bluuebunny/crossref_metadata_2025_split huggingface dataset:
Specific Midgut Region Controlling the Symbiont Population in an Insect-Microbe Gut Symbiotic Association
Authors: Kim Jiyeun Kate , Kim Na Hyang , Jang Ho Am , Kikuchi Yoshitomo , Kim Chan-Hee , Fukatsu Takema , Lee Bok Luel 
Published: September 2013

ABSTRACT

Many insects possess symbiotic bacteria that affect the biology of the host. The level of the symbiont population in the host is a pivotal factor that modulates the biological outcome of the symbiotic association. Hence, the symbiont population should be maintained at a proper level by the host's control mechanisms. Several mechanisms for controlling intracellular symbionts of insects have been reported, while mechanisms for controlling extracellular gut symbionts of insects are poorly understood. The bean bug
Riptortus pedestris
harbors a betaproteobacterial extracellular symbiont of the genus
Burkholderia
in the midgut symbiotic organ designated the M4 region. We found that the M4B region, which is directly connected to the M4 region, also harbors
Burkholderia
symbiont cells, but the symbionts therein are mostly dead. A series of experiments demonstrated that the M4B region exhibits antimicrobial activity, and the antimicrobial activity is specifically potent against the
Burkholderia
symbiont but not the cultured
Burkholderia
and other bacteria. The antimicrobial activity of the M4B region was detected in symbiotic host insects, reaching its highest point at the fifth instar, but not in aposymbiotic host insects, which suggests the possibility of symbiont-mediated induction of the antimicrobial activity. This antimicrobial activity was not associated with upregulation of antimicrobial peptides of the host. Based on these results, we propose that the M4B region is a specialized gut region of
R. pedestris
that plays a critical role in controlling the population of the
Burkholderia
gut symbiont. The molecular basis of the antimicrobial activity is of great interest and deserves future study.
Species Co-Occurrence Patterns among Lyme Borreliosis Pathogens in the Tick Vector Ixodes ricinus
Authors: Herrmann Coralie , Gern Lise , Voordouw Maarten J. 
Published: September 2013

ABSTRACT

Mixed infections have important consequences for the ecology and evolution of host-parasite interactions. In vector-borne diseases, interactions between pathogens occur in both the vertebrate host and the arthropod vector. Spirochete bacteria belonging to the
Borrelia burgdorferi
sensu lato
genospecies complex are transmitted by
Ixodes
ticks and cause Lyme borreliosis in humans. In Europe, there is a high diversity of
Borrelia
pathogens, and the main tick vector,
Ixodes ricinus
, is often infected with multiple
Borrelia
genospecies. In the present study, we characterized the pairwise interactions between five
B. burgdorferi
sensu lato
genospecies in a large data set of
I. ricinus
ticks collected from the same field site in Switzerland. We measured two types of pairwise interactions: (i) co-occurrence, whether double infections occurred more or less often than expected, and (ii) spirochete load additivity, whether the total spirochete load in double infections was greater or less than the sum of the single infections. Mixed infections of
Borrelia
genospecies specialized on different vertebrate reservoir hosts occurred less frequently than expected (negative co-occurrence) and had joint spirochete loads that were lower than the additive expectation (inhibition). In contrast, mixed infections of genospecies that share the same reservoir hosts were more common than expected (positive co-occurrence) and had joint spirochete loads that were similar to or greater than the additive expectation (facilitation). Our study suggests that the vertebrate host plays an important role in structuring the community of
B. burgdorferi
sensu lato
genospecies inside the tick vector.
Development of a Tiered Multilocus Sequence Typing Scheme for Members of the Lactobacillus acidophilus Complex
Authors: Ramachandran Padmini , Lacher David W. , Pfeiler Erika A. , Elkins Christopher A. 
Published: September 2013

