bluuebunny/crossref_metadata_2025_split huggingface dataset:
AguR, a Transmembrane Transcription Activator of the Putrescine Biosynthesis Operon in Lactococcus lactis, Acts in Response to the Agmatine Concentration
Authors: Linares Daniel M. , del Rio Beatriz , Redruello Begoña , Ladero Victor , Martin M. Cruz , de Jong Anne , Kuipers Oscar P. , Fernandez Maria , Alvarez Miguel A. 
Published: June 2015

ABSTRACT

Dairy industry fermentative processes mostly use
Lactococcus lactis
as a starter. However, some dairy
L. lactis
strains produce putrescine, a biogenic amine that raises food safety and spoilage concerns, via the agmatine deiminase (AGDI) pathway. The enzymatic activities responsible for putrescine biosynthesis in this bacterium are encoded by the AGDI gene cluster. The role of the catabolic genes
aguB
,
aguD
,
aguA
, and
aguC
has been studied, but knowledge regarding the role of
aguR
(the first gene in the cluster) remains limited. In the present work,
aguR
was found to be a very low level constitutively expressed gene that is essential for putrescine biosynthesis and is transcribed independently of the polycistronic mRNA encoding the catabolic genes (
aguBDAC
). In response to agmatine, AguR acts as a transcriptional activator of the
aguB
promoter (P

aguB

), which drives the transcription of the
aguBDAC
operon. Inverted sequences required for P

aguB

activity were identified by deletion analysis. Further work indicated that AguR is a transmembrane protein which might function as a one-component signal transduction system that senses the agmatine concentration of the medium and, accordingly, regulates the transcription of the
aguBDAC
operon through a C-terminal cytoplasmic DNA-binding domain typically found in LuxR-like proteins.
Cable Bacteria in Freshwater Sediments
Authors: Risgaard-Petersen Nils , Kristiansen Michael , Frederiksen Rasmus B. , Dittmer Anders Lindequist , Bjerg Jesper Tataru , Trojan Daniela , Schreiber Lars , Damgaard Lars Riis , Schramm Andreas , Nielsen Lars Peter 
Published: June 2015

ABSTRACTIn marine sediments cathodic oxygen reduction at the sediment surface can be coupled to anodic sulfide oxidation in deeper anoxic layers through electrical currents mediated by filamentous, multicellular bacteria of theDesulfobulbaceaefamily, the so-called cable bacteria. Until now, cable bacteria have only been reported from marine environments. In this study, we demonstrate that cable bacteria also occur in freshwater sediments. In a first step, homogenized sediment collected from the freshwater stream Giber Å, Denmark, was incubated in the laboratory. After 2 weeks, pH signatures and electric fields indicated electron transfer between vertically separated anodic and cathodic half-reactions. Fluorescencein situhybridization revealed the presence ofDesulfobulbaceaefilaments. In addition,in situmeasurements of oxygen, pH, and electric potential distributions in the waterlogged banks of Giber Å demonstrated the presence of distant electric redox coupling in naturally occurring freshwater sediment. At the same site, filamentousDesulfobulbaceaewith cable bacterium morphology were found to be present. Their 16S rRNA gene sequence placed them as a distinct sister group to the known marine cable bacteria, with the genusDesulfobulbusas the closest cultured lineage. The results of the present study indicate that electric currents mediated by cable bacteria could be important for the biogeochemistry in many more environments than anticipated thus far and suggest a common evolutionary origin of the cable phenotype withinDesulfobulbaceaewith subsequent diversification into a freshwater and a marine lineage.
Clostridium botulinum Group II Isolate Phylogenomic Profiling Using Whole-Genome Sequence Data
Authors: Weedmark K. A. , Mabon P. , Hayden K. L. , Lambert D. , Van Domselaar G. , Austin J. W. , Corbett C. R. 
Published: June 2015

ABSTRACT

Clostridium botulinum
group II isolates (
n
= 163) from different geographic regions, outbreaks, and neurotoxin types and subtypes were characterized
in silico
using whole-genome sequence data. Two clusters representing a variety of botulinum neurotoxin (BoNT) types and subtypes were identified by multilocus sequence typing (MLST) and core single nucleotide polymorphism (SNP) analysis. While one cluster included BoNT/B4/F6/E9 and nontoxigenic members, the other comprised a wide variety of different BoNT/E subtype isolates and a nontoxigenic strain.
In silico
MLST and core SNP methods were consistent in terms of clade-level isolate classification; however, core SNP analysis showed higher resolution capability. Furthermore, core SNP analysis correctly distinguished isolates by outbreak and location. This study illustrated the utility of next-generation sequence-based typing approaches for isolate characterization and source attribution and identified discrete SNP loci and MLST alleles for isolate comparison.
Phenotypic and Phylogenetic Identification of Coliform Bacteria Obtained Using 12 Coliform Methods Approved by the U.S. Environmental Protection Agency
Authors: Zhang Ya , Hong Pei-Ying , LeChevallier Mark W. , Liu Wen-Tso 
Published: June 2015

