bluuebunny/crossref_metadata_2025 huggingface dataset:
Abiotic Stress Resistance, a Novel Moonlighting Function of Ribosomal Protein RPL44 in the Halophilic Fungus Aspergillus glaucus
Authors: Liu Xiao-Dan , Xie Lixia , Wei Yi , Zhou Xiaoyang , Jia Baolei , Liu Jinliang , Zhang Shihong
Published: May 2014

Ribosomal proteins are highly conserved components of basal cellular organelles, primarily involved in the translation of mRNA leading to protein synthesis. However, certain ribosomal proteins moonlight in the development and differentiation of organisms. In this study, the ribosomal protein L44 (RPL44), associated with salt resistance, was screened from the halophilic fungus
Aspergillus glaucus
(AgRPL44), and its activity was investigated in
Saccharomyces cerevisiae
and
Nicotiana tabacum
. Sequence alignment revealed that AgRPL44 is one of the proteins of the large ribosomal subunit 60S. Expression of
AgRPL44
was upregulated via treatment with salt, sorbitol, or heavy metals to demonstrate its response to osmotic stress. A homologous sequence from the model fungus
Magnaporthe oryzae
, MoRPL44, was cloned and compared with
AgRPL44
in a yeast expression system. The results indicated that yeast cells with overexpressed
AgRPL44
were more resistant to salt, drought, and heavy metals than were yeast cells expressing
MoRPL44
at a similar level of stress. When
AgRPL44
was introduced into
M. oryzae
, the transformants displayed obviously enhanced tolerance to salt and drought, indicating the potential value of
AgRPL44
for genetic applications. To verify the value of its application in plants, tobacco was transformed with
AgRPL44
, and the results were similar. Taken together, we conclude that
AgRPL44
supports abiotic stress resistance and may have value for genetic application.
Modeling the Infection Dynamics of Bacteriophages in Enteric Escherichia coli: Estimating the Contribution of Transduction to Antimicrobial Gene Spread
Authors: Volkova Victoriya V. , Lu Zhao , Besser Thomas , Gröhn Yrjö T.
Published: May 2014

Animal-associated bacterial communities are infected by bacteriophages, although the dynamics of these infections are poorly understood. Transduction by bacteriophages may contribute to transfer of antimicrobial resistance genes, but the relative importance of transduction among other gene transfer mechanisms is unknown. We therefore developed a candidate deterministic mathematical model of the infection dynamics of enteric coliphages in commensal
Escherichia coli
in the large intestine of cattle. We assumed the phages were associated with the intestine and were predominantly temperate. Model simulations demonstrated how, given the bacterial ecology and infection dynamics, most (>90%) commensal enteric
E. coli
bacteria may become lysogens of enteric coliphages during intestinal transit. Using the model and the most liberal assumptions about transduction efficiency and resistance gene frequency, we approximated the upper numerical limits (“worst-case scenario”) of gene transfer through specialized and generalized transduction in
E. coli
by enteric coliphages when the transduced genetic segment is picked at random. The estimates were consistent with a relatively small contribution of transduction to lateral gene spread; for example, generalized transduction delivered the chromosomal resistance gene to up to 8
E. coli
bacteria/hour within the population of 1.47 × 10
8
E. coli
bacteria/liter luminal contents. In comparison, the plasmidic
bla
CMY-2
gene carried by ∼2% of enteric
E. coli
was transferred by conjugation at a rate at least 1.4 × 10
3
times greater than our generalized transduction estimate. The estimated numbers of transductants varied nonlinearly depending on the ecology of bacteria available for phages to infect, that is, on the assumed rates of turnover and replication of enteric
E. coli
.
A Tailored
galK
Counterselection System for Efficient Markerless Gene Deletion and Chromosomal Tagging in Magnetospirillum gryphiswaldense
Authors: Raschdorf Oliver , Plitzko Jürgen M. , Schüler Dirk , Müller Frank D.
Published: May 2014

Magnetotactic bacteria have emerged as excellent model systems to study bacterial cell biology, biomineralization, vesicle formation, and protein targeting because of their ability to synthesize single-domain magnetite crystals within unique organelles (magnetosomes). However, only few species are amenable to genetic manipulation, and the limited methods for site-specific mutagenesis are tedious and time-consuming. Here, we report the adaptation and application of a fast and convenient technique for markerless chromosomal manipulation of
Magnetospirillum gryphiswaldense
using a single antibiotic resistance cassette and
galK
-based counterselection for marker recycling. We demonstrate the potential of this technique by genomic excision of the
phbCAB
operon, encoding enzymes for polyhydroxyalkanoate (PHA) synthesis, followed by chromosomal fusion of magnetosome-associated proteins to fluorescent proteins. Because of the absence of interfering PHA particles, these engineered strains are particularly suitable for microscopic analyses of cell biology and magnetosome biosynthesis.
Assessing Genetic Diversity among Brettanomyces Yeasts by DNA Fingerprinting and Whole-Genome Sequencing
Authors: Crauwels Sam , Zhu Bo , Steensels Jan , Busschaert Pieter , De Samblanx Gorik , Marchal Kathleen , Willems Kris A. , Verstrepen Kevin J. , Lievens Bart
Published: May 2014

