bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Endothelial Adherence of Bartonella henselae and Acinetobacter baumannii Using a Dynamic Human
Ex Vivo
Infection Model
Authors: Weidensdorfer Marko , Chae Ju Ik , Makobe Celestine , Stahl Julia , Averhoff Beate , Müller Volker , Schürmann Christoph , Brandes Ralf P. , Wilharm Gottfried , Ballhorn Wibke , Christ Sara , Linke Dirk , Fischer Doris , Göttig Stephan , Kempf Volkhard A. J. 
Published: December 2015

ABSTRACT

Bacterial adherence determines the virulence of many human-pathogenic bacteria. Experimental approaches elucidating this early infection event in greater detail have been performed using mainly methods of cellular microbiology. However,
in vitro
infections of cell monolayers reflect the
in vivo
situation only partially, and animal infection models are not available for many human-pathogenic bacteria. Therefore,
ex vivo
infection of human organs might represent an attractive method to overcome these limitations. We infected whole human umbilical cords
ex vivo
with
Bartonella henselae
or
Acinetobacter baumannii
under dynamic flow conditions mimicking the
in vivo
infection situation of human endothelium. For this purpose, methods for quantifying endothelium-adherent wild-type and trimeric autotransporter adhesin (TAA)-deficient bacteria were set up. Data revealed that (i)
A. baumannii
binds in a TAA-dependent manner to endothelial cells, (ii) this organ infection model led to highly reproducible adherence rates, and furthermore, (iii) this model allowed to dissect the biological function of TAAs in the natural course of human infections. These findings indicate that infection models using
ex vivo
human tissue samples (“organ microbiology”) might be a valuable tool in analyzing bacterial pathogenicity with the capacity to replace animal infection models at least partially.
ISC, a Novel Group of Bacterial and Archaeal DNA Transposons That Encode Cas9 Homologs
Authors: Kapitonov Vladimir V. , Makarova Kira S. , Koonin Eugene V. 
Published: December 2015

ABSTRACT

Bacterial genomes encode numerous homologs of Cas9, the effector protein of the type II CRISPR-Cas systems. The homology region includes the arginine-rich helix and the HNH nuclease domain that is inserted into the RuvC-like nuclease domain. These genes, however, are not linked to
cas
genes or CRISPR. Here, we show that Cas9 homologs represent a distinct group of nonautonomous transposons, which we denote ISC (
i
nsertion
s
equences
C
as9-like). We identify many diverse families of full-length ISC transposons and demonstrate that their terminal sequences (particularly 3′ termini) are similar to those of IS
605
superfamily transposons that are mobilized by the Y1 tyrosine transposase encoded by the TnpA gene and often also encode the TnpB protein containing the RuvC-like endonuclease domain. The terminal regions of the ISC and IS
605
transposons contain palindromic structures that are likely recognized by the Y1 transposase. The transposons from these two groups are inserted either exactly in the middle or upstream of specific 4-bp target sites, without target site duplication. We also identify autonomous ISC transposons that encode TnpA-like Y1 transposases. Thus, the nonautonomous ISC transposons could be mobilized in
trans
either by Y1 transposases of other, autonomous ISC transposons or by Y1 transposases of the more abundant IS
605
transposons. These findings imply an evolutionary scenario in which the ISC transposons evolved from IS
605
family transposons, possibly via insertion of a mobile group II intron encoding the HNH domain, and Cas9 subsequently evolved via immobilization of an ISC transposon.

IMPORTANCE
Cas9 endonucleases, the effectors of type II CRISPR-Cas systems, represent the new generation of genome-engineering tools. Here, we describe in detail a novel family of transposable elements that encode the likely ancestors of Cas9 and outline the evolutionary scenario connecting different varieties of these transposons and Cas9.
BfpI, BfpJ, and BfpK Minor Pilins Are Important for the Function and Biogenesis of Bundle-Forming Pili Expressed by Enteropathogenic Escherichia coli
Authors: Martinez de la Peña Claudia F. , De Masi Leon , Nisa Shahista , Mulvey George , Tong Jesse , Donnenberg Michael S. , Armstrong Glen D. 
Published: December 2015

