bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-Time PCR Reveals Rapid Dissemination of Leptospira interrogans after Intraperitoneal and Conjunctival Inoculation of Hamsters
Authors: Wunder Elsio A. , Figueira Claudio P. , Santos Gisele R. , Lourdault Kristel , Matthias Michael A. , Vinetz Joseph M. , Ramos Eduardo , Haake David A. , Picardeau Mathieu , dos Reis Mitermayer G. , Ko Albert I. 
Published: May 2016

ABSTRACT

The pathogen
Leptospira interrogans
is a highly motile spirochete that causes acute and fulminant infections in humans and other accidental hosts. Hematogenous dissemination is important for infection by the pathogen but remains poorly understood because few animal model studies have used sensitive tools to quantify the bacteria. We evaluated the kinetics of leptospiral infection in Golden Syrian hamsters by a sensitive quantitative real-time PCR (TaqMan) with
lipl32
as the target gene. The dissemination and bacterial burden were measured after intraperitoneal infection with a high dose (10
8
) or low dose (2.5 × 10
2
) of leptospires. We also examined the conjunctival challenge route to mimic the natural history of infection. Quantification of leptospires in perfused animals revealed that pathogens were detected in all organs of intraperitoneally infected hamsters, including the eye and brain, within 1 h after inoculation of 10
8
virulent
L. interrogans
bacteria. Peaks of 10
5
to 10
8
leptospires per gram or per milliliter were achieved in blood and all tissues between day 4 and day 8 after intraperitoneal inoculation of high- and low-dose challenges, respectively, coinciding with macroscopic and histological changes. The conjunctival route resulted in a delay in the time to peak organ burden in comparison to intraperitoneal infection, indicating that although infection could be established, penetration efficiency was low across this epithelial barrier. Surprisingly, infection with a large inoculum of high-passage-number attenuated
L. interrogans
strains resulted in dissemination to all organs in the first 4 days postinfection, albeit with a lower burden, followed by clearance from the blood and organs 7 days postinfection and survival of all animals. These results demonstrate that leptospiral dissemination and tissue invasion occur. In contrast, development of a critical level of tissue burden and pathology are dependent on the virulence of the infecting strain.
Rapid Curtailing of the Stringent Response by Toxin-Antitoxin Module-Encoded mRNases
Authors: Tian Chengzhe , Roghanian Mohammad , Jørgensen Mikkel Girke , Sneppen Kim , Sørensen Michael Askvad , Gerdes Kenn , Mitarai Namiko 
Published: May 2016

ABSTRACT

Escherichia coli
regulates its metabolism to adapt to changes in the environment, in particular to stressful downshifts in nutrient quality. Such shifts elicit the so-called stringent response, coordinated by the alarmone guanosine tetra- and pentaphosphate [(p)ppGpp]. On sudden amino acid (aa) starvation, RelA [(p)ppGpp synthetase I] activity is stimulated by binding of uncharged tRNAs to a vacant ribosomal site; the (p)ppGpp level increases dramatically and peaks within the time scale of a few minutes. The decrease of the (p)ppGpp level after the peak is mediated by the decreased production of mRNA by (p)ppGpp-associated transcriptional regulation, which reduces the vacant ribosomal A site and thus constitutes negative feedback to the RelA-dependent (p)ppGpp synthesis. Here we showed that on sudden isoleucine starvation, this peak was higher in an
E. coli
strain that lacks the 10 known mRNase-encoding toxin-antitoxin (TA) modules present in the wild-type (wt) strain. This observation suggested that toxins are part of the negative-feedback mechanism to control the (p)ppGpp level during the early stringent response. We built a ribosome trafficking model to evaluate the fold increase in RelA activity just after the onset of aa starvation. Combining this with a feedback model between the (p)ppGpp level and the mRNA level, we obtained reasonable fits to the experimental data for both strains. The analysis revealed that toxins are activated rapidly, within a minute after the onset of starvation, reducing the mRNA half-life by ∼30%.

