bluuebunny/crossref_metadata_2025_split huggingface dataset:
Borrelia burgdorferi, the Causative Agent of Lyme Disease, Forms Drug-Tolerant Persister Cells
Authors: Sharma Bijaya , Brown Autumn V. , Matluck Nicole E. , Hu Linden T. , Lewis Kim 
Published: May 2015

ABSTRACT

Borrelia burgdorferi
is the causative agent of Lyme disease, which affects an estimated 300,000 people annually in the United States. When treated early, the disease usually resolves, but when left untreated, it can result in symptoms such as arthritis and encephalopathy. Treatment of the late-stage disease may require multiple courses of antibiotic therapy. Given that antibiotic resistance has not been observed for
B. burgdorferi
, the reason for the recalcitrance of late-stage disease to antibiotics is unclear. In other chronic infections, the presence of drug-tolerant persisters has been linked to recalcitrance of the disease. In this study, we examined the ability of
B. burgdorferi
to form persisters. Killing growing cultures of
B. burgdorferi
with antibiotics used to treat the disease was distinctly biphasic, with a small subpopulation of surviving cells. Upon regrowth, these cells formed a new subpopulation of antibiotic-tolerant cells, indicating that these are persisters rather than resistant mutants. The level of persisters increased sharply as the culture transitioned from the exponential to stationary phase. Combinations of antibiotics did not improve killing. Daptomycin, a membrane-active bactericidal antibiotic, killed stationary-phase cells but not persisters. Mitomycin C, an anticancer agent that forms adducts with DNA, killed persisters and eradicated growing and stationary cultures of
B. burgdorferi
. Finally, we examined the ability of pulse dosing an antibiotic to eliminate persisters. After addition of ceftriaxone, the antibiotic was washed away, surviving persisters were allowed to resuscitate, and the antibiotic was added again. Four pulse doses of ceftriaxone killed persisters, eradicating all live bacteria in the culture.
Artemether Exhibits Amoebicidal Activity against Acanthamoeba castellanii through Inhibition of the Serine Biosynthesis Pathway
Authors: Deng Yihong , Ran Wei , Man Suqin , Li Xueping , Gao Hongjian , Tang Wei , Tachibana Hiroshi , Cheng Xunjia 
Published: May 2015

ABSTRACT

Acanthamoeba
sp. parasites are the causative agents of
Acanthamoeba
keratitis, fatal granulomatous amoebic encephalitis, and cutaneous infections. However, there are currently no effective drugs for these organisms. Here, we evaluated the activity of the antimalarial agent artemether against
Acanthamoeba castellanii
trophozoites and identified potential targets of this agent through a proteomic approach. Artemether exhibited
in vitro
amoebicidal activity in a time- and dose-dependent manner and induced ultrastructural modification and cell apoptosis. The iTRAQ quantitative proteomic analysis identified 707 proteins that were differentially expressed after artemether treatment. We focused on phosphoglycerate dehydrogenase and phosphoserine aminotransferase in the serine biosynthesis pathway because of their importance to the growth and proliferation of protozoan and cancer cells. The expression of these proteins in
Acanthamoeba
was validated using quantitative real-time PCR and Western blotting after artemether treatment. The changes in the expression levels of phosphoserine aminotransferase were consistent with those of phosphoglycerate dehydrogenase. Therefore, the downregulation of phosphoserine aminotransferase may be due to the downregulation of phosphoglycerate dehydrogenase. Furthermore, exogenous serine might antagonize the activity of artemether against
Acanthamoeba
trophozoites. These results indicate that the serine biosynthesis pathway is important to amoeba survival and that targeting these enzymes would improve the treatment of
Acanthamoeba
infections. Artemether may be used as a phosphoglycerate dehydrogenase inhibitor to control or block
Acanthamoeba
infections.
Four-Component Staphylococcus aureus Vaccine 4C-Staph Enhances Fcγ Receptor Expression in Neutrophils and Monocytes and Mitigates S. aureus Infection in Neutropenic Mice
Authors: Torre Antonina , Bacconi Marta , Sammicheli Chiara , Galletti Bruno , Laera Donatello , Fontana Maria Rita , Grandi Guido , De Gregorio Ennio , Bagnoli Fabio , Nuti Sandra , Bertholet Sylvie , Bensi Giuliano 
Published: May 2015

