bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tree carbon allocation dynamics determined using a carbon mass balance approach
Authors: Klein Tamir , Hoch Günter 
Published: December 2014

Summary

Tree internal carbon (C) fluxes between compound and compartment pools are difficult to measure directly. Here we used a C mass balance approach to decipher these fluxes and provide a full description of tree C allocation dynamics.

We collected independent measurements of tree C sinks, source and pools in Pinus halepensis in a semi‐arid forest, and converted all fluxes to g C per tree d−1. Using this data set, a process flowchart was created to describe and quantify the tree C allocation on diurnal to annual time‐scales.

The annual C source of 24.5 kg C per tree yr−1 was balanced by C sinks of 23.5 kg C per tree yr−1, which partitioned into 70%, 17% and 13% between respiration, growth, and litter (plus export to soil), respectively. Large imbalances (up to 57 g C per tree d−1) were observed as C excess during the wet season, and as C deficit during the dry season. Concurrent changes in C reserves (starch) were sufficient to buffer these transient C imbalances.

The C pool dynamics calculated using the flowchart were in general agreement with the observed pool sizes, providing confidence regarding our estimations of the timing, magnitude, and direction of the internal C fluxes.
Ecological mechanisms for the coevolution of mating systems and defence
Authors: Campbell Stuart A. 
Published: December 2014

SummaryThe diversity of flowering plants is evident in two seemingly unrelated aspects of life history: sexual reproduction, exemplified by the stunning variation in flower form and function, and defence, often in the form of an impressive arsenal of secondary chemistry. Researchers are beginning to appreciate that plant defence and reproduction do not evolve independently, but, instead, may have reciprocal and interactive (coevolutionary) effects on each other. Understanding the mechanisms for mating–defence interactions promises to broaden our understanding of how ecological processes can generate these two rich sources of angiosperm diversity. Here, I review current research on the role of herbivory as a driver of mating system evolution, and the role of mating systems in the evolution of defence strategies. I outline different ecological mechanisms and processes that could generate these coevolutionary patterns, and summarize theoretical and empirical support for each. I provide a conceptual framework for linking plant defence with mating system theory to better integrate these two research fields.
Social cognitive theory and physical activity: a systematic review and meta‐analysis
Authors: Young M. D. , Plotnikoff R. C. , Collins C. E. , Callister R. , Morgan P. J. 
Published: November 2014

SummaryThis review investigated three research questions (i) What is the utility of social cognitive theory (SCT) to explain physical activity (PA)?; (ii) Is the effectiveness of SCT moderated by sample or methodological characteristics? and (iii) What is the frequency of significant associations between the core SCT constructs and PA? Ten electronic databases were searched with no date or sample restrictions. Forty‐four studies were retrieved containing 55 SCT models of PA. Methodological quality was assessed using a standardized tool. A random‐effects meta‐analysis revealed that SCT accounted for 31% of the variance in PA. However, methodological quality was mostly poor for these models. Methodological quality and sample age moderated the PA effect size, with increases in both associated with greater variance explained. Although self‐efficacy and goals were consistently associated with PA, outcome expectations and socio‐structural factors were not. This review determined that SCT is a useful framework to explain PA behaviour. Higher quality models explained more PA variance, but overall methodological quality was poor. As such, high‐quality studies examining the utility of SCT to explain PA are warranted.
The first wheezing episode: respiratory virus etiology, atopic characteristics, and illness severity
Authors: Turunen Riitta , Koistinen Annamari , Vuorinen Tytti , Arku Benedict , Söderlund‐Venermo Maria , Ruuskanen Olli , Jartti Tuomas 
Published: December 2014

