bluuebunny/crossref_metadata_2025_split huggingface dataset:
Regulation of Gene Expression during the Onset of Ligninolytic Oxidation by Phanerochaete chrysosporium on Spruce Wood
Authors: Korripally Premsagar , Hunt Christopher G. , Houtman Carl J. , Jones Don C. , Kitin Peter J. , Cullen Dan , Hammel Kenneth E. 
Published: September 2015

ABSTRACT

Since uncertainty remains about how white rot fungi oxidize and degrade lignin in wood, it would be useful to monitor changes in fungal gene expression during the onset of ligninolysis on a natural substrate. We grew
Phanerochaete chrysosporium
on solid spruce wood and included oxidant-sensing beads bearing the fluorometric dye BODIPY 581/591 in the cultures. Confocal fluorescence microscopy of the beads showed that extracellular oxidation commenced 2 to 3 days after inoculation, coincident with cessation of fungal growth. Whole transcriptome shotgun sequencing (RNA-seq) analyses based on the v.2.2
P. chrysosporium
genome identified 356 genes whose transcripts accumulated to relatively high levels at 96 h and were at least four times the levels found at 40 h. Transcripts encoding some lignin peroxidases, manganese peroxidases, and auxiliary enzymes thought to support their activity showed marked apparent upregulation. The data were also consistent with the production of ligninolytic extracellular reactive oxygen species by the action of manganese peroxidase-catalyzed lipid peroxidation, cellobiose dehydrogenase-catalyzed Fe
3+
reduction, and oxidase-catalyzed H
2
O
2
production, but the data do not support a role for iron-chelating glycopeptides. In addition, transcripts encoding a variety of proteins with possible roles in lignin fragment uptake and processing, including 27 likely transporters and 18 cytochrome P450s, became more abundant after the onset of extracellular oxidation. Genes encoding cellulases showed little apparent upregulation and thus may be expressed constitutively. Transcripts corresponding to 165 genes of unknown function accumulated more than 4-fold after oxidation commenced, and some of them may merit investigation as possible contributors to ligninolysis.
Single-Domain Peptidyl-Prolyl
cis
/
trans
Isomerase FkpA from Corynebacterium glutamicum Improves the Biomass Yield at Increased Growth Temperatures
Authors: Kallscheuer Nicolai , Bott Michael , van Ooyen Jan , Polen Tino 
Published: September 2015

ABSTRACT

Peptidyl-prolyl
cis
/
trans
isomerases (PPIases) catalyze the rate-limiting protein folding step at peptidyl bonds preceding proline residues and were found to be involved in several biological processes, including gene expression, signal transduction, and protein secretion. Representative enzymes were found in almost all sequenced genomes, including
Corynebacterium glutamicum
, a facultative anaerobic Gram-positive and industrial workhorse for the production of amino acids. In
C. glutamicum
, a predicted single-domain FK-506 (tacrolimus) binding protein (FKBP)-type PPIase (FkpA) is encoded directly downstream of
gltA
, which encodes citrate synthase (CS). This gene cluster is also present in other
Actinobacteria
. Here we carried out
in vitro
and
in vivo
experiments to study the function and influence of predicted FkpA in
C. glutamicum
.
In vitro
, FkpA indeed shows typical PPIase activity with artificial substrates and is inhibited by FK-506. Furthermore, FkpA delays the aggregation of CS, which is also inhibited by FK-506. Surprisingly, FkpA has a positive effect on the activity and temperature range of CS
in vitro
. Deletion of
fkpA
causes a 50% reduced biomass yield compared to that of the wild type when grown at 37°C, whereas there is only a 10% reduced biomass yield at the optimal growth temperature of 30°C accompanied by accumulation of 7 mM
l
-glutamate and 22 mM 2-oxoglutarate. Thus, FkpA may be exploited for improved product formation in biotechnical processes. Comparative transcriptome analysis revealed 69 genes which exhibit ≥2-fold mRNA level changes in
C. glutamicum
Δ
fkpA
, giving insight into the transcriptional response upon mild heat stress when FkpA is absent.
Control of Gene Expression in Leptospira spp. by Transcription Activator-Like Effectors Demonstrates a Potential Role for LigA and LigB in Leptospira interrogans Virulence
Authors: Pappas Christopher J. , Picardeau Mathieu 
Published: September 2015

