bluuebunny/crossref_metadata_2025_split huggingface dataset:
Toll-Like Receptor 2 and NALP2 Mediate Induction of Human Beta-Defensins byFusobacterium nucleatumin Gingival Epithelial Cells
Authors: Ji Suk , Shin Ji Eun , Kim Young Sook , Oh Ju-Eun , Min Byung-Moo , Choi Youngnim 
Published: December 2008

ABSTRACTWe previously reported that infection byFusobacterium nucleatumstrongly induced the expression of both human beta-defensin 2 (HBD-2) and HBD-3 by gingival epithelial cells. The aim of this study was to characterize the pattern recognition receptors (PRRs) and regulatory mechanisms involved in the induction of HBD-2 and -3 expression byF. nucleatumin gingival epithelial cells. Immortalized human gingival epithelial HOK-16B cells were infected with live or heat-killedF. nucleatum, and the expression of HBDs and interleukin-8 (IL-8) was examined by real-time reverse transcription-PCR and enzyme-linked immunosorbent assay, respectively. Live, but not heat-killed,F. nucleatuminvaded HOK-16B cells, as seen by confocal microscopy and flow cytometry. LiveF. nucleatuminduced both HBD-2 and -3 efficiently, whereas heat-killed bacteria induced only HBD-3 at a reduced level. Knockdown of NACHT-LRR- and pyrin domain-containing protein 2 (NALP2), the most abundant intracellular PRR in HOK-16B cells, by RNA interference (RNAi) significantly reduced the induction of HBD-3 but not HBD-2 and IL-8. In addition, knockdown of Toll-like receptor 2 (TLR2) by RNAi reduced the upregulation of HBD-2 and -3 but not IL-8. Heat-killedF. nucleatumwas hindered in its ability to activate TLR2 and JNK signaling pathways. Theses data show that TLR2 and NALP2 mediate the induction of HBDs byF. nucleatumin gingival epithelial cells, but thresholds for the two HBD genes are different.
An Engineered Human Antibody Fab Fragment Specific for
Pseudomonas aeruginosa
PcrV Antigen Has Potent Antibacterial Activity
Authors: Baer Mark , Sawa Teiji , Flynn Peter , Luehrsen Kenneth , Martinez David , Wiener-Kronish Jeanine P. , Yarranton Geoffrey , Bebbington Christopher 
Published: December 2008

ABSTRACT

Pseudomonas aeruginosa
is an opportunistic pathogen that can cause acute lung injury and mortality through the delivery of exotoxins by the type III secretion system (TTSS). PcrV is an important structural protein of the TTSS. An engineered human antibody Fab fragment that binds to the
P. aeruginosa
PcrV protein with high affinity has been identified and has potent in vitro neutralization activity against the TTSS. The instillation of a single dose of Fab into the lungs of mice provided protection against lethal pulmonary challenge of
P. aeruginosa
and led to a substantial reduction of viable bacterial counts in the lungs. These results demonstrate that blocking of the TTSS by a Fab lacking antibody Fc-mediated effector functions can be sufficient for the effective clearance of pulmonary
P. aeruginosa
infection.
Role of NADPH Phagocyte Oxidase in Host Defense against Acute Respiratory
Acinetobacter baumannii
Infection in Mice
Authors: Qiu Hongyu , KuoLee Rhonda , Harris Greg , Chen Wangxue 
Published: December 2008

