bluuebunny/crossref_metadata_2025_split huggingface dataset:
Larval connectivity across temperature gradients and its potential effect on heat tolerance in coral populations
Authors: Kleypas Joan A. , Thompson Diane M. , Castruccio Frederic S. , Curchitser Enrique N. , Pinsky Malin , Watson James R. 
Published: May 2016

AbstractCoral reefs are increasingly exposed to elevated temperatures that can cause coral bleaching and high levels of mortality of corals and associated organisms. The temperature threshold for coral bleaching depends on the acclimation and adaptation of corals to the local maximum temperature regime. However, because of larval dispersal, coral populations can receive larvae from corals that are adapted to very different temperature regimes. We combine an offline particle tracking routine with output from a high‐resolution physical oceanographic model to investigate whether connectivity of coral larvae between reefs of different thermal regimes could alter the thermal stress threshold of corals. Our results suggest that larval transport between reefs of widely varying temperatures is likely in the Coral Triangle and that accounting for this connectivity may be important in bleaching predictions. This has important implications in conservation planning, because connectivity may allow some reefs to have an inherited heat tolerance that is higher or lower than predicted based on local conditions alone.
Regional atmospheric cooling and wetting effect of permafrost thaw‐induced boreal forest loss
Authors: Helbig Manuel , Wischnewski Karoline , Kljun Natascha , Chasmer Laura E. , Quinton William L. , Detto Matteo , Sonnentag Oliver 
Published: May 2016

AbstractIn the sporadic permafrost zone of North America, thaw‐induced boreal forest loss is leading to permafrost‐free wetland expansion. These land cover changes alter landscape‐scale surface properties with potentially large, however, still unknown impacts on regional climates. In this study, we combine nested eddy covariance flux tower measurements with satellite remote sensing to characterize the impacts of boreal forest loss on albedo, eco‐physiological and aerodynamic surface properties, and turbulent energy fluxes of a lowland boreal forest region in the Northwest Territories, Canada. Planetary boundary layer modelling is used to estimate the potential forest loss impact on regional air temperature and atmospheric moisture. We show that thaw‐induced conversion of forests to wetlands increases albedo: and bulk surface conductance for water vapour and decreases aerodynamic surface temperature. At the same time, heat transfer efficiency is reduced. These shifts in land surface properties increase latent at the expense of sensible heat fluxes, thus, drastically reducing Bowen ratios. Due to the lower albedo of forests and their masking effect of highly reflective snow, available energy is lower in wetlands, especially in late winter. Modelling results demonstrate that a conversion of a present‐day boreal forest–wetland to a hypothetical homogeneous wetland landscape could induce a near‐surface cooling effect on regional air temperatures of up to 3–4 °C in late winter and 1–2 °C in summer. An atmospheric wetting effect in summer is indicated by a maximum increase in water vapour mixing ratios of 2 mmol mol−1. At the same time, maximum boundary layer heights are reduced by about a third of the original height. In fall, simulated air temperature and atmospheric moisture between the two scenarios do not differ. Therefore, permafrost thaw‐induced boreal forest loss may modify regional precipitation patterns and slow down regional warming trends.
Dental caries and periodontal disease among U.S. pregnant women and nonpregnant women of reproductive age, National Health and Nutrition Examination Survey, 1999–2004
Authors: Azofeifa Alejandro , Yeung Lorraine F. , Alverson C. J. , Beltrán‐Aguilar Eugenio 
Published: May 2016

