bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cofactor Specificity of the Bifunctional Alcohol and Aldehyde Dehydrogenase (AdhE) in Wild-Type and Mutant Clostridium thermocellum and Thermoanaerobacteriumsaccharolyticum
Authors: Zheng Tianyong , Olson Daniel G. , Tian Liang , Bomble Yannick J. , Himmel Michael E. , Lo Jonathan , Hon Shuen , Shaw A. Joe , van Dijken Johannes P. , Lynd Lee R. 
Published: May 2015

ABSTRACT

Clostridium thermocellum
and
Thermoanaerobacterium
saccharolyticum
are thermophilic bacteria that have been engineered to produce ethanol from the cellulose and hemicellulose fractions of biomass, respectively. Although engineered strains of
T. saccharolyticum
produce ethanol with a yield of 90% of the theoretical maximum, engineered strains of
C. thermocellum
produce ethanol at lower yields (∼50% of the theoretical maximum). In the course of engineering these strains, a number of mutations have been discovered in their
adhE
genes, which encode both alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) enzymes. To understand the effects of these mutations, the
adhE
genes from six strains of
C. thermocellum
and
T. saccharolyticum
were cloned and expressed in
Escherichia coli
, the enzymes produced were purified by affinity chromatography, and enzyme activity was measured. In wild-type strains of both organisms, NADH was the preferred cofactor for both ALDH and ADH activities. In high-ethanol-producing (ethanologen) strains of
T. saccharolyticum
, both ALDH and ADH activities showed increased NADPH-linked activity. Interestingly, the AdhE protein of the ethanologenic strain of
C. thermocellum
has acquired high NADPH-linked ADH activity while maintaining NADH-linked ALDH and ADH activities at wild-type levels. When single amino acid mutations in AdhE that caused increased NADPH-linked ADH activity were introduced into
C. thermocellum
and
T. saccharolyticum
, ethanol production increased in both organisms. Structural analysis of the wild-type and mutant AdhE proteins was performed to provide explanations for the cofactor specificity change on a molecular level.

IMPORTANCE
This work describes the characterization of the AdhE enzyme from different strains of
C. thermocellum
and
T. saccharolyticum
.
C. thermocellum
and
T. saccharolyticum
are thermophilic anaerobes that have been engineered to make high yields of ethanol and can solubilize components of plant biomass and ferment the sugars to ethanol. In the course of engineering these strains, several mutations arose in the bifunctional ADH/ALDH protein AdhE, changing both enzyme activity and cofactor specificity. We show that changing AdhE cofactor specificity from mostly NADH linked to mostly NADPH linked resulted in higher ethanol production by
C. thermocellum
and
T. saccharolyticum
.
A Trigger Residue for Transmembrane Signaling in the Escherichia coli Serine Chemoreceptor
Authors: Kitanovic Smiljka , Ames Peter , Parkinson John S. 
Published: May 2015

ABSTRACT

The transmembrane Tsr protein of
Escherichia coli
mediates chemotactic responses to environmental serine gradients. Serine binds to the periplasmic domain of the homodimeric Tsr molecule, promoting a small inward displacement of one transmembrane helix (TM2). TM2 piston displacements, in turn, modulate the structural stability of the Tsr-HAMP domain on the cytoplasmic side of the membrane to control the autophosphorylation activity of the signaling CheA kinase bound to the membrane-distal cytoplasmic tip of Tsr. A five-residue control cable segment connects TM2 to the AS1 helix of HAMP and transmits stimulus and sensory adaptation signals between them. To explore the possible role of control cable helicity in transmembrane signaling by Tsr, we characterized the signaling properties of mutant receptors with various control cable alterations. An all-alanine control cable shifted Tsr output toward the kinase-on state, whereas an all-glycine control cable prevented Tsr from reaching either a fully on or fully off output state. Restoration of the native isoleucine (I214) in these synthetic control cables largely alleviated their signaling defects. Single amino acid replacements at Tsr-I214 shifted output toward the kinase-off (L, N, H, and R) or kinase-on (A and G) states, whereas other control cable residues tolerated most amino acid replacements with little change in signaling behavior. These findings indicate that changes in control cable helicity might mediate transitions between the kinase-on and kinase-off states during transmembrane signaling by chemoreceptors. Moreover, the Tsr-I214 side chain plays a key role, possibly through interaction with the membrane interfacial environment, in triggering signaling changes in response to TM2 piston displacements.