ABSTRACT

Acinetobacter baumannii
is an emerging bacterial pathogen that rapidly develops multiple-drug resistance and is responsible for many nosocomial pulmonary infections. This study investigated the role of the NADPH phagocyte oxidase (phox) and inducible nitric oxide synthase (NOS2) in the host defense against respiratory infection with
A. baumannii
in mouse models of intranasal
A. baumannii
infection. gp91
phox−/−
mice showed higher susceptibility to
A. baumannii
infection than wild-type (WT) C57BL/6 mice, with significantly greater bacterial counts in their lungs (1,000-fold) (
P
< 0.005) and spleens (10-fold) (
P
< 0.05). Moreover, all of the gp91
phox−/−
mice succumbed to infection within 48 h. In contrast, only a moderate increase in bacterial burdens was detected in the lungs of NOS2
−/−
mice, and all NOS2
−/−
mice survived infection. Compared to WT mice, the pulmonary influx of inflammatory cells and serum and local inflammatory cytokine/chemokine responses were not obviously impaired at 4 h and were significantly higher at 24 h (
P
< 0.05) in gp91
phox−/−
mice, but NADPH-deficient neutrophils were unable to control bacterial replication and extrapulmonary dissemination. Thus, NADPH phagocyte oxidase appears to play a crucial role in the neutrophil-mediated host defense against
A. baumannii
.
Role of the
dosR
-
dosS
Two-Component Regulatory System in
Mycobacterium tuberculosis
Virulence in Three Animal Models
Authors: Converse Paul J. , Karakousis Petros C. , Klinkenberg Lee G. , Kesavan Anup K. , Ly Lan H. , Allen Shannon Sedberry , Grosset Jacques H. , Jain Sanjay K. , Lamichhane Gyanu , Manabe Yukari C. , McMurray David N. , Nuermberger Eric L. , Bishai William R. 
Published: December 2008

ABSTRACT

The
Mycobacterium tuberculosis dosR
gene (Rv3133c) is part of an operon, Rv3134c-Rv3132c, and encodes a response regulator that has been shown to be upregulated by hypoxia and other in vitro stress conditions and may be important for bacterial survival within granulomatous lesions found in tuberculosis. DosR is activated in response to hypoxia and nitric oxide by DosS (Rv3132c) or DosT (Rv2027c). We compared the virulence levels of an
M. tuberculosis dosR
-
dosS
deletion mutant (Δ
dosR
-
dosS
[Δ
dosR-S
]), a
dosR
-complemented strain, and wild-type H37Rv in rabbits, guinea pigs, and mice infected by the aerosol route and in a mouse hollow-fiber model that may mimic in vivo granulomatous conditions. In the mouse and the guinea pig models, the Δ
dosR
-
S
mutant exhibited a growth defect. In the rabbit, the Δ
dosR
-
S
mutant did not replicate more than the wild type. In the hollow-fiber model, the mutant phenotype was not different from that of the wild-type strain. Our analyses reveal that the
dosR
and
dosS
genes are required for full virulence and that there may be differences in the patterns of attenuation of this mutant between the animal models studied.
Characterization of a γ-Aminobutyric Acid Transport System of
Rhizobium leguminosarum
bv. viciae 3841
Authors: White J. P. , Prell J. , Ramachandran V. K. , Poole P. S. 
Published: December 2008

ABSTRACT

Spontaneous mutants of
Rhizobium leguminosarum
bv. viciae 3841 were isolated that grow faster than the wild type on γ-aminobutyric acid (GABA) as the sole carbon and nitrogen source. These strains (RU1736 and RU1816) have frameshift mutations (
gtsR101
and
gtsR102
, respectively) in a GntR-type regulator (GtsR) that result in a high rate of constitutive GABA transport. Tn
5
mutagenesis and quantitative reverse transcription-PCR showed that GstR regulates expression of a large operon (pRL100242 to pRL100252) on the Sym plasmid that is required for GABA uptake. An ABC transport system, GtsABCD (for GABA transport system) (pRL100248-51), of the spermidine/putrescine family is part of this operon. GtsA is a periplasmic binding protein, GtsB and GtsC are integral membrane proteins, and GtsD is an ATP-binding subunit. Expression of
gtsABCD
from a
lacZ
promoter confirmed that it alone is responsible for high rates of GABA transport, enabling rapid growth of strain 3841 on GABA. Gts transports open-chain compounds with four or five carbon atoms with carboxyl and amino groups at, or close to, opposite termini. However, aromatic compounds with similar spacing between carboxyl and amino groups are excellent inhibitors of GABA uptake so they may also be transported. In addition to the ABC transporter, the operon contains two putative mono-oxygenases, a putative hydrolase, a putative aldehyde dehydrogenase, and a succinate semialdehyde dehydrogenase. This suggests the operon may be involved in the transport and breakdown of a more complex precursor to GABA. Gts is not expressed in pea bacteroids, and
gtsB
mutants are unaltered in their symbiotic phenotype, suggesting that Bra is the only GABA transport system available for amino acid cycling.
Characterization of the Autocleavage Process of the
Escherichia coli
HtrA Protein: Implications for its Physiological Role
Authors: Jomaa Ahmad , Iwanczyk Jack , Tran Julie , Ortega Joaquin 
Published: December 2008