IMPORTANCE
The early stringent response elicited by amino acid starvation is controlled by a sharp increase of the cellular (p)ppGpp level. Toxin-antitoxin module-encoded mRNases are activated by (p)ppGpp through enhanced degradation of antitoxins. The present work shows that this activation happens over a very short time scale and that the activated mRNases negatively affect the (p)ppGpp level. The proposed mathematical model of (p)ppGpp regulation through the mRNA level highlights the importance of several feedback loops in early (p)ppGpp regulation.
Promoter Recognition by Extracytoplasmic Function σ Factors: Analyzing DNA and Protein Interaction Motifs
Authors: Guzina Jelena , Djordjevic Marko 
Published: May 2016

ABSTRACT

E
xtra
c
ytoplasmic
f
unction (ECF) σ factors are the largest and the most diverse group of alternative σ factors, but their mechanisms of transcription are poorly studied. This subfamily is considered to exhibit a rigid promoter structure and an absence of mixing and matching; both −35 and −10 elements are considered necessary for initiating transcription. This paradigm, however, is based on very limited data, which bias the analysis of diverse ECF σ subgroups. Here we investigate DNA and protein recognition motifs involved in ECF σ factor transcription by a computational analysis of canonical ECF subfamily members, much less studied ECF σ subgroups, and the group outliers, obtained from recently sequenced bacteriophages. The analysis identifies an extended −10 element in promoters for phage ECF σ factors; a comparison with bacterial σ factors points to a putative 6-amino-acid motif just C-terminal of domain σ
2
, which is responsible for the interaction with the identified extension of the −10 element. Interestingly, a similar protein motif is found C-terminal of domain σ
2
in canonical ECF σ factors, at a position where it is expected to interact with a conserved motif further upstream of the −10 element. Moreover, the phiEco32 ECF σ factor lacks a recognizable −35 element and σ
4
domain, which we identify in a homologous phage, 7-11, indicating that the extended −10 element can compensate for the lack of −35 element interactions. Overall, the results reveal greater flexibility in promoter recognition by ECF σ factors than previously recognized and raise the possibility that mixing and matching also apply to this group, a notion that remains to be biochemically tested.

IMPORTANCE
ECF σ factors are the most numerous group of alternative σ factors but have been little studied. Their promoter recognition mechanisms are obscured by the large diversity within the ECF σ factor group and the limited similarity with the well-studied housekeeping σ factors. Here we extensively compare bacterial and bacteriophage ECF σ factors and their promoters in order to infer DNA and protein recognition motifs involved in transcription initiation. We predict a more flexible promoter structure than is recognized by the current paradigm, which assumes rigidness, and propose that ECF σ promoter elements may complement (mix and match with) each other's strengths. These results warrant the refocusing of research efforts from the well-studied housekeeping σ factors toward the physiologically highly important, but insufficiently understood, alternative σ factors.
Diurnal Regulation of Cellular Processes in the Cyanobacterium
Synechocystis
sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses
Authors: Saha Rajib , Liu Deng , Hoynes-O’Connor Allison , Liberton Michelle , Yu Jingjie , Bhattacharyya-Pakrasi Maitrayee , Balassy Andrea , Zhang Fuzhong , Moon Tae Seok , Maranas Costas D. , Pakrasi Himadri B. 
Published: May 2016

ABSTRACT

Synechocystis
sp. strain PCC 6803 is the most widely studied model cyanobacterium, with a well-developed omics level knowledgebase. Like the lifestyles of other cyanobacteria, that of
Synechocystis
PCC 6803 is tuned to diurnal changes in light intensity. In this study, we analyzed the expression patterns of all of the genes of this cyanobacterium over two consecutive diurnal periods. Using stringent criteria, we determined that the transcript levels of nearly 40% of the genes in
Synechocystis
PCC 6803 show robust diurnal oscillating behavior, with a majority of the transcripts being upregulated during the early light period. Such transcripts corresponded to a wide array of cellular processes, such as light harvesting, photosynthetic light and dark reactions, and central carbon metabolism. In contrast, transcripts of membrane transporters for transition metals involved in the photosynthetic electron transport chain (e.g., iron, manganese, and copper) were significantly upregulated during the late dark period. Thus, the pattern of global gene expression led to the development of two distinct transcriptional networks of coregulated oscillatory genes. These networks help describe how
Synechocystis
PCC 6803 regulates its metabolism toward the end of the dark period in anticipation of efficient photosynthesis during the early light period. Furthermore,
in silico
flux prediction of important cellular processes and experimental measurements of cellular ATP, NADP(H), and glycogen levels showed how this diurnal behavior influences its metabolic characteristics. In particular, NADPH/NADP
+
showed a strong correlation with the majority of the genes whose expression peaks in the light. We conclude that this ratio is a key endogenous determinant of the diurnal behavior of this cyanobacterium.