AbstractBackgroundSusceptibility to early rhinovirus‐induced wheezing has been recognized as an important risk factor for childhood asthma, but data on the first wheezing episode are limited. The aim of this selected population study was to investigate virus etiology, atopic characteristics, and illness severity, as well as their interrelation, among first‐time wheezing children.MethodsWe studied 111 first‐time wheezing children aged between 3 and 23 months (88/23 in‐/outpatients). The investigated factors included atopy, food, perennial and aeroallergen sensitization, eczema, atopic eczema, elevated blood eosinophil count, and parental allergic rhinitis, asthma, and smoking. Nasopharyngeal aspirates were analyzed for adenovirus, coronaviruses, enteroviruses, bocavirus‐1 (also serologically confirmed), influenza viruses, metapneumovirus, parainfluenza viruses, rhinovirus, and respiratory syncytial virus using PCR methods.ResultsThe mean age of the study patients was 12 months (standard deviation 6.0). Atopic characteristics could be found in 56%, atopic eczema in 16%, and sensitization in 23% of the cases. In all samples (100%), ≥1 viruses were detected as follows: rhinovirus (76%), respiratory syncytial virus (29%), bocavirus (18%, acute infections), and other viruses <10% each. Virus coinfections occurred in 38% of the children. Rhinovirus infection was positively associated with age, blood eosinophil count, eczema, and duration of cough, as well as parental allergic rhinitis and smoking but negatively associated with virus coinfection (all p < 0.05).ConclusionsA respiratory virus infection can be detected in all first‐time wheezing children. Rhinovirus dominated the findings and was linked to atopic characteristics, prolonged cough, and parental smoking.
Phenotypic and marker‐assisted pyramiding of genes for resistance to zucchini yellow mosaic virus in oilseed pumpkin (Cucurbita pepo)
Authors: Pachner Martin , Paris Harry S. , Winkler Johanna , Lelley Tamas 
Published: December 2014

AbstractWe report on the identification of phenotypic and molecular markers for genes introgressed into oilseed pumpkin Cucurbita pepo from C. moschata germplasm originating in Nigeria, Portugal and Puerto Rico, which provide resistance against zucchini yellow mosaic virus (ZYMV) and on pyramiding these genes for improved and long‐lasting field protection of oilseed pumpkins. One SCAR and two SSR markers have been found for three dominant resistance genes, Zym‐0, Zym‐1 and Zym‐2. Characteristic reactions to ZYMV inoculation of plants carrying the recessive genes for resistance zym‐4* and zym‐6 have been defined. Described are procedures and results of pyramiding various combinations of these genes in oilseed pumpkin using the three markers and the specific phenotypic reactions to infection of some of these genes. The putative combination of all six resistance genes in one genotype resulted in a resistance that appeared to be at least as strong as or even stronger than that of the resistance source germplasm in C. moschata.
Retrospective study of the prevalence of keratoconjunctivitis sicca in diabetic and nondiabetic dogs after phacoemulsification
Authors: Gemensky‐Metzler Anne J. , Sheahan Jennifer E. , Rajala‐Schultz Paivi J. , Wilkie David A. , Harrington Jay 
Published: November 2014

AbstractObjectiveTo evaluate the prevalence of keratoconjunctivitis sicca (KCS) in diabetic and nondiabetic dogs following phacoemulsification.ProceduresMedical records were reviewed for signalment, body weight, diabetes status, andSTTat the preoperative and all postoperative examinations. A clinical diagnosis ofKCSwas defined as aSTT<15 mm/min with compatible clinical signs. Schirmer tear test values and the prevalence ofKCSbased onSTT<15 mm/min were evaluated at 2–4, 5–8, 9–14, 15–20, and 41–52 weeks postoperatively. Size of dog (large, >10 kg; small, ≤10 kg) andSTTranges (<15 mm/min, 15–22 mm/min and >22 mm/min) were categorized for analysis of effect of body weight andSTTon prevalence ofKCS.ResultsOne hundred and seventeen nondiabetic (198 eyes) and 118 diabetic dogs (228 eyes) were evaluated.KCSwas diagnosed in nearly twice as many diabetics as nondiabetics (27.4% vs. 15.4%) within 2 weeks postoperatively (P = 0.0088). Percentage of eyes withKCSamong all dogs decreased over time and did not differ significantly after the first postoperative visit. Diabetic small dogs were 1.7 times more likely to haveKCSthan nondiabetic small dogs (P = 0.0052). PreoperativeSTTwas significantly associated with likelihood of postoperativeKCSamong large (P < 0.0001), but not small dogs (P = 0.0781). Among large dogs, eyes withSTTs between 15 and 22 mm/min were approximately 3 times more likely to be diagnosed withKCSafter surgery than those withSTT>22 mm/min.ConclusionThe greatest risk forKCSfor all dogs is during the first 2 weeks postoperatively. Populations at greatest risk for postoperativeKCSare small dogs, small diabetic dogs, and large dogs with preoperativeSTT≤22.
Epitranscriptional regulation of cardiovascular development and disease
Authors: Dorn Gerald W. , Matkovich Scot J. 
Published: November 2014