ABSTRACT

Staphylococcus aureus
is a human bacterial pathogen causing a variety of diseases. The occurrence of multidrug-resistant strains of
Staphylococcus aureus
underlines the need for a vaccine. Defining immune correlates of protection may support the design of an effective vaccine. We used a murine
Staphylococcus aureus
infection model, in which bacteria were inoculated in an air pouch generated on the back of the animal. Analysis of the air-pouch content in mice immunized or not with an adjuvanted multiantigen vaccine formulation, four-component
S. aureus
vaccine (4C-Staph), prior to infection allowed us to measure bacteria, cytokines, and 4C-Staph-specific antibodies and to analyze host immune cells recruited to the infection site. Immunization with 4C-Staph resulted in accumulation of antigen-specific antibodies in the pouch and mitigated the infection. Neutrophils were the most abundant cells in the pouch, and they showed the upregulation of Fcγ receptor (FcγR) following immunization with 4C-Staph. Reduction of the infection was also obtained in mice immunized with 4C-Staph and depleted of neutrophils; these mice showed an increase in monocytes and macrophages. Upregulation of the FcγR and the presence of antigen-specific antibodies induced by immunization with 4C-Staph may contribute to increase bacterial opsonophagocytosis. Protection in neutropenic mice indicated that an effective vaccine could activate alternative protection mechanisms compensating for neutropenia, a condition often occurring in
S. aureus
-infected patients.
Host-Like Carbohydrates Promote Bloodstream Survival of Vibrio vulnificusIn Vivo
Authors: Lubin Jean-Bernard , Lewis Warren G. , Gilbert Nicole M. , Weimer Cory M. , Almagro-Moreno Salvador , Boyd E. Fidelma , Lewis Amanda L. 
Published: May 2015

ABSTRACTSialic acids are found on all vertebrate cell surfaces and are part of a larger class of molecules known as nonulosonic acids. Many bacterial pathogens synthesize related nine-carbon backbone sugars; however, the role(s) of these non-sialic acid molecules in host-pathogen interactions is poorly understood.Vibrio vulnificusis the leading cause of seafood-related death in the United States due to its ability to quickly access the host bloodstream, which it can accomplish through gastrointestinal or wound infection. However, little is known about how this organism persists systemically. Here we demonstrate that sialic acid-like molecules are present on the lipopolysaccharide ofV. vulnificus, are required for full motility and biofilm formation, and also contribute to the organism's natural resistance to polymyxin B. Further experiments in a murine model of intravenousV. vulnificusinfection demonstrated that expression of nonulosonic acids had a striking benefit for bacterial survival during bloodstream infection and dissemination to other tissuesin vivo. In fact, levels of bacterial persistence in the blood corresponded to the overall levels of these molecules expressed byV. vulnificusisolates. Taken together, these results suggest that molecules similar to sialic acids evolved to facilitate the aquatic lifestyle ofV. vulnificusbut that their emergence also resulted in a gain of function with life-threatening potential in the human host.
Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal
Authors: Erill Ivan 
Published: May 2015

ABSTRACT
Experimentally verified transcription factor-binding sites represent an information-rich and highly applicable data type that aptly summarizes the results of time-consuming experiments and inference processes. Currently, there is no centralized repository for this type of data, which is routinely embedded in articles and extremely hard to mine. CollecTF provides the first standardized resource for submission and deposition of these data into the NCBI RefSeq database, maximizing its accessibility and prompting the community to adopt direct submission policies.
Copper Tolerance and Characterization of a Copper-Responsive Operon,
copYAZ
, in an M1T1 Clinical Strain of Streptococcus pyogenes
Authors: Young Christie A. , Gordon Lily D. , Fang Zhong , Holder Robert C. , Reid Sean D. 
Published: May 2015