ABSTRACT

The
Escherichia coli
HtrA protein is a periplasmic protease/chaperone that is upregulated under stress conditions. The protease and chaperone activities of HtrA eliminate or refold damaged and unfolded proteins in the bacterial periplasm that are generated upon stress conditions. In the absence of substrates, HtrA oligomerizes into a hexameric cage, but binding of misfolded proteins transforms the hexamers into bigger 12-mer and 24-mer cages that encapsulate the substrates for degradation or refolding. HtrA also undergoes partial degradation as a consequence of self-cleavage of the mature protein, producing short-HtrA protein (s-HtrA). The aim of this study was to examine the physiological role of this self-cleavage process. We found that the only requirement for self-cleavage of HtrA into s-HtrA in vitro was the hydrolysis of protein substrates. In fact, peptides resulting from the hydrolysis of the protein substrates were sufficient to induce autocleavage. However, the continuous presence of full-length substrate delayed the process. In addition, we observed that the hexameric cage structure is required for autocleavage and that s-HtrA accumulates only late in the degradation reaction. These results suggest that self-cleavage occurs when HtrA reassembles back into the resting hexameric structure and peptides resulting from substrate hydrolysis are allosterically stimulating the HtrA proteolytic activity. Our data support a model in which the physiological role of the self-cleavage process is to eliminate the excess of HtrA once the stress conditions cease.
An Intramolecular Upstream Helix Ensures the Stability of a Toxin-Encoding RNA inEnterococcus faecalis
Authors: Shokeen Sonia , Greenfield Tony J. , Ehli Erik A. , Rasmussen Jessica , Perrault Brian E. , Weaver Keith E. 
Published: December 2008

ABSTRACTTheparstability determinant is required for the stable inheritance of the plasmid pAD1 in its native host,Enterococcus faecalis.It is the only antisense RNA-regulated addiction module identified to date in gram-positive bacteria. It encodes two small, convergently transcribed RNAs, RNA I and RNA II. RNA I encodes the Fst toxin and RNA II acts as the antitoxin by interacting with RNA I posttranscriptionally. As the toxin-encoding component of the system, it is important that RNA I is more stable than RNA II. This study reveals that a helix sequestering the 5′ end of RNA I plays a crucial role in maintaining the stability of the RNA I. An adjacent structure previously determined to regulate Fst translation was not required to enhance stability. Results indicated that endoribonuclease J2 contributes significantly to the degradation of a mutant disrupting the upstream helix (UH) of RNA I inBacillus subtilis.Finally, it was shown that interaction with RNA II stabilized the UH mutant of RNA I.
Prediction of protein-protein binding site by using core interface residue and support vector machine
Authors: Li Nan , Sun Zhonghua , Jiang Fan 
Published: December 2008

Abstract

Background
The prediction of protein-protein binding site can provide structural annotation to the protein interaction data from proteomics studies. This is very important for the biological application of the protein interaction data that is increasing rapidly. Moreover, methods for predicting protein interaction sites can also provide crucial information for improving the speed and accuracy of protein docking methods.

Results
In this work, we describe a binding site prediction method by designing a new residue neighbour profile and by selecting only the core-interface residues for SVM training. The residue neighbour profile includes both the sequential and the spatial neighbour residues of an interface residue, which is a more complete description of the physical and chemical characteristics surrounding the interface residue. The concept of core interface is applied in selecting the interface residues for training the SVM models, which is shown to result in better discrimination between the core interface and other residues.
The best SVM model trained was tested on a test set of 50 randomly selected proteins. The sensitivity, specificity, and MCC for the prediction of the core interface residues were 60.6%, 53.4%, and 0.243, respectively. Our prediction results on this test set were compared with other three binding site prediction methods and found to perform better. Furthermore, our method was tested on the 101 unbound proteins from the protein-protein interaction benchmark v2.0. The sensitivity, specificity, and MCC of this test were 57.5%, 32.5%, and 0.168, respectively.