AbstractDevelopment, homeostasis and responses to stress in the heart all depend on appropriate control of mRNA expression programmes, which may be enacted at the level of DNA sequence, DNA accessibility and RNA‐mediated control of mRNA output. Diverse mechanisms underlie promoter‐driven transcription of coding mRNAs and their translation into protein, and the ways in which sequence alteration of DNA can make an impact on these processes have been studied for some time. The field of epigenetics explores changes in DNA structure that influence its accessibility by transcriptional machinery, and we are continuing to develop our understanding of how these processes modify cardiac RNA production. In this topical review, we do not focus on how DNA sequence and methylation, and histone interactions, may alter its accessibility, but rather on newly described mechanisms by which some transcribed RNAs may alter initial transcription or downstream processing of other RNAs, involving both short non‐coding RNAs (microRNAs) and long non‐coding RNAs (lncRNAs). Here we present examples of how these two classes of non‐coding RNAs mediate widespread effects on cardiac transcription and protein output in processes for which we use the broad term ‘epitranscriptional regulation’ and that are complementary to the DNA methylation and histone modification events studied by classical epigenetics.
Molecular Mechanisms of Fluconazole Resistance in Candida parapsilosis Isolates from a U.S. Surveillance System
Authors: Grossman Nina T. , Pham Cau D. , Cleveland Angela A. , Lockhart Shawn R. 
Published: December 2014

ABSTRACT

Candida parapsilosis
is the second or third most common cause of candidemia in many countries. The Infectious Diseases Society of America recommends fluconazole as the primary therapy for
C. parapsilosis
candidemia. Although the rate of fluconazole resistance among
C. parapsilosis
isolates is low in most U.S. institutions, the resistance rate can be as high as 7.5%. This study was designed to assess the mechanisms of fluconazole resistance in 706 incident bloodstream isolates from U.S. hospitals. We sequenced the
ERG11
and
MRR1
genes of 122
C. parapsilosis
isolates with resistant (30 isolates; 4.2%), susceptible dose-dependent (37 isolates; 5.2%), and susceptible (55 isolates) fluconazole MIC values and used real-time PCR of RNA from 17 isolates to investigate the regulation of
MDR1
. By comparing these isolates to fully fluconazole-susceptible isolates, we detected at least two mechanisms of fluconazole resistance: an amino acid substitution in the 14-α-demethylase gene
ERG11
and overexpression of the efflux pump
MDR1
, possibly due to point mutations in the
MRR1
transcription factor that regulates
MDR1
. The
ERG11
single nucleotide polymorphism (SNP) was found in 57% of the fluconazole-resistant isolates and in no susceptible isolates. The
MRR1
SNPs were more difficult to characterize, as not all resulted in overexpression of
MDR1
and not all
MDR1
overexpression was associated with an SNP in
MRR1
. Further work to characterize the
MRR1
SNPs and search for overexpression of other efflux pumps is needed.
Burkholderia cepacia Complex Phage-Antibiotic Synergy (PAS): Antibiotics Stimulate Lytic Phage Activity
Authors: Kamal Fatima , Dennis Jonathan J. 
Published: December 2014

ABSTRACT

The
Burkholderia cepacia
complex (Bcc) is a group of at least 18 species of Gram-negative opportunistic pathogens that can cause chronic lung infection in cystic fibrosis (CF) patients. Bcc organisms possess high levels of innate antimicrobial resistance, and alternative therapeutic strategies are urgently needed. One proposed alternative treatment is phage therapy, the therapeutic application of bacterial viruses (or bacteriophages). Recently, some phages have been observed to form larger plaques in the presence of sublethal concentrations of certain antibiotics; this effect has been termed phage-antibiotic synergy (PAS). Those reports suggest that some antibiotics stimulate increased production of phages under certain conditions. The aim of this study is to examine PAS in phages that infect
Burkholderia cenocepacia
strains C6433 and K56-2. Bcc phages KS12 and KS14 were tested for PAS, using 6 antibiotics representing 4 different drug classes. Of the antibiotics tested, the most pronounced effects were observed for meropenem, ciprofloxacin, and tetracycline. When grown with subinhibitory concentrations of these three antibiotics, cells developed a chain-like arrangement, an elongated morphology, and a clustered arrangement, respectively. When treated with progressively higher antibiotic concentrations, both the sizes of plaques and phage titers increased, up to a maximum.
B. cenocepacia
K56-2-infected
Galleria mellonella
larvae treated with phage KS12 and low-dose meropenem demonstrated increased survival over controls treated with KS12 or antibiotic alone. These results suggest that antibiotics can be combined with phages to stimulate increased phage production and/or activity and thus improve the efficacy of bacterial killing.
Passage of Wolbachia pipientis through Mutant Drosophila melanogaster Induces Phenotypic and Genomic Changes
Authors: Newton Irene L. G. , Sheehan Kathy B. 
Published: December 2014