ABSTRACT

Leptospirosis is a zoonotic disease that affects ∼1 million people annually, with a mortality rate of >10%. Currently, there is an absence of effective genetic manipulation tools for targeted mutagenesis in pathogenic leptospires. Transcription activator-like effectors (TALEs) are a recently described group of repressors that modify transcriptional activity in prokaryotic and eukaryotic cells by directly binding to a targeted sequence within the host genome. To determine the applicability of TALEs within
Leptospira
spp., two TALE constructs were designed. First, a constitutively expressed TALE gene specific for the
lacO
-like region upstream of
bgaL
was
trans
inserted in the saprophyte
Leptospira biflexa
(the TALE
βgal
strain). Reverse transcriptase PCR (RT-PCR) analysis and enzymatic assays demonstrated that BgaL was not expressed in the TALE
βgal
strain. Second, to study the role of LigA and LigB in pathogenesis, a constitutively expressed TALE gene with specificity for the homologous promoter regions of
ligA
and
ligB
was
cis
inserted into the pathogen
Leptospira interrogans
(TALE

lig

). LigA and LigB expression was studied by using three independent clones: TALE

lig1

, TALE

lig2

, and TALE

lig3

. Immunoblot analysis of osmotically induced TALE

lig

clones demonstrated 2- to 9-fold reductions in the expression levels of LigA and LigB, with the highest reductions being noted for TALE

lig1

and TALE

lig2

, which were avirulent
in vivo
and nonrecoverable from animal tissues. This study reconfirms galactosidase activity in the saprophyte and suggests a role for LigA and LigB in pathogenesis. Collectively, this study demonstrates that TALEs are effective at reducing the expression of targeted genes within saprophytic and pathogenic strains of
Leptospira
spp., providing an additional genetic manipulation tool for this genus.
The Cytosolic pH of Individual Saccharomyces cerevisiae Cells Is a Key Factor in Acetic Acid Tolerance
Authors: Fernández-Niño Miguel , Marquina Maribel , Swinnen Steve , Rodríguez-Porrata Boris , Nevoigt Elke , Ariño Joaquín 
Published: September 2015

ABSTRACT

It was shown recently that individual cells of an isogenic
Saccharomyces cerevisiae
population show variability in acetic acid tolerance, and this variability affects the quantitative manifestation of the trait at the population level. In the current study, we investigated whether cell-to-cell variability in acetic acid tolerance could be explained by the observed differences in the cytosolic pHs of individual cells immediately before exposure to the acid. Results obtained with cells of the strain CEN.PK113-7D in synthetic medium containing 96 mM acetic acid (pH 4.5) showed a direct correlation between the initial cytosolic pH and the cytosolic pH drop after exposure to the acid. Moreover, only cells with a low initial cytosolic pH, which experienced a less severe drop in cytosolic pH, were able to proliferate. A similar correlation between initial cytosolic pH and cytosolic pH drop was also observed in the more acid-tolerant strain MUCL 11987-9. Interestingly, a fraction of cells in the MUCL 11987-9 population showed initial cytosolic pH values below the minimal cytosolic pH detected in cells of the strain CEN.PK113-7D; consequently, these cells experienced less severe drops in cytosolic pH. Although this might explain in part the difference between the two strains with regard to the number of cells that resumed proliferation, it was observed that all cells from strain MUCL 11987-9 were able to proliferate, independently of their initial cytosolic pH. Therefore, other factors must also be involved in the greater ability of MUCL 11987-9 cells to endure strong drops in cytosolic pH.
Abundance of Antibiotic Resistance Genes in Bacteriophage following Soil Fertilization with Dairy Manure or Municipal Biosolids, and Evidence for Potential Transduction
Authors: Ross Joseph , Topp Edward 
Published: September 2015

ABSTRACT
Animal manures and municipal biosolids recycled onto crop production land carry antibiotic-resistant bacteria that can influence the antibiotic resistome of agricultural soils, but little is known about the contribution of bacteriophage to the dissemination of antibiotic resistance genes (ARGs) in this context. In this work, we quantified a set of ARGs in the bacterial and bacteriophage fractions of agricultural soil by quantitative PCR. All tested ARGs were present in both the bacterial and phage fractions. We demonstrate that fertilization of soil with dairy manure or human biosolids increases ARG abundance in the bacterial fraction but not the bacteriophage fraction and further show that pretreatment of dairy manure can impact ARG abundance in the bacterial fraction. Finally, we show that purified bacteriophage can confer increased antibiotic resistance to soil bacteria when combined with selective pressure. The results indicate that soilborne bacteriophage represents a substantial reservoir of antibiotic resistance and that bacteriophage could play a significant role in the horizontal transfer of resistance genes in the context of an agricultural soil microbiome. Overall, our work reinforces the advisability of composting or digesting fecal material prior to field application and suggests that application of some antibiotics at subclinical concentrations can promote bacteriophage-mediated horizontal transfer of ARGs in agricultural soil microbiomes.
Autoinduction Specificities of the Lantibiotics Subtilin and Nisin
Authors: Spieß Tobias , Korn Sophie Marianne , Kötter Peter , Entian Karl-Dieter 
Published: September 2015