IMPORTANCE
Cyanobacteria are photosynthetic microbes that use energy from sunlight and CO
2
as feedstock. Certain cyanobacterial strains are amenable to facile genetic manipulation, thus enabling synthetic biology and metabolic engineering applications. Such strains are being developed as a chassis for the sustainable production of food, feed, and fuel. To this end, a holistic knowledge of cyanobacterial physiology and its correlation with gene expression patterns under the diurnal cycle is warranted. In this report, a genomewide transcriptional analysis of
Synechocystis
PCC 6803, the most widely studied model cyanobacterium, sheds light on the global coordination of cellular processes during diurnal periods. Furthermore, we found that, in addition to light, the redox level of NADP(H) is an important endogenous regulator of diurnal entrainment of
Synechocystis
PCC 6803.
Sustained Local Diversity of Vibrio cholerae O1 Biotypes in a Previously Cholera-Free Country
Authors: Boucher Yan 
Published: May 2016

ABSTRACT

Although the current cholera pandemic can trace its origin to a specific time and place, many variants of
Vibrio cholerae
have caused this disease over the last 50 years. The relative clinical importance and geographical distribution of these variants have changed with time, but most remain in circulation. Some countries, such as Mexico and Haiti, had escaped the current pandemic, until large epidemics struck them in 1991 and 2010, respectively. Cholera has been endemic in these countries ever since. A recent retrospective study in
mBio
presents the results of more than 3 decades of
V. cholerae
monitoring from environmental and clinical sources in Mexico (S. Y. Choi et al., mBio 7:e02160-15, 2016,
http://dx.doi.org/10.1128/mBio.02160-15
). It reveals that multiple
V. cholerae
variants, including classical strains from the previous pandemic, as well as completely novel biotypes, have been circulating in Mexico. This discovery has important implications for the epidemiology and evolution of
V. cholerae
.
Risk Factors for Osteoporosis in a Subgroup of Elderly Men in a Veterans Administration Nursing Home
Authors: Yeh Shing-Shing , Phanumas Donna , Hafner Alice , Schuster Michael W. 
Published: May 2016

Background General risk factors for osteoporosis in men include cigarette smoking, alcohol consumption, and diseases known to affect calcium or bone turnover. The aim of this study was to determine the specific incidence and major risk factors for osteoporosis in those at high risk for falling in a Veterans Administration nursing home that included a high proportion of psychiatric patients. Methods We performed a cross-sectional analysis of Veterans Administration Medical Center nursing home residents with high fall risk. Thirty-nine men with a previous episode of falling or who were considered to be at high fall risk were enrolled. A review of the medical histories and pertinent hormonal and biochemical laboratory values was performed. Bone mineral density was measured by performing dual energy x-ray absorptiometry for all participants. Results We reviewed the medical records of 39 male nursing home residents with high fall risk. The patients’ mean age was 74.7±6.8 years. A significant (p=0.00045) association was found between chronic obstructive pulmonary disease and osteoporosis independent of oral corticosteroid use. Additional risk factors found to be associated with osteoporosis included hypogonadism, lower body weight, antipsychotic medication use, and smoking. Conclusion In a Veterans Administration nursing home population at high risk for falls, including psychiatric patients, chronic obstructive pulmonary disease independent of the use of corticosteroids, lower body weight, hypogonadism, use of antipsychotic medications, and smoking was found to be associated with osteoporosis.
Malignancy incidence in 5294 patients with juvenile arthritis
Authors: Zahedi Niaki Omid , Clarke Ann E , Ramsey-Goldman Rosalind , Yeung Rae , Hayward Kristen , Oen Kiem , Duffy Ciarán M , Rosenberg Alan , O'Neil Kathleen M , von Scheven Emily , Schanberg Laura , Labrecque Jeremy , Tse Shirley M L , Hasija Rachana , Lee Jennifer L F , Bernatsky Sasha 
Published: May 2016