ABSTRACT

Wolbachia pipientis
is a nearly ubiquitous, maternally transmitted bacterium that infects the germ line of insect hosts. Estimates are that
Wolbachia
infects 40 to 60% of insect species on the planet, making it one of the most prevalent infections on Earth. However, we know surprisingly little about the molecular mechanisms used by
Wolbachia
to infect its hosts. We passaged
Wolbachia
through normally restrictive
Drosophila melanogaster
hosts, bottlenecking
Wolbachia
through stochastic segregation while simultaneously selecting for mutants that could recolonize these previously restrictive hosts. Here, we show that
Wolbachia
alters its behavior when passaged through heterozygous mutant flies. After only three generations,
Wolbachia
was able to colonize the previously restrictive hosts at control titers. Additionally, the
Wolbachia
organisms passaged through heterozygous mutant
D. melanogaster
alter their pattern of tissue-specific Wsp protein production, suggesting a behavioral response to the host genotype. Using whole-genome resequencing, we identified the mutations accumulated by these lineages of
Wolbachia
and confirmed the existence and persistence of the mutations through clone library Sanger sequencing. Our results suggest that
Wolbachia
can quickly adapt to new host contexts, with genomic mutants arising after only two generations.
Use of an Endogenous Plasmid Locus for Stable in
trans
Complementation in Borrelia burgdorferi
Authors: Kasumba Irene N. , Bestor Aaron , Tilly Kit , Rosa Patricia A. 
Published: December 2014

ABSTRACT

Targeted mutagenesis and complementation are important tools for studying genes of unknown function in the Lyme disease spirochete
Borrelia burgdorferi
. A standard method of complementation is reintroduction of a wild-type copy of the targeted gene on a shuttle vector. However, shuttle vectors are present at higher copy numbers than
B. burgdorferi
plasmids and are potentially unstable in the absence of selection, thereby complicating analyses in the mouse-tick infectious cycle.
B. burgdorferi
has over 20 plasmids, with some, such as linear plasmid 25 (lp25), carrying genes required by the spirochete
in vivo
but relatively unstable during
in vitro
cultivation. We propose that complementation on an endogenous plasmid such as lp25 would overcome the copy number and
in vivo
stability issues of shuttle vectors. In addition, insertion of a selectable marker on lp25 could ensure its stable maintenance by spirochetes in culture. Here, we describe the construction of a multipurpose allelic-exchange vector containing a multiple-cloning site and either of two selectable markers. This suicide vector directs insertion of the complementing gene into the
bbe02
locus, a site on lp25 that was previously shown to be nonessential during both
in vitro
and
in vivo
growth. We demonstrate the functional utility of this strategy by restoring infectivity to an
ospC
mutant through complementation at this site on lp25 and stable maintenance of the
ospC
gene throughout mouse infection. We conclude that this represents a convenient and widely applicable method for stable gene complementation in
B. burgdorferi
.
Draft Genome Sequences of Eight Enterohepatic
Helicobacter
Species Isolated from Both Laboratory and Wild Rodents
Authors: Sheh Alexander , Shen Zeli , Fox James G. 
Published: November 2014

ABSTRACT

The draft genome sequences of eight enterohepatic
Helicobacter
species,
H. muridarum, H. trogontum, H. typhlonius
, and five unnamed helicobacters, are presented here. Using laboratory mice pervasively infected with helicobacters, we characterized the presence of known virulence factors.
Draft Genome Sequence of Fish Pathogenic Vibrio vulnificus Biotype 2
Authors: Koton Yael , Eghbaria Saleh , Gordon Michal , Chalifa-Caspi Vered , Bisharat Naiel 
Published: November 2014

ABSTRACT

Vibrio vulnificus
is a marine pathogen capable of causing severe soft tissue infections and septicemia in humans.
V. vulnificus
biotype 2 is the etiological agent of fish vibriosis. We describe here the first draft genome sequence of
V. vulnificus
biotype 2, strain ES-7601, isolated from an infected eel in Japan.
Complete Genome Sequence of
Francisella endociliophora
Strain FSC1006, Isolated from a Laboratory Culture of the Marine Ciliate
Euplotes raikovi
Authors: Sjödin Andreas , Öhrman Caroline , Bäckman Stina , Lärkeryd Adrian , Granberg Malin , Lundmark Eva , Karlsson Edvin , Nilsson Elin , Vallesi Adriana , Tellgren-Roth Christian , Stenberg Per , Thelaus Johanna 
Published: November 2014

