasma (FFP). Tolerance is the main residual issue in FFP transfusion, and only large series observations are powered enough to identify significantly elevated levels of hazards. We report here on 15 133 new transfusions of AI‐FFP, over the previously published 36 035, which in all represents one of the largest series observed by means of a highly standardized surveillance (51 168 observations). There is no noticeable difference in terms of tolerance of AI‐FFP compared to 5875 transfusions of Quarantine (Q)‐FFP. There was no significant difference in terms of advance events, between the two types of FFP (P = 0·98); further, no difference was recorded either when the total number of AI‐FFP (51 168) was compared to the corresponding number of Q‐FFP (5875; P = 0·62).
Transcriptomic and Proteomic Profiling of Anabaena sp. Strain 90 under Inorganic Phosphorus Stress
Authors: Teikari Jonna , Österholm Julia , Kopf Matthias , Battchikova Natalia , Wahlsten Matti , Aro Eva-Mari , Hess Wolfgang R. , Sivonen Kaarina 
Published: May 2015

ABSTRACT

Inorganic phosphorus (P
i
) is one of the main growth-limiting factors of diazotrophic cyanobacteria. Due to human activity, the availability of P
i
has increased in water bodies, resulting in eutrophication and the formation of massive cyanobacterial blooms. In this study, we examined the molecular responses of the cyanobacterium
Anabaena
sp. strain 90 to phosphorus deprivation, aiming at the identification of candidate genes to monitor the P
i
status in cyanobacteria. Furthermore, this study increased the basic understanding of how phosphorus affects diazotrophic and bloom-forming cyanobacteria as a major growth-limiting factor. Based on RNA sequencing data, we identified 246 differentially expressed genes after phosphorus starvation and 823 differentially expressed genes after prolonged P
i
limitation, most of them related to central metabolism and cellular growth. The transcripts of the genes related to phosphorus transport and assimilation (
pho
regulon) were most upregulated during phosphorus depletion. One of the most increased transcripts encodes a giant protein of 1,869 amino acid residues, which contains, among others, a phytase-like domain. Our findings predict its crucial role in phosphorus starvation, but future studies are still needed. Using two-dimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), we found 43 proteins that were differentially expressed after prolonged phosphorus stress. However, correlation analysis unraveled an association only to some extent between the transcriptomic and proteomic abundances. Based on the present results, we suggest that the method used for monitoring the P
i
status in cyanobacterial bloom should contain wider combinations of
pho
regulon genes (e.g., PstABCS transport systems) in addition to the commonly used alkaline phosphatase gene alone.
Novel HIV-1 Recombinant Identified in a Foreign Heterosexual Resident in Japan: Relatedness to Recently Reported CRF69_01B, Detected Primarily among Japanese Men Who Have Sex with Men
Authors: Kusagawa Shigeru , Yokota Yuko , Negishi Masayoshi , Kondo Makiko , Matano Tetsuro , Kato Shingo , Takebe Yutaka 
Published: May 2015

ABSTRACT

We report here an HIV-1 recombinant composed of CRF01_AE and subtype B, with a total of eight recombination breakpoints in the
gag-pol
and
vpr-tat
regions. This recombinant was identified from a Myanmarese heterosexual male in Japan and showed the chimera structure identical to recently reported CRF69_01B, detected primarily among men who have sex with men in Japan.
Draft Genome Sequence of
Bacillus
sp. Strain CMAA 1185, a Cellullolytic Bacterium Isolated from Stain House Lake, Antarctic Peninsula
Authors: Santos Suikinai Nobre , Kavamura Vanessa Nessner , Taketani Rodrigo Gouvêa , Vasconcellos Rafael L. F. , Zucchi Tiago Domingues , Melo Itamar Soares 
Published: May 2015

ABSTRACT

The aim of this study was to report the genome sequence of the cellulolytic
Bacillus
sp. strain CMAA 1185, isolated from Stain House Lake, Antarctica.
Draft Genome Sequences of 24 Microbial Strains Assembled from Direct Sequencing from 4 Stool Samples
Authors: Jeraldo Patricio , Hernández Álvaro , White Bryan A. , O’Brien Daniel , Ahlquist David , Boardman Lisa , Chia Nicholas 
Published: May 2015