ABSTRACT

The biosynthesis of the lantibiotics subtilin and nisin is regulated by autoinduction via two-component systems. Although subtilin is structurally closely related to nisin and contains the same lanthionine ring structure, both lantibiotics specifically autoinduce their biosynthesis. Subtilin and also the subtilin-like lantibiotics entianin and ericin autoinduce the two-component system SpaRK of
Bacillus subtilis
, whereas the biosynthesis of nisin is autoinduced via the two-component system NisRK of
Lactococcus lactis
. Autoinduction is highly specific for the respective lantibiotic and therefore of major importance for the functional expression of genetically engineered subtilin-like lantibiotics. To identify the structural features required for subtilin autoinduction, subtilin-nisin hybrids and specific point mutations of amino acid position 1 were generated. For subtilin autoinduction, the N-terminal tryptophan is the most important for full SpaK activation. The failure of subtilin to autoinduce the histidine kinase NisK mainly depends on the N-terminal tryptophan, as its single exchange to the aliphatic amino acid residues isoleucine, leucine, and valine provided NisK autoinduction. In addition, the production of subtilin variants which did not autoinduce their own biosynthesis could be rescued upon heterologous coexpression in
B. subtilis
DSM15029 by the autoinducing subtilin-like lantibiotic entianin.
pH Regulates White-Opaque Switching and Sexual Mating in Candida albicans
Authors: Sun Yuan , Cao Chengjun , Jia Wei , Tao Li , Guan Guobo , Huang Guanghua 
Published: September 2015

ABSTRACT

As a successful commensal and pathogen of humans,
Candida albicans
encounters a wide range of environmental conditions. Among them, ambient pH, which changes frequently and affects many biological processes in this species, is an important factor, and the ability to adapt to pH changes is tightly linked with pathogenesis and morphogenesis. In this study, we report that pH has a profound effect on white-opaque switching and sexual mating in
C. albicans
. Acidic pH promotes white-to-opaque switching under certain culture conditions but represses sexual mating. The Rim101-mediated pH-sensing pathway is involved in the control of pH-regulated white-opaque switching and the mating response. Phr2 and Rim101 could play a major role in acidic pH-induced opaque cell formation. Despite the fact that the cyclic AMP (cAMP) signaling pathway does not play a major role in pH-regulated white-opaque switching and mating, white and opaque cells of the
cyr1/cyr1
mutant, which is defective in the production of cAMP, showed distinct growth defects under acidic and alkaline conditions. We further discovered that acidic pH conditions repressed sexual mating due to the failure of activation of the Ste2-mediated α-pheromone response pathway in opaque
a
cells. The effects of pH changes on phenotypic switching and sexual mating could involve a balance of host adaptation and sexual reproduction in
C. albicans
.
Associations between time in bed and suicidal thoughts, plans and attempts in Korean adolescents
Authors: Kim Jae-Hyun , Park Eun-Cheol , Lee Sang Gyu , Yoo Ki-Bong 
Published: September 2015

ObjectivesTo examine the hypothesis that respondents with any of three specific sleep patterns would have a higher likelihood of suicidality than those without reports of these patterns in Korean adolescents.SettingData from the 2011–2013 Korea Youth Risk Behavior Web-based Survey were used.Participants191 642 subjects were included. The survey's target population was students in grades 7 through 12 in South Korea.Independent variableSleep time.Primary and secondary outcome measuresSuicidal thoughts, plans and attempts.ResultsThe odds of suicidal thoughts in subjects with very short or long time in bed were 1.487-fold higher (95% CI 1.219 to 1.815) or 0.611-fold lower (95% CI 0.460 to 0.811), respectively, than for subjects with 7 h/day in bed; the odds were similar for suicidal plans. The odds of suicidal thoughts in subjects with early or late awakening times were 1.231-fold higher (95% CI 1.050 to 1.442) or 1.528-fold lower (95% CI 1.000 to 2.334), respectively, than for subjects with 7 h/day in bed; these odds were lower for suicidal plans and attempts. The odds of suicidal thoughts in subjects with early bedtime were 1.748-fold higher (95% CI 1.302 to 2.346), the odds of suicidal plans in people with an early bedtime were 2.494-fold higher (95% CI 1.671 to 3.722) and the odds of suicide attempts in subjects with late bedtime were 1.313-fold higher (95% CI 1.005 to 1.716) than for subjects with a bedtime of 23:00.ConclusionsThe sleep-related time is associated with suicide-related behaviours in Korean adolescents. Multilateral approaches are needed to identify the greatest risk factors for suicidal behaviours.
Sustained reductions in time to antibiotic delivery in febrile immunocompromised children: results of a quality improvement collaborative
Authors: Dandoy Christopher E , Hariharan Selena , Weiss Brian , Demmel Kathy , Timm Nathan , Chiarenzelli Janis , Dewald Mary Katherine , Kennebeck Stephanie , Langworthy Shawna , Pomales Jennifer , Rineair Sylvia , Sandfoss Erin , Volz-Noe Pamela , Nagarajan Rajaram , Alessandrini Evaline 
Published: September 2015