ABSTRACT

Members of the
Lactobacillus acidophilus
complex are associated with functional foods and dietary supplements because of purported health benefits they impart to the consumer. Many characteristics of these microorganisms are reported to be strain specific. Therefore, proper strain typing is essential for safety assessment and product labeling, and also for monitoring strain integrity for industrial production purposes. Fifty-two strains of the
L. acidophilus
complex (
L. acidophilus
,
L. amylovorus
,
L. crispatus
,
L. gallinarum
,
L. gasseri
, and
L. johnsonii
) were genotyped using two established methods and compared to a novel multilocus sequence typing (MLST) scheme. PCR restriction fragment length polymorphism (PCR-RFLP) analysis of the
hsp60
gene with AluI and TaqI successfully clustered 51 of the 52 strains into the six species examined, but it lacked strain-level discrimination. Random amplified polymorphic DNA PCR (RAPD-PCR) targeting the M13 sequence resulted in highly discriminatory profiles but lacked reproducibility. In this study, an MLST scheme was developed using the conserved housekeeping genes
fusA
,
gpmA
,
gyrA
,
gyrB
,
lepA
,
pyrG
, and
recA
, which identified 40 sequence types that successfully clustered all of the strains into the six species. Analysis of the observed alleles suggests that nucleotide substitutions within five of the seven MLST loci have reached saturation, a finding that emphasizes the highly diverse nature of the
L. acidophilus
complex and our unconventional application of a typically intraspecies molecular typing tool. Our MLST results indicate that this method could be useful for characterization and strain discrimination of a multispecies complex, with the potential for taxonomic expansion to a broader collection of
Lactobacillus
species.
Detection of Achromobacter xylosoxidans in Hospital, Domestic, and Outdoor Environmental Samples and Comparison with Human Clinical Isolates
Authors: Amoureux Lucie , Bador Julien , Fardeheb Sakina , Mabille Cédric , Couchot Charlyne , Massip Clémence , Salignon Anne-Lise , Berlie Guillaume , Varin Véronique , Neuwirth Catherine 
Published: September 2013

ABSTRACT

Achromobacter xylosoxidans
is an aerobic nonfermentative Gram-negative rod considered an important emerging pathogen among cystic fibrosis (CF) patients worldwide and among immunocompromised patients. This increased prevalence remains unexplained, and to date no environmental reservoir has been identified. The aim of this study was to identify potential reservoirs of
A. xylosoxidans
in hospital, domestic, and outdoor environments and to compare the isolates with clinical ones. From 2011 to 2012, 339 samples were collected in Dijon's university hospital, in healthy volunteers' homes in the Dijon area, and in the outdoor environment in Burgundy (soil, water, mud, and plants). We designed a protocol to detect
A. xylosoxidans
in environmental samples based on a selective medium: MCXVAA (MacConkey agar supplemented with xylose, vancomycin, aztreonam, and amphotericin B). Susceptibility testing, genotypic analysis by pulsed-field gel electrophoresis, and
bla
OXA-114
sequencing were performed on the isolates. A total of 50 strains of
A. xylosoxidans
were detected in hospital (33 isolates), domestic (9 isolates), and outdoor (8 isolates) samples, mainly in hand washing sinks, showers, and water. Most of them were resistant to ciprofloxacin (49 strains). Genotypic analysis and
bla
OXA-114
sequencing revealed a wide diversity among the isolates, with 35 pulsotypes and 18 variants of oxacillinases. Interestingly, 10 isolates from hospital environment were clonally related to clinical isolates previously recovered from hospitalized patients, and one domestic isolate was identical to one recovered from a CF patient. These results indicate that
A. xylosoxidans
is commonly distributed in various environments and therefore that CF patients or immunocompromised patients are surrounded by these reservoirs.
Identification of CtpL as a Chromosomally Encoded Chemoreceptor for 4-Chloroaniline and Catechol in Pseudomonas aeruginosa PAO1
Authors: Vangnai Alisa S. , Takeuchi Kazuki , Oku Shota , Kataoka Naoya , Nitisakulkan Tisana , Tajima Takahisa , Kato Junichi 
Published: September 2013

ABSTRACT

Bacterial chemotaxis influences the ability of bacteria to survive and thrive in most environments, including polluted ones. Despite numerous reports of the phenotypic characterization of chemotactic bacteria, only a few molecular details of chemoreceptors for aromatic pollutants have been described. In this study, the molecular basis of chemotaxis toward an environmentally toxic chlorinated aromatic pollutant, 4-chloroaniline (4CA), was evaluated. Among the three
Pseudomonas
spp. tested,
Pseudomonas aeruginosa
PAO1 exhibited positive chemotaxis both to the nonmetabolizable 4CA, where 4-chloroacetanilide was formed as a dead-end transformation product, and to the metabolizable catechol. Molecular analysis of all 26 mutants with a disrupted methyl-accepting chemotaxis gene revealed that CtpL, a chromosomally encoded chemoreceptor, was responsible for the positive chemotactic response toward 4CA. Since CtpL has previously been described to be a major chemoreceptor for inorganic phosphate at low concentrations in PAO1, this report describes a fortuitous ability of CtpL to function toward aromatic pollutants. In addition, its regulation not only was dependent on the presence of the chemoattractant inducer but also was regulated by conditions of phosphate starvation. These results expand the range of known chemotactic transducers and their function in the environmental bacterium PAO1.
Accumulation and Inactivation of Avian Influenza Virus by the Filter-Feeding Invertebrate Daphnia magna
Authors: Meixell Brandt W. , Borchardt Mark A. , Spencer Susan K. 
Published: September 2013