Brettanomycesyeasts, with the speciesBrettanomyces(Dekkera)bruxellensisbeing the most important one, are generally reported to be spoilage yeasts in the beer and wine industry due to the production of phenolic off flavors. However,B. bruxellensisis also known to be a beneficial contributor in certain fermentation processes, such as the production of certain specialty beers. Nevertheless, despite its economic importance,Brettanomycesyeasts remain poorly understood at the genetic and genomic levels. In this study, the genetic relationship between more than 50Brettanomycesstrains from all presently known species and from several sources was studied using a combination of DNA fingerprinting techniques. This revealed an intriguing correlation between theB. bruxellensisfingerprints and the respective isolation source. To further explore this relationship, we sequenced a (beneficial) beer isolate ofB. bruxellensis(VIB X9085; ST05.12/22) and compared its genome sequence with the genome sequences of two wine spoilage strains (AWRI 1499 and CBS 2499). ST05.12/22 was found to be substantially different from both wine strains, especially at the level of single nucleotide polymorphisms (SNPs). In addition, there were major differences in the genome structures between the strains investigated, including the presence of large duplications and deletions. Gene content analysis revealed the presence of 20 genes which were present in both wine strains but absent in the beer strain, including many genes involved in carbon and nitrogen metabolism, and vice versa, no genes that were missing in both AWRI 1499 and CBS 2499 were found in ST05.12/22. Together, this study provides tools to discriminateBrettanomycesstrains and provides a first glimpse at the genetic diversity and genome plasticity ofB. bruxellensis.
Microbial Population Dynamics in the Hemolymph of Manduca sexta Infected with Xenorhabdus nematophila and the Entomopathogenic Nematode Steinernema carpocapsae
Authors: Singh Swati , Reese Jordan M. , Casanova-Torres Ángel M. , Goodrich-Blair Heidi , Forst Steven
Published: May 2014

Xenorhabdus nematophila
engages in a mutualistic association with the nematode
Steinernema carpocapsae
. The nematode invades and traverses the gut of susceptible insects.
X. nematophila
is released in the insect blood (hemolymph), where it suppresses host immune responses and functions as a pathogen.
X. nematophila
produces diverse antimicrobials in laboratory cultures. The natural competitors that
X. nematophila
encounters in the hemolymph and the role of antimicrobials in interspecies competition in the host are poorly understood. We show that gut microbes translocate into the hemolymph when the nematode penetrates the insect intestine. During natural infection,
Staphylococcus saprophyticus
was initially present and subsequently disappeared from the hemolymph, while
Enterococcus faecalis
proliferated.
S. saprophyticus
was sensitive to
X. nematophila
antibiotics and was eliminated from the hemolymph when coinjected with
X. nematophila
. In contrast,
E. faecalis
was relatively resistant to
X. nematophila
antibiotics. When injected by itself,
E. faecalis
persisted (∼10
3
CFU/ml), but when coinjected with
X. nematophila
, it proliferated to ∼10
9
CFU/ml. Injection of
E. faecalis
into the insect caused the upregulation of an insect antimicrobial peptide, while the transcript levels were suppressed when
E. faecalis
was coinjected with
X. nematophila
. Its relative antibiotic resistance together with suppression of the host immune system by
X. nematophila
may account for the growth of
E. faecalis
. At higher injected levels (10
6
CFU/insect),
E. faecalis
could kill insects, suggesting that it may contribute to virulence in an
X. nematophila
infection. These findings provide new insights into the competitive events that occur early in infection after
S. carpocapsae
invades the host hemocoel.
Physiological and Transcriptional Responses of Anaerobic Chemostat Cultures of Saccharomyces cerevisiae Subjected to Diurnal Temperature Cycles
Authors: Hebly Marit , de Ridder Dick , de Hulster Erik A. F. , de la Torre Cortes Pilar , Pronk Jack T. , Daran-Lapujade Pascale
Published: May 2014

Diurnal temperature cycling is an intrinsic characteristic of many exposed microbial ecosystems. However, its influence on yeast physiology and the yeast transcriptome has not been studied in detail. In this study, 24-h sinusoidal temperature cycles, oscillating between 12°C and 30°C, were imposed on anaerobic, glucose-limited chemostat cultures of
Saccharomyces cerevisiae
. After three diurnal temperature cycles (DTC), concentrations of glucose and extracellular metabolites as well as CO
2
production rates showed regular, reproducible circadian rhythms. DTC also led to waves of transcriptional activation and repression, which involved one-sixth of the yeast genome. A substantial fraction of these DTC-responsive genes appeared to respond primarily to changes in the glucose concentration. Elimination of known glucose-responsive genes revealed an overrepresentation of previously identified temperature-responsive genes as well as genes involved in the cell cycle and
de novo
purine biosynthesis. In-depth analysis demonstrated that DTC led to a partial synchronization of the cell cycle of the yeast populations in chemostat cultures, which was lost upon release from DTC. Comparison of DTC results with data from steady-state cultures showed that the 24-h DTC was sufficiently slow to allow
S. cerevisiae
chemostat cultures to acclimate their transcriptome and physiology at the DTC temperature maximum and to approach acclimation at the DTC temperature minimum. Furthermore, this comparison and literature data on growth rate-dependent cell cycle phase distribution indicated that cell cycle synchronization was most likely an effect of imposed fluctuations of the relative growth rate (μ/μ
max
) rather than a direct effect of temperature.
Discovery of Bovine Digital Dermatitis-Associated Treponema spp. in the Dairy Herd Environment by a Targeted Deep-Sequencing Approach
Authors: Klitgaard Kirstine , Nielsen Martin W. , Ingerslev Hans-Christian , Boye Mette , Jensen Tim K.
Published: May 2014

