bluuebunny/crossref_metadata_2025_split huggingface dataset:
Poor sleep quality impairs cognitive performance in older adults
Authors: Miyata Seiko , Noda Akiko , Iwamoto Kunihiro , Kawano Naoko , Okuda Masato , Ozaki Norio 
Published: April 2013

SummaryThe prevalence of insomnia increases with age. Short sleep duration is associated with deficits in cognitive performance. We hypothesized that short sleep duration and sleep quality influence cognitive performance in older adults. The study included 78 adults aged 60 years and over (72.2 ± 5.9 years). Total sleep time and sleep efficiency (total sleep time/time in bed × 100) were calculated using actigraphy. We evaluated cognitive performance with the continuous performance test‐identical pairs and the number‐back test. Sleep apnea was evaluated overnight with a portable home monitoring system. The accuracy of the 0‐back test significantly decreased in participants with total sleep time less than 5 h compared with those with total sleep time greater than 7 h, but there was no significant difference in continuous performance test‐identical pairs between the two groups. Participants with sleep efficiency <85% showed a significant decrease in 0‐ and 1‐back test accuracy compared with those with sleep efficiency ≥85%. There were no significant differences in the accuracy of number‐back tests and continuous performance test‐identical pairs between apnea–hypopnea index ≥15 h−1 and apnea–hypopnea index <15 h−1 groups, or among lowest SpO2 ≥ 90%, lowest 80–90%, and lowest SpO2 < 80% groups. Age, total sleep time and sleep efficiency were significantly correlated with accuracy on the 0‐back test. Age and sleep efficiency were significantly correlated with accuracy on the 1‐back test. Multiple regression analysis revealed that total sleep time was independently correlated with accuracy on the 0‐back test, while age was independently correlated with accuracy on the 1‐back test. Our findings suggest that sleep duration and sleep quality may play a role in cognitive performance in older adults.
Deciphering the aetiology of a mixed fungal infection by broad‐range PCR with sequencing and fluorescence in situ hybridisation
Authors: Rickerts V. , McCormick Smith I. , Mousset S. , Kommedal O. , Fredricks D. N. 
Published: April 2013

SummarySimultaneous infections with multiple fungi may be misinterpreted as monomicrobial infections by current diagnostics with ramifications for the choice of antimicrobial agents that may impact patient outcomes. The application of molecular methods on tissue samples may be useful to decipher the aetiology of mixed fungal infections. We present a leukaemic patient who died from sepsis due to candidaemia. The postmortem examination documented fungal elements in lung tissue. Fungal DNA was amplified from the lung sample by broad‐range PCR assays targeting the 28S ribosomal RNA gene or the internal transcribed spacer 2 (ITS‐2). Fluorescence in situ hybridisation (FISH) using differentially labelled fungal probes was applied on the tissue. Sequencing identified the PCR amplicons as Aspergillus fumigatus (28S assay) and Candida tropicalis (ITS‐2 assay). As a chromatogram suggested mixed amplicons, the Isentio ripseq® tool for in silico analysis was applied and confirmed the presence of both amplicons in the PCR products of both assays. FISH confirmed the presence of Aspergillus and Candida within the infectious process, a prerequisite for inferring a causal relationship with the infection. The combination of broad‐range PCR with sequence analysis and FISH applied on tissue samples is a powerful approach to identify the aetiology of invasive fungal infections, including mixed infections.
Osteopontin gene SNPs (rs9138, rs11730582) mediate susceptibility to external root resorption in orthodontic patients
Authors: Iglesias‐Linares A , Yañez‐Vico RM , Moreno‐Fernández AM , Mendoza‐Mendoza A , Orce‐Romero A , Solano‐Reina E 
Published: April 2013