BackgroundTimely delivery of antibiotics to febrile immunocompromised (F&I) paediatric patients in the emergency department (ED) and outpatient clinic reduces morbidity and mortality.ObjectiveThe aim of this quality improvement initiative was to increase the percentage of F&I patients who received antibiotics within goal in the clinic and ED from 25% to 90%.MethodsUsing the Model of Improvement, we performed Plan-Do-Study-Act cycles to design, test and implement high-reliability interventions to decrease time to antibiotics. Pre-arrival interventions were tested and implemented, followed by post-arrival interventions in the ED. Many processes were spread successfully to the outpatient clinic. The Chronic Care Model was used, in addition to active family engagement, to inform and improve processes.ResultsThe study period was from January 2010 to January 2015. Pre-arrival planning improved our F&I time to antibiotics in the ED from 137 to 88 min. This was sustained until October 2012, when further interventions including a pre-arrival huddle decreased the median time to <50 min. Implementation of the various processes to the clinic delivery system increased the mean percentage of patients receiving antibiotics within 60 min to >90%. In September 2014, we implemented a rapid response team to improve reliable venous access in the ED, which increased our mean percentage of patients receiving timely antibiotics to its highest rate (95%).ConclusionsThis stepwise approach with pre-arrival planning using the Chronic Care Model, followed by standardisation of processes, created a sustainable improvement of timely antibiotic delivery in F&I patients.
Next day discharge after elective intracranial aneurysm coiling: is it safe?
Authors: Zakhari Nader , Lum Cheemun , Quateen Aiman , Iancu Daniela , Lesiuk Howard 
Published: September 2015

BackgroundThere is a paucity of literature on early discharge after elective aneurysm treatment. We hypothesize that patient discharge on the next day is not associated with an increase in post-discharge adverse events.MethodsWe retrospectively reviewed elective coiling procedures between 2009 and 2013. The primary outcome measure was 30-day adverse events (emergency department visits, readmission or prolonged admission >30 days, and death). We evaluated the association between early and standard discharge for the primary outcome using the Fisher exact test. We also assessed the association of the primary outcome with other patient and technical variables as well as findings on pre-discharge diffusion weighted imaging.ResultsWe included 97 patients. Median length of hospital stay (LOS) was 2.52 days, and in 26 patients (26.8%) LOS was <2 days. There was no significant difference in post-discharge adverse outcome rates between early and standard discharge groups (19.2% vs 18.3%; p=1.000). The primary outcome was significantly associated with the use of flow diverters (p=0.0287) and change in modified Rankin Scale category at discharge (p=0.0329). No significant association was noted between the outcome and the other variables including the presence of diffusion restriction pre-discharge (p>0.05).ConclusionsPatient discharge the next day after elective intracranial aneurysm coiling is not associated with an increase in 30-day adverse outcomes. A prospective study investigating early discharge in elective treatment is warranted.Trial numberOHSN-REB #20130786-01H.
Technology in postgraduate medical education: a dynamic influence on learning?
Authors: Bullock Alison , Webb Katie 
Published: September 2015