ABSTRACT

Infection with
Streptococcus pyogenes
is associated with a breadth of clinical manifestations ranging from mild pharyngitis to severe necrotizing fasciitis. Elevated levels of intracellular copper are highly toxic to this bacterium, and thus, the microbe must tightly regulate the level of this metal ion by one or more mechanisms, which have, to date, not been clearly defined. In this study, we have identified two virulence mechanisms by which
S. pyogenes
protects itself against copper toxicity. We defined a set of putative genes,
copY
(for a regulator),
copA
(for a P1-type ATPase), and
copZ
(for a copper chaperone), whose expression is regulated by copper. Our results indicate that these genes are highly conserved among a range of clinical
S. pyogenes
isolates. The
copY
,
copA
, and
copZ
genes are induced by copper and are transcribed as a single unit. Heterologous expression assays revealed that
S. pyogenes
CopA can confer copper tolerance in a copper-sensitive
Escherichia coli
mutant by preventing the accumulation of toxic levels of copper, a finding that is consistent with a role for CopA in copper export. Evaluation of the effect of copper stress on
S. pyogenes
in a planktonic or biofilm state revealed that biofilms may aid in protection during initial exposure to copper. However, copper stress appears to prevent the shift from the planktonic to the biofilm state. Therefore, our results indicate that
S. pyogenes
may use several virulence mechanisms, including altered gene expression and a transition to and from planktonic and biofilm states, to promote survival during copper stress.

IMPORTANCE
Bacterial pathogens encounter multiple stressors at the host-pathogen interface. This study evaluates a virulence mechanism(s) utilized by
S. pyogenes
to combat copper at sites of infection. A better understanding of pathogen tolerance to stressors such as copper is necessary to determine how host-pathogen interactions impact bacterial survival during infections. These insights may lead to the identification of novel therapeutic targets that can be used to address antibiotic resistance.
Critical Components of the Conjugation Machinery of the Integrative and Conjugative Element ICE
Bs1
of Bacillus subtilis
Authors: Leonetti Cori T. , Hamada Matt A. , Laurer Stephanie J. , Broulidakis Matthew P. , Swerdlow Kyle J. , Lee Catherine A. , Grossman Alan D. , Berkmen Melanie B. 
Published: May 2015

ABSTRACT

Conjugation, or mating, plays a profound role in bacterial evolution by spreading genes that allow bacteria to adapt to and colonize new niches. ICE
Bs1
, an integrative and conjugative element of
Bacillus subtilis
, can transfer itself and mobilize resident plasmids. DNA transfer is mediated by a type IV secretion system (T4SS). Characterized components of the ICE
Bs1
T4SS include the conserved VirB4-like ATPase ConE, the bifunctional cell wall hydrolase CwlT, and the presumed VirD4-like coupling protein ConQ. A fusion of ConE to green fluorescent protein (GFP) localizes to the membrane preferentially at the cell poles. One or more ICE
Bs1
proteins are required for ConE's localization at the membrane, as ConE lacks predicted transmembrane segments and ConE-GFP is found dispersed throughout the cytoplasm in cells lacking ICE
Bs1
. Here, we analyzed five ICE
Bs1
genes to determine if they are required for DNA transfer and/or ConE-GFP localization. We found that
conB
,
conC
,
conD
, and
conG
, but not
yddF
, are required for both ICE
Bs1
transfer and plasmid mobilization. All four required genes encode predicted integral membrane proteins.
conB
and, to some extent,
conD
were required for localization of ConE-GFP to the membrane. Using an adenylate cyclase-based bacterial two-hybrid system, we found that ConE interacts with ConB. We propose a model in which the ICE
Bs1
conjugation machinery is composed of ConB, ConC, ConD, ConE, ConG, CwlT, ConQ, and possibly other ICE
Bs1
proteins, and that ConB interacts with ConE, helping to recruit and/or maintain ConE at the membrane.

IMPORTANCE
Conjugation is a major form of horizontal gene transfer and has played a profound role in bacterial evolution by moving genes, including those involved in antibiotic resistance, metabolism, symbiosis, and infectious disease. During conjugation, DNA is transferred from cell to cell through the conjugation machinery, a type of secretion system. Relatively little is known about the conjugation machinery of Gram-positive bacteria. Here, we analyzed five genes of the integrative and conjugative element ICE
Bs1
of
Bacillus subtilis
. Our research identifies four new components of the ICE
Bs1
conjugation machinery (ConB, ConC, ConD, and ConG) and shows an interaction between ConB and ConE that is required for ConE to associate with the cell membrane.
A Mutant Chaperonin That Is Functional at Lower Temperatures Enables Hyperthermophilic Archaea To Grow under Cold-Stress Conditions
Authors: Gao Le , Imanaka Tadayuki , Fujiwara Shinsuke 
Published: May 2015