ABSTRACT

The principal mode of avian influenza A virus (AIV) transmission among wild birds is thought to occur via an indirect fecal-oral route, whereby individuals are exposed to virus from the environment through contact with virus-contaminated water. AIV can remain viable for an extended time in water; however, little is known regarding the influence of the biotic community (i.e., aquatic invertebrates) on virus persistence and infectivity in aquatic environments. We conducted laboratory experiments to investigate the ability of an aquatic filter-feeding invertebrate,
Daphnia magna
, to accumulate virus from AIV-dosed water under the hypothesis that they represent a potential vector of AIV to waterfowl hosts. We placed live daphnids in test tubes dosed with low-pathogenicity AIV (H3N8 subtype isolated from a wild duck) and sampled
Daphnia
tissue and the surrounding water using reverse transcription-quantitative PCR (RT-qPCR) at 3- to 120-min intervals for up to 960 min following dosing. Concentrations of viral RNA averaged 3 times higher in
Daphnia
tissue than the surrounding water shortly after viral exposure, but concentrations decreased exponentially through time for both. Extracts from
Daphnia
tissue were negative for AIV by cell culture, whereas AIV remained viable in water without
Daphnia
present. Our results suggest daphnids can accumulate AIV RNA and effectively remove virus particles from water. Although concentrations of viral RNA were consistently higher in
Daphnia
tissue than the water, additional research is needed on the time scale of AIV inactivation after
Daphnia
ingestion to fully elucidate
Daphnia
's role as a potential vector of AIV infection to aquatic birds.
Regiospecificities and Prenylation Mode Specificities of the Fungal Indole Diterpene Prenyltransferases AtmD and PaxD
Authors: Liu Chengwei , Minami Atsushi , Noike Motoyoshi , Toshima Hiroaki , Oikawa Hideaki , Dairi Tohru 
Published: September 2013

ABSTRACT

We recently reported the function of
paxD
, which is involved in the paxilline (compound 1) biosynthetic gene cluster in
Penicillium paxilli
. Recombinant PaxD catalyzed a stepwise regular-type diprenylation at the 21 and 22 positions of compound 1 with dimethylallyl diphosphate (DMAPP) as the prenyl donor. In this study,
atmD
, which is located in the aflatrem (compound 2) biosynthetic gene cluster in
Aspergillus flavus
and encodes an enzyme with 32% amino acid identity to PaxD, was characterized using recombinant enzyme. When compound 1 and DMAPP were used as substrates, two major products and a trace of minor product were formed. The structures of the two major products were determined to be reversely monoprenylated compound 1 at either the 20 or 21 position. Because compound 2 and β-aflatrem (compound 3), both of which are compound 1-related compounds produced by
A. flavus
, have the same prenyl moiety at the 20 and 21 position, respectively, AtmD should catalyze the prenylation in compound 2 and 3 biosynthesis. More importantly and surprisingly, AtmD accepted paspaline (compound 4), which is an intermediate of compound 1 biosynthesis that has a structure similar to that of compound 1, and catalyzed a regular monoprenylation of compound 4 at either the 21 or 22 position, though the reverse prenylation was observed with compound 1. This suggests that fungal indole diterpene prenyltransferases have the potential to alter their position and regular/reverse specificities for prenylation and could be applicable for the synthesis of industrially useful compounds.
Bacterial Persister Cell Formation and Dormancy
Authors: Wood Thomas K. , Knabel Stephen J. , Kwan Brian W. 
Published: September 2013