ObjectiveTo determine cancer incidence in a large clinical juvenile-onset arthritis population.MethodsWe combined data from 6 existing North American juvenile-onset arthritis cohorts. Patients with juvenile-onset arthritis were linked to regional cancer registries to detect incident cancers after cohort entry, defined as first date seen in the paediatric rheumatology clinic. The expected number of malignancies was obtained by multiplying the person-years observed (defined from cohort entry to end of follow-up) by the geographically matched age, sex and calendar year-specific cancer rates. The standardised incidence ratios (SIR; ratio of cancers observed to expected) were generated, with 95% CIs.ResultsThe 6 juvenile arthritis registries provided a total of 5294 patients. The mean age at cohort entry was 8.9 (SD 5.0) years and 68% of participants were female. The mean duration of follow-up was 6.8 years with a total of 36 063 person-years spanning 1978–2012. During follow-up, 9 invasive cancers occurred, compared with 10.9 expected (SIR 0.82, 95% CI 0.38 to 1.5). 3 of these were haematological (Hodgkin's, non-Hodgkin's lymphoma and leukaemia). 6 of the patients with cancer were exposed to disease-modifying drugs; 5 of these had also been exposed to biological agents.ConclusionsWe did not clearly demonstrate an increase in overall malignancy risk in patients with juvenile-onset arthritis followed for an average of almost 7 years. 3 of the 9 observed cancers were haematological. 5 of the cancers arose in children exposed to biological agents. Longer follow-up of this population is warranted, with further study of drug effects.
Activation of the Lin28/let-7 Axis by Loss of ESE3/EHF Promotes a Tumorigenic and Stem-like Phenotype in Prostate Cancer
Authors: Albino Domenico , Civenni Gianluca , Dallavalle Cecilia , Roos Martina , Jahns Hartmut , Curti Laura , Rossi Simona , Pinton Sandra , D'Ambrosio Gioacchino , Sessa Fausto , Hall Jonathan , Catapano Carlo V. , Carbone Giuseppina M. 
Published: May 2016

Abstract
Although cancer stem-like cells (CSC) are thought to be the most tumorigenic, metastatic, and therapy-resistant cell subpopulation within human tumors, current therapies target bulk tumor cells while tending to spare CSC. In seeking to understand mechanisms needed to acquire and maintain a CSC phenotype in prostate cancer, we investigated connections between the ETS transcription factor ESE3/EHF, the Lin28/let-7 microRNA axis, and the CSC subpopulation in this malignancy. In normal cells, we found that ESE3/EHF bound and repressed promoters for the Lin28A and Lin28B genes while activating transcription and maturation of the let-7 microRNAs. In cancer cells, reduced expression of ESE3/EHF upregulated Lin28A and Lin28B and downregulated the let-7 microRNAs. Notably, we found that deregulation of the Lin28/let-7 axis with reduced production of let-7 microRNAs was critical for cell transformation and expansion of prostate CSC. Moreover, targeting Lin28A/Lin28B in cell lines and tumor xenografts mimicked the effects of ESE3/EHF and restrained tumor-initiating and self-renewal properties of prostate CSC both in vitro and in vivo. These results establish that tight control by ESE3/EHF over the Lin28/let-7 axis is a critical barrier to malignant transformation, and they also suggest new strategies to antagonize CSC in human prostate cancer for therapeutic purposes. Cancer Res; 76(12); 3629–43. ©2016 AACR.
GR and ER Coactivation Alters the Expression of Differentiation Genes and Associates with Improved ER+ Breast Cancer Outcome
Authors: West Diana C. , Pan Deng , Tonsing-Carter Eva Y. , Hernandez Kyle M. , Pierce Charles F. , Styke Sarah C. , Bowie Kathleen R. , Garcia Tzintzuni I. , Kocherginsky Masha , Conzen Suzanne D. 
Published: May 2016

Abstract
In estrogen receptor (ER)–negative breast cancer, high tumor glucocorticoid receptor (GR) expression has been associated with a relatively poor outcome. In contrast, using a meta-analysis of several genomic datasets, here we find that tumor GR mRNA expression is associated with improved ER+ relapse-free survival (RFS; independently of progesterone receptor expression). To understand the mechanism by which GR expression is associated with a better ER+ breast cancer outcome, the global effect of GR-mediated transcriptional activation in ER+ breast cancer cells was studied. Analysis of GR chromatin immunoprecipitation followed by high-throughput sequencing in ER+/GR+ MCF-7 cells revealed that upon coactivation of GR and ER, GR chromatin association became enriched at proximal promoter regions. Furthermore, following ER activation, increased GR chromatin association was observed at ER, FOXO, and AP1 response elements. In addition, ER associated with GR response elements, suggesting that ER and GR interact in a complex. Coactivation of GR and ER resulted in increased expression (relative to ER activation alone) of transcripts that encode proteins promoting cellular differentiation (e.g., KDM4B, VDR) and inhibiting the Wnt signaling pathway (IGFBP4). Finally, expression of these individual prodifferentiation genes was associated with significantly improved RFS in ER+ breast cancer patients. Together, these data suggest that the coexpression and subsequent activity of tumor cell GR and ER contribute to the less aggressive natural history of early-stage breast cancer by coordinating the altered expression of genes favoring differentiation.
Implications: The interaction between ER and GR activity highlights the importance of context-dependent nuclear receptor function in cancer. Mol Cancer Res; 14(8); 707–19. ©2016 AACR.
AMPK Causes Cell Cycle Arrest in LKB1-Deficient Cells via Activation of CAMKK2
Authors: Fogarty Sarah , Ross Fiona A. , Vara Ciruelos Diana , Gray Alexander , Gowans Graeme J. , Hardie D. Grahame 
Published: May 2016