AbstractObjectivesThis study assessed and compared the prevalence and severity of dental caries and the prevalence of periodontal disease among pregnant and nonpregnant women of reproductive age (15–44 years) using data from the National Health and Nutrition Examination Survey, NHANES (1999–2004).MethodsEstimates were derived from a sample of 897 pregnant women and 3,971 nonpregnant women. Chi‐square and two‐sample t‐tests were used to assess differences between groups stratified by age, race/ethnicity, education, and poverty. Bonferroni method was applied to adjust for multiple comparisons.ResultsIn general, there were no statistically significant differences in the prevalence estimates of dental caries and periodontal disease between pregnant women and nonpregnant women. However, results showed significant differences when stratified by sociodemographic characteristics. For example, the prevalence of untreated dental caries among women aged 15–24 years was significantly higher in pregnant women than in nonpregnant women (41 percent versus 24 percent, P = 0.001). Regardless of their pregnancy status, racial/ethnic minorities or women with less education or lower family income had higher prevalence of untreated dental caries, severity of dental caries, and periodontal disease compared to the respective reference groups of non‐Hispanic whites or women with more education or higher family income.ConclusionResults of this study show few clinical differences in dental caries and periodontal disease between pregnant and nonpregnant women but persistent disparities by sociodemographic characteristics. In order to reduce oral health disparities in the United States, it is important to improve access to oral health care particularly among vulnerable groups. Integrating oral health into the overall health care could benefit and improve women's oral health outcomes.
Effect of vitamin D on gastrointestinal symptoms and health‐related quality of life in irritable bowel syndrome patients: a randomized double‐blind clinical trial
Authors: Abbasnezhad A. , Amani R. , Hajiani E. , Alavinejad P. , Cheraghian B. , Ghadiri A. 
Published: May 2016

AbstractBackgroundLow‐grade mucosal inflammation and immune activation are involved in the pathogenesis of irritable bowel syndrome (IBS). Furthermore, IBS symptoms are associated with a significantly higher prevalence of psychological distress, which in itself results into an impaired quality of life (QoL). Vitamin D could ameliorate the symptoms of patients suffering from IBS through its beneficial effects on psychological factors and inflammation.MethodsA total of 90 IBS patients participated in this double‐blind, randomized, placebo‐controlled study. Participants were randomly selected to receive either 50 000 IU vitamin D3 or a placebo fortnightly for a period of 6 months. Patients reported their IBS symptoms at the baseline and monthly during intervention periods. The IBS severity score system (IBSSS) and IBS‐specific QoL questionnaires were used at the baseline and postintervention.Key ResultsOver the 6‐month intervention period, a significantly greater improvement in IBS symptoms such as abdominal pain and distention, flatulence, rumbling, and overall gastrointestinal (GI) symptoms (except dissatisfaction with bowel habits) was observed in the patients receiving vitamin D as compared to the placebo group. The IBSSS and the IBS‐QoL scores in the vitamin D group significantly improved compared to the placebo group postintervention (mean IBSSS score change: −53.82 ± 23.3 vs −16.85 ± 25.01, p < 0.001, respectively; mean IBS‐QoL score change: 14.26 ± 3 vs 11 ± 2.34, p < 0.001, respectively).Conclusions & InferencesVitamin D seems to be an effective and safe option to improve QoL and symptoms of IBS. ClinicalTrials.gov (NCT02579902).
In situ embryo rescue for generation of wide intra‐ and interspecific hybrids of Panicum virgatum L.
Authors: Kausch Albert P. , Tilelli Michael , Hague Joel , Heffelfinger Christopher , Cunha David , Moreno Maria , Dellaporta Stephen L. , Nelson Kimberly 
Published: May 2016

SummaryWide crosses have been used for decades as a method for transferring novel genetic material and traits in plant breeding. Historically, many products of wide crosses require tedious and inefficient surgical embryo rescue prior to embryo abortion to recover single plantlets. We have utilized transgenic switchgrass (Panicum virgatum L. cv Alamo) as a pollen donor in conjunction with antibiotic or herbicide selection for recovery of intra‐and interspecific F1 crosses by using developing ovules from the female parent and selecting for embryogenic cultures derived from the in situ immature embryo. Using this approach, several intravarietial crosses were generated between transgenic Alamo and the switchgrass varieties Kanlow, Blackwell and Cave‐in‐Rock as well as an interspecific cross with Atlantic coastal panicgrass. This procedure selected F1 embryogenic callus produced from the developing embryo contained within isolated immature ovules. Several clonal plants were successfully regenerated from each cross. Southern blot, PCR, phenotypic analyses and genomic analysis confirmed F1 hybrids. Using genotyping‐by‐sequencing shows the hybridization of the recovered plants by determining the ratio of transgressive markers to total compared markers between parents and their potential offspring. The ratio of transgressive markers to total compared markers was significantly lower between parents and their predicted offspring than between parents and offspring unrelated to them. This approach provides the possibility to move useful transgenes into varieties that are recalcitrant to direct transformation which can be optionally segregated thus useful to create new hybrids, as well as recovery of wide crosses that are either difficult or impossible using traditional techniques.
Identification and molecular characterization of the nicotianamine synthase gene family in bread wheat
Authors: Bonneau Julien , Baumann Ute , Beasley Jesse , Li Yuan , Johnson Alexander A. T. 
Published: May 2016