ObjectiveExternal apical root resorption (EARR) is a frequent iatrogenic effect of orthodontic treatment. Substantial variability in responses to postorthodontic EARR has been observed among patients even when similar treatment protocols were used. This observation suggests that environmental and/or genetic variations between individuals may confer susceptibility or resistance to developing EARR. The objective of this study is to determine whether variants in the osteopontin gene, an essential mediator in the odontoclast fusion and attachment process, are positively/negatively associated with postorthodontic EARR.Materials and MethodsGenetic screening of eighty‐seven orthodontic patients was performed for two polymorphisms in the osteopontin gene cluster (rs9138 and rs11730582). Subjects were divided into groups, according to the presence or absence of EARR (>2 mm). Genotype distributions and allelic frequencies were calculated using the chi‐square test. Logistic regression analysis was used to assess the extent to which clinical‐related parameters interfered with the EARR. Odds ratios (OR) and 95% confidence intervals were also calculated.ResultsData from this study show that subjects heterozygous and homozygous for the most frequent allele of the osteopontin gene at position 89261521 [OR: 0.035 (P = 0.035*) (allele A)] and 89253600 [OR: 0.20 (P = 0.025*) (allele T)], respectively, are protected against postorthodontic EARR. Nevertheless, a highly significant association was found in the comparative analysis of homozygous subjects [2/2 (CC)] for the osteopontin gene (rs9138), resulting in an increased risk of suffering postorthodontic EARR[OR: 4.10; P = 0.045*;CI: 95%]. Subjects who were homozygous [2/2 (CC)] for the osteopontin gene (rs11730582) were more likely, and to a greater extent, to be affected with EARR [OR: 11.68; P < 0.039*;CI: 95%] compared with other genotypes.ConclusionVariations in the osteopontin gene (rs9138 and rs11730582) are determinants of a genetic predisposition to suffer EARR secondary to orthodontic treatment.
Spatial and Temporal Variation in Enterococcal Abundance and Its Relationship to the Microbial Community in Hawaii Beach Sand and Water
Authors: Cui Henglin , Yang Kun , Pagaling Eulyn , Yan Tao 
Published: April 2013

ABSTRACTRecent studies have reported high levels of fecal indicator enterococci in marine beach sand. This study aimed to determine the spatial and temporal variation of enterococcal abundance and to evaluate its relationships with microbial community parameters in Hawaii beach sand and water. Sampling at 23 beaches on the Island of Oahu detected higher levels of enterococci in beach foreshore sand than in beach water on a mass unit basis. Subsequent 8-week consecutive samplings at two selected beaches (Waialae and Kualoa) consistently detected significantly higher levels of enterococci in backshore sand than in foreshore/nearshore sand and beach water. Comparison between the abundance of enterococci and the microbial communities showed that enterococci correlated significantly with totalVibrioin all beach zones but less significantly with total bacterial density andEscherichia coli. Samples from the different zones of Waialae beach were sequenced by 16S rRNA gene pyrosequencing to determine the microbial community structure and diversity. The backshore sand had a significantly more diverse community and contained different major bacterial populations than the other beach zones, which corresponded to the spatial distribution pattern of enterococcal abundance. Taken together, multiple lines of evidence support the possibility of enterococci as autochthonous members of the microbial community in Hawaii beach sand.
Genetic Diversity and Geographical Distribution of Indigenous Soybean-Nodulating Bradyrhizobia in the United States
Authors: Shiro Sokichi , Matsuura Syota , Saiki Rina , Sigua Gilbert C. , Yamamoto Akihiro , Umehara Yosuke , Hayashi Masaki , Saeki Yuichi 
Published: April 2013

ABSTRACT

We investigated the relationship between the genetic diversity of indigenous soybean-nodulating bradyrhizobia and their geographical distribution in the United States using nine soil isolates from eight states. The bradyrhizobia were inoculated on three soybean
Rj
genotypes (non-
Rj
,
Rj
2
Rj
3
, and
Rj
4
). We analyzed their genetic diversity and community structure by means of restriction fragment length polymorphisms of PCR amplicons to target the 16S-23S rRNA gene internal transcribed spacer region, using 11 USDA
Bradyrhizobium
strains as reference strains. We also performed diversity analysis, multidimensional scaling analysis based on the Bray-Curtis index, and polar ordination analysis to describe the structure and geographical distribution of the soybean-nodulating bradyrhizobial community. The major clusters were
Bradyrhizobium japonicum
Bj123, in the northern United States, and
Bradyrhizobium elkanii
, in the middle to southern regions. Dominance of bradyrhizobia in a community was generally larger for the cluster belonging to
B. elkanii
than for the cluster belonging to
B. japonicum
. The indigenous American soybean-nodulating bradyrhizobial community structure was strongly correlated with latitude. Our results suggest that this community varies geographically.
Simultaneous Catabolism of Plant-Derived Aromatic Compounds Results in Enhanced Growth for Members of the Roseobacter Lineage
Authors: Gulvik Christopher A. , Buchan Alison 
Published: April 2013