ABSTRACT

The current definition of coliform bacteria is method dependent, and when different culture-based methods are used, discrepancies in results can occur and affect the accuracy of identification of true coliforms. This study used an alternative approach to the identification of true coliforms by combining the phenotypic traits of the coliform isolates and the phylogenetic affiliation of 16S rRNA gene sequences with the use of
lacZ
and
uidA
genes. A collection of 1,404 isolates detected by 12 U.S. Environmental Protection Agency-approved coliform-testing methods were characterized based on their phylogenetic affiliations and responses to their original isolation media and lauryl tryptose broth, m-Endo, and MI agar media. Isolates were phylogenetically classified into 32 true-coliform, or targeted
Enterobacteriaceae
(TE), groups and 14 noncoliform, or nontargeted
Enterobacteriaceae
(NTE), groups. It was shown statistically that detecting true-positive (TP) events is more challenging than detecting true-negative (TN) events. Furthermore, most false-negative (FN) events were associated with four TE groups (i.e.,
Serratia
group I and the
Providencia
,
Proteus
, and
Morganella
groups) and most false-positive (FP) events with two NTE groups, the
Aeromonas
and
Plesiomonas
groups. In
Escherichia coli
testing, 18 out of 145
E. coli
isolates identified by enzymatic methods were validated as FN. The reasons behind the FP and FN reactions could be explained through analysis of the
lacZ
and
uidA
genes. Overall, combining the analyses of the 16S rRNA,
lacZ
, and
uidA
genes with the growth responses of TE and NTE on culture-based media is an effective way to evaluate the performance of coliform detection methods.
Development of Spatial Distribution Patterns by Biofilm Cells
Authors: Haagensen Janus A. J. , Hansen Susse K. , Christensen Bjarke B. , Pamp Sünje J. , Molin Søren 
Published: June 2015

ABSTRACT

Confined spatial patterns of microbial distribution are prevalent in nature, such as in microbial mats, soil communities, and water stream biofilms. The symbiotic two-species consortium of
Pseudomonas putida
and
Acinetobacter
sp. strain C6, originally isolated from a creosote-polluted aquifer, has evolved a distinct spatial organization in the laboratory that is characterized by an increased fitness and productivity. In this consortium,
P. putida
is reliant on microcolonies formed by
Acinetobacter
sp. C6, to which it attaches. Here we describe the processes that lead to the microcolony pattern by
Acinetobacter
sp. C6. Ecological spatial pattern analyses revealed that the microcolonies were not entirely randomly distributed and instead were arranged in a uniform pattern. Detailed time-lapse confocal microscopy at the single-cell level demonstrated that the spatial pattern was the result of an intriguing self-organization: small multicellular clusters moved along the surface to fuse with one another to form microcolonies. This active distribution capability was dependent on environmental factors (carbon source and oxygen) and historical contingency (formation of phenotypic variants). The findings of this study are discussed in the context of species distribution patterns observed in macroecology, and we summarize observations about the processes involved in coadaptation between
P. putida
and
Acinetobacter
sp. C6. Our results contribute to an understanding of spatial species distribution patterns as they are observed in nature, as well as the ecology of engineered communities that have the potential for enhanced and sustainable bioprocessing capacity.
Evaluation of a New Environmental Sampling Protocol for Detection of Human Norovirus on Inanimate Surfaces
Authors: Park Geun Woo , Lee David , Treffiletti Aimee , Hrsak Mario , Shugart Jill , Vinjé Jan 
Published: June 2015

