bluuebunny/crossref_metadata_2025 huggingface dataset:
Expanding the molecular toolbox for Lactococcus lactis: construction of an inducible thioredoxin gene fusion expression system
Authors: Douillard François P , O'Connell-Motherway Mary , Cambillau Christian , van Sinderen Douwe
Published: August 2011

Background

The development of the Nisin Inducible Controlled Expression (NICE) system in the food-grade bacterium Lactococcus lactis subsp. cremoris represents a cornerstone in the use of Gram-positive bacterial expression systems for biotechnological purposes. However, proteins that are subjected to such over-expression in L. lactis may suffer from improper folding, inclusion body formation and/or protein degradation, thereby significantly reducing the yield of soluble target protein. Although such drawbacks are not specific to L. lactis, no molecular tools have been developed to prevent or circumvent these recurrent problems of protein expression in L. lactis.

Results

Mimicking thioredoxin gene fusion systems available for E. coli, two nisin-inducible expression vectors were constructed to over-produce various proteins in L. lactis as thioredoxin fusion proteins. In this study, we demonstrate that our novel L. lactis fusion partner expression vectors allow high-level expression of soluble heterologous proteins Tuc2009 ORF40, Bbr_0140 and Tuc2009 BppU/BppL that were previously insoluble or not expressed using existing L. lactis expression vectors. Over-expressed proteins were subsequently purified by Ni-TED affinity chromatography. Intact heterologous proteins were detected by immunoblotting analyses. We also show that the thioredoxin moiety of the purified fusion protein was specifically and efficiently cleaved off by enterokinase treatment.

Conclusions

This study is the first description of a thioredoxin gene fusion expression system, purposely developed to circumvent problems associated with protein over-expression in L. lactis. It was shown to prevent protein insolubility and degradation, allowing sufficient production of soluble proteins for further structural and functional characterization.
Iron and zinc content of selected foods in the diet of schoolchildren in Kumi district, east of Uganda: a cross-sectional study
Authors: Tidemann-Andersen Ida , Acham Hedwig , Maage Amund , Malde Marian K
Published: August 2011

Background

Iron and zinc are essential micronutrients for humans and deficiency of the two elements is widespread in the world with the highest prevalence in less developed countries. There are few data on dietary intake of iron and zinc in Uganda, and no food composition table is available. There is hardly any widely published literature that clearly documents the quality of Ugandan children's diet. Thus information of both food intake and the concentration of these trace elements in local food ingredients are needed in order to assess daily intake.

Methods

The present study focused on the iron and zinc content in selected foods and intake of the micronutrients iron and zinc among schoolchildren in Kumi District, Uganda. Over a period of 4 weeks single 24-hour dietary recall interviews were carried out on a convenience sample of 178 schoolchildren (9-15 years old). Data from the dietary recalls was used when selecting foods for chemical analysis.

Results

Results from this study showed that the iron concentrations varied, and were high in some cereals and vegetables. The zinc concentrations in foods generally corresponded with results from other African countries (Mali and Kenya). Data from the 24-hour dietary recall showed that the daily Recommended Nutrient Intake (RNI) was met for iron but not for zinc.

Conclusions

The schoolchildren of Kumi district had a predominantly vegetable based diet. Foods of animal origin were consumed occasionally. The iron content in the selected foods was high and variable, and higher than in similar ingredients from Kenya and Mali, while the zinc concentrations were generally in accordance with reported values. The total daily zinc (mg) intake does not meet the daily RNI. The iron intake is adequate according to RNI, but due to iron contamination and reduced bioavailability, RNI may not be met in a vegetable based diet. More studies are needed to investigate possible sources of contamination.
Antihypertensive and antioxidant effects of dietary black sesame meal in pre-hypertensive humans
Authors: Wichitsranoi Jatuporn , Weerapreeyakul Natthida , Boonsiri Patcharee , Settasatian Chatri , Settasatian Nongnuch , Komanasin Nantarat , Sirijaichingkul Suchart , Teerajetgul Yaovalak , Rangkadilok Nuchanart , Leelayuwat Naruemon
Published: August 2011

Background

It has been known that hypertension is an independent risk factor for cardiovascular disease (CVD). CVD is the major cause of morbidity and mortality in developed and developing countries. Elevation of blood pressure (BP) increases the adverse effect for cardiovascular outcomes. Prevention of increased BP plays a crucial role in a reduction of those outcomes, leading to a decrease in mortality. Therefore, the purpose of this study was to investigate the effects of dietary black sesame meal on BP and oxidative stress in individuals with prehypertension.

