bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generation of a phage‐display library of single‐domain camelid VHH antibodies directed against Chlamydomonas reinhardtii antigens, and characterization of VHHs binding cell‐surface antigens
Authors: Jiang Wenzhi , Rosenberg Julian N. , Wauchope Akelia D. , Tremblay Jacqueline M. , Shoemaker Charles B. , Weeks Donald P. , Oyler George A. 
Published: August 2013

SummarySingle‐domain antibodies (sdAbs) are powerful tools for the detection, quantification, purification and subcellular localization of proteins of interest in biological research. We have generated camelid (Lama pacos) heavy chain‐only variable VH domain (VHH) libraries against antigens in total cell lysates from Chlamydomonas reinhardtii. The sdAbs in the sera from immunized animals and VHH antibody domains isolated from the library show specificity to C. reinhardtii and lack of reactivity to antigens from four other algae: Chlorella variabilis, Coccomyxa subellipsoidea, Nannochloropsis oceanica and Thalassiosira pseudonana. Antibodies were produced against a diverse representation of antigens as evidenced by sera ELISA and protein‐blot analyses. A phage‐display library consisting of the VHH region contained at least 106 individual transformants, and thus should represent a wide range of C. reinhardtii antigens. The utility of the phage library was demonstrated by using live C. reinhardtii cells to pan for VHH clones with specific recognition of cell‐surface epitopes. The lead candidate VHH clones (designated B11 and H10) bound to C. reinhardtii with EC50 values ≤0.5 nm. Treatment of cells with VHH B11 fused to the mCherry or green fluorescent proteins allowed brilliant and specific staining of the C. reinhardtii cell wall and analysis of cell‐wall genesis during cell division. Such high‐complexity VHH antibody libraries for algae will be valuable tools for algal researchers and biotechnologists.
A BAC physical map of aus rice cultivar ‘Kasalath’, and the map‐based genomic sequence of ‘Kasalath’ chromosome 1
Authors: Kanamori Hiroyuki , Fujisawa Masaki , Katagiri Satoshi , Oono Youko , Fujisawa Hiroko , Karasawa Wataru , Kurita Kanako , Sasaki Harumi , Mori Satomi , Hamada Masao , Mukai Yoshiyuki , Yazawa Takayuki , Mizuno Hiroshi , Namiki Nobukazu , Sasaki Takuji , Katayose Yuichi , Matsumoto Takashi , Wu Jianzhong 
Published: August 2013

SummaryComparative analysis using available genomic resources within closely related species is an effective way to investigate genomic sequence and structural diversity. Rice (Oryza sativa L.) has undergone significant physiological and morphological changes during its domestication and local adaptation. We present a complete bacterial artificial chromosome (BAC) physical map for the aus rice cultivar ‘Kasalath’, which covers 90% of the sequence of temperate japonica rice cultivar ‘Nipponbare’. Examination of physical distances between computational and experimental measurements of ‘Kasalath’ BAC insert size revealed the presence of more than 500 genomic regions that appear to have significant chromosome structural changes between the two cultivars. In particular, a genomic region on the long arm of ‘Kasalath’ chromosome 11 carrying a disease‐resistance gene cluster was greatly expanded relative to the ‘Nipponbare’ genome. We also decoded 41.37 Mb of high‐quality genomic sequence from ‘Kasalath’ chromosome 1. Extensive comparisons of chromosome 1 between ‘Kasalath’ and ‘Nipponbare’ led to the discovery of 317 843 single‐nucleotide polymorphisms (SNPs) and 66 331 insertion/deletion (indel) sites. Nearly two‐thirds of the expressed genes on rice chromosome 1 carried natural variations involving SNPs and/or indels that resulted in substitutions, insertions or deletions of amino acids in one cultivar relative to the other. We also observed gain and loss of genes caused by large indels. This study provides an important framework and an invaluable dataset for further understanding of the molecular mechanisms underlying the evolution and functions of the rice genome.
Homeostasis of Glutathione Is Associated with Polyamine-Mediated β-Lactam Susceptibility in Acinetobacter baumannii ATCC 19606
Authors: Kwon Dong H. , Hekmaty Saboor , Seecoomar Gomattie 
Published: August 2013