ABSTRACT

Enteropathogenic
Escherichia coli
(EPEC) remains a significant cause of infant diarrheal illness and associated morbidity and mortality in developing countries. EPEC strains are characterized by their ability to colonize the small intestines of their hosts by a multistep program involving initial loose attachment to intestinal epithelial cells followed by an intimate adhesion phase. The initial loose interaction of typical EPEC with host intestinal cells is mediated by bundle-forming pili (BFP). BFP are type 4b pili (T4bP) based on structural and functional properties shared with T4bP expressed by other bacteria. The major structural subunit of BFP is called bundlin, a T4b pilin expressed from the
bfpA
gene in the BFP operon, which contains three additional genes that encode the pilin-like proteins BfpI, BfpJ, and BfpK. In this study, we show that, in the absence of the BFP retraction ATPase (BfpF), BfpI, BfpJ, and BfpK are dispensable for BFP biogenesis. We also demonstrate that these three minor pilins are incorporated along with bundlin into the BFP filament and contribute to its structural integrity and host cell adhesive properties. The results confirm that previous findings in T4aP systems can be extended to a model T4bP such as BFP.

IMPORTANCE
Bundle-forming pili contribute to the host colonization strategy of enteropathogenic
Escherichia coli
. The studies described here investigate the role for three minor pilin subunits in the structure and function of BFP in EPEC. The studies also suggest that these subunits could be antigens for vaccine development.
Pathogenic Acinetobacter: from the Cell Surface to Infinity and Beyond
Authors: Weber Brent S. , Harding Christian M. , Feldman Mario F. 
Published: December 2015

ABSTRACT

The genus
Acinetobacter
encompasses multiple nosocomial opportunistic pathogens that are of increasing worldwide relevance because of their ability to survive exposure to various antimicrobial and sterilization agents. Among these,
Acinetobacter baumannii
,
Acinetobacter nosocomialis
, and
Acinetobacter pittii
are the most frequently isolated in hospitals around the world. Despite the growing incidence of multidrug-resistant
Acinetobacter
spp., little is known about the factors that contribute to pathogenesis. New strategies for treating and managing infections caused by multidrug-resistant
Acinetobacter
strains are urgently needed, and this requires a detailed understanding of the pathobiology of these organisms. In recent years, some virulence factors important for
Acinetobacter
colonization have started to emerge. In this review, we focus on several recently described virulence factors that act at the bacterial surface level, such as the capsule,
O
-linked protein glycosylation, and adhesins. Furthermore, we describe the current knowledge regarding the type II and type VI secretion systems present in these strains.
Iron Acquisition in Mycobacterium avium subsp. paratuberculosis
Authors: Wang Joyce , Moolji Jalal , Dufort Alex , Staffa Alfredo , Domenech Pilar , Reed Michael B. , Behr Marcel A. 
Published: December 2015

ABSTRACT

Mycobacterium avium
subsp.
paratuberculosis
is a host-adapted pathogen that evolved from the environmental bacterium
M. avium
subsp.
hominissuis
through gene loss and gene acquisition. Growth of
M. avium
subsp.
paratuberculosis
in the laboratory is enhanced by supplementation of the media with the iron-binding siderophore mycobactin J. Here we examined the production of mycobactins by related organisms and searched for an alternative iron uptake system in
M. avium
subsp.
paratuberculosis
. Through thin-layer chromatography and radiolabeled iron-uptake studies, we showed that
M. avium
subsp.
paratuberculosis
is impaired for both mycobactin synthesis and iron acquisition. Consistent with these observations, we identified several mutations, including deletions, in
M. avium
subsp.
paratuberculosis
genes coding for mycobactin synthesis. Using a transposon-mediated mutagenesis screen conditional on growth without myobactin, we identified a potential mycobactin-independent iron uptake system on a
M. avium
subsp.
paratuberculosis
-specific genomic island, LSP
P
15. We obtained a transposon (Tn) mutant with a disruption in the LSP
P
15 gene
MAP3776c
for targeted study. The mutant manifests increased iron uptake as well as intracellular iron content, with genes downstream of the transposon insertion (
MAP3775c
to
MAP3772c
[
MAP3775-2c
]) upregulated as the result of a polar effect. As an independent confirmation, we observed the same iron uptake phenotypes by overexpressing
MAP3775-2c
in wild-type
M. avium
subsp.
paratuberculosis
. These data indicate that the horizontally acquired LSP
P
15 genes contribute to iron acquisition by
M. avium
subsp.
paratuberculosis
, potentially allowing the subsequent loss of siderophore production by this pathogen.