The bacteria associated with the infectious claw disease bovine digital dermatitis (DD) are spirochetes of the genus
Treponema
; however, their environmental reservoir remains unknown. To our knowledge, the current study is the first report of the discovery and phylogenetic characterization of rRNA gene sequences from DD-associated treponemes in the dairy herd environment. Although the spread of DD appears to be facilitated by wet floors covered with slurry, no DD-associated treponemes have been isolated from this environment previously. Consequently, there is a lack of knowledge about the spread of this disease among cows within a herd as well as between herds. To address the issue of DD infection reservoirs, we searched for evidence of DD-associated treponemes in fresh feces, in slurry, and in hoof lesions by deep sequencing of the V3 and V4 hypervariable regions of the 16S rRNA gene coupled with identification at the operational-taxonomic-unit level. Using treponeme-specific primers in this high-throughput approach, we identified small amounts of DNA (on average 0.6% of the total amount of sequence reads) from DD-associated treponemes in 43 of 64 samples from slurry and cow feces collected from six geographically dispersed dairy herds. Species belonging to the
Treponema denticola
/
Treponema pedis
-like and
Treponema phagedenis
-like phylogenetic clusters were among the most prevalent treponemes in both the dairy herd environment and the DD lesions. By the high-throughput approach presented here, we have demonstrated that cow feces and environmental slurry are possible reservoirs of DD-associated treponemes. This method should enable further clarification of the etiopathogenesis of DD.
Functional Heterologous Production of Reductive Dehalogenases from Desulfitobacterium hafniense Strains
Authors: Mac Nelly Anita , Kai Marco , Svatoš Aleš , Diekert Gabriele , Schubert Torsten
Published: May 2014

The anaerobic dehalogenation of organohalides is catalyzed by the reductive dehalogenase (RdhA) enzymes produced in phylogenetically diverse bacteria. These enzymes contain a cobamide cofactor at the active site and two iron-sulfur clusters. In this study, the tetrachloroethene (PCE) reductive dehalogenase (PceA) of the Gram-positive
Desulfitobacterium hafniense
strain Y51 was produced in a catalytically active form in the nondechlorinating, cobamide-producing bacterium
Shimwellia blattae
(ATCC 33430), a Gram-negative gammaproteobacterium. The formation of recombinant catalytically active PceA enzyme was significantly enhanced when its dedicated PceT chaperone was coproduced and when 5,6-dimethylbenzimidazole and hydroxocobalamin were added to the
S. blattae
cultures. The experiments were extended to
D. hafniense
DCB-2, a reductively dehalogenating bacterium harboring multiple
rdhA
genes. To elucidate the substrate spectrum of the
rdhA3
gene product of this organism, the recombinant enzyme was tested for the conversion of different dichlorophenols (DCP) in crude extracts of an RdhA3-producing
S. blattae
strain. 3,5-DCP, 2,3-DCP, and 2,4-DCP, but not 2,6-DCP and 3,4-DCP, were reductively dechlorinated by the recombinant RdhA3. In addition, this enzyme dechlorinated PCE to trichloroethene at low rates.
Starter Culture Selection for Making Chinese Sesame-Flavored Liquor Based on Microbial Metabolic Activity in Mixed-Culture Fermentation
Authors: Wu Qun , Ling Jie , Xu Yan
Published: May 2014

Selection of a starter culture with excellent viability and metabolic activity is important for inoculated fermentation of traditional food. To obtain a suitable starter culture for making Chinese sesame-flavored liquor, the yeast and bacterium community structures were investigated during spontaneous and solid-state fermentations of this type of liquor. Five dominant species in spontaneous fermentation were identified:Saccharomyces cerevisiae,Pichia membranaefaciens,Issatchenkia orientalis,Bacillus licheniformis, andBacillus amyloliquefaciens. The metabolic activity of each species in mixed and inoculated fermentations of liquor was investigated in 14 different cocultures that used different combinations of these species. The relationships between the microbial species and volatile metabolites were analyzed by partial least-squares (PLS) regression analysis. We found thatS. cerevisiaewas positively correlated to nonanal, andB. licheniformiswas positively associated with 2,3-butanediol, isobutyric acid, guaiacol, and 4-vinyl guaiacol, whileI. orientaliswas positively correlated to butyric acid, isovaleric acid, hexanoic acid, and 2,3-butanediol. These three species are excellent flavor producers for Chinese liquor. AlthoughP. membranaefaciensandB. amyloliquefacienswere not efficient flavor producers, the addition of them alleviated competition among the other three species and altered their growth rates and flavor production. As a result, the coculture of all five dominant species produced the largest amount of flavor compounds. The result indicates that flavor producers and microbial interaction regulators are important for inoculated fermentation of Chinese sesame-flavored liquor.
The Plasmid Complement of Lactococcus lactis UC509.9 Encodes Multiple Bacteriophage Resistance Systems
Authors: Ainsworth Stuart , Mahony Jennifer , van Sinderen Douwe
Published: May 2014

Lactococcus lactis
subsp.
cremoris
strains are used globally for the production of fermented dairy products, particularly hard cheeses. Believed to be of plant origin,
L. lactis
strains that are used as starter cultures have undergone extensive adaptation to the dairy environment, partially through the acquisition of extrachromosomal DNA in the form of plasmids that specify technologically important phenotypic traits. Here, we present a detailed analysis of the eight plasmids of
L. lactis
UC509.9, an Irish dairy starter strain. Key industrial phenotypes were mapped, and genes that are typically associated with lactococcal plasmids were identified. Four distinct, plasmid-borne bacteriophage resistance systems were identified, including two abortive infection systems, AbiB and AbiD1, thereby supporting the observed phage resistance of
L. lactis
UC509.9. AbiB escape mutants were generated for phage sk1, which were found to carry mutations in
orf6
, which encodes the major capsid protein of this phage.
Metabolism of Sialic Acid by Bifidobacterium breve UCC2003
Authors: Egan Muireann , O'Connell Motherway Mary , Ventura Marco , van Sinderen Douwe
Published: May 2014