ABSTRACT
The influence of technology in medical workplace learning is explored by focusing on three uses: m-learning (notably apps), simulation and social media. Smartphones with point-of-care tools (such as textbooks, drug guides and medical calculators) can support workplace learning and doctors’ decision-making. Simulations can help develop technical skills and team interactions, and ‘in situ’ simulations improve the match between the virtual and the real. Social media (wikis, blogs, networking, YouTube) heralds a more participatory and collaborative approach to knowledge development. These uses of technology are related to Kolb’s learning cycle and Eraut’s intentions of informal learning. Contentions and controversies with these technologies exist. There is a problem with the terminology commonly adopted to describe the use of technology to enhance learning. Using learning technology in the workplace changes the interaction with others and raises issues of professionalism and etiquette. Lack of regulation makes assessment of app quality a challenge. Distraction and dependency are charges levelled at smartphone use in the workplace and these need further research. Unless addressed, these and other challenges will impede the benefits that technology may bring to postgraduate medical education.
Breast Cancer Cells Respond Differentially to Modulation of TGFβ2 Signaling after Exposure to Chemotherapy or Hypoxia
Authors: O'Brien Siobhan K. , Chen Liang , Zhong Wenyan , Armellino Douglas , Yu Jiyang , Loreth Christine , Follettie Maximillian , Damelin Marc 
Published: September 2015

Abstract
Intratumoral heterogeneity helps drive the selection for diverse therapy-resistant cell populations. In this study, we demonstrate the coexistence of two therapy-resistant populations with distinct properties that are reproducibly enriched under conditions that characterize tumor pathophysiology. Breast cancer cells that survived chemotherapy or hypoxia were enriched for cells expressing the major hyaluronic acid receptor CD44. However, only CD44hi cells that survived chemotherapy exhibited cancer stem cell (CSC) phenotypes based on growth potential and gene expression signatures that represent oncogenic signaling and metastatic prowess. Strikingly, we identified TGFβ2 as a key growth promoter of CD44hi cells that survived chemotherapy but also as a growth inhibitor of cells that survived hypoxia. Expression of the TGFβ receptor TGFβR1 and its effector molecule SMAD4 was required for enrichment of CD44hi cells exposed to the chemotherapeutic drug epirubicin, which suggests a feed-forward loop to enrich for and enhance the function of surviving CSCs. Our results reveal context-dependent effects of TGFβ2 signaling in the same tumor at the same time. The emergence of distinct resistant tumor cell populations as a consequence of prior therapeutic intervention or microenvironmental cues has significant implications for the responsiveness of recurring tumors to therapy. Cancer Res; 75(21); 4605–16. ©2015 AACR.
Post-transcriptional Modifications Contribute to the Upregulation of Cyclin D2 in Multiple Myeloma
Authors: Misiewicz-Krzeminska Irena , Sarasquete María E. , Vicente-Dueñas Carolina , Krzeminski Patryk , Wiktorska Katarzyna , Corchete Luis Antonio , Quwaider Dalia , Rojas Elizabeta A. , Corral Rocío , Martín Ana A. , Escalante Fernando , Bárez Abelardo , García Juan Luis , Sánchez-García Isidro , García-Sanz Ramón , San Miguel Jesús F. , Gutiérrez Norma C. 
Published: September 2015

Abstract
Purpose: Dysregulation of one of the three D-cyclin genes has been observed in virtually all multiple myeloma tumors. The mechanisms by which CCND2 is upregulated in a set of multiple myeloma are not completely deciphered. We investigated the role of post-transcriptional regulation through the interaction between miRNAs and their binding sites at 3′UTR in CCND2 overexpression in multiple myeloma.
Experimental Design: Eleven myeloma cell lines and 45 primary myeloma samples were included in the study. Interactions between miRNAs deregulated in multiple myeloma and mRNA targets were analyzed by 3′UTR-luciferase plasmid assay. The presence of CCND2 mRNA isoforms different in length was explored using qRT-PCR, Northern blot, mRNA FISH, and 3′ rapid amplification of cDNA ends (RACE)-PCR.
Results: We detected the presence of short CCND2 mRNA, both in the multiple myeloma cell lines and primary cells. The results obtained by 3′RACE experiments revealed that changes in CCND2 3′UTR length are explained by alternative polyadenylation. The luciferase assays using plasmids harboring the truncated CCND2 mRNA strongly confirmed the loss of miRNA sites in the shorter CCND2 mRNA isoform. Those multiple myelomas with greater abundance of the shorter 3′UTR isoform were associated with significant higher level of total CCND2 mRNA expression. Furthermore, functional analysis showed significant CCND2 mRNA shortening after CCND1 silencing and an increased relative expression of longer isoform after CCND1 and CCND3 overexpression, suggesting that cyclin D1 and D3 could regulate CCND2 levels through modifications in polyadenylation-cleavage reaction.
Conclusions: Overall, these results highlight the impact of CCND2 3′UTR shortening on miRNA-dependent regulation of CCND2 in multiple myeloma. Clin Cancer Res; 22(1); 207–17. ©2015 AACR.