SummaryNicotianamine (NA) is a non‐protein amino acid involved in fundamental aspects of metal uptake, transport and homeostasis in all plants and constitutes the biosynthetic precursor of mugineic acid family phytosiderophores (MAs) in graminaceous plant species. Nicotianamine synthase (NAS) genes, which encode enzymes that synthesize NA from S‐adenosyl‐L‐methionine (SAM), are differentially regulated by iron (Fe) status in most plant species and plant genomes have been found to contain anywhere from 1 to 9 NAS genes. This study describes the identification of 21 NAS genes in the hexaploid bread wheat (Triticum aestivum L.) genome and their phylogenetic classification into two distinct clades. The TaNAS genes are highly expressed during germination, seedling growth and reproductive development. Fourteen of the clade I NAS genes were up‐regulated in root tissues under conditions of Fe deficiency. Protein sequence analyses revealed the presence of endocytosis motifs in all of the wheat NAS proteins as well as chloroplast, mitochondrial and secretory transit peptide signals in four proteins. These results greatly expand our knowledge of NAS gene families in graminaceous plant species as well as the genetics underlying Fe nutrition in bread wheat.
Differential expression of microRNAs and potential targets under drought stress in barley
Authors: Ferdous Jannatul , Sanchez‐Ferrero Juan Carlos , Langridge Peter , Milne Linda , Chowdhury Jamil , Brien Chris , Tricker Penny J. 
Published: May 2016

AbstractDrought is a crucial environmental constraint limiting crop production in many parts of the world. microRNA (miRNA) based gene regulation has been shown to act in several pathways, including crop response to drought stress. Sequence based profiling and computational analysis have revealed hundreds of miRNAs and their potential targets in different plant species under various stress conditions, but few have been biologically verified. In this study, 11 candidate miRNAs were tested for their expression profiles in barley. Differences in accumulation of only four miRNAs (Ath‐miR169b, Osa‐miR1432, Hv‐miRx5 and Hv‐miR166b/c) were observed between drought‐treated and well‐watered barley in four genotypes. miRNA targets were predicted using degradome analysis of two, different genotypes, and genotype‐specific target cleavage was observed. Inverse correlation of mature miRNA accumulation with miRNA target transcripts was also genotype dependent under drought treatment. Drought‐responsive miRNAs accumulated predominantly in mesophyll tissues. Our results demonstrate genotype‐specific miRNA regulation under drought stress and evidence for their role in mediating expression of target genes for abiotic stress response in barley.
A mutation in the Cdon gene potentiates congenital nevus development mediated by NRASQ61K
Authors: Chitsazan Arash , Ferguson Blake , Ram Ramesh , Mukhopadhyay Pamela , Handoko Herlina Y. , Gabrielli Brian , Soyer Peter H , Morahan Grant , Walker Graeme J. 
Published: May 2016