IMPORTANCE
Many microbes are able to scavenge iron from their surroundings by producing iron-chelating siderophores. One exception is
Mycobacterium avium
subsp.
paratuberculosis
, a fastidious, slow-growing animal pathogen whose growth needs to be supported by exogenous mycobacterial siderophore (mycobactin) in the laboratory. Data presented here demonstrate that, compared to other closely related
M. avium
subspecies, mycobactin production and iron uptake are different in
M. avium
subsp.
paratuberculosis
, and these phenotypes may be caused by numerous deletions in its mycobactin biosynthesis pathway. Using a genomic approach, supplemented by targeted genetic and biochemical studies, we identified that LSP
P
15, a horizontally acquired genomic island, may encode an alternative iron uptake system. These findings shed light on the potential physiological consequence of horizontal gene transfer in
M. avium
subsp.
paratuberculosis
evolution.
Study of structural and magnetic properties of melt spun Nd2Fe13.6Zr0.4B ingot and ribbon
Authors: Amin Muhammad , Siddiqi Saadat A. , Ashfaq Ahmad , Saleem Murtaza , Ramay Shahid M. , Mahmood Asif , Al-Zaghayer Yousef S. 
Published: December 2015

Nd2Fe[Formula: see text]Zr[Formula: see text]B hard magnetic material were prepared using arc-melting technique on a water-cooled copper hearth kept under argon gas atmosphere. The prepared samples, Nd2Fe[Formula: see text]Zr[Formula: see text]B ingot and ribbon are characterized using X-ray diffraction (XRD), scanning electron microscopy (SEM) for crystal structure determination and morphological studies, respectively. The magnetic properties of the samples have been explored using vibrating sample magnetometer (VSM). The lattice constants slightly increased due to the difference in the ionic radii of Fe and that of Zr. The bulk density decreased due to smaller molar weight and low density of Zr as compared to that of Fe. Ingot sample shows almost single crystalline phase with larger crystallite sizes whereas ribbon sample shows a mixture of amorphous and crystalline phases with smaller crystallite sizes. The crystallinity of the material was highly affected with high thermal treatments. Magnetic measurements show noticeable variation in magnetic behavior with the change in crystallite size. The sample prepared in ingot type shows soft while ribbon shows hard magnetic behavior.
Differential Serum Cytokine Levels and Risk of Lung Cancer Between African and European Americans
Authors: Pine Sharon R. , Mechanic Leah E. , Enewold Lindsey , Bowman Elise D. , Ryan Bríd M. , Cote Michele L. , Wenzlaff Angela S. , Loffredo Christopher A. , Olivo-Marston Susan , Chaturvedi Anil , Caporaso Neil E. , Schwartz Ann G. , Harris Curtis C. 
Published: December 2015

Abstract
Background: African Americans have a higher risk of developing lung cancer than European Americans. Previous studies suggested that certain circulating cytokines were associated with lung cancer. We hypothesized that variations in serum cytokine levels exist between African Americans and European Americans, and increased circulating cytokine levels contribute to lung cancer differently in the two races.
Methods: Differences in 10 serum cytokine levels, IL1β, IL4, IL5, IL6, IL8, IL10, IL12, granulocyte macrophage colony-stimulating factor, IFNγ, and TNFα, between 170 African-American and 296 European-American controls from the National Cancer Institute-Maryland (NCI-MD) case–control study were assessed. Associations of the serum cytokine levels with lung cancer were analyzed. Statistically significant results were replicated in the prospective Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial and the Wayne State University Karmanos Cancer Institute case–control study.
Results: Six cytokines, IL4, IL5, IL8, IL10, IFNγ, and TNFα, were significantly higher among European-American as compared with African-American controls. Elevated IL6 and IL8 levels were associated with lung cancer among both races in all three studies. Elevated IL1β, IL10, and TNFα levels were associated with lung cancer only among African Americans. The association between elevated TNFα levels and lung cancer among European Americans was significant after adjustment for additional factors.
Conclusions: Serum cytokine levels vary by race and might contribute to lung cancer differently between African Americans and European Americans.
Impact: Future work examining risk prediction models of lung cancer can measure circulating cytokines to accurately characterize risk within racial groups. Cancer Epidemiol Biomarkers Prev; 25(3); 488–97. ©2015 AACR.
Dietary Intake of One-Carbon Metabolism–Related Nutrients and Pancreatic Cancer Risk: The Singapore Chinese Health Study
Authors: Huang Joyce Y. , Butler Lesley M. , Wang Renwei , Jin Aizhen , Koh Woon-Puay , Yuan Jian-Min 
Published: December 2015