ABSTRACT

Thermococcus kodakarensis
grows optimally at 85°C and possesses two chaperonins, cold-inducible CpkA and heat-inducible CpkB, which are involved in adaptation to low and high temperatures, respectively. The two chaperonins share a high sequence identity (77%), except in their C-terminal regions. CpkA, which contains tandem repeats of a GGM motif, shows its highest ATPase activity at 60°C to 70°C, whereas CpkB shows its highest activity at temperatures higher than 90°C. To clarify the effects of changes in ATPase activity on chaperonin function at lower temperatures, various CpkA variants were constructed by introducing single point mutations into the C-terminal region. A CpkA variant in which Glu530 was replaced with Gly (CpkA-E530G) showed increased ATPase activity, with its highest activity at 50°C. The efficacy of the CpkA variants against denatured indole-3-glycerol-phosphate synthase of
T. kodakarensis
(TrpC

Tk

), which is a CpkA target, was then examined
in vitro
. CpkA-E530G was more effective than wild-type CpkA at facilitating the refolding of chemically unfolded TrpC

Tk

at 50°C. The effect of
cpkA-E530G
on cell growth was then examined by introducing
cpkA-E530G
into the genome of
T. kodakarensis
KU216 (
pyrF
). The mutant strain, DA4 (
pyrF cpkA-E530G
), grew as well as the parental KU216 strain at 60°C. In contrast, DA4 grew more vigorously than KU216 at 50°C. These results suggested that the CpkA-E530G mutation prevented cold denaturation of proteins under cold-stress conditions, thereby enabling cells to grow in cooler environments. Thus, a single base pair substitution in a chaperonin gene allows cells to grow vigorously in a new environment.

IMPORTANCE
Thermococcus kodakarensis
possesses two group II chaperonins, cold-inducible CpkA and heat-inducible CpkB, which are involved in adaptation to low and high temperatures, respectively. CpkA might act as an “adaptive allele” to adapt to cooler environments. In this study, we compared the last 20 amino acids within the C termini of the chaperonins and found a clear correlation between the CpkA-type chaperonin gene copy number and growth temperature. Furthermore, we introduced single mutations into the CpkA C-terminal region to clarify its role in cold adaptation, and we showed that a single base substitution allowed the organism to adapt to a lower temperature. The present data suggest that hyperthermophiles have evolved by obtaining mutations in chaperonins that allow them to adapt to a colder environment.
Databases for Microbiologists
Authors: Zhulin Igor B. 
Published: May 2015

ABSTRACT
Databases play an increasingly important role in biology. They archive, store, maintain, and share information on genes, genomes, expression data, protein sequences and structures, metabolites and reactions, interactions, and pathways. All these data are critically important to microbiologists. Furthermore, microbiology has its own databases that deal with model microorganisms, microbial diversity, physiology, and pathogenesis. Thousands of biological databases are currently available, and it becomes increasingly difficult to keep up with their development. The purpose of this minireview is to provide a brief survey of current databases that are of interest to microbiologists.
Cooperative Roles for Fimbria and Filamentous Hemagglutinin inBordetellaAdherence and Immune Modulation
Authors: Scheller Erich V. , Melvin Jeffrey A. , Sheets Amanda J. , Cotter Peggy A. 
Published: May 2015