ABSTRACT

Plant-derived aromatic compounds are important components of the dissolved organic carbon pool in coastal salt marshes, and their mineralization by resident bacteria contributes to carbon cycling in these systems. Members of the roseobacter lineage of marine bacteria are abundant in coastal salt marshes, and several characterized strains, including
Sagittula stellata
E-37, utilize aromatic compounds as primary growth substrates. The genome sequence of
S. stellata
contains multiple, potentially competing, aerobic ring-cleaving pathways. Preferential hierarchies in substrate utilization and complex transcriptional regulation have been demonstrated to be the norm in many soil bacteria that also contain multiple ring-cleaving pathways. The purpose of this study was to ascertain whether substrate preference exists in
S. stellata
when the organism is provided a mixture of aromatic compounds that proceed through different ring-cleaving pathways. We focused on the protocatechuate (
pca
) and the aerobic benzoyl coenzyme A (
box
) pathways and the substrates known to proceed through them,
p
-hydroxybenzoate (POB) and benzoate, respectively. When these two substrates were provided at nonlimiting carbon concentrations, temporal patterns of cell density, gene transcript abundance, enzyme activity, and substrate concentrations indicated that
S. stellata
simultaneously catabolized both substrates. Furthermore, enhanced growth rates were observed when
S. stellata
was provided both compounds simultaneously compared to the rates of cells grown singly with an equimolar concentration of either substrate alone. This simultaneous-catabolism phenotype was also demonstrated in another lineage member,
Ruegeria pomeroyi
DSS-3. These findings challenge the paradigm of sequential aromatic catabolism reported for soil bacteria and contribute to the growing body of physiological evidence demonstrating the metabolic versatility of roseobacters.
Comparison of 26 Sphingomonad Genomes Reveals Diverse Environmental Adaptations and Biodegradative Capabilities
Authors: Aylward Frank O. , McDonald Bradon R. , Adams Sandra M. , Valenzuela Alejandra , Schmidt Rebeccah A. , Goodwin Lynne A. , Woyke Tanja , Currie Cameron R. , Suen Garret , Poulsen Michael 
Published: April 2013

ABSTRACT

Sphingomonads comprise a physiologically versatile group within the
Alphaproteobacteria
that includes strains of interest for biotechnology, human health, and environmental nutrient cycling. In this study, we compared 26 sphingomonad genome sequences to gain insight into their ecology, metabolic versatility, and environmental adaptations. Our multilocus phylogenetic and average amino acid identity (AAI) analyses confirm that
Sphingomonas
,
Sphingobium
,
Sphingopyxis
, and
Novosphingobium
are well-resolved monophyletic groups with the exception of
Sphingomonas
sp. strain SKA58, which we propose belongs to the genus
Sphingobium
. Our pan-genomic analysis of sphingomonads reveals numerous species-specific open reading frames (ORFs) but few signatures of genus-specific cores. The organization and coding potential of the sphingomonad genomes appear to be highly variable, and plasmid-mediated gene transfer and chromosome-plasmid recombination, together with prophage- and transposon-mediated rearrangements, appear to play prominent roles in the genome evolution of this group. We find that many of the sphingomonad genomes encode numerous oxygenases and glycoside hydrolases, which are likely responsible for their ability to degrade various recalcitrant aromatic compounds and polysaccharides, respectively. Many of these enzymes are encoded on megaplasmids, suggesting that they may be readily transferred between species. We also identified enzymes putatively used for the catabolism of sulfonate and nitroaromatic compounds in many of the genomes, suggesting that plant-based compounds or chemical contaminants may be sources of nitrogen and sulfur. Many of these sphingomonads appear to be adapted to oligotrophic environments, but several contain genomic features indicative of host associations. Our work provides a basis for understanding the ecological strategies employed by sphingomonads and their role in environmental nutrient cycling.
Differentiation of Bacillus anthracis, B. cereus, and B. thuringiensis on the Basis of the
csaB
Gene Reflects Host Source
Authors: Zheng Jinshui , Peng Donghai , Song Xiaoling , Ruan Lifang , Mahillon Jacques , Sun Ming 
Published: April 2013