ABSTRACT
Bacterial cells may escape the effects of antibiotics without undergoing genetic change; these cells are known as persisters. Unlike resistant cells that grow in the presence of antibiotics, persister cells do not grow in the presence of antibiotics. These persister cells are a small fraction of exponentially growing cells (due to carryover from the inoculum) but become a significant fraction in the stationary phase and in biofilms (up to 1%). Critically, persister cells may be a major cause of chronic infections. The mechanism of persister cell formation is not well understood, and even the metabolic state of these cells is debated. Here, we review studies relevant to the formation of persister cells and their metabolic state and conclude that the best model for persister cells is still dormancy, with the latest mechanistic studies shedding light on how cells reach this dormant state.
The Polyketide Synthase Gene
pks4
of Trichoderma reesei Provides Pigmentation and Stress Resistance
Authors: Atanasova Lea , Knox Benjamin P. , Kubicek Christian P. , Druzhinina Irina S. , Baker Scott E. 
Published: September 2013

ABSTRACT

Species of the fungal genus
Trichoderma
(Hypocreales, Ascomycota) are well-known for their production of various secondary metabolites. Nonribosomal peptides and polyketides represent a major portion of these products. In a recent phylogenomic investigation of
Trichoderma
polyketide synthase (PKS)-encoding genes, the
pks4
from
T. reesei
was shown to be an orthologue of pigment-forming PKSs involved in synthesis of aurofusarin and bikaverin in
Fusarium
spp. In this study, we show that deletion of this gene in
T. reesei
results in loss of green conidial pigmentation and in pigmentation alteration of teleomorph structures. It also has an impact on conidial cell wall stability and the antagonistic abilities of
T. reesei
against other fungi, including formation of inhibitory metabolites. In addition, deletion of
pks4
significantly influences the expression of other PKS-encoding genes of
T. reesei
. To our knowledge, this is the first indication that a low-molecular-weight pigment-forming PKS is involved in defense, mechanical stability, and stress resistance in fungi.
Murine Models of Candida Gastrointestinal Colonization and Dissemination
Authors: Koh Andrew Y. 
Published: September 2013

ABSTRACT

Ninety-five percent of infectious agents enter through exposed mucosal surfaces, such as the respiratory and gastrointestinal (GI) tracts. The human GI tract is colonized with trillions of commensal microbes, including numerous
Candida
spp. Some commensal microbes in the GI tract can cause serious human infections under specific circumstances, typically involving changes in the gut environment and/or host immune conditions. Therefore, utilizing animal models of fungal GI colonization and dissemination can lead to significant insights into the complex pathophysiology of transformation from a commensal organism to a pathogen and host-pathogen interactions. This paper will review the methodologic approaches used for modeling GI colonization versus dissemination, the insights learned from these models, and finally, possible future directions using these animal modeling systems.
Loss of Mitochondrial Protein Fus1 Augments Host Resistance to Acinetobacter baumannii Infection
Authors: Hood M. Indriati , Uzhachenko Roman , Boyd Kelli , Skaar Eric P. , Ivanova Alla V. 
Published: September 2013

ABSTRACTFus1 is a tumor suppressor protein with recently described immunoregulatory functions. Although its role in sterile inflammation is being elucidated, its role in regulating immune responses to infectious agents has not been examined. We used here a murine model ofAcinetobacter baumanniipneumonia to identify the role of Fus1 in antibacterial host defenses. We found that the loss of Fus1 in mice results in significantly increased resistance toA. baumanniipneumonia. We observed earlier and more robust recruitment of neutrophils and macrophages to the lungs of infected Fus1−/−mice, with a concomitant increase in phagocytosis of invading bacteria and more rapid clearance. Such a prompt and enhanced immune response to bacterial infection in Fus1−/−mice stems from early activation of proinflammatory pathways (NF-κB and phosphatidylinositol 3-kinase/Akt/mammalian target of rapamycin [mTOR]), most likely due to significantly increased mitochondrial membrane potential and mitochondrial reactive oxygen species production. Significant early upregulation of interleukin-17 (IL-17) in Fus1−/−immune cells was also observed, together with significant downregulation of IL-10. Depletion of neutrophils eliminates the enhanced antibacterial defenses of the Fus1−/−mice, suggesting that ultimately it is the enhanced immune cell recruitment that mediates the increased resistance of Fus1−/−mice toA. baumanniipneumonia. Taken together, our data define the novel role for Fus1 in the immune response toA. baumanniipneumonia and highlight new avenues for immune modulating therapeutic targets for this treatment-resistant nosocomial pathogen.
The Sulfolobus Initiator Element Is an Important Contributor to Promoter Strength
Authors: Ao Xiang , Li Yingjun , Wang Fan , Feng Mingxia , Lin Yanxu , Zhao Shumiao , Liang Yunxiang , Peng Nan 
Published: September 2013