IMPORTANCE
The Tsr protein of
E. coli
mediates chemotactic responses to environmental serine gradients. Stimulus signals from the Tsr periplasmic sensing domain reach its cytoplasmic kinase control domain through piston displacements of a membrane-spanning helix and an adjoining five-residue control cable segment. We characterized the signaling properties of Tsr variants to elucidate the transmembrane signaling role of the control cable, an element present in many microbial sensory proteins. Both the kinase-on and kinase-off output states of Tsr depended on control cable helicity, but only one residue, I214, was critical for triggering responses to attractant inputs. These findings suggest that signal transmission in Tsr involves modulation of control cable helicity through interaction of the I214 side chain with the cytoplasmic membrane.
Secreted Cyclic Di-GMP Induces Stalk Cell Differentiation in the Eukaryote Dictyostelium discoideum
Authors: Chen Zhi-hui , Schaap Pauline 
Published: May 2015

ABSTRACT

Cyclic di-GMP (c-di-GMP) is currently recognized as the most widely used intracellular signal molecule in prokaryotes, but roles in eukaryotes were only recently discovered. In the social amoeba
Dictyostelium discoideum
, c-di-GMP, produced by a prokaryote-type diguanylate cyclase, induces the differentiation of stalk cells, thereby enabling the formation of spore-bearing fruiting bodies. In this review, we summarize the currently known mechanisms that control the major life cycle transitions of
Dictyostelium
and focus particularly on the role of c-di-GMP in stalk formation. Stalk cell differentiation has characteristics of autophagic cell death, a process that also occurs in higher eukaryotes. We discuss the respective roles of c-di-GMP and of another signal molecule, differentiation-inducing factor 1, in autophagic cell death
in vitro
and in stalk formation
in vivo
.
Temporal Hierarchy of Gene Expression Mediated by Transcription Factor Binding Affinity and Activation Dynamics
Authors: Gao Rong , Stock Ann M. 
Published: May 2015

ABSTRACT

Understanding cellular responses to environmental stimuli requires not only the knowledge of specific regulatory components but also the quantitative characterization of the magnitude and timing of regulatory events. The two-component system is one of the major prokaryotic signaling schemes and is the focus of extensive interest in quantitative modeling and investigation of signaling dynamics. Here we report how the binding affinity of the PhoB two-component response regulator (RR) to target promoters impacts the level and timing of expression of PhoB-regulated genes. Information content has often been used to assess the degree of conservation for transcription factor (TF)-binding sites. We show that increasing the information content of PhoB-binding sites in designed
phoA
promoters increased the binding affinity and that the binding affinity and concentration of phosphorylated PhoB (PhoB~P) together dictate the level and timing of expression of
phoA
promoter variants. For various PhoB-regulated promoters with distinct promoter architectures, expression levels appear not to be correlated with TF-binding affinities, in contrast to the intuitive and oversimplified assumption that promoters with higher affinity for a TF tend to have higher expression levels. However, the expression timing of the core set of PhoB-regulated genes correlates well with the binding affinity of PhoB~P to individual promoters and the temporal hierarchy of gene expression appears to be related to the function of gene products during the phosphate starvation response. Modulation of the information content and binding affinity of TF-binding sites may be a common strategy for temporal programming of the expression profile of RR-regulated genes.

IMPORTANCE
A single TF often orchestrates the expression of multiple genes in response to environmental stimuli. It is not clear how different TF-binding sites within the regulon dictate the expression profile. Our studies of
Escherichia coli
PhoB, a response regulator that controls expression of a core set of phosphate assimilation genes in response to phosphate starvation, showed that expression levels of PhoB-regulated genes are under sophisticated control and do not follow a simple correlation with the binding affinity of PhoB~P to individual promoters. However, the expression timing correlates with the PhoB-binding affinity and gene functions. Genes involved in direct P
i
uptake contain high-affinity sites and are transcribed earlier than genes involved in phosphorus scavenging. This illustrates an elaborate mechanism of temporally programmed gene expression, even for nondevelopmental pathways.
A review on out-of-sequence deformation in the Himalaya
Authors: Mukherjee Soumyajit 
Published: May 2015