Bifidobacteria constitute a specific group of commensal bacteria that inhabit the gastrointestinal tracts of humans and other mammals.
Bifidobacterium breve
UCC2003 has previously been shown to utilize several plant-derived carbohydrates that include cellodextrins, starch, and galactan. In the present study, we investigated the ability of this strain to utilize the mucin- and human milk oligosaccharide (HMO)-derived carbohydrate sialic acid. Using a combination of transcriptomic and functional genomic approaches, we identified a gene cluster dedicated to the uptake and metabolism of sialic acid. Furthermore, we demonstrate that
B. breve
UCC2003 can cross feed on sialic acid derived from the metabolism of 3′-sialyllactose, an abundant HMO, by another infant gut bifidobacterial strain,
Bifidobacterium bifidum
PRL2010.
Stress Induces Changes in the Phosphorylation of Trypanosoma cruzi RNA Polymerase II, Affecting Its Association with Chromatin and RNA Processing
Authors: Rocha Antônio Augusto , Moretti Nilmar Silvio , Schenkman Sergio
Published: May 2014

The phosphorylation of the carboxy-terminal heptapeptide repeats of the largest subunit of RNA polymerase II (Pol II) controls several transcription-related events in eukaryotes. Trypanosomatids lack these typical repeats and display an unusual transcription control. RNA Pol II associates with the transcription site of the spliced leader (SL) RNA, which is used in the
trans
-splicing of all mRNAs transcribed on long polycistronic units. We found that
Trypanosoma cruzi
RNA Pol II associated with chromatin is highly phosphorylated. When transcription is inhibited by actinomycin D, the enzyme runs off from SL genes, remaining hyperphosphorylated and associated with polycistronic transcription units. Upon heat shock, the enzyme is dephosphorylated and remains associated with the chromatin. Transcription is partially inhibited with the accumulation of housekeeping precursor mRNAs, except for heat shock genes. DNA damage caused dephosphorylation and transcription arrest, with RNA Pol II dissociating from chromatin although staying at the SL. In the presence of calyculin A, the hyperphosphorylated form detached from chromatin, including the SL loci. These results indicate that in trypanosomes, the unusual RNA Pol II is phosphorylated during the transcription of SL and polycistronic operons. Different types of stresses modify its phosphorylation state, affecting pre-RNA processing.
Literature-Based Gene Curation and Proposed Genetic Nomenclature for Cryptococcus
Authors: Inglis Diane O. , Skrzypek Marek S. , Liaw Edward , Moktali Venkatesh , Sherlock Gavin , Stajich Jason E.
Published: May 2014

Cryptococcus
, a major cause of disseminated infections in immunocompromised patients, kills over 600,000 people per year worldwide. Genes involved in the virulence of the meningitis-causing fungus are being characterized at an increasing rate, and to date, at least 648
Cryptococcus
gene names have been published. However, these data are scattered throughout the literature and are challenging to find. Furthermore, conflicts in locus identification exist, so that named genes have been subsequently published under new names or names associated with one locus have been used for another locus. To avoid these conflicts and to provide a central source of
Cryptococcus
gene information, we have collected all published
Cryptococcus
gene names from the scientific literature and associated them with standard
Cryptococcus
locus identifiers and have incorporated them into FungiDB (
www.fungidb.org
). FungiDB is a panfungal genome database that collects gene information and functional data and provides search tools for 61 species of fungi and oomycetes. We applied these published names to a manually curated ortholog set of all
Cryptococcus
species currently in FungiDB, including
Cryptococcus neoformans
var.
neoformans
strains JEC21 and B-3501A,
C. neoformans
var.
grubii
strain H99, and
Cryptococcus gattii
strains R265 and WM276, and have written brief descriptions of their functions. We also compiled a protocol for gene naming that summarizes guidelines proposed by members of the
Cryptococcus
research community. The centralization of genomic and literature-based information for
Cryptococcus
at FungiDB will help researchers communicate about genes of interest, such as those related to virulence, and will further facilitate research on the pathogen.
PvdP Is a Tyrosinase That Drives Maturation of the Pyoverdine Chromophore in Pseudomonas aeruginosa
Authors: Nadal-Jimenez Pol , Koch Gudrun , Reis Carlos R. , Muntendam Remco , Raj Hans , Jeronimus-Stratingh C. Margot , Cool Robbert H. , Quax Wim J.
Published: May 2014

The iron binding siderophore pyoverdine constitutes a major adaptive factor contributing to both virulence and survival in fluorescent pseudomonads. For decades, pyoverdine production has allowed the identification and classification of fluorescent and nonfluorescent pseudomonads. Here, we demonstrate that PvdP, a periplasmic enzyme of previously unknown function, is a tyrosinase required for the maturation of the pyoverdine chromophore in
Pseudomonas aeruginosa
. PvdP converts the nonfluorescent ferribactin, containing two iron binding groups, into a fluorescent pyoverdine, forming a strong hexadentate complex with ferrous iron, by three consecutive oxidation steps. PvdP represents the first characterized member of a small family of tyrosinases present in fluorescent pseudomonads that are required for siderophore maturation and are capable of acting on large peptidic substrates.
The Rip1 Protease of Mycobacterium tuberculosis Controls the SigD Regulon
Authors: Schneider Jessica S. , Sklar Joseph G. , Glickman Michael S.
Published: May 2014