ABSTRACTBordetellafimbriae (FIM) are generally considered to function as adhesins despite a lack of experimental evidence supporting this conclusion forBordetella pertussisand evidence against a requirement for FIM in adherence ofBordetella bronchisepticato mammalian cell lines. UsingB. bronchisepticaand mice, we developed anin vivoadherence assay that revealed that FIM do function as critically important adhesins in the lower respiratory tract. In the first few days postinoculation, FIM-deficientB. bronchisepticainduced a more robust inflammatory response than wild-type bacteria did, suggesting that FIM, like filamentous hemagglutinin (FHA), allowB. bronchisepticato suppress the innate immune response to infection. Localization analyses indicated that FIM are required for efficient attachment to airway epithelium, as bacteria lacking FIM localized to alveoli. FHA-deficient bacteria, in contrast, localized to airways. Bacteria unable to produce both FIM and FHA localized to alveoli and caused increased inflammation and histopathology identical to that caused by FIM-deficient bacteria, demonstrating that lack of FIM is epistatic to lack of FHA. Coinoculation experiments provided evidence that wild-typeB. bronchisepticasuppresses inflammation locally within the respiratory tract and that both FHA and FIM are required for defense against clearance by the innate immune system. Altogether, our data suggest that FIM-mediated adherence to airway epithelium is a critical first step inBordetellainfection that allows FHA-dependent interactions to mediate tight adherence, suppression of inflammation, and resistance to inflammatory cell-mediated clearance. Our results suggest that mucosal antibodies capable of blocking FIM-mediated interactions could prevent bacterial colonization of the lower respiratory tract.IMPORTANCEAlthough fimbriae (FIM) have been shown to be important mediators of adherence for many bacterial pathogens, there is surprisingly little experimental evidence supporting this role forBordetellafimbria. Our results provide the first demonstration thatBordetellaFIM function as adhesinsin vivo, specifically to airway epithelium. Furthermore, our results suggest that FIM mediate initial interactions with airway epithelial cells that are followed by tight filamentous hemagglutinin (FHA)-mediated binding and that together, FIM and FHA allowBordetellato suppress inflammation, leading to prolonged colonization. Given the shortcoming of the current acellular component pertussis (aP) vaccine in preventing colonization, these findings suggest that generation of antibodies capable of blocking FIM-mediated adherence could potentially preventBordetellacolonization.
Niemann-Pick C1 Is Essential for Ebolavirus Replication and Pathogenesis
In Vivo
Authors: Herbert Andrew S. , Davidson Cristin , Kuehne Ana I. , Bakken Russell , Braigen Stephen Z. , Gunn Kathryn E. , Whelan Sean P. , Brummelkamp Thijn R. , Twenhafel Nancy A. , Chandran Kartik , Walkley Steven U. , Dye John M. 
Published: May 2015

ABSTRACT

Recent work demonstrated that the Niemann-Pick C1 (NPC1) protein is an essential entry receptor for filoviruses. While previous studies focused on filovirus entry requirements of NPC1
in vitro
, its roles in filovirus replication and pathogenesis
in vivo
remain unclear. Here, we evaluated the importance of NPC1, and its partner in cholesterol transport, NPC2, by using a mouse model of Ebolavirus (EBOV) disease. We found that, whereas wild-type mice had high viral loads and succumbed to EBOV infection,

Npc1
−/−

mice were entirely free of viral replication and completely protected from EBOV disease. Interestingly,

Npc1
+/−

mice transiently developed high levels of viremia, but were nevertheless substantially protected from EBOV challenge. We also found

Npc2
−/−

mice to be fully susceptible to EBOV infection, while

Npc1
−/−

mice treated to deplete stored lysosomal cholesterol remained completely resistant to EBOV infection. These results provide mechanistic evidence that NPC1 is directly required for EBOV infection
in vivo
, with little or no role for NPC1/NPC2-dependent cholesterol transport. Finally, we assessed the
in vivo
antiviral efficacies of three compounds known to inhibit NPC1 function or NPC1-glycoprotein binding
in vitro
. Two compounds reduced viral titers
in vivo
and provided a modest, albeit not statistically significant, degree of protection. Taken together, our results show that NPC1 is critical for replication and pathogenesis in animals and is a bona fide target for development of antifilovirus therapeutics. Additionally, our findings with

Npc1
+/−

mice raise the possibility that individuals heterozygous for NPC1 may have a survival advantage in the face of EBOV infection.

IMPORTANCE
Researchers have been searching for an essential filovirus receptor for decades, and numerous candidate receptors have been proposed. However, none of the proposed candidate receptors has proven essential in all
in vitro
scenarios, nor have they proven essential when evaluated using animal models. In this report, we provide the first example of a knockout mouse that is completely refractory to EBOV infection, replication, and disease. The findings detailed here provide the first critical
in vivo
data illustrating the absolute requirement of NPC1 for filovirus infection in mice. Our work establishes NPC1 as a legitimate target for the development of anti-EBOV therapeutics. However, the limited success of available NPC1 inhibitors to protect mice from EBOV challenge highlights the need for new molecules or approaches to target NPC1
in vivo
.