AbstractBackground: Nutrients involved in one-carbon metabolism are hypothesized to protect against pancreatic cancer development.Methods: The Singapore Chinese Health Study database was used to prospectively examine the association between intake of one-carbon metabolism–related nutrients and pancreatic cancer risk. Between 1993 and 1998, 63,257 men and women ages 45 to 74 years were enrolled into the cohort. The daily intakes of the following one-carbon metabolism–related nutrients were assessed at enrollment using a 165-item food frequency questionnaire: betaine, choline, folate, and vitamins B2, B6, and B12. Multivariable HRs and 95% confidence intervals (CI) for pancreatic cancer risk associated with dietary intakes of one-carbon metabolism–related nutrients were calculated.Results: As of December 2013, 271 incident pancreatic cancer cases were identified during an average of 16.3 years of follow-up. Higher intakes of vitamin B6 and choline were associated with statistically significant decreases in the risk of developing pancreatic cancer. Compared with the lowest quartile, HRs (95% CIs) for the highest quartiles of vitamin B6 and choline were 0.52 (0.36–0.74; P trend = 0.001) and 0.67 (0.48–0.93; P trend = 0.04), respectively. There were no clear associations between the other one-carbon metabolism–related nutrients and pancreatic cancer risk.Conclusion: Our study suggests that higher intake of vitamin B6 and choline may lower the risk of pancreatic cancer.Impact: Our prospective findings are consistent with the in vivo evidence for protective roles of vitamin B6 and choline on pancreatic cancer development. Cancer Epidemiol Biomarkers Prev; 25(2); 417–24. ©2015 AACR.
Performance of Three-Biomarker Immunohistochemistry for Intrinsic Breast Cancer Subtyping in the AMBER Consortium
Authors: Allott Emma H. , Cohen Stephanie M. , Geradts Joseph , Sun Xuezheng , Khoury Thaer , Bshara Wiam , Zirpoli Gary R. , Miller C. Ryan , Hwang Helena , Thorne Leigh B. , O'Connor Siobhan , Tse Chiu-Kit , Bell Mary B. , Hu Zhiyuan , Li Yan , Kirk Erin L. , Bethea Traci N. , Perou Charles M. , Palmer Julie R. , Ambrosone Christine B. , Olshan Andrew F. , Troester Melissa A. 
Published: December 2015

Abstract
Background: Classification of breast cancer into intrinsic subtypes has clinical and epidemiologic importance. To examine accuracy of IHC-based methods for identifying intrinsic subtypes, a three-biomarker IHC panel was compared with the clinical record and RNA-based intrinsic (PAM50) subtypes.
Methods: Automated scoring of estrogen receptor (ER), progesterone receptor (PR), and HER2 was performed on IHC-stained tissue microarrays comprising 1,920 cases from the African American Breast Cancer Epidemiology and Risk (AMBER) consortium. Multiple cores (1–6/case) were collapsed to classify cases, and automated scoring was compared with the clinical record and to RNA-based subtyping.
Results: Automated analysis of the three-biomarker IHC panel produced high agreement with the clinical record (93% for ER and HER2, and 88% for PR). Cases with low tumor cellularity and smaller core size had reduced agreement with the clinical record. IHC-based definitions had high agreement with the clinical record regardless of hormone receptor positivity threshold (1% vs. 10%), but a 10% threshold produced highest agreement with RNA-based intrinsic subtypes. Using a 10% threshold, IHC-based definitions identified the basal-like intrinsic subtype with high sensitivity (86%), although sensitivity was lower for luminal A, luminal B, and HER2-enriched subtypes (76%, 40%, and 37%, respectively).
Conclusion: Three-biomarker IHC-based subtyping has reasonable accuracy for distinguishing basal-like from nonbasal-like, although additional biomarkers are required for accurate classification of luminal A, luminal B, and HER2-enriched cancers.
Impact: Epidemiologic studies relying on three-biomarker IHC status for subtype classification should use caution when distinguishing luminal A from luminal B and when interpreting findings for HER2-enriched cancers. Cancer Epidemiol Biomarkers Prev; 25(3); 470–8. ©2015 AACR.
Effective Clinical Responses in Metastatic Melanoma Patients after Vaccination with Primary Myeloid Dendritic Cells
Authors: Schreibelt Gerty , Bol Kalijn F. , Westdorp Harm , Wimmers Florian , Aarntzen Erik H.J.G. , Duiveman-de Boer Tjitske , van de Rakt Mandy W.M.M. , Scharenborg Nicole M. , de Boer Annemiek J. , Pots Jeanette M. , Olde Nordkamp Michel A.M. , van Oorschot Tom G.M. , Tel Jurjen , Winkels Gregor , Petry Katja , Blokx Willeke A.M. , van Rossum Michelle M. , Welzen Marieke E.B. , Mus Roel D.M. , Croockewit Sandra A.J. , Koornstra Rutger H.T. , Jacobs Joannes F.M. , Kelderman Sander , Blank Christian U. , Gerritsen Winald R. , Punt Cornelis J.A. , Figdor Carl G. , de Vries I. Jolanda M. 
Published: December 2015