Abstract

Out-of-sequence deformation in the Himalaya has been caused mainly by thrusting. Out-of-sequence thrusts, usually north- to NE-dipping foreshear planes, occur inside the Sub-Himalaya (SH), Lesser Himalaya (LH) and Greater Himalayan Crystalline (GHC) sequences. Where absolute dates are available, the youngest slip within the SH occurred near the Janauri Anticline (India) at
c.
AD 1400–1460. The Munsiari Thrust (India) activated within the LH at
c.
1–2 Ma and the Main Central Thrust zone in the Marsyandi valley (Nepal) in the GHC was formed during the Holocene (
c.
0.3 ka). Except for the Riasi Thrust (Kashmir, India), the Paonta Thrust (Himachal Pradesh, India) in the Siwalik and the Tons Thrust (Garhwal region, India) within the Main Central Thrust zone, crustal shortening related to out-of-sequence thrusting in the Himalaya has been insignificant. The major litho-/stratigraphic contacts within the SH and the GHC at some places acted as out-of-sequence thrusts. Out-of-sequence thrusts in the SH have been detected mainly based on geomorphological observations. However, more quantitative geochronological studies have detected out-of-sequence thrusting from
c.
22 Ma up to Holocene age in the GHC based on age jumps, especially within the Main Central Thrust zone. Crustal channel flow (specifically for the GHC) and/or the critical taper model with or without erosion can be used to explain the Himalayan out-of-sequence thrusts.
Partitioned Global Address Space Languages
Authors: De Wael Mattias , Marr Stefan , De Fraine Bruno , Van Cutsem Tom , De Meuter Wolfgang 
Published: May 2015

The Partitioned Global Address Space (PGAS) model is a parallel programming model that aims to improve programmer productivity while at the same time aiming for high performance. The main premise of PGAS is that a globally shared address space improves productivity, but that a distinction between local and remote data accesses is required to allow performance optimizations and to support scalability on large-scale parallel architectures. To this end, PGAS preserves the global address space while embracing awareness of nonuniform communication costs.
Today, about a dozen languages exist that adhere to the PGAS model. This survey proposes a definition and a taxonomy along four axes: how parallelism is introduced, how the address space is partitioned, how data is distributed among the partitions, and finally, how data is accessed across partitions. Our taxonomy reveals that today’s PGAS languages focus on distributing regular data and distinguish only between local and remote data access cost, whereas the distribution of irregular data and the adoption of richer data access cost models remain open challenges.
Nicotine Metabolite Ratio (3-Hydroxycotinine/Cotinine) in Plasma and Urine by Different Analytical Methods and Laboratories: Implications for Clinical Implementation
Authors: Tanner Julie-Anne , Novalen Maria , Jatlow Peter , Huestis Marilyn A. , Murphy Sharon E. , Kaprio Jaakko , Kankaanpää Aino , Galanti Laurence , Stefan Cristiana , George Tony P. , Benowitz Neal L. , Lerman Caryn , Tyndale Rachel F. 
Published: May 2015

Abstract
Background: The highly genetically variable enzyme CYP2A6 metabolizes nicotine to cotinine (COT) and COT to trans-3′-hydroxycotinine (3HC). The nicotine metabolite ratio (NMR, 3HC/COT) is commonly used as a biomarker of CYP2A6 enzymatic activity, rate of nicotine metabolism, and total nicotine clearance; NMR is associated with numerous smoking phenotypes, including smoking cessation. Our objective was to investigate the impact of different measurement methods, at different sites, on plasma and urinary NMR measures from ad libitum smokers.
Methods: Plasma (n = 35) and urine (n = 35) samples were sent to eight different laboratories, which used similar and different methods of COT and 3HC measurements to derive the NMR. We used Bland–Altman analysis to assess agreement, and Pearson correlations to evaluate associations, between NMR measured by different methods.
Results: Measures of plasma NMR were in strong agreement between methods according to Bland–Altman analysis (ratios, 0.82–1.16) and were highly correlated (all Pearson r &gt; 0.96, P &lt; 0.0001). Measures of urinary NMR were in relatively weaker agreement (ratios 0.62–1.71) and less strongly correlated (Pearson r values of 0.66–0.98, P &lt; 0.0001) between different methods. Plasma and urinary COT and 3HC concentrations, while weaker than NMR, also showed good agreement in plasma, which was better than that in urine, as was observed for NMR.
Conclusions: Plasma is a very reliable biologic source for the determination of NMR, robust to differences in these analytical protocols or assessment site.
Impact: Together this indicates a reduced need for differential interpretation of plasma NMR results based on the approach used, allowing for direct comparison of different studies. Cancer Epidemiol Biomarkers Prev; 24(8); 1239–46. ©2015 AACR.
Integrated Genomic Analysis Suggests MLL3 Is a Novel Candidate Susceptibility Gene for Familial Nasopharyngeal Carcinoma
Authors: Sasaki Mark M. , Skol Andrew D. , Bao Riyue , Rhodes Lindsay V. , Chambers Rachelle , Vokes Everett E. , Cohen Ezra E.W. , Onel Kenan 
Published: May 2015