Abstract
The AMP-activated protein kinase (AMPK) is activated by phosphorylation at Thr172, either by the tumor suppressor kinase LKB1 or by an alternate pathway involving the Ca2+/calmodulin-dependent kinase, CAMKK2. Increases in AMP:ATP and ADP:ATP ratios, signifying energy deficit, promote allosteric activation and net Thr172 phosphorylation mediated by LKB1, so that the LKB1–AMPK pathway acts as an energy sensor. Many tumor cells carry loss-of-function mutations in the STK11 gene encoding LKB1, but LKB1 reexpression in these cells causes cell-cycle arrest. Therefore, it was investigated as to whether arrest by LKB1 is caused by activation of AMPK or of one of the AMPK-related kinases, which are also dependent on LKB1 but are not activated by CAMKK2. In three LKB1-null tumor cell lines, treatment with the Ca2+ ionophore A23187 caused a G1 arrest that correlated with AMPK activation and Thr172 phosphorylation. In G361 cells, expression of a truncated, Ca2+/calmodulin-independent CAMKK2 mutant also caused G1 arrest similar to that caused by expression of LKB1, while expression of a dominant-negative AMPK mutant, or a double knockout of both AMPK-α subunits, also prevented the cell-cycle arrest caused by A23187. These mechanistic findings confirm that AMPK activation triggers cell-cycle arrest, and also suggest that the rapid proliferation of LKB1-null tumor cells is due to lack of the restraining influence of AMPK. However, cell-cycle arrest can be restored by reexpressing LKB1 or a constitutively active CAMKK2, or by pharmacologic agents that increase intracellular Ca2+ and thus activate endogenous CAMKK2.
Implications: Evidence here reveals that the rapid growth and proliferation of cancer cells lacking the tumor suppressor LKB1 is due to reduced activity of AMPK, and suggests a therapeutic approach by which this block might be circumvented. Mol Cancer Res; 14(8); 683–95. ©2016 AACR.
Association between Circulating Vitamin D Metabolites and Fecal Bile Acid Concentrations
Authors: Jacobs Elizabeth T. , Haussler Mark R. , Alberts David S. , Kohler Lindsay N. , Lance Peter , Martínez María Elena , Roe Denise J. , Jurutka Peter W. 
Published: May 2016

AbstractAlthough hydrophobic bile acids have been demonstrated to exhibit cytotoxic and carcinogenic effects in the colorectum, ursodeoxycholic acid (UDCA) has been investigated as a potential chemopreventive agent. Vitamin D has been shown to play a role in both bile acid metabolism and in the development of colorectal neoplasia. Using a cross-sectional design, we sought to determine whether baseline circulating concentrations of the vitamin D metabolites 25(OH)D and 1,25(OH)2D were associated with baseline fecal bile acid concentrations in a trial of UDCA for the prevention of colorectal adenoma recurrence. We also prospectively evaluated whether vitamin D metabolite concentrations modified the effect of UDCA on adenoma recurrence. After adjustment for age, sex, BMI, physical activity, and calcium intake, adequate concentrations of 25(OH)D (≥30 ng/mL) were statistically significantly associated with reduced odds for high levels of total [OR, 0.61; 95% confidence interval (CI), 0.38–0.97], and primary (OR, 0.61; 95% CI, 0.38–0.96) bile acids, as well as individually with chenodeoxycholic acid (OR, 0.39; 95% CI, 0.24–0.63) and cholic acid (OR, 0.56; 95% CI, 0.36–0.90). No significant associations were observed for 1,25(OH)2D and high versus low fecal bile acid concentrations. In addition, neither 25(OH)D nor 1,25(OH)2D modified the effect of UDCA on colorectal adenoma recurrence. In conclusion, this is the first study to demonstrate an inverse relationship between circulating levels of 25(OH)D and primary fecal bile acid concentrations. These results support prior data demonstrating that vitamin D plays a key role in bile acid metabolism, and suggest a potential mechanism of action for 25(OH)D in colorectal cancer prevention. Cancer Prev Res; 9(7); 589–97. ©2016 AACR.