Conclusion
By improving both the descriptions of the interface residues and their surrounding environment and the training strategy, better SVM models were obtained and shown to outperform previous methods. Our tests on the unbound protein structures suggest further improvement is possible.
The meaning of alignment: lessons from structural diversity
Authors: Pirovano Walter , Feenstra K Anton , Heringa Jaap 
Published: December 2008

Abstract

Background
Protein structural alignment provides a fundamental basis for deriving principles of functional and evolutionary relationships. It is routinely used for structural classification and functional characterization of proteins and for the construction of sequence alignment benchmarks. However, the available techniques do not fully consider the implications of protein structural diversity and typically generate a single alignment between sequences.

Results
We have taken alternative protein crystal structures and generated simulation snapshots to explicitly investigate the impact of structural changes on the alignments. We show that structural diversity has a significant effect on structural alignment. Moreover, we observe alignment inconsistencies even for modest spatial divergence, implying that the biological interpretation of alignments is less straightforward than commonly assumed. A salient example is the GroES 'mobile loop' where sub-Ångstrom variations give rise to contradictory sequence alignments.

Conclusion
A comprehensive treatment of ambiguous alignment regions is crucial for further development of structural alignment applications and for the representation of alignments in general. For this purpose we have developed an on-line database containing our data and new ways of visualizing alignment inconsistencies, which can be found at http://www.ibi.vu.nl/databases/stralivari.
An evolutionary and structural characterization of mammalian protein complex organization
Authors: Wong Philip , Althammer Sonja , Hildebrand Andrea , Kirschner Andreas , Pagel Philipp , Geissler Bernd , Smialowski Pawel , Blöchl Florian , Oesterheld Matthias , Schmidt Thorsten , Strack Normann , Theis Fabian J , Ruepp Andreas , Frishman Dmitrij 
Published: December 2008

Abstract

Background
We have recently released a comprehensive, manually curated database of mammalian protein complexes called CORUM. Combining CORUM with other resources, we assembled a dataset of over 2700 mammalian complexes. The availability of a rich information resource allows us to search for organizational properties concerning these complexes.

Results
As the complexity of a protein complex in terms of the number of unique subunits increases, we observed that the number of such complexes and the mean non-synonymous to synonymous substitution ratio of associated genes tend to decrease. Similarly, as the number of different complexes a given protein participates in increases, the number of such proteins and the substitution ratio of the associated gene also tends to decrease. These observations provide evidence relating natural selection and the organization of mammalian complexes. We also observed greater homogeneity in terms of predicted protein isoelectric points, secondary structure and substitution ratio in annotated versus randomly generated complexes. A large proportion of the protein content and interactions in the complexes could be predicted from known binary protein-protein and domain-domain interactions. In particular, we found that large proteins interact preferentially with much smaller proteins.

Conclusion
We observed similar trends in yeast and other data. Our results support the existence of conserved relations associated with the mammalian protein complexes.
Hairy-root organ cultures for the production of human acetylcholinesterase
Authors: Woods Ryan R , Geyer Brian C , Mor Tsafrir S 
Published: December 2008

Abstract

Background
Human cholinesterases can be used as a bioscavenger of organophosphate toxins used as pesticides and chemical warfare nerve agents. The practicality of this approach depends on the availability of the human enzymes, but because of inherent supply and regulatory constraints, a suitable production system is yet to be identified.