ABSTRACT

csaB
gene analysis clustered 198 strains of
Bacillus anthracis
,
Bacillus cereus
, and
Bacillus thuringiensis
into two groups related to mammalian and insect hosts, respectively. Mammal-related group I strains also have more S-layer homology (SLH) protein genes than group II strains. This indicates that
csaB
-based differentiation reflects selective pressure from animal hosts.
Alternative Sigma Factor SigK Has a Role in Stress Tolerance of Group I Clostridium botulinum Strain ATCC 3502
Authors: Dahlsten Elias , Kirk David , Lindstrï¿½m Miia , Korkeala Hannu 
Published: April 2013

ABSTRACT

The role of the alternative sigma factor SigK in cold and osmotic stress tolerance of
Clostridium botulinum
ATCC 3502 was demonstrated by induction of
sigK
after temperature downshift and exposure to hyperosmotic conditions and by impaired growth of the
sigK
mutants under the respective conditions.
Comparative Transcriptomics of Infectious Spores from the Fungal Pathogen Histoplasma capsulatum Reveals a Core Set of Transcripts That Specify Infectious and Pathogenic States
Authors: Inglis Diane O. , Voorhies Mark , Hocking Murray Davina R. , Sil Anita 
Published: April 2013

ABSTRACT

Histoplasma capsulatum
is a fungal pathogen that infects both healthy and immunocompromised hosts. In regions where it is endemic,
H. capsulatum
grows in the soil and causes respiratory and systemic disease when inhaled by humans. An interesting aspect of
H. capsulatum
biology is that it adopts specialized developmental programs in response to its environment. In the soil, it grows as filamentous chains of cells (mycelia) that produce asexual spores (conidia). When the soil is disrupted, conidia aerosolize and are inhaled by mammalian hosts. Inside a host, conidia germinate into yeast-form cells that colonize immune cells and cause disease. Despite the ability of conidia to initiate infection and disease, they have not been explored on a molecular level. We developed methods to purify
H. capsulatum
conidia, and we show here that these cells germinate into filaments at room temperature and into yeast-form cells at 37°C. Conidia internalized by macrophages germinate into the yeast form and proliferate within macrophages, ultimately lysing the host cells. Similarly, infection of mice with purified conidia is sufficient to establish infection and yield viable yeast-form cells
in vivo
. To characterize conidia on a molecular level, we performed whole-genome expression profiling of conidia, yeast, and mycelia from two highly divergent
H. capsulatum
strains. In parallel, we used homology and protein domain analysis to manually annotate the predicted genes of both strains. Analyses of the resultant data defined sets of transcripts that reflect the unique molecular states of
H. capsulatum
conidia, yeast, and mycelia.
Pbp1 Is Involved in Ccr4- and Khd1-Mediated Regulation of Cell Growth through Association with Ribosomal Proteins Rpl12a and Rpl12b
Authors: Kimura Yuichi , Irie Kaoru , Irie Kenji 
Published: April 2013

ABSTRACT

The
Saccharomyces cerevisiae
Pbp1 [poly(A)-binding protein (Pab1)-binding protein] is believed to be involved in RNA metabolism and regulation of translation, since Pbp1 regulates a length of poly(A) tail and is involved in stress granule (SG) formation. However, a physiological function of Pbp1 remains unclear, since the
pbp1
Δ mutation has no obvious effect on cell growth. In this study, we showed that
PBP1
genetically interacts with
CCR4
and
KHD1
, which encode a cytoplasmic deadenylase and an RNA-binding protein, respectively. Ccr4 and Khd1 modulate a signal from Rho1 in the cell wall integrity pathway by regulating the expression of RhoGEF and RhoGAP, and the double deletion of
CCR4
and
KHD1
confers a severe growth defect displaying cell lysis. We found that the
pbp1
Δ mutation suppressed the growth defect caused by the
ccr4Δ khd1
Δ mutation. The
pbp1
Δ mutation also suppressed the growth defect caused by double deletion of
POP2
, encoding another cytoplasmic deadenylase, and
KHD1
. Deletion of the gene encoding previously known Pbp1-interacting factor Lsm12, Pbp4, or Mkt1 did not suppress the growth defect of the
ccr4Δ khd1
Δ mutant, suggesting that Pbp1 acts independently of these factors in this process. We then screened novel Pbp1-interacting factors and found that Pbp1 interacts with ribosomal proteins Rpl12a and Rpl12b. Similarly to the
pbp1
Δ mutation, the
rpl12a
Δ and
rpl12b
Δ mutations also suppressed the growth defect caused by the
ccr4Δ khd1
Δ mutation. Our results suggest that Pbp1 is involved in the Ccr4- and Khd1-mediated regulation of cell growth through the association with Rpl12a and Rpl12b.
Endogenous Mutagenesis in Recombinant Sulfolobus Plasmids
Authors: Sakofsky Cynthia J. , Grogan Dennis W. 
Published: April 2013