Methods

Twenty-two women and eight men (aged 49.8 ± 6.6 years) with prehypertension were randomly divided into two groups, 15 subjects per group. They ingested 2.52 g black sesame meal capsules or placebo capsules each day for 4 weeks. Blood samples were obtained after overnight fasting for measurement of plasma lipid, malondialdehyde (MDA) and vitamin E levels. Anthropometry, body composition and BP were measured before and after 4-week administration of black sesame meal or a placebo.

Results

The results showed that 4-week administration of black sesame meal significantly decreased systolic BP (129.3 ± 6.8 vs. 121.0 ± 9.0 mmHg, P < 0.05) and MDA level (1.8 ± 0.6 vs. 1.2 ± 0.6 μmol/L, P < 0.05), and increased vitamin E level (29.4 ± 6.0 vs. 38.2 ± 7.8 μmol/L, P < 0.01). In the black sesame meal group, the change in SBP tended to be positively related to the change in MDA (R = 0.50, P = 0.05), while the change in DBP was negatively related to the change in vitamin E (R = -0.55, P < 0.05). There were no correlations between changes in BP and oxidative stress in the control group.

Conclusions

These results suggest the possible antihypertensive effects of black sesame meal on improving antioxidant status and decreasing oxidant stress. These data may imply a beneficial effect of black sesame meal on prevention of CVD.
Inhibition of telomerase activity preferentially targets aldehyde dehydrogenase-positive cancer stem-like cells in lung cancer
Authors: Serrano Diego , Bleau Anne-Marie , Fernandez-Garcia Ignacio , Fernandez-Marcelo Tamara , Iniesta Pilar , Ortiz-de-Solorzano Carlos , Calvo Alfonso
Published: August 2011

Background

Mortality rates for advanced lung cancer have not declined for decades, even with the implementation of novel chemotherapeutic regimens or the use of tyrosine kinase inhibitors. Cancer Stem Cells (CSCs) are thought to be responsible for resistance to chemo/radiotherapy. Therefore, targeting CSCs with novel compounds may be an effective approach to reduce lung tumor growth and metastasis. We have isolated and characterized CSCs from non-small cell lung cancer (NSCLC) cell lines and measured their telomerase activity, telomere length, and sensitivity to the novel telomerase inhibitor MST312.

Results

The aldehyde dehydrogenase (ALDH) positive lung cancer cell fraction is enriched in markers of stemness and endowed with stem cell properties. ALDH+ CSCs display longer telomeres than the non-CSC population. Interestingly, MST312 has a strong antiproliferative effect on lung CSCs and induces p21, p27 and apoptosis in the whole tumor population. MST312 acts through activation of the ATM/pH2AX DNA damage pathway (short-term effect) and through decrease in telomere length (long-term effect). Administration of this telomerase inhibitor (40 mg/kg) in the H460 xenograft model results in significant tumor shrinkage (70% reduction, compared to controls). Combination therapy consisting of irradiation (10Gy) plus administration of MST312 did not improve the therapeutic efficacy of the telomerase inhibitor alone. Treatment with MST312 reduces significantly the number of ALDH+ CSCs and their telomeric length in vivo.

Conclusions

We conclude that antitelomeric therapy using MST312 mainly targets lung CSCs and may represent a novel approach for effective treatment of lung cancer.
Tropically stable novel oral lipid formulation of amphotericin B (iCo-010): biodistribution and toxicity in a mouse model
Authors: Sivak Olena , Gershkovich Pavel , Lin Molly , Wasan Ellen K , Zhao Jinying , Owen David , Clement John G , Wasan Kishor M
Published: August 2011

Background

The purpose of this study was to evaluate the biodistribution and toxicity of amphotericin B (AmB) following multiple oral administrations of a novel tropically stable lipid-based formulation (iCo-010).

Methods

BALB/c mice were allocated into six groups: oral iCo-010 twice daily for 5 days in the dose of 20, 10, 5 and 2.5 mg/kg; vehicle control; and intravenous boluses of Fungizone® 2 mg/kg once daily for 5 days. The animals were sacrificed 12 h following the last administration and blood and tissues were collected.