ABSTRACT

Inanimate surfaces are regarded as key vehicles for the spread of human norovirus during outbreaks. ISO method 15216 involves the use of cotton swabs for environmental sampling from food surfaces and fomites for the detection of norovirus genogroup I (GI) and GII. We evaluated the effects of the virus drying time (1, 8, 24, or 48 h), swab material (cotton, polyester, rayon, macrofoam, or an antistatic wipe), surface (stainless steel or a toilet seat), and area of the swabbed surface (25.8 cm
2
to 645.0 cm
2
) on the recovery of human norovirus. Macrofoam swabs produced the highest rate of recovery of norovirus from surfaces as large as 645 cm
2
. The rates of recovery ranged from 2.2 to 36.0% for virus seeded on stainless-steel coupons (645.0 cm
2
) to 1.2 to 33.6% for toilet seat surfaces (700 cm
2
), with detection limits of 3.5 log
10
and 4.0 log
10
RNA copies. We used macrofoam swabs to collect environmental samples from several case cabins and common areas of a cruise ship where passengers had reported viral gastroenteritis symptoms. Seventeen (18.5%) of 92 samples tested positive for norovirus GII, and 4 samples could be sequenced and had identical GII.1 sequences. The viral loads of the swab samples from the cabins of the sick passengers ranged from 80 to 31,217 RNA copies, compared with 16 to 113 RNA copies for swab samples from public spaces. In conclusion, our swab protocol for norovirus may be a useful tool for outbreak investigations when no clinical samples are available to confirm the etiology.
The Centriole Cartwheel Protein SAS-6 in Trypanosoma brucei Is Required for Probasal Body Biogenesis and Flagellum Assembly
Authors: Hu Huiqing , Liu Yi , Zhou Qing , Siegel Sara , Li Ziyin 
Published: June 2015

ABSTRACT

The centriole in eukaryotes functions as the cell's microtubule-organizing center (MTOC) to nucleate spindle assembly, and its biogenesis requires an evolutionarily conserved protein, SAS-6, which assembles the centriole cartwheel.
Trypanosoma brucei
, an early branching protozoan, possesses the basal body as its MTOC to nucleate flagellum biogenesis. However, little is known about the components of the basal body and their roles in basal body biogenesis and flagellum assembly. Here, we report that the
T. brucei
SAS-6 homolog, TbSAS-6, is localized to the mature basal body and the probasal body throughout the cell cycle. RNA interference (RNAi) of TbSAS-6 inhibited probasal body biogenesis, compromised flagellum assembly, and caused cytokinesis arrest. Surprisingly, overexpression of TbSAS-6 in
T. brucei
also impaired probasal body duplication and flagellum assembly, contrary to SAS-6 overexpression in humans, which produces supernumerary centrioles. Furthermore, we showed that depletion of
T. brucei
Polo-like kinase, TbPLK, or inhibition of TbPLK activity did not abolish TbSAS-6 localization to the basal body, in contrast to the essential role of Polo-like kinase in recruiting SAS-6 to centrioles in animals. Altogether, these results identified the essential role of TbSAS-6 in probasal body biogenesis and flagellum assembly and suggest the presence of a TbPLK-independent pathway governing basal body duplication in
T. brucei
.
Comparative Analysis of Transmembrane Regulators of the Filamentous Growth Mitogen-Activated Protein Kinase Pathway Uncovers Functional and Regulatory Differences
Authors: Adhikari Hema , Caccamise Lauren M. , Pande Tanaya , Cullen Paul J. 
Published: June 2015

ABSTRACT
Filamentous growth is a microbial differentiation response that involves the concerted action of multiple signaling pathways. In budding yeast, one pathway that regulates filamentous growth is a Cdc42p-dependent mitogen-activated protein kinase (MAPK) pathway. Several transmembrane (TM) proteins regulate the filamentous growth pathway, including the signaling mucin Msb2p, the tetraspan osmosensor Sho1p, and an adaptor Opy2p. The TM proteins were compared to identify common and unique features. Msb2p, Sho1p, and Opy2p associated by coimmunoprecipitation analysis but showed predominantly different localization patterns. The different localization patterns of the proteins resulted in part from different rates of turnover from the plasma membrane (PM). In particular, Msb2p (and Opy2p) were turned over rapidly compared to Sho1p. Msb2p signaled from the PM, and its turnover was a rate-limiting step in MAPK signaling. Genetic analysis identified unique phenotypes of cells overexpressing the TM proteins. Therefore, each TM regulator of the filamentous growth pathway has its own regulatory pattern and specific function in regulating filamentous growth. This specialization may be important for fine-tuning and potentially diversifying the filamentation response.
Does valvuloarterial impedance impact prognosis after surgery for severe aortic stenosis in the elderly?
Authors: Katayama Minako , Najib Mohammad Q , Marella Punnaiah C , Temkit M'hamed H , Belohlavek Marek , Chaliki Hari P 
Published: June 2015