Regulated intramembrane proteolysis of membrane-embedded substrates by site-2 proteases (S2Ps) is a widespread mechanism of transmembrane signal transduction in bacteria and bacterial pathogens. We previously demonstrated that the
Mycobacterium tuberculosis
S2P Rip1 is required for full virulence in the mouse model of infection. Rip1 controls transcription in part through proteolysis of three transmembrane anti-sigma factors, anti-SigK, -L, and -M, but there are also Rip1-dependent, SigKLM-independent pathways. To determine the contribution of the sigma factors K, L, and M to the Δ
rip1
attenuation phenotype, we constructed an
M. tuberculosis
Δ
sigK
Δ
sigL
Δ
sigM
mutant and found that this strain fails to recapitulate the marked attenuation of Δ
rip1
in mice. In a search for additional pathways controlled by Rip1, we demonstrated that the SigD regulon is positively regulated by the Rip1 pathway. Rip1 cleavage of transmembrane anti-SigD is required for expression of SigD target genes. In the absence of Rip1, proteolytic maturation of RsdA is impaired. These findings identify RsdA/SigD as a fourth arm of the branched pathway controlled by Rip1 in
M. tuberculosis
.
Tolerance of a Phage Element by Streptococcus pneumoniae Leads to a Fitness Defect during Colonization
Authors: DeBardeleben Hilary K. , Lysenko Elena S. , Dalia Ankur B. , Weiser Jeffrey N.
Published: May 2014

The pathogenesis of the disease caused by
Streptococcus pneumoniae
begins with colonization of the upper respiratory tract. Temperate phages have been identified in the genomes of up to 70% of clinical isolates. How these phages affect the bacterial host during colonization is unknown. Here, we examined a clinical isolate that carries a novel prophage element, designated Spn1, which was detected in both integrated and episomal forms. Surprisingly, both lytic and lysogenic Spn1 genes were expressed under routine growth conditions. Using a mouse model of asymptomatic colonization, we demonstrate that the Spn1
−
strain outcompeted the Spn1
+
strain >70-fold. To determine if Spn1 causes a fitness defect through a
trans
-acting factor, we constructed an Spn1
+
mutant that does not become an episome or express phage genes. This mutant competed equally with the Spn1
−
strain, indicating that expression of phage genes or phage lytic activity is required to confer this fitness defect.
In vitro
, we demonstrate that the presence of Spn1 correlated with a defect in LytA-mediated autolysis. Furthermore, the Spn1
+
strain displayed increased chain length and resistance to lysis by penicillin compared to the Spn
−
strain, indicating that Spn1 alters the cell wall physiology of its host strain. We posit that these changes in cell wall physiology allow for tolerance of phage gene products and are responsible for the relative defect of the Spn1
+
strain during colonization. This study provides new insight into how bacteria and prophages interact and affect bacterial fitness
in vivo
.
How Many Initiator tRNA Genes Does Escherichia coli Need?
Authors: Samhita Laasya , Nanjundiah Vidyanand , Varshney Umesh
Published: May 2014

Multiple copies of a gene require enhanced investment on the part of the cell and, as such, call for an explanation. The observation that
Escherichia coli
has four copies of initiator tRNA (tRNA

i

) genes, encoding a special tRNA (tRNA
fMet
) required to start protein synthesis, is puzzling particularly because the cell appears to be unaffected by the removal of one copy. However, the fitness of an organism has both absolute and relative connotations. Thus, we carried out growth competition experiments between
E. coli
strains that differ in the number of tRNA

i

genes they contain. This has enabled us to uncover an unexpected link between the number of tRNA

i

genes and protein synthesis, nutritional status, and fitness. Wild-type strains with the canonical four tRNA

i

genes are favored in nutrient-rich environments, and those carrying fewer are favored in nutrient-poor environments. Auxotrophs behave as if they have a nutritionally poor internal environment. A heuristic model that links tRNA

i

gene copy number, genetic stress, and growth rate accounts for the findings. Our observations provide strong evidence that natural selection can work through seemingly minor quantitative variations in gene copy number and thereby impact organismal fitness.
Alginate-Dependent Gene Expression Mechanism in Sphingomonas sp. Strain A1
Authors: Hayashi Chie , Takase Ryuichi , Momma Keiko , Maruyama Yukie , Murata Kousaku , Hashimoto Wataru
Published: May 2014

Sphingomonas
sp. strain A1, a Gram-negative bacterium, directly incorporates alginate polysaccharide into the cytoplasm through a periplasmic alginate-binding protein-dependent ATP-binding cassette transporter. The polysaccharide is degraded to monosaccharides via the formation of oligosaccharides by endo- and exotype alginate lyases. The strain A1 proteins for alginate uptake and degradation are encoded in both strands of a genetic cluster in the bacterial genome and inducibly expressed in the presence of alginate. Here we show the function of the alginate-dependent transcription factor AlgO and its mode of action on the genetic cluster and alginate oligosaccharides. A putative gene within the genetic cluster seems to encode a transcription factor-like protein (AlgO). Mutant strain A1 (ΔAlgO mutant) cells with a disrupted
algO
gene constitutively produced alginate-related proteins. DNA microarray analysis indicated that wild-type cells inducibly transcribed the genetic cluster only in the presence of alginate, while ΔAlgO mutant cells constitutively expressed the genetic cluster. A gel mobility shift assay showed that AlgO binds to the specific intergenic region between
algO
and
algS
(
algO-algS
). Binding of AlgO to the
algO-algS
intergenic region diminished with increasing alginate oligosaccharides. These results demonstrated a novel alginate-dependent gene expression mechanism. In the absence of alginate, AlgO binds to the
algO-algS
intergenic region and represses the expression of both strands of the genetic cluster, while in the presence of alginate, AlgO dissociates from the
algO-algS
intergenic region via binding to alginate oligosaccharides produced through the lyase reaction and subsequently initiates transcription of the genetic cluster. This is the first report on the mechanism by which alginate regulates the expression of the gene cluster.
Adding maps (GPS) to accelerometry data to improve study participants’ recall of physical activity: a methodological advance in physical activity research
Authors: Brown Barbara B , Wilson Laura , Tribby Calvin P , Werner Carol M , Wolf Jean , Miller Harvey J , Smith Ken R
Published: May 2014

Objective

Obtaining the ‘when, where and why’ of healthy bouts of moderate-to-vigorous physical activity (MVPA) provides insights into natural PA.