Results
As a promising alternative, we report the creation of "hairy root" organ cultures derived via Agrobacterium rhizogenes-mediated transformation from human acetylcholinesterase-expressing transgenic Nicotiana benthamiana plants. Acetylcholinesterase-expressing hairy root cultures had a slower growth rate, reached to the stationary phase faster and grew to lower maximal densities as compared to wild type control cultures. Acetylcholinesterase accumulated to levels of up to 3.3% of total soluble protein, ~3 fold higher than the expression level observed in the parental plant. The enzyme was purified to electrophoretic homogeneity. Enzymatic properties were nearly identical to those of the transgenic plant-derived enzyme as well as to those of mammalian cell culture derived enzyme. Pharmacokinetic properties of the hairy-root culture derived enzyme demonstrated a biphasic clearing profile. We demonstrate that master banking of plant material is possible by storage at 4°C for up to 5 months.

Conclusion
Our results support the feasibility of using plant organ cultures as a successful alternative to traditional transgenic plant and mammalian cell culture technologies.
Human cellular microRNA hsa-miR-29a interferes with viral nef protein expression and HIV-1 replication
Authors: Ahluwalia Jasmine K , Khan Sohrab Zafar , Soni Kartik , Rawat Pratima , Gupta Ankit , Hariharan Manoj , Scaria Vinod , Lalwani Mukesh , Pillai Beena , Mitra Debashis , Brahmachari Samir K 
Published: December 2008

Abstract

Background
Cellular miRNAs play an important role in the regulation of gene expression in eukaryotes. Recently, miRNAs have also been shown to be able to target and inhibit viral gene expression. Computational predictions revealed earlier that the HIV-1 genome includes regions that may be potentially targeted by human miRNAs. Here we report the functionality of predicted miR-29a target site in the HIV-1 nef gene.

Results
We find that the human miRNAs hsa-miR-29a and 29b are expressed in human peripheral blood mononuclear cells. Expression of a luciferase reporter bearing the nef miR-29a target site was decreased compared to the luciferase construct without the target site. Locked nucleic acid modified anti-miRNAs targeted against hsa-miR-29a and 29b specifically reversed the inhibitory effect mediated by cellular miRNAs on the target site. Ectopic expression of the miRNA results in repression of the target Nef protein and reduction of virus levels.

Conclusion
Our results show that the cellular miRNA hsa-miR29a downregulates the expression of Nef protein and interferes with HIV-1 replication.
Traditional Indian medicine and homeopathy for HIV/AIDS: a review of the literature
Authors: Fritts M , Crawford CC , Quibell D , Gupta A , Jonas WB , Coulter I , Andrade SA 
Published: December 2008

AbstractBackgroundAllopathic practitioners in India are outnumbered by practitioners of traditional Indian medicine and homeopathy (TIMH), which is used by up to two-thirds of its population to help meet primary health care needs, particularly in rural areas. India has an estimated 2.5 million HIV infected persons. However, little is known about TIMH use, safety or efficacy in HIV/AIDS management in India, which has one of the largest indigenous medical systems in the world. The purpose of this review was to assess the quality of peer-reviewed, published literature on TIMH for HIV/AIDS care and treatment.ResultsOf 206 original articles reviewed, 21 laboratory studies, 17 clinical studies, and 6 previous reviews of the literature were identified that covered at least one system of TIMH, which includes Ayurveda, Unani medicine, Siddha medicine, homeopathy, yoga and naturopathy. Most studies examined either Ayurvedic or homeopathic treatments. Only 4 of these studies were randomized controlled trials, and only 10 were published in MEDLINE-indexed journals. Overall, the studies reported positive effects and even "cure" and reversal of HIV infection, but frequent methodological flaws call into question their internal and external validity. Common reasons for poor quality included small sample sizes, high drop-out rates, design flaws such as selection of inappropriate or weak outcome measures, flaws in statistical analysis, and reporting flaws such as lack of details on products and their standardization, poor or no description of randomization, and incomplete reporting of study results.ConclusionThis review exposes a broad gap between the widespread use of TIMH therapies for HIV/AIDS, and the dearth of high-quality data supporting their effectiveness and safety. In light of the suboptimal effectiveness of vaccines, barrier methods and behavior change strategies for prevention of HIV infection and the cost and side effects of antiretroviral therapy (ART) for its treatment, it is both important and urgent to develop and implement a rigorous research agenda to investigate the potential risks and benefits of TIMH and to identify its role in the management of HIV/AIDS and associated illnesses in India.