BackgroundValvuloarterial impedance (Zva) was introduced as a prognostic measure in patients with aortic stenosis (AS). However, it is unclear whether Zva has a prognostic impact on survival after surgical aortic valve replacement (AVR) in patients with severe AS with preserved ejection fraction (EF).MethodsWe retrospectively reviewed 929 consecutive patients who had AVR. We investigated 170 elderly patients (age >65 years, mean 76 years) who had AVR secondary to severe AS (mean gradient ≥40 mm Hg; aortic valve area ≤1 cm2; peak velocity ≥4 m/s). Patients with EF <50%, greater than moderate aortic regurgitation, prior heart surgery and concomitant mitral or tricuspid valve surgery were excluded. Zva was calculated and the patients were divided into two groups; low Zva, Zva <4.3 (n=82) and high Zva, Zva ≥4.3 (n=88). The end point was all-cause of death. Survival curves were calculated according to Kaplan-Meier method.ResultsAge, prevalence of hypertension, diabetes, chronic kidney disease (CKD), atrial fibrillation, symptoms, EF, E/e′ and concomitant coronary artery bypass graft were not different between the groups. Survival was not different between the groups at 5 years (70% in low Zva and 81% in high Zva; p=0.21) and for the entire follow-up period (p=0.23). Only age was a significant factor in predicting survival by multivariate analyses in Cox proportional hazards model after adjusting for Zva, CKD, atrial fibrillation and hypertension.ConclusionsOur results suggest that preoperative Zva does not have a prognostic impact on postoperative survival in elderly patients with severe AS with preserved EF. Further investigation is needed to elucidate the controversial results.
Molecular Pathways: Activating T Cells after Cancer Cell Phagocytosis from Blockade of CD47 “Don't Eat Me” Signals
Authors: McCracken Melissa N. , Cha Adriel C. , Weissman Irving L. 
Published: June 2015

Abstract
Recent advances with immunotherapy agents for the treatment of cancer have provided remarkable, and in some cases, curative results. Our laboratory has identified CD47 as an important “don't eat me” signal expressed on malignant cells. Blockade of the CD47:SIRP-α axis between tumor cells and innate immune cells (monocytes, macrophages, and dendritic cells) increases tumor cell phagocytosis in both solid tumors (including, but not limited to, bladder, breast, colon, lung, and pancreatic) and hematologic malignancies. These phagocytic innate cells are also professional antigen-presenting cells (APC), providing a link from innate to adaptive antitumor immunity. Preliminary studies have demonstrated that APCs present antigens from phagocytosed tumor cells, causing T-cell activation. Therefore, agents that block the CD47:SIRP-α engagement are attractive therapeutic targets as a monotherapy or in combination with additional immune-modulating agents for activating antitumor T cells in vivo. Clin Cancer Res; 21(16); 3597–601. ©2015 AACR.
Dual Targeting of Protein Degradation Pathways with the Selective HDAC6 Inhibitor ACY-1215 and Bortezomib Is Synergistic in Lymphoma
Authors: Amengual Jennifer E. , Johannet Paul , Lombardo Maximilian , Zullo Kelly , Hoehn Daniela , Bhagat Govind , Scotto Luigi , Jirau-Serrano Xavier , Radeski Dejan , Heinen Jennifer , Jiang Hongfeng , Cremers Serge , Zhang Yuan , Jones Simon , O'Connor Owen A. 
Published: June 2015

Abstract
Purpose: Pan-class histone deacetylase (HDAC) inhibitors are effective treatments for select lymphomas. Isoform-selective HDAC inhibitors are emerging as potentially more targeted agents. HDAC6 is a class IIb deacetylase that facilitates misfolded protein transport to the aggresome for degradation. We investigated the mechanism and therapeutic impact of the selective HDAC6 inhibitor ACY-1215 alone and in combination with bortezomib in preclinical models of lymphoma.
Experimental Design: Concentration–effect relationships were defined for ACY-1215 across 16 lymphoma cell lines and for synergy with bortezomib. Mechanism was interrogated by immunoblot and flow cytometry. An in vivo xenograft model of DLBCL was used to confirm in vitro findings. A collection of primary lymphoma samples were surveyed for markers of the unfolded protein response (UPR).
Results: Concentration–effect relationships defined maximal cytotoxicity at 48 hours with IC50 values ranging from 0.9 to 4.7 μmol/L. Strong synergy was observed in combination with bortezomib. Treatment with ACY-1215 led to inhibition of the aggresome evidenced by acetylated α-tubulin and accumulated polyubiquitinated proteins and upregulation of the UPR. All pharmacodynamic effects were enhanced with the addition of bortezomib. Findings were validated in vivo where mice treated with the combination demonstrated significant tumor growth delay and prolonged overall survival. Evaluation of a collection of primary lymphoma samples for markers of the UPR revealed increased HDAC6, GRP78, and XBP-1 expression as compared with reactive lymphoid tissue.
Conclusions: These data are the first results to demonstrate that dual targeting of protein degradation pathways represents an innovative and rational approach for the treatment of lymphoma. Clin Cancer Res; 21(20); 4663–75. ©2015 AACR.
Ingenol Mebutate Signals via PKC/MEK/ERK in Keratinocytes and Induces Interleukin Decoy Receptors IL1R2 and IL13RA2
Authors: Freiberger Sandra N. , Cheng Phil F. , Iotzova-Weiss Guergana , Neu Johannes , Liu Qinxiu , Dziunycz Piotr , Zibert John R. , Dummer Reinhard , Skak Kresten , Levesque Mitchell P. , Hofbauer Günther F.L. 
Published: June 2015