Design

In Salt Lake City, Utah, adults wore accelerometer and Global Positioning System (GPS) loggers for a week in a cross-sectional study to establish baseline travel and activity patterns near a planned Complete Street intervention involving a new rail line, new sidewalks and a bike path.

Results

At the end of the week, research assistants met with the 918 participants who had at least three 10 h days of good accelerometer readings. Accelerometer and GPS data were uploaded and integrated within a custom application, and participants were provided with maps and time information for past MVPA bouts of ≥3 min to help them recall bout details. Participants said that ‘getting someplace’ was, on average, a more important motivation for their bouts than leisure or exercise. A series of recall tests showed that participants recalled most bouts they were asked about, regardless of the duration of the bout, suggesting that participant perceptions of their shorter lifestyle bouts can be studied with this methodology. Visual prompting with a map depicting where each bout took place yielded more accurate recall than prompting with time cues alone.

Conclusions

These techniques provide a novel way to understand participant memories of the context and subjective assessments associated with healthy bouts of PA. Prompts with time-stamped maps that illustrate places of MVPA offer an effective method to improve understanding of activity and its supportive sociophysical contexts.
Why has the pedestrian death rate decreased in Spain between 1993 and 2011? An application of the decomposition method
Authors: Jiménez-Mejías Eladio , Onieva-García María Ángeles , Robles-Martín Jessica , Martínez-Ruiz Virginia , Luna-del-Castillo Juan de Dios , Lardelli-Claret Pablo
Published: May 2014

A decomposition procedure was used to estimate the percentage contributions of exposure, risk of collision and fatality to explain the decreases in pedestrian collision death rates observed in Spain from 1993 to 2011. Information was obtained from the Spanish National Institute of Statistics and the Spanish Register of Road Crashes with Victims. A quasi-induced method was used to obtain estimates of annual pedestrian exposure. Poisson regression was used to obtain age-adjusted and sex-adjusted estimates of the mean annual percentage decrease in pedestrian death rates attributable to exposure, collision and fatality; these values were +2.28%, −45.86% and −51.86%, respectively. The results suggest that the decrease in fatality rates and, to a lesser extent, collision rates were the most important determinants of the reduction in pedestrian collision death rates, whereas the contribution of exposure was irrelevant.
Risky driving, mental health, and health-compromising behaviours: risk clustering in late adolescents and adults
Authors: McDonald Catherine C , Sommers Marilyn S , Fargo Jamison D
Published: May 2014

Background

Health-compromising behaviours in adolescents and adults co-occur. Because motor vehicle crashes are the leading cause of death and disability for these age groups, understanding the association between risky driving and other health-compromising behaviours is critical.

Methods

We performed a secondary analysis of data from a randomised controlled trial of an intervention for participants who screened positive for risky driving and problem drinking. Using baseline data, we examined relationships among conduct behaviour problems before and after age 15 years, depressive symptoms, sleep, problem drinking, and risky driving (hostile, reckless and drinking and driving) in late adolescents ages 18–24 (n=110) years, and adults ages 25–44 (n=202) years. We developed a measurement model for the entire sample using confirmatory factor analysis, which was then specified as a multigroup structural equation model.

Results

Late adolescents and adults had some similar associations for pathways through problem drinking to drinking and driving; depression to reckless driving; and conduct behaviour problems after 15 years of age to hostile driving. Late adolescents, however, had more complex relationships: depressive symptoms and conduct behaviour problems before 15 years of age were associated with more risky driving behaviours through multiple pathways, and males reported more risky driving.

Conclusions

Risky driving is associated with other health-compromising behaviours and mental health factors. It is a multidimensional phenomenon more pronounced in late adolescence than adulthood. In order to promote safe driving, the findings support the need to consider behaviours that are a health threat in the late adolescent population during driving training and licensure.

Trial registration number:

NCT00164294.
Low neurologic intensive care unit hemoglobin as a predictor for intra-arterial vasospasm therapy and poor discharge modified Rankin Scale in aneurysmal subarachnoid haemorrhage-induced cerebral vasospasm
Authors: Bell Donnie L , Kimberly W Taylor , Yoo Albert J , Leslie-Mazwi Thabele M , Rabinov James D , Bell Jania E , Mehta Brijesh P , Hirsch Joshua A
Published: May 2014

Background

Intra-arterial vasospasm therapy (IAVT) with vasodilators, balloon angioplasty, and cerebral blood flow augmentation devices are therapies for aneurysmal subarachnoid hemorrhage-induced symptomatic cerebral vasospasm refractory to maximal medical management. Our aim was to identify clinical factors predictive of IAVT and/or poor outcome.

Methods

A cross-sectional retrospective analysis was performed of 130 patients with aneurysmal subarachnoid hemorrhage including patients without and with symptomatic cerebral vasospasm requiring IAVT. The data were analysed by Student t test, univariate analysis and binary logistic regression.