SummaryCongenital nevi develop before birth and sometimes cover large areas of the body. They are presumed to arise from the acquisition of a gene mutation in an embryonic melanocyte that becomes trapped in the dermis during development. Mice bearing the Cdk4R24C::Tyr‐NRASQ61K transgenes develop congenital nevus‐like lesions by post‐natal day 10, from melanocytes escaping the confines of hair follicles. We interbred these mice with the collaborative cross (CC), a resource that enables identification of modifier genes for complex diseases (those where multiple genes are involved). We examined variation in nevus cell density in 66 CC strains and mapped a large‐effect quantitative trait locus (QTL) controlling nevus cell density to murine chromosome 9. The best candidate for a gene that exacerbates congenital nevus development in the context of an NRAS mutation is Cdon, a positive regulator of sonic hedgehog (Shh) that is expressed mainly in keratinocytes.
Culturing Synechocystis sp. Strain PCC 6803 with N
2
and CO
2
in a Diel Regime Reveals Multiphase Glycogen Dynamics with Low Maintenance Costs
Authors: Angermayr S. Andreas , van Alphen Pascal , Hasdemir Dicle , Kramer Gertjan , Iqbal Muzamal , van Grondelle Wilmar , Hoefsloot Huub C. , Choi Young Hae , Hellingwerf Klaas J. 
Published: May 2016

ABSTRACT

Investigating the physiology of cyanobacteria cultured under a diel light regime is relevant for a better understanding of the resulting growth characteristics and for specific biotechnological applications that are foreseen for these photosynthetic organisms. Here, we present the results of a multiomics study of the model cyanobacterium
Synechocystis
sp. strain PCC 6803, cultured in a lab-scale photobioreactor in physiological conditions relevant for large-scale culturing. The culture was sparged with N
2
and CO
2
, leading to an anoxic environment during the dark period. Growth followed the availability of light. Metabolite analysis performed with
1
H nuclear magnetic resonance analysis showed that amino acids involved in nitrogen and sulfur assimilation showed elevated levels in the light. Most protein levels, analyzed through mass spectrometry, remained rather stable. However, several high-light-response proteins and stress-response proteins showed distinct changes at the onset of the light period. Microarray-based transcript analysis found common patterns of ∼56% of the transcriptome following the diel regime. These oscillating transcripts could be grouped coarsely into genes that were upregulated and downregulated in the dark period. The accumulated glycogen was degraded in the anaerobic environment in the dark. A small part was degraded gradually, reflecting basic maintenance requirements of the cells in darkness. Surprisingly, the largest part was degraded rapidly in a short time span at the end of the dark period. This degradation could allow rapid formation of metabolic intermediates at the end of the dark period, preparing the cells for the resumption of growth at the start of the light period.

IMPORTANCE
Industrial-scale biotechnological applications are anticipated for cyanobacteria. We simulated large-scale high-cell-density culturing of
Synechocystis
sp. PCC 6803 under a diel light regime in a lab-scale photobioreactor. In BG-11 medium,
Synechocystis
grew only in the light. Metabolite analysis grouped the collected samples according to the light and dark conditions. Proteome analysis suggested that the majority of enzyme-activity regulation was not hierarchical but rather occurred through enzyme activity regulation. An abrupt light-on condition induced high-light-stress proteins. Transcript analysis showed distinct patterns for the light and dark periods. Glycogen gradually accumulated in the light and was rapidly consumed in the last quarter of the dark period. This suggests that the circadian clock primed the cellular machinery for immediate resumption of growth in the light.
Comparative Analysis of the Antimicrobial Activities of Plant Defensin-Like and Ultrashort Peptides against Food-Spoiling Bacteria
Authors: Kraszewska Joanna , Beckett Michael C. , James Tharappel C. , Bond Ursula 
Published: May 2016

ABSTRACT

Antimicrobial peptides offer potential as novel therapeutics to combat food spoilage and poisoning caused by pathogenic and nonpathogenic bacteria. Our previous studies identified the peptide human beta-defensin 3 (HBD3) as a potent antimicrobial agent against a wide range of beer-spoiling bacteria. Thus, HBD3 is an excellent candidate for development as an additive to prevent food and beverage spoilage. To expand the repertoire of peptides with antimicrobial activity against bacteria associated with food spoilage and/or food poisoning, we carried out an
in silico
discovery pipeline to identify peptides with structure and activity similar to those of HBD3, focusing on peptides of plant origin. Using a standardized assay, we compared the antimicrobial activities of nine defensin-like plant peptides to the activity of HBD3. Only two of the peptides, fabatin-2 and Cp-thionin-2, displayed antimicrobial activity; however, the peptides differed from HBD3 in being sensitive to salt and were thermostable. We also compared the activities of several ultrashort peptides to that of HBD3. One of the peptides, the synthetic tetrapeptide O3TR, displayed biphasic antimicrobial activity but had a narrower host range than HBD3. Finally, to determine if the peptides might act in concert to improve antimicrobial activity, we compared the activities of the peptides in pairwise combinations. The plant defensin-like peptides fabatin-2 and Cp-thionin-2 displayed a synergistic effect with HBD3, while O3TR was antagonistic. Thus, some plant defensin-like peptides are effective antimicrobials and may act in concert with HBD3 to control bacteria associated with food spoilage and food poisoning.