Results

The plasma concentrations of AmB were similar to previously reported after administration of iCo-009. Somewhat lower concentrations of AmB were detected in reticulo-endothelial system in the case of iCo-010 when compared with iCo-009. The concentration in kidney was higher with iCo-010 than with iCo-009. The creatinine levels in all oral treatment groups were in a normal range as in the case of iCo-009. Administration of Fungizone® resulted in elevated plasma creatinine levels. Histopathology analysis detected no GI, liver or kidney toxicity following multiple dose oral administration of iCo-010. Fungizone® treatment induced necrotic changes in hepatic and kidney tissues.

Conclusions

Given the tropical stability of iCo-010, near identical activity against visceral leishmaniasis and significant concentrations in target organs this formulation has a potential to become a treatment of choice in tropical developing countries.
Ovarian sensitivity index is strongly related to circulating AMH and may be used to predict ovarian response to exogenous gonadotropins in IVF
Authors: Biasoni Valentina , Patriarca Ambra , Dalmasso Paola , Bertagna Angela , Manieri Chiara , Benedetto Chiara , Revelli Alberto
Published: August 2011

Background

Serum anti-Mullerian hormone (AMH) is currently considered the best marker of ovarian reserve and of ovarian responsiveness to gonadotropins in in-vitro fertilization (IVF). AMH assay, however, is not available in all IVF Units and is quite expensive, a reason that limits its use in developing countries. The aim of this study is to assess whether the "ovarian sensitivity index" precisely reflects AMH so that this index may be used as a surrogate for AMH in prediction of ovarian response during an IVF cycle.

Methods

AMH serum levels were measured in 61 patients undergoing IVF with a "long" stimulation protocol including the GnRH agonist buserelin and recombinant follicle-stimulating hormone (rFSH). Patients were divided into four subgroups according to the percentile of serum AMH and their ovarian stimulation was prospectively followed. Ovarian sensitivity index (OSI) was calculated dividing the total administered FSH dose by the number of retrieved oocytes.

Results

AMH and OSI show a highly significant negative correlation (r = -0.67; p = 0.0001) that is stronger than the one between AMH and the total number of retrieved oocytes and than the one between AMH and the total FSH dose.

Conclusions

OSI reflects quite satisfactory the AMH level and may be proposed as a surrogate of AMH assay in predicting ovarian responsiveness to FSH in IVF. Being very easy to calculate and costless, its use could be proposed where AMH measurement is not available or in developing countries where limiting costs is of primary importance.
CGB and GNRH1 expression analysis as a method of tumor cells metastatic spread detection in patients with gynecological malignances
Authors: Andrusiewicz Mirosław , Szczerba Anna , Wołuń-Cholewa Maria , Warchoł Wojciech , Nowak-Markwitz Ewa , Gąsiorowska Emilia , Adamska Krystyna , Jankowska Anna
Published: August 2011

Background

Metastasis is a common feature of many advanced stage cancers and metastatic spread is thought to be responsible for cancer progression. Most cancer cells are localized in the primary tumor and only a small population of circulating tumor cells (CTC) has metastatic potential. CTC amount reflects the aggressiveness of tumors, therefore their detection can be used to determine the prognosis and treatment of cancer patients.

The aim of this study was to evaluate human chorionic gonadotropin beta subunit (CGB) and gonadoliberin type 1 (GNRH1) expression as markers of tumor cells circulating in peripheral blood of gynecological cancer patients, indicating the metastatic spread of tumor.

Methods

CGB and GNRH1 expression level in tumor tissue and blood of cancer patients was assessed by real-time RT-PCR. The data was analyzed using the Mann-Whitney U and Spearman tests. In order to distinguish populations with homogeneous genes' expression the maximal likelihood method for one- and multiplied normal distribution was used.

Result

Real time RT-PCR results revealed CGB and GNRH1 genes activity in both tumor tissue and blood of gynecological cancers patients. While the expression of both genes characterized all examined tumor tissues, in case of blood analysis, the transcripts of GNRH1 were found in all cancer patients while CGB were present in 93% of patients. CGB and GNRH1 activity was detected also in control group, which consisted of tissue lacking cancerous changes and blood of healthy volunteers. The log-transformation of raw data fitted to multiplied normal distribution model showed that CGB and GNRH1 expression is heterogeneous and more than one population can be distinguished within defined groups.

Based on CGB gene activity a critical value indicating the presence of cancer cells in studied blood was distinguished. In case