Abstract
Background: Little is known about genetic factors associated with nasopharyngeal carcinoma (NPC). To gain insight into NPC etiology, we performed whole exome sequencing on germline and tumor DNA from three closely related family members with NPC.
Methods: The family was ascertained through the Pediatric Familial Cancer Clinic at The University of Chicago (Chicago, IL). The diagnosis of NPC was confirmed pathologically for each individual. For each sample sequenced, 97.3% of the exome was covered at 5×, with an average depth of 44×. Candidate germline and somatic variants associated with NPC were identified and prioritized using a custom pipeline.
Results: We discovered 72 rare deleterious germline variants in 56 genes shared by all three individuals. Of these, only three are in previously identified NPC-associated genes, all of which are located within MLL3, a gene known to be somatically altered in NPC. One variant introduces an early stop codon in MLL3, which predicts complete loss-of-function. Tumor DNA analysis revealed somatic mutations and Epstein–Barr virus (EBV) integration events; none, however, were shared among all three individuals.
Conclusions: These data suggest that inherited mutations in MLL3 may have predisposed these three individuals from a single family to develop NPC, and may cooperate with individually acquired somatic mutations or EBV integration events in NPC etiology.
Impact: Our finding is the first instance of a plausible candidate high penetrance inherited mutation predisposing to NPC. Cancer Epidemiol Biomarkers Prev; 24(8); 1222–8. ©2015 AACR.
Upregulation of ER Signaling as an Adaptive Mechanism of Cell Survival in HER2-Positive Breast Tumors Treated with Anti-HER2 Therapy
Authors: Giuliano Mario , Hu Huizhong , Wang Yen-Chao , Fu Xiaoyong , Nardone Agostina , Herrera Sabrina , Mao Sufeng , Contreras Alejandro , Gutierrez Carolina , Wang Tao , Hilsenbeck Susan G. , De Angelis Carmine , Wang Nicholas J. , Heiser Laura M. , Gray Joe W. , Lopez-Tarruella Sara , Pavlick Anne C. , Trivedi Meghana V. , Chamness Gary C. , Chang Jenny C. , Osborne C. Kent , Rimawi Mothaffar F. , Schiff Rachel 
Published: May 2015

AbstractPurpose: To investigate the direct effect and therapeutic consequences of epidermal growth factor receptor 2 (HER2)-targeting therapy on expression of estrogen receptor (ER) and Bcl2 in preclinical models and clinical tumor samples.Experimental design: Archived xenograft tumors from two preclinical models (UACC812 and MCF7/HER2-18) treated with ER and HER2-targeting therapies and also HER2+ clinical breast cancer specimens collected in a lapatinib neoadjuvant trial (baseline and week 2 posttreatment) were used. Expression levels of ER and Bcl2 were evaluated by immunohistochemistry and Western blot analysis. The effects of Bcl2 and ER inhibition, by ABT-737 and fulvestrant, respectively, were tested in parental versus lapatinib-resistant UACC812 cells in vitro.Results: Expression of ER and Bcl2 was significantly increased in xenograft tumors with acquired resistance to anti-HER2 therapy compared with untreated tumors in both preclinical models (UACC812: ER P = 0.0014; Bcl2 P &lt; 0.001 and MCF7/HER2-18: ER P = 0.0007; Bcl2 P = 0.0306). In the neoadjuvant clinical study, lapatinib treatment for 2 weeks was associated with parallel upregulation of ER and Bcl2 (Spearman coefficient: 0.70; P = 0.0002). Importantly, 18% of tumors originally ER-negative (ER−) converted to ER+ upon anti-HER2 therapy. In ER−/HER2+ MCF7/HER2-18 xenografts, ER reexpression was primarily observed in tumors responding to potent combination of anti-HER2 drugs. Estrogen deprivation added to this anti-HER2 regimen significantly delayed tumor progression (P = 0.018). In the UACC812 cells, fulvestrant, but not ABT-737, was able to completely inhibit anti–HER2-resistant growth (P &lt; 0.0001).Conclusions: HER2 inhibition can enhance or restore ER expression with parallel Bcl2 upregulation, representing an ER-dependent survival mechanism potentially leading to anti-HER2 resistance. Clin Cancer Res; 21(17); 3995–4003. ©2015 AACR.
MCL-1 Is a Key Determinant of Breast Cancer Cell Survival: Validation of MCL-1 Dependency Utilizing a Highly Selective Small Molecule Inhibitor
Authors: Xiao Yu , Nimmer Paul , Sheppard George S. , Bruncko Milan , Hessler Paul , Lu Xin , Roberts-Rapp Lisa , Pappano William N. , Elmore Steven W. , Souers Andrew J. , Leverson Joel D. , Phillips Darren C. 
Published: May 2015