Abstract
Squamous cell carcinoma (SCC) is the second most common human skin cancer and the second leading cause of skin cancer–related death. Recently, a new compound, ingenol mebutate, was approved for treatment of actinic keratosis, a precursor of SCC. As the mechanism of action is poorly understood, we have further investigated the mechanism of ingenol mebutate–induced cell death. We elucidate direct effects of ingenol mebutate on primary keratinocytes, patient-derived SCC cells, and a SCC cell line. Transcriptional profiling followed by pathway analysis was performed on ingenol mebutate–treated primary keratinocytes and patient-derived SCC cells to find key mediators and identify the mechanism of action. Activation of the resulting pathways was confirmed in cells and human skin explants and supported by a phosphorylation screen of treated primary cells. The necessity of these pathways was demonstrated by inhibition of certain pathway components. Ingenol mebutate inhibited viability and proliferation of all keratinocyte-derived cells in a biphasic manner. Transcriptional profiling identified the involvement of PKC/MEK/ERK signaling in the mechanism of action and inhibition of this signaling pathway rescued ingenol mebutate–induced cell death after treatment with 100 nmol/L ingenol mebutate, the optimal concentration for the first peak of response. We found the interleukin decoy receptors IL1R2 and IL13RA2 induced by ingenol mebutate in a PKC/MEK/ERK–dependent manner. Furthermore, siRNA knockdown of IL1R2 and IL13RA2 partially rescued ingenol mebutate–treated cells. In conclusion, we have shown that ingenol mebutate–induced cell death is mediated through the PKCδ/MEK/ERK pathway, and we have functionally linked the downstream induction of IL1R2 and IL13RA2 expression to the reduced viability of ingenol mebutate–treated cells. Mol Cancer Ther; 14(9); 2132–42. ©2015 AACR.
YU238259 Is a Novel Inhibitor of Homology-Dependent DNA Repair That Exhibits Synthetic Lethality and Radiosensitization in Repair-Deficient Tumors
Authors: Stachelek Gregory C. , Peterson-Roth Elizabeth , Liu Yanfeng , Fernandez Rafael J. , Pike Luke R.G. , Qian Jack M. , Abriola Laura , Hoyer Denton , Hungerford William , Merkel Janie , Glazer Peter M. 
Published: June 2015

Abstract
Radiotherapy and DNA-damaging chemotherapy are frequently utilized in the treatment of solid tumors. Innate or acquired resistance to these therapies remains a major clinical challenge in oncology. The development of small molecules that sensitize cancers to established therapies represents an attractive approach to extending survival and quality of life in patients. Here, we demonstrate that YU238259, a member of a novel class of DNA double-strand break repair inhibitors, exhibits potent synthetic lethality in the setting of DNA damage response and DNA repair defects. YU238259 specifically inhibits homology-dependent DNA repair, but not non-homologous end-joining, in cell-based GFP reporter assays. Treatment with YU238259 is not only synergistic with ionizing radiation, etoposide, and PARP inhibition, but this synergism is heightened by BRCA2 deficiency. Further, growth of BRCA2-deficient human tumor xenografts in nude mice is significantly delayed by YU238259 treatment even in the absence of concomitant DNA-damaging therapy. The cytotoxicity of these small molecules in repair-deficient cells results from an accumulation of unresolved DNA double-strand breaks. These findings suggest that YU238259 or related small molecules may have clinical benefit to patients with advanced BRCA2-negative tumors, either as a monotherapy or as an adjuvant to radiotherapy and certain chemotherapies.
Implications: We have identified a novel series of compounds that demonstrate synthetic lethality in DNA repair–deficient cell and animal models and have strong potential for clinical translation. Mol Cancer Res; 13(10); 1389–97. ©2015 AACR.