ABSTRACT
The ability to assemble genomes from metagenomic sequencing avoids the need for culture and any associated culture biases. We assembled 24 essentially complete draft genomes from metagenomic pair-end and size-selected mate pair sequencing from 4 stool samples, 2 from subjects diagnosed with colorectal cancer and 2 from healthy controls.
Whole-Genome Sequence of Serratia liquefaciens HUMV-21, a Cytotoxic, Quorum-Sensing, and Biofilm-Producing Clinical Isolate
Authors: Lázaro-Díez María , Acosta Felix , Remuzgo-Martínez Sara , Ocampo-Sosa Alain , Ocejo-Vinyals Javier Gonzalo , Bravo Jimena , El Aamri Fátima , Escuela Oliver , Martínez-Martínez Luis , Ramos-Vivas José 
Published: May 2015

ABSTRACT

A clinical isolate of
Serratia liquefaciens
(strain HUMV-21) was obtained from a skin ulcer of an adult patient. We report here its complete genome assembly using PacBio single-molecule real-time (SMRT) sequencing, which resulted in a single circular chromosome with 5.3 Mb. About 5,844 protein-coding genes are predicted from this assembly.
Draft Genome Sequence of Mycoparasite
Clonostachys rosea
Strain 67-1
Authors: Sun Zhan-Bin , Sun Man-Hong , Li Shi-Dong 
Published: May 2015

ABSTRACT

Clonostachys rosea
is a promising mycoparasite. In this study, we sequenced the draft genome of the highly effective strain 67-1 using the Illumina HiSeq 2500 sequencing platform. The genome is 55.4 Mb with a G+C content of 49.2% and provides a powerful resource for future studies on the molecular mechanisms underlying
Clonostachys rosea
's antagonism on fungal pathogens.
Complete Genome Sequence of Sulfolobus solfataricus Strain 98/2 and Evolved Derivatives
Authors: McCarthy Samuel , Gradnigo Julien , Johnson Tyler , Payne Sophie , Lipzen Anna , Martin Joel , Schackwitz Wendy , Moriyama Etsuko , Blum Paul 
Published: May 2015

ABSTRACT

Sulfolobus solfataricus
is a thermoacidophilic crenarcheote with a 3.0-Mb genome. Here, we report the genome sequence of
S. solfataricus
strain 98/2, along with several evolved derivatives generated through experimental microbial evolution for enhanced thermoacidophily.
Complete Genome Sequence of a Novel Circovirus from Zebra Finch
Authors: Rinder Monika , Schmitz Anna , Peschel Andrea , Korbel Rüdiger 
Published: May 2015

ABSTRACT

A novel circovirus was identified in zebra finches (
Taeniopygia guttata
). The genome of the circovirus strain, designated 8454V25-1, comprised 1,982 nucleotides with two major open reading frames encoding a replication-associated protein and a viral capsid protein.
Draft Genome Sequence of Isoproturon-Mineralizing
Sphingomonas
sp. SRS2, Isolated from an Agricultural Field in the United Kingdom
Authors: Nielsen Tue Kjærgaard , Sørensen Sebastian R. , Hansen Lars Hestbjerg 
Published: May 2015

ABSTRACT

Sphingomonas
sp. SRS2 was the first described pure strain that is capable of mineralizing the phenylurea herbicide isoproturon and some of its related compounds. This strain has been studied thoroughly and shows potential for bioremediation purposes. We present the draft genome sequence of this bacterium, which will aid future studies.
Complete Genome Sequence of Corynebacterium kutscheri DSM 20755, a Corynebacterial Type Strain with Remarkably Low G+C Content of Chromosomal DNA
Authors: Rückert Christian , Albersmeier Andreas , Winkler Anika , Tauch Andreas 
Published: May 2015

ABSTRACT

The complete genome sequence of the type strain
Corynebacterium kutscheri
DSM 20755 comprises 2,354,065 bp and 2,047 protein-coding genes. The mean G+C content of the chromosomal DNA is 46.46%, which is the lowest value detected so far in a member of the genus
Corynebacterium
.