Abstract
Hyperexpression of antiapoptotic BCL-2 family proteins allows cells to survive despite the receipt of signals that would ordinarily induce their deletion, a facet frequently exploited by tumors. Tumors addicted to the BCL-2 family proteins for survival are now being targeted therapeutically. For example, navitoclax, a BCL-2/BCL-XL/BCL-W inhibitor, is currently in phase I/II clinical trials in numerous malignancies. However, the related family member, MCL-1, limits the efficacy of navitoclax and other chemotherapeutic agents. In the present study, we identify breast cancer cell lines that depend upon MCL-1 for survival and subsequently determine the mechanism of apoptosis mediated by the MCL-1 selective inhibitor A-1210477. We demonstrate that apoptosis resulting from a loss in MCL-1 function requires expression of the proapoptotic protein BAK. However, expression of BCL-XL can limit apoptosis resulting from loss in MCL-1 function through sequestration of free BIM. Finally, we demonstrate substantial synergy between navitoclax and MCL-1 siRNA, the direct MCL-1 inhibitor A-1210477, or the indirect MCL-1 inhibitor flavopiridol, highlighting the therapeutic potential for inhibiting BCL-XL and MCL-1 in breast cancer. Mol Cancer Ther; 14(8); 1837–47. ©2015 AACR.
PTK6 Potentiates Gemcitabine-Induced Apoptosis by Prolonging S-phase and Enhancing DNA Damage in Pancreatic Cancer
Authors: Ono Hiroaki , Basson Marc D. , Ito Hiromichi 
Published: May 2015

Abstract
Protein Tyrosine Kinase 6 (PTK6) is a non-receptor–type tyrosine kinase known to be expressed in various cancers, including pancreatic cancer. The role of PTK6 in cancer chemoresistance remains unclear. Therefore, it was hypothesized that PTK6 mechanistically regulates gemcitabine resistance in pancreatic cancer. Gemcitabine treatment stimulated endogenous PTK6 overexpression in MIAPaCa2 and Panc1 cells. PTK6 gene silencing increased cell survival after gemcitabine treatment and decreased apoptosis, whereas PTK6 overexpression decreased cell survival and increased apoptosis. Selection for gemcitabine resistance revealed substantially lower PTK6 expression in the gemcitabine-resistant subclones compared with the parental lines, while restoring PTK6 rescued gemcitabine sensitivity. Gemcitabine induced phosphorylation of H2AX (γ-H2AX) and ataxia-telangiectasia mutated kinase (pATM), specific markers for DNA double-strand breaks. Both gemcitabine-induced phosphorylation of H2AX and ATM were reduced by PTK6 knockdown and increased by PTK6 overexpression. PTK6 overexpression also increased the S-phase fraction 48 hours after gemcitabine treatment. Although gemcitabine activated both caspase-8 (CASP8) and caspase-9 (CASP9), the effect of PTK6 on gemcitabine-induced apoptosis required CASP8 but not CASP9. In mouse xenografts, PTK6 overexpression in subcutaneous tumors attenuated tumor growth after gemcitabine treatment. In conclusion, PTK6 prolongs S-phase and increases the ability of gemcitabine to cause DNA damage in vitro and in vivo.
Implications: PTK6 affects cell cycle and DNA damage, thus making it an important therapeutic target to improve the outcomes of patients with pancreatic cancer. Mol Cancer Res; 13(8); 1174–84. ©2015 AACR.