ABSTRACT

A strain of
Francisella endociliophora
was isolated from a laboratory culture of the marine ciliate
Euplotes raikovi
. Here, we report the complete genome sequence of the bacterial strain FSC1006 (
Francisella
Strain Collection, Swedish Defence Research Agency, Umeå, Sweden).
Draft Genome Sequence of
Chryseobacterium
sp. Strain P1-3, a Keratinolytic Bacterium Isolated from Poultry Waste
Authors: Park Gun-Seok , Hong Sung-Jun , Lee Chang-Hyun , Khan Abdur Rahim , Ullah Ihsan , Jung Byung Kwon , Choi JungBae , Kwak Yunyoung , Back Chang-Gi , Jung Hee-Young , Shin Jae-Ho 
Published: November 2014

ABSTRACT

Chryseobacterium
sp. strain P1-3, harboring keratin degrading activity, has recently been isolated from poultry waste. Here, we report the 4.6-Mbp draft genome sequence of the keratinolytic bacterium with a G+C content of 37.0% and 4,087 protein-coding genes.
Characteristics of Emerging Human-Pathogenic Escherichia coli O26:H11 Strains Isolated in France between 2010 and 2013 and Carrying the
stx
2d
Gene Only
Authors: Delannoy Sabine , Mariani-Kurkdjian Patricia , Bonacorsi Stephane , Liguori Sandrine , Fach Patrick 
Published: November 2014

ABSTRACT

Strains of
Escherichia coli
O26:H11 that were positive for
stx
2
alone (
n
= 23), which were not epidemiologically related or part of an outbreak, were isolated from pediatric patients in France between 2010 and 2013. We were interested in comparing these strains with the new highly virulent
stx
2a
-positive
E. coli
O26 clone sequence type 29 (ST29) that has emerged recently in Europe, and we tested them by multilocus sequence typing (MLST),
stx
2
subtyping, clustered regularly interspaced short palindromic repeat (CRISPR) sequencing, and plasmid (
ehxA
,
katP
,
espP
, and
etpD
) and chromosomal (Z2098,
espK
, and
espV
) virulence gene profiling. We showed that 16 of the 23 strains appeared to correspond to this new clone, but the characteristics of 12 strains differed significantly from the previously described characteristics, with negative results for both plasmid and chromosomal genetic markers. These 12 strains exhibited a ST29 genotype and related CRISPR arrays (CRISPR2a alleles 67 or 71), suggesting that they evolved in a common environment. This finding was corroborated by the presence of
stx
2d
in 7 of the 12 ST29 strains. This is the first time that
E. coli
O26:H11 carrying
stx
2d
has been isolated from humans. This is additional evidence of the continuing evolution of virulent Shiga toxin-producing
E. coli
(STEC) O26 strains. A new O26:H11 CRISPR PCR assay, SP_O26_E, has been developed for detection of these 12 particular ST29 strains of
E. coli
O26:H11. This test is useful to better characterize the
stx
2
-positive O26:H11 clinical isolates, which are associated with severe clinical outcomes such as bloody diarrhea and hemolytic uremic syndrome.
Leukodepletion as a Point-of-Care Method for Monitoring HIV-1 Viral Load in Whole Blood
Authors: Titchmarsh Logan , Zeh Clement , Verpoort Thierry , Allain Jean-Pierre , Lee Helen 
Published: November 2014

ABSTRACT
In order to limit the interference of HIV-1 cellular nucleic acids in estimating viral load (VL), the feasibility of leukodepletion of a small whole-blood (WB) volume to eliminate only leukocyte cell content was investigated, using a selection of filters. The efficacy of leukocyte filtration was evaluated by counting, CD45 quantitative PCR, and HIV-1 DNA quantification. Plasma HIV-1 was tested by real-time reverse transcription (RT)-PCR. A specific, miniaturized filter was developed and tested for leukocyte and plasma virus retention, WB sample dilution, and filtration parameters in HIV-1-spiked WB samples. This device proved effective to retain >99.9% of white blood cells in 100 μl of WB without affecting plasma VL. The Samba sample preparation chemistry was adapted to use a leukodepleted WB sample for VL monitoring using the point-of-care Samba-1 semiautomated system. The clinical performance of the assay was evaluated by testing 207 consecutive venous EDTA WB samples from HIV-1-infected patients attending a CD4 testing clinic. Most patients were on antiretroviral treatment (ART), but their VL status was unknown. Compared to the Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test, the new Samba assay had a concordance of 96.5%. The use of the Samba system with a VL test for WB might contribute to HIV-1 ART management and reduce loss-to-follow-up rates in resource-limited settings.