ABSTRACT

Glutathione is a tripeptide (
l
-γ-glutamyl–
l
-cysteinyl–glycine) thiol compound existing in many bacteria and maintains a proper cellular redox state, thus protecting cells against toxic substances such as reactive oxygen species. Polyamines (spermine and spermidine) are low-molecular-weight aliphatic polycations ubiquitously presenting in all living cells and modulate many cellular functions. We previously reported that exogenous polyamines significantly enhanced β-lactam susceptibility of β-lactam-associated multidrug-resistant
Acinetobacter baumannii
. In this study, three genes differentially associated with the polyamine effects on β-lactam susceptibility were identified by transposon mutagenesis of
A. baumannii
ATCC 19606. All three genes encoded components of membrane transport systems. Inactivation of one of the genes encoding a putative glutathione transport ATP-binding protein increased the accumulation of intracellular glutathione (∼150 to ∼200%) and significantly decreased the polyamine effects on β-lactam susceptibility in
A. baumannii
ATCC 19606. When the cells were grown with polyamines, the levels of intracellular glutathione in
A. baumannii
ATCC 19606 significantly decreased from ∼0.5 to ∼0.2 nmol, while the levels of extracellular glutathione were correspondingly increased. However, the levels of total glutathione (intra- plus extracellular) were unchanged when the cells were grown with or without polyamines. Overall, these results suggest that exogenous polyamines induce glutathione export, resulting in decreased levels of intracellular glutathione, which may produce an improper cellular redox state that is associated with the polyamine-mediated β-lactam susceptibility of
A. baumannii
. This finding may provide a clue for development of new antimicrobial agents and/or novel strategies to treat multidrug-resistant
A. baumannii
.
Effects of Bacteriocins on Methicillin-Resistant Staphylococcus aureus Biofilm
Authors: Okuda Ken-ichi , Zendo Takeshi , Sugimoto Shinya , Iwase Tadayuki , Tajima Akiko , Yamada Satomi , Sonomoto Kenji , Mizunoe Yoshimitsu 
Published: August 2013

ABSTRACT

Control of biofilms formed by microbial pathogens is an important subject for medical researchers, since the development of biofilms on foreign-body surfaces often causes biofilm-associated infections in patients with indwelling medical devices. The present study examined the effects of different kinds of bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by certain bacteria, on biofilms formed by a clinical isolate of methicillin-resistant
Staphylococcus aureus
(MRSA). The activities and modes of action of three bacteriocins with different structures (nisin A, lacticin Q, and nukacin ISK-1) were evaluated. Vancomycin, a glycopeptide antibiotic used in the treatment of MRSA infections, showed bactericidal activity against planktonic cells but not against biofilm cells. Among the tested bacteriocins, nisin A showed the highest bactericidal activity against both planktonic cells and biofilm cells. Lacticin Q also showed bactericidal activity against both planktonic cells and biofilm cells, but its activity against biofilm cells was significantly lower than that of nisin A. Nukacin ISK-1 showed bacteriostatic activity against planktonic cells and did not show bactericidal activity against biofilm cells. Mode-of-action studies indicated that pore formation leading to ATP efflux is important for the bactericidal activity against biofilm cells. Our results suggest that bacteriocins that form stable pores on biofilm cells are highly potent for the treatment of MRSA biofilm infections.
Staphylococcus aureus Fatty Acid Auxotrophs Do Not Proliferate in Mice
Authors: Parsons Joshua B. , Frank Matthew W. , Rosch Jason W. , Rock Charles O. 
Published: August 2013

ABSTRACT

Inactivation of acetyl-coenzyme A (acetyl-CoA) carboxylase confers resistance to fatty acid synthesis inhibitors in
Staphylococcus aureus
on media supplemented with fatty acids. The addition of
anteiso
-fatty acids (1 mM) plus lipoic acid supports normal growth of Δ
accD
strains, but supplementation with mammalian fatty acids was less efficient. Mice infected with strain RN6930 developed bacteremia, but bacteria were not detected in mice infected with its Δ
accD
derivative.
S. aureus
bacteria lacking acetyl-CoA carboxylase can be propagated
in vitro
but were unable to proliferate in mice, suggesting that the acquisition of inactivating mutations in this enzyme is not a mechanism for the evasion of fatty acid synthesis inhibitors.
Lack of Pharmacokinetic Interaction between Rilpivirine and Integrase Inhibitors Dolutegravir and GSK1265744
Authors: Ford Susan L. , Gould Elizabeth , Chen Shuguang , Margolis David , Spreen William , Crauwels Herta , Piscitelli Stephen 
Published: August 2013