ABSTRACT

Basal elements in archaeal promoters, except for putative initiator elements encompassing transcription start sites, are well characterized. Here, we employed the
Sulfolobus
araS
promoter as a model to study the function of the initiator element (Inr) in archaea. We have provided evidence for the presence of a third core promoter element, the
Sulfolobus
Inr, whose action depends on a TATA box and the TF
B
r
ecognition
e
lement (BRE). Substitution mutations in the
araS
Inr did not alter the location of the transcription start site. Using systematic mutagenesis, the most functional
araS
Inr was defined as +1 GAGAMK +6 (where M is A/C and K is G/T). Furthermore, WebLogo analysis of a subset of promoters with coding sequences for 5′ untranslated regions (UTRs) larger than 4 nucleotides (nt) in
Sulfolobus solfataricus
P2 identified an Inr consensus that exactly matches the functional
araS
Inr sequence. Moreover, mutagenesis of 3 randomly selected promoters confirmed the Inr sequences to be important for basal promoter strength in the subgroup. Importantly, the result of the
araS
Inr being added to the Inr-less promoters indicates that the
araS
Inr, the core promoter element, is able to enhance the strength of Inr-less promoters. We infer that transcription factor B (TFB) and subunits of RNA polymerase bind the Inr to enhance promoter strength. Taken together, our data suggest that the presence or absence of an Inr on basal promoters is important for global gene regulation in
Sulfolobus
.
Control of RNA Stability by NrrF, an Iron-Regulated Small RNA in Neisseria gonorrhoeae
Authors: Jackson Lydgia A. , Pan Jing-Cao , Day Michael W. , Dyer David W. 
Published: September 2013

ABSTRACT

Regulation of gene expression by small noncoding RNAs (sRNAs) plays a critical role in bacterial response to physiological stresses. NrrF, a
trans
-acting sRNA in
Neisseria meningitidis
and
Neisseria gonorrhoeae
, has been shown in the meningococcus to control indirectly, in response to iron (Fe) availability, the transcription of genes encoding subunits of succinate dehydrogenase, a Fe-requiring enzyme. Given that in other organisms, sRNAs target multiple mRNAs to control gene expression, we used a global approach to examine the role of NrrF in controlling gonococcal transcription. Three strains, including
N. gonorrhoeae
FA1090, an
nrrF
deletion mutant, and a complemented derivative, were examined using a custom CombiMatrix microarray to assess the role of this sRNA in controlling gene expression in response to Fe availability. In the absence of NrrF, the mRNA half-lives for 12 genes under Fe-depleted growth conditions were longer than those in FA1090. The 12 genes controlled by NrrF encoded proteins with biological functions including energy metabolism, oxidative stress, antibiotic resistance, and amino acid synthesis, as well as hypothetical proteins and a regulatory protein whose functions are not fully understood.
Streptomyces coelicolor Polynucleotide Phosphorylase Can Polymerize Nucleoside Diphosphates under Phosphorolysis Conditions, with Implications for the Degradation of Structured RNAs
Authors: Jones George H. , Mackie George A. 
Published: September 2013

ABSTRACT

We have examined the ability of wild-type polynucleotide phosphorylase (PNPase) from
Streptomyces coelicolor
and two mutant forms of the enzyme, N459D and C468A, to function in the polymerization of ADP and in the phosphorolysis of RNA substrates derived from the
S. coelicolor rpsO-pnp
operon. The wild-type enzyme was twice as active in polymerization as N459D and four times as active as C468A. The
k
cat
/

K
m

value for phosphorolysis of a structured RNA substrate by N459D was essentially the same as that observed for the wild-type enzyme, while C468A was 50% as active with this substrate. A mixture of all four common nucleoside diphosphates increased the
k
cat
/

K
m

for phosphorolysis of the structured substrate by the wild-type enzyme by a factor of 1.7 but did not affect phosphorolysis catalyzed by N459D or C468A. We conducted phosphorolysis of the structured substrate in the presence of nucleoside diphosphates and labeled the 3′ ends of the products of those reactions using [
32
P]pCp. Digestion of the end-labeled RNAs and display of the products on a sequencing gel revealed that wild-type
S. coelicolor
PNPase was able to synthesize RNA 3′ tails under phosphorolysis conditions while the N459D and C468A mutants could not. The wild-type enzyme did not add 3′ tails to a substrate that already possessed an unstructured 3′ tail. We propose a model in which the transient synthesis of 3′ tails facilitates the phosphorolysis of structured substrates by
Streptomyces
PNPase.