IMPORTANCE
Food spoilage and food poisoning caused by bacteria can have major health and economic implications for human society. With the rise in resistance to conventional antibiotics, there is a need to identify new antimicrobials to combat these outbreaks in our food supply. Here we screened plant peptide databases to identify peptides that share structural similarity with the human defensin peptide HBD3, which has known antimicrobial activity against food-spoiling bacteria. We show that two of the plant peptides display antimicrobial activity against bacteria associated with food spoilage. When combined with HBD3, the peptides are highly effective. We also analyzed the activity of an easily made ultrashort synthetic peptide, O3TR. We show that this small peptide also displays antimicrobial activity against food-spoiling bacteria but is not as effective as HBD3 or the plant peptides. The plant peptides identified are good candidates for development as natural additives to prevent food spoilage.
The Cooperative and Interdependent Roles of GerA, GerK, and Ynd in Germination of Bacillus licheniformis Spores
Authors: Borch-Pedersen Kristina , Lindbäck Toril , Madslien Elisabeth H. , Kidd Shani W. , O'Sullivan Kristin , Granum Per Einar , Aspholm Marina 
Published: May 2016

ABSTRACT

When nutrients are scarce,
Bacillus
species form metabolically dormant and extremely resistant spores that enable survival over long periods of time under conditions not permitting growth. The presence of specific nutrients triggers spore germination through interaction with germinant receptors located in the spore's inner membrane.
Bacillus licheniformis
is a biotechnologically important species, but it is also associated with food spoilage and food-borne disease. The
B. licheniformis
ATCC 14580/DSM13 genome exhibits three
gerA
family operons (
gerA
,
gerK
, and
ynd
) encoding germinant receptors. We show that spores of
B. licheniformis
germinate efficiently in response to a range of different single
l
-amino acid germinants, in addition to a weak germination response seen with
d
-glucose. Mutational analyses revealed that the GerA and Ynd germination receptors function cooperatively in triggering an efficient germination response with single
l
-amino acid germinants, whereas the GerK germination receptor is essential for germination with
d
-glucose. Mutant spores expressing only GerA and GerK or only Ynd and GerK show reduced or severely impaired germination responses, respectively, with single
l
-amino acid germinants. Neither GerA nor Ynd could function alone in stimulating spore germination. Together, these results functionally characterize the germination receptor operons present in
B. licheniformis
. We demonstrate the overlapping germinant recognition patterns of the GerA and Ynd germination receptors and the cooperative functionalities between GerA, Ynd, and GerK in inducing germination.

IMPORTANCE
To ensure safe food production and durable foods, there is an obvious need for more knowledge on spore-forming bacteria. It is the process of spore germination that ultimately leads to food spoilage and food poisoning.
Bacillus licheniformis
is a biotechnologically important species that is also associated with food spoilage and food-borne disease. Despite its importance, the mechanisms of spore germination are poorly characterized in this species. This study provides novel knowledge on germination of
B. licheniformis
spores. We characterize the germinant recognition profiles of the three germinant receptors present in
B. licheniformis
spores and demonstrate that the GerA germinant receptor cooperates with the Ynd and GerK germinant receptors to enable an effective germination response to
l
-amino acids. We also demonstrate that GerK is required for germination in response to the single germinant glucose. This study demonstrates the complex interactions between germinant receptors necessary for efficient germination of
B. licheniformis
spores.