ABSTRACT

Dolutegravir (DTG) and GSK1265744 are HIV integrase inhibitors (INIs) in clinical development. The oral formulation of rilpivirine (RPV), a nonnucleoside reverse transcriptase inhibitor (NNRTI), has been approved for treatment-naive HIV infection. Long-acting depot injections of GSK1265744 and RPV are also being developed. This study evaluated the potential for drug interactions between RPV and these INIs. This phase 1, open-label, two-cohort, three-period, single-sequence crossover study evaluated oral coadministration of RPV with DTG or GSK1265744. Healthy subjects received DTG (50 mg every 24 h for 5 days) or GSK1265744 (30 mg every 24 h for 12 days) in period 1 followed by a washout, RPV (25 mg every 24 h for 11 or 12 days) in period 2, immediately followed by RPV (25 mg every 24 h) plus DTG (50 mg every 24 h) for 5 days or GSK1265744 (30 mg every 24 h) for 12 days in period 3. Steady-state pharmacokinetic (PK) parameters were estimated using noncompartmental analysis of data collected on the last day of each period. The combinations of RPV and DTG (
n
= 16) and of RPV and GSK1265744 (
n
= 11) were well tolerated; no grade 3 or 4 adverse events (AEs) or AE-related discontinuations were observed. The 90% confidence intervals for the area under the curve from time zero until the end of the dosage interval [AUC
0–τ
] and maximum concentration of drug in serum (
C
max
) geometric mean ratios were within 0.8 to 1.25. Following administration of DTG + RPV, DTG and RPV
C
τ increased by 22% and 21%, respectively. Following administration of GSK1265744 + RPV, RPV
C
τ decreased 8%. DTG and GSK1265744 can be administered with RPV without dosage adjustment for either agent. These results support coadministration of RPV with DTG or GSK1265744 as either oral or long-acting depot injection regimens. (This study has been registered at ClinicalTrials.gov under registration no. NCT01467531.)
Mutational Analysis of Quinolone Resistance Protein QnrB1
Authors: Jacoby George A. , Corcoran Marian A. , Mills Debra M. , Griffin Caitlin M. , Hooper David C. 
Published: August 2013

ABSTRACT

Alanine substitutions and selected deletions have been used to localize amino acids in QnrB essential for its protective activity. Essential amino acids are found at positions i and i
−2
in the pentapeptide repeat module and in the larger of two loops, where deletion of only a single amino acid compromises activity. Deletion of 10 amino acids at the N terminus is tolerated, but removal of 3 amino acids in the C-terminal dimerization unit destroys activity.
Flucytosine Antagonism of Azole Activity versus Candida glabrata: Role of Transcription Factor Pdr1 and Multidrug Transporter Cdr1
Authors: Steier Zoë , Vermitsky John-Paul , Toner Geoffrey , Gygax Scott E. , Edlind Thomas , Katiyar Santosh 
Published: August 2013

ABSTRACT

Infections with the opportunistic yeast
Candida glabrata
have increased dramatically in recent years. Antifungal therapy of yeast infections commonly employs azoles, such as fluconazole (FLC), but
C. glabrata
frequently develops resistance to these inhibitors of ergosterol biosynthesis. The pyrimidine analog flucytosine (5-fluorocytosine [5FC]) is highly active versus
C. glabrata
but is now rarely used clinically due to similar concerns over resistance and, a related concern, the toxicity associated with high doses used to counter resistance. Azole-5FC combination therapy would potentially address these concerns; however, previous studies suggest that 5FC may antagonize azole activity versus
C. glabrata
. Here, we report that 5FC at subinhibitory concentrations antagonized the activity of FLC 4- to 16-fold versus 8 of 8
C. glabrata
isolates tested. 5FC antagonized the activity of other azoles similarly but had only indifferent effects in combination with unrelated antifungals. Since azole resistance in
C. glabrata
results from transcription factor Pdr1-dependent upregulation of the multidrug transporter gene
CDR1
, we reasoned that 5FC antagonism might be similarly mediated. Indeed, 5FC-FLC antagonism was abrogated in
pdr1
Δ and
cdr1
Δ strains. In further support of this hypothesis, 5FC exposure induced
CDR1
expression 6-fold, and this upregulation was Pdr1 dependent. In contrast to azoles, 5FC is not a Cdr1 substrate and so its activation of Pdr1 was unexpected. We observed, however, that 5FC exposure readily induced petite mutants, which exhibit Pdr1-dependent
CDR1
upregulation. Thus, mitochondrial dysfunction resulting in Pdr1 activation is the likely basis for 5FC antagonism of azole activity versus
C. glabrata
.
Relative Contributions of Lipooligosaccharide Inner and Outer Core Modifications to Nontypeable Haemophilus influenzae Pathogenesis
Authors: Morey Pau , Viadas Cristina , Euba Begoña , Hood Derek W. , Barberán Montserrat , Gil Carmen , Grilló María Jesús , Bengoechea José Antonio , Garmendia Junkal 
Published: August 2013