Results

The mean±SD patient age was 54±12.2 years, admission hemoglobin was 13.6±1.5 g/dL, and neurologic intensive care unit (NICU) hemoglobin 11±1.4 g/dL. The median Hunt and Hess grade was 2 (range 1,4), Fisher grade 3 (range 3,3), and discharge modified Rankin Scale (mRS) 0.5 (range 0,2). Lower mean NICU hemoglobin was found in patients receiving IAVT than in those not receiving IAVT (M=10.4±0.9 g/dL vs M=11.2±1.4 g/dL, t(115)=−2.52, p=0.01). Further, lower mean NICU hemoglobin was associated with increased IAVT (ρ=−0.3, p<0.01) and higher discharge mRS (ρ=−0.5, p<0.01). In binary logistic regression, lower mean NICU hemoglobin was an independent predictor of IAVT (OR 0.6, 95% CI 0.4 to 0.9, p<0.05) as well as poor discharge mRS (OR 0.6, 95% CI 0.4 to 0.9, p<0.05). Hunt and Hess grade was also an independent predictor of these outcomes.

Conclusions

Lower mean hemoglobin during the acute phase of aneurysmal subarachnoid hemorrhage-induced cerebral vasospasm is an independent predictor of IAVT and poor discharge mRS. This relationship warrants further evaluation.
An early Late Cretaceous (Cenomanian) sturgeon (Acipenseriformes) from the Dunvegan Formation, northwestern Alberta, Canada
Authors: Vavrek Matthew J. , Murray Alison M. , Bell Phil R.
Published: May 2014

A recent survey of the middle Cenomanian Dunvegan Formation along the Peace River, Alberta, has yielded a partial skull of a large acipenseriform fish. The fossil was from an animal approximately 5 m in length, based on comparisons with living relatives. Though incomplete, this represents an important record of mid-Cretaceous fish from northern North America, as formations of this age are virtually unexplored in northern regions. This fossil is the oldest acipenserid from North America, and one of the most northerly known.
National forest inventories in the service of small area estimation of stem volume
Authors: Magnussen Steen , Mandallaz Daniel , Breidenbach Johannes , Lanz Adrian , Ginzler Christian
Published: May 2014

This study introduces five facets that can improve inference in small area estimation (SAE) problems: (1) model groups, (2) test of area effects, (3) conditional EBLUPs, (4) model selection, and (5) model averaging. Two contrasting case studies with data from the Swiss and Norwegian national forest inventories demonstrate the five facets. The target variable of interest was mean stem volume per hectare on forested land in 108 Swiss forest districts (FD) and in 14 Norwegian municipalities (KOM) in the County of Vestfold. Auxiliary variables from airborne laser scanning (Switzerland) and photogrammetric point clouds (Vestfold) with full coverage and a resolution of 25 m × 25 m (Switzerland) and 16 m × 16 m (Vestfold) were available. Only the data metric mean canopy height was statistically significant. Ten linear fixed-effects models and three mixed linear models were assessed. Area effects were statistically significant in the Swiss case but not in Vestfold case. A model selection based on AIC favored separate linear regression models for each FD and a single common regression model in Vestfold. Model averaging increased, on average, an estimated variance by 15%. Reported estimates of uncertainty were consistently larger than corresponding unconditional EBLUPs.
Gi proteins mediate activation of the canonical hedgehog pathway in the myocardium
Authors: Carbe Christian J. , Cheng Lan , Addya Sankar , Gold Jessica I. , Gao Erhe , Koch Walter J. , Riobo Natalia A.
Published: May 2014

During myocardial ischemia, upregulation of the hedgehog (Hh) pathway promotes neovascularization and increases cardiomyocyte survival. The canonical Hh pathway activates a transcriptional program through the Gli family of transcription factors by derepression of the seven-transmembrane protein smoothened (Smo). The mechanisms linking Smo to Gli are complex and, in some cell types, involve coupling of Smo to Gi proteins. In the present study, we investigated, for the first time, the transcriptional response of cardiomyocytes to sonic hedgehog (Shh) and the role of Gi protein utilization. Our results show that Shh strongly activates Gli1 expression by quantitative PCR in a Smo-dependent manner in neonatal rat ventricular cardiomyocytes. Microarray analysis of gene expression changes elicited by Shh and sensitive to a Smo inhibitor identified a small subset of 37 cardiomyocyte-specific genes regulated by Shh, including some in the PKA and purinergic signaling pathways. In addition, neonatal rat ventricular cardiomyocytes infected with an adenovirus encoding GiCT, a peptide that impairs receptor-Gi protein coupling, showed reduced activation of Hh targets. In vitro data were confirmed in transgenic mice with cardiomyocyte-inducible GiCT expression. Transgenic GiCT mice showed specific reduction of Gli1 expression in the heart under basal conditions and failed to upregulate the Hh pathway upon ischemia and reperfusion injury, unlike their littermate controls. This study characterizes, for the first time, the transcriptional response of cardiomyocytes to Shh and establishes a critical role for Smo coupling to Gi in Hh signaling in the normal and ischemic myocardium.
Systemic vascular effects of acute electrical baroreflex stimulation
Authors: Burgoyne Steven , Georgakopoulos Dimitrios , Belenkie Israel , Tyberg John V.
Published: May 2014