ABSTRACT

Low rates of replication errors in chromosomal genes of
Sulfolobus
spp. demonstrate that these extreme thermoacidophiles can maintain genome integrity in environments with high temperature and low pH. In contrast to this genetic stability, we observed unusually frequent mutation of the β-
d
-glycosidase gene (
lacS
) of a shuttle plasmid (pJ
lacS
) propagated in
Sulfolobus acidocaldarius
. The resulting Lac
−
mutants also grew faster than the Lac
+
parent, thereby amplifying the impact of the frequent
lacS
mutations on the population. We developed a mutant accumulation assay and corrections for the effects of copy number and differential growth for this system; the resulting measurements and calculations yielded a corrected rate of 5.1 × 10
−4
mutational events at the
lacS
gene per plasmid replication. Analysis of independent
lacS
mutants revealed three types of mutations: (i) G·C-to-A·T transitions, (ii) slipped-strand events, and (iii) deletions. These mutations were frequent in plasmid-borne
lacS
expressed at a high level but not in single-copy
lacS
in the chromosome or at lower levels of expression in a plasmid. Substitution mutations arose at only two of 12 potential priming sites of the DNA primase of the pRN1 replicon, but nearly all these mutations created nonsense (chain termination) codons. The spontaneous mutation rate of plasmid-borne
lacS
was 175-fold higher under high-expression than under low-expression conditions. The results suggest that important DNA repair or replication fidelity functions are impaired or overwhelmed in pJ
lacS
, with results analogous to those of the “transcription-associated mutagenesis” seen in bacteria and eukaryotes.
Secretion of TcpF by the Vibrio cholerae Toxin-Coregulated Pilus Biogenesis Apparatus Requires an N-Terminal Determinant
Authors: Megli Christina J. , Taylor Ronald K. 
Published: April 2013

ABSTRACT

Type IV pili are important for microcolony formation, biofilm formation, twitching motility, and attachment. We and others have shown that type IV pili are important for protein secretion across the outer membrane, similar to type II secretion systems. This study explored the relationship between protein secretion and pilus formation in
Vibrio cholerae
. The toxin-coregulated pilus (TCP), a type IV pilus required for
V. cholerae
pathogenesis, is necessary for the secretion of the colonization factor TcpF (T. J. Kirn, N. Bose, and R. K. Taylor, Mol. Microbiol.
49:
81–92, 2003). This phenomenon is not unique to
V. cholerae
; secreted virulence factors that are dependent on the presence of components of the type IV pilus biogenesis apparatus for secretion have been reported with
Dichelobacter nodosus
(R. M. Kennan, O. P. Dhungyel, R. J. Whittington, J. R. Egerton, and J. I. Rood, J. Bacteriol.
183:
4451–4458, 2001) and
Francisella tularensis
(A. J. Hager et al., Mol. Microbiol.
62:
227–237, 2006). Using site-directed mutagenesis, we demonstrated that the secretion of TcpF is dependent on the presence of selected amino acid R groups at position five. We were unable to find other secretion determinants, suggesting that Y5 is the major secretion determinant within TcpF. We also report that proteins secreted in a type IV pilus biogenesis apparatus-dependent manner have a YXS motif within the first 15 amino acids following the Sec cleavage site. The YXS motif is not present in proteins secreted by type II secretion systems, indicating that this is unique to type IV pilus-mediated secretion. Moreover, we show that TcpF interacts with the pilin TcpA, suggesting that these proteins are secreted by the type IV pilus biogenesis system. These data provide a starting point for understanding how type IV pili can mediate secretion of virulence factors important for bacterial pathogenesis.