ABSTRACT

Nontypeable
Haemophilus influenzae
(NTHi) is a frequent commensal of the human nasopharynx that causes opportunistic infection in immunocompromised individuals. Existing evidence associates lipooligosaccharide (LOS) with disease, but the specific and relative contributions of NTHi LOS modifications to virulence properties of the bacterium have not been comprehensively addressed. Using NTHi strain 375, an isolate for which the detailed LOS structure has been determined, we compared systematically a set of isogenic mutant strains expressing sequentially truncated LOS. The relative contributions of 2-keto-3-deoxyoctulosonic acid, the triheptose inner core, oligosaccharide extensions on heptoses I and III, phosphorylcholine, digalactose, and sialic acid to NTHi resistance to antimicrobial peptides (AMP), self-aggregation, biofilm formation, cultured human respiratory epithelial infection, and murine pulmonary infection were assessed. We show that
opsX
,
lgtF
,
lpsA
,
lic1
, and
lic2A
contribute to bacterial resistance to AMP;
lic1
is related to NTHi self-aggregation;
lgtF
,
lic1
, and
siaB
are involved in biofilm growth;
opsX
and
lgtF
participate in epithelial infection; and
opsX
,
lgtF
, and
lpsA
contribute to lung infection. Depending on the phenotype, the involvement of these LOS modifications occurs at different extents, independently or having an additive effect in combination. We discuss the relative contribution of LOS epitopes to NTHi virulence and frame a range of pathogenic traits in the context of infection.
The Acyl-Homoserine Lactone Synthase YenI from Yersinia enterocolitica Modulates Virulence Gene Expression in Enterohemorrhagic Escherichia coli O157:H7
Authors: Nguyen Y N. , Sheng Haiqing , Dakarapu Rambabu , Falck John R. , Hovde Carolyn J. , Sperandio Vanessa 
Published: August 2013

ABSTRACTThe human pathogen enterohemorrhagicEscherichia coli(EHEC) O157:H7 colonizes the rectoanal junction (RAJ) in cattle, its natural reservoir. Colonization at the RAJ poses a serious risk for fecal shedding and contamination of the environment. We previously demonstrated that EHEC senses acyl-homoserine lactones (AHLs) produced by the microbiota in the rumen to activate thegadacid resistance genes necessary for survival through the acidic stomachs in cattle and to repress the locus of enterocyte effacement (LEE) genes important for colonization of the RAJ, but unnecessary in the rumen. Devoid of AHLs, the RAJ is the prominent site of colonization of EHEC in cattle. To determine if the presence of AHLs in the RAJ could repress colonization at this site, we engineered EHEC to express theYersinia enterocoliticaAHL synthase geneyenI, which constitutively produces AHLs, to mimic a constant exposure of AHLs in the environment. TheyenI+EHEC produces oxo-C6-homoserine lactone (oxo-C6-HSL) and had a significant reduction in LEE expression, effector protein secretion, and attaching and effacing (A/E) lesion formationin vitrocompared to the wild type (WT). TheyenI+EHEC also activated expression of thegadgenes. To assess whether AHL production, which decreases LEE expression, would decrease RAJ colonization by EHEC, cattle were challenged at the RAJ with WT oryenI+EHEC. Although theyenI+EHEC colonized the RAJ with efficiency equal to that of the WT, there was a trend for the cattle to shed the WT strain longer than theyenI+EHEC.
Cellular Response to Trypanosoma cruzi Infection Induces Secretion of Defensin α-1, Which Damages the Flagellum, Neutralizes Trypanosome Motility, and Inhibits Infection
Authors: Johnson Candice A. , Rachakonda Girish , Kleshchenko Yuliya Y. , Nde Pius N. , Madison M. Nia , Pratap Siddharth , Cardenas Tatiana C. , Taylor Chase , Lima Maria F. , Villalta Fernando 
Published: August 2013