Abstract
Purpose: Thus far, dendritic cell (DC)-based immunotherapy of cancer was primarily based on in vitro–generated monocyte-derived DCs, which require extensive in vitro manipulation. Here, we report on a clinical study exploiting primary CD1c+ myeloid DCs, naturally circulating in the blood.
Experimental Design: Fourteen stage IV melanoma patients, without previous systemic treatment for metastatic disease, received autologous CD1c+ myeloid DCs, activated by only brief (16 hours) ex vivo culture and loaded with tumor-associated antigens of tyrosinase and gp100.
Results: Our results show that therapeutic vaccination against melanoma with small amounts (3–10 × 106) of myeloid DCs is feasible and without substantial toxicity. Four of 14 patients showed long-term progression-free survival (12–35 months), which directly correlated with the development of multifunctional CD8+ T-cell responses in three of these patients. In particular, high CD107a expression, indicative for cytolytic activity, and IFNγ as well as TNFα and CCL4 production was observed. Apparently, these T-cell responses are essential to induce tumor regression and promote long-term survival by stalling tumor growth.
Conclusions: We show that vaccination of metastatic melanoma patients with primary myeloid DCs is feasible and safe and results in induction of effective antitumor immune responses that coincide with improved progression-free survival. Clin Cancer Res; 22(9); 2155–66. ©2015 AACR.
Identification of an Immunogenic Subset of Metastatic Uveal Melanoma
Authors: Rothermel Luke D. , Sabesan Arvind C. , Stephens Daniel J. , Chandran Smita S. , Paria Biman C. , Srivastava Abhishek K. , Somerville Robert , Wunderlich John R. , Lee Chyi-Chia R. , Xi Liqiang , Pham Trinh H. , Raffeld Mark , Jailwala Parthav , Kasoji Manjula , Kammula Udai S. 
Published: December 2015

Abstract
Purpose: Uveal melanoma is a rare melanoma variant with no effective therapies once metastases develop. Although durable cancer regression can be achieved in metastatic cutaneous melanoma with immunotherapies that augment naturally existing antitumor T-cell responses, the role of these treatments for metastatic uveal melanoma remains unclear. We sought to define the relative immunogenicity of these two melanoma variants and determine whether endogenous antitumor immune responses exist against uveal melanoma.
Experimental Design: We surgically procured liver metastases from uveal melanoma (n = 16) and cutaneous melanoma (n = 35) patients and compared the attributes of their respective tumor cell populations and their infiltrating T cells (TIL) using clinical radiology, histopathology, immune assays, and whole-exomic sequencing.
Results: Despite having common melanocytic lineage, uveal melanoma and cutaneous melanoma metastases differed in their melanin content, tumor differentiation antigen expression, and somatic mutational profile. Immunologic analysis of TIL cultures expanded from these divergent forms of melanoma revealed cutaneous melanoma TIL were predominantly composed of CD8+ T cells, whereas uveal melanoma TIL were CD4+ dominant. Reactivity against autologous tumor was significantly greater in cutaneous melanoma TIL compared with uveal melanoma TIL. However, we identified TIL from a subset of uveal melanoma patients which had robust antitumor reactivity comparable in magnitude with cutaneous melanoma TIL. Interestingly, the absence of melanin pigmentation in the parental tumor strongly correlated with the generation of highly reactive uveal melanoma TIL.
Conclusions: The discovery of this immunogenic group of uveal melanoma metastases should prompt clinical efforts to determine whether patients who harbor these unique tumors can benefit from immunotherapies that exploit endogenous antitumor T-cell populations. Clin Cancer Res; 22(9); 2237–49. ©2015 AACR.