We intended to determine if acute baroreflex activation therapy (BAT) increases venous capacitance and aortic conductance. BAT is effective in resistant hypertension, but its effect on the systemic vasculature is poorly understood. Left ventricular (LV) and aortic pressures and subdiaphragmatic aortic and caval flows (ultrasonic) were measured in six anesthetized dogs. Changes in abdominal blood volume (Vabdominal) were estimated as the integrated difference in abdominal aortic inflow and caval outflow. An electrode was implanted on the right carotid sinus. Data were measured during control and BAT. Next, sodium nitroprusside (SNP) was infused and BAT was subsequently added. Finally, angiotensin II (ANG II) was infused, and three increased BAT currents were added. We found that BAT decreased mean aortic pressure (PAo) by 22.5 ± 1.3 mmHg ( P < 0.001) and increased aortic conductance by 16.2 ± 4.9% ( P < 0.01) and Vabdominal at a rate of 2.2 ± 0.6 ml·kg−1·min−1 ( P < 0.01). SNP decreased PAo by 17.4 ± 0.7 mmHg ( P < 0.001) and increased Vabdominal at a rate of 2.2 ± 0.7 ml·kg−1·min−1 ( P < 0.05). During the SNP infusion, BAT decreased PAo further, by 26.0 ± 2.1 mmHg ( P < 0.001). ANG II increased PAo by 40.4 ± 3.5 mmHg ( P = 0.001). When an increased BAT current was added, PAo decreased to baseline ( P < 0.01) while aortic conductance increased from 62.3 ± 5.2% to 80.2 ± 3.3% ( P < 0.05) of control. Vabdominal increased at a rate of 1.8 ± 0.9 ml·kg−1·min−1 ( P < 0.01), reversing the ANG II effects. In conclusion, BAT increases arterial conductance, decreases PAo, and increases venous capacitance even in the presence of powerful vasoactive drugs. Increasing venous capacitance may be an important effect of BAT in hypertension.
Maternal nutrient restriction during pregnancy impairs an endothelium-derived hyperpolarizing factor-like pathway in sheep fetal coronary arteries
Authors: Shukla Praveen , Ghatta Srinivas , Dubey Nidhi , Lemley Caleb O. , Johnson Mary Lynn , Modgil Amit , Vonnahme Kimberly , Caton Joel S. , Reynolds Lawrence P. , Sun Chengwen , O'Rourke Stephen T.
Published: May 2014

The mechanisms underlying developmental programming are poorly understood but may be associated with adaptations by the fetus in response to changes in the maternal environment during pregnancy. We hypothesized that maternal nutrient restriction during pregnancy alters vasodilator responses in fetal coronary arteries. Pregnant ewes were fed a control [100% U.S. National Research Council (NRC)] or nutrient-restricted (60% NRC) diet from days 50 to 130 of gestation (term = 145 days); fetal tissues were collected at day 130. In coronary arteries isolated from control fetal lambs, relaxation to bradykinin was unaffected by nitro-l-arginine (NLA). Iberiotoxin or contraction with KCl abolished the NLA-resistant response to bradykinin. In fetal coronary arteries from nutrient-restricted ewes, relaxation to bradykinin was fully suppressed by NLA. Large-conductance, calcium-activated potassium channel (BKCa) currents did not differ in coronary smooth muscle cells from control and nutrient-restricted animals. The BKCa openers, BMS 191011 and NS1619, and 14,15-epoxyeicosatrienoic acid [a putative endothelium-derived hyperpolarizing factor (EDHF)] each caused fetal coronary artery relaxation and BKCa current activation that was unaffected by maternal nutrient restriction. Expression of BKCa-channel subunits did not differ in fetal coronary arteries from control or undernourished ewes. The results indicate that maternal undernutrition during pregnancy results in loss of the EDHF-like pathway in fetal coronary arteries in response to bradykinin, an effect that cannot be explained by a decreased number or activity of BKCa channels or by decreased sensitivity to mediators that activate BKCa channels in vascular smooth muscle cells. Under these conditions, bradykinin-induced relaxation is completely dependent on nitric oxide, which may represent an adaptive response to compensate for the absence of the EDHF-like pathway.
Pim1 kinase protects airway epithelial cells from cigarette smoke-induced damage and airway inflammation
Authors: de Vries M. , Heijink I. H. , Gras R. , den Boef L. E. , Reinders-Luinge M. , Pouwels S. D. , Hylkema M. N. , van der Toorn M. , Brouwer U. , van Oosterhout A. J. M. , Nawijn M. C.
Published: May 2014

Exposure to cigarette smoke (CS) is the main risk factor for developing chronic obstructive pulmonary disease and can induce airway epithelial cell damage, innate immune responses, and airway inflammation. We hypothesized that cell survival factors might decrease the sensitivity of airway epithelial cells to CS-induced damage, thereby protecting the airways against inflammation upon CS exposure. Here, we tested whether Pim survival kinases could protect from CS-induced inflammation. We determined expression of Pim kinases in lung tissue, airway inflammation, and levels of keratinocyte-derived cytokine (KC) and several damage-associated molecular patterns in bronchoalveolar lavage in mice exposed to CS or air. Human bronchial epithelial BEAS-2B cells were treated with CS extract (CSE) in the presence or absence of Pim1 inhibitor and assessed for loss of mitochondrial membrane potential, induction of cell death, and release of heat shock protein 70 (HSP70). We observed increased expression of Pim1, but not of Pim2 and Pim3, in lung tissue after exposure to CS. Pim1-deficient mice displayed a strongly enhanced neutrophilic airway inflammation upon CS exposure compared with wild-type controls. Inhibition of Pim1 activity in BEAS-2B cells increased the loss of mitochondrial membrane potential and reduced cell viability upon CSE treatment, whereas release of HSP70 was enhanced. Interestingly, we observed release of S100A8 but not of double-strand DNA or HSP70 in Pim1-deficient mice compared with wild-type controls upon CS exposure. In conclusion, we show that expression of Pim1 protects against CS-induced cell death in vitro and neutrophilic airway inflammation in vivo. Our data suggest that the underlying mechanism involves CS-induced release of S100A8 and KC.