ABSTRACTHuman defensins play a fundamental role in the initiation of innate immune responses to some microbial pathogens. Here we show that colonic epithelial model HCT116 cells respond toTrypanosoma cruziinfection by secreting defensin α-1, which reduces infection. We also report the early effects of defensin α-1 on invasive trypomastigotes that involve damage of the flagellar structure to inhibit parasite motility and reduce cellular infection. Short exposure of defensin α-1 to trypomastigotes shows that defensin α-1 binds to the flagellum, resulting in flagellar membrane and axoneme alterations, followed by breaking of the flagellar membrane connected to the trypanosome body, leading to detachment and release of the parasite flagellum. In addition, defensin α-1 induces a significant reduction in parasite motility in a peptide concentration-dependent manner, which is abrogated by anti-defensin α-1 IgG. Preincubation of trypomastigotes with a concentration of defensin α-1 that inhibits 50% trypanosome motility significantly reduced cellular infection by 80%. Thus, human defensin α-1 is an innate immune molecule that is secreted by HCT116 cells in response toT. cruziinfection, inhibitsT. cruzimotility, and plays an important role in reducing cellular infection. This is the first report showing a novel cellular innate immune response to a human parasite by secretion of defensin α-1, which neutralizes the motility of a human parasite to reduce cellular infection. The mode of activity of human defensin α-1 againstT. cruziand its function may provide insights for the development of new antiparasitic strategies.
Mri Evaluation of Metal Acupuncture Needles
Authors: Mei Ling , Long Xiaojing , Diao Yanjun , Yu Haibo , Yang Wanzhang , Standish Leanna J , Qiu Bensheng 
Published: August 2013

Objective To evaluate the MR compatibility of three metal acupuncture needles (a standard stainless steel needle, a gold needle and an austenitic stainless steel needle) by comparing their imaging artefacts, radiofrequency heating effects and ease of operation. Methods The MRI artefacts of the three metal needles were first evaluated by placing them in an agar gel phantom and performing MRI of the phantom. The increase in temperature during MRI was recorded using an MR-compatible fibreoptic thermometer. MRI of acupuncture at SP6 was performed using the MR-compatible gold needle and the austenitic stainless steel needle. Results The standard stainless steel acupuncture needle produced large imaging artefacts on MRI. The gold needle was superior for MRI but not rigid enough for some clinical applications such as scalp acupuncture. The austenitic stainless steel needle is non-ferromagnetic and compatible with MRI. None of these acupuncture needles introduced radiofrequency heating during MRI. Conclusions The evaluation of MR compatibility showed that gold and austenitic stainless steel needles are MR-compatible and therefore can be used for MRI of acupuncture.
Survey and taxonomy of botnet research through life-cycle
Authors: Rodríguez-Gómez Rafael A. , Maciá-Fernández Gabriel , García-Teodoro Pedro 
Published: August 2013

Of all current threats to cybersecurity, botnets are at the top of the list. In consequence, interest in this problem is increasing rapidly among the research community and the number of publications on the question has grown exponentially in recent years. This article proposes a taxonomy of botnet research and presents a survey of the field to provide a comprehensive overview of all these contributions. Furthermore, we hope to provide researchers with a clear perspective of the gaps that remain to be filled in our defenses against botnets. The taxonomy is based upon the botnet's life-cycle, defined as the sequence of stages a botnet needs to pass through in order to reach its goal.
This approach allows us to consider the problem of botnets from a global perspective, which constitutes a key difference from other taxonomies that have been proposed. Under this novel taxonomy, we conclude that all attempts to defeat botnets should be focused on one or more stages of this life-cycle. In fact, the sustained hindering of any of the stages makes it possible to thwart a botnet's progress and thus render it useless. We test the potential capabilities of our taxonomy by means of a survey of current botnet research, and find it genuinely useful in understanding the focus of the different contributions in this field.
Analyzing and defending against web-based malware
Authors: Chang Jian , Venkatasubramanian Krishna K. , West Andrew G. , Lee Insup 
Published: August 2013

Web-based malware is a growing threat to today's Internet security. Attacks of this type are prevalent and lead to serious security consequences. Millions of malicious URLs are used as distribution channels to propagate malware all over the Web. After being infected, victim systems fall in the control of attackers, who can utilize them for various cyber crimes such as stealing credentials, spamming, and distributed denial-of-service attacks. Moreover, it has been observed that traditional security technologies such as firewalls and intrusion detection systems have only limited capability to mitigate this new problem.
In this article, we survey the state-of-the-art research regarding the analysis of—and defense against—Web-based malware attacks. First, we study the attack model, the root cause, and the vulnerabilities that enable these attacks. Second, we analyze the status quo of the Web-based malware problem. Third, three categories of defense mechanisms are discussed in detail: (1) building honeypots with virtual machines or signature-based detection system to discover existing threats; (2) using code analysis and testing techniques to identify the vulnerabilities of Web applications; and (3) constructing reputation-based blacklists or smart sandbox systems to protect end-users from attacks. We show that these three categories of approaches form an extensive solution space to the Web-based malware problem. Finally, we compare the surveyed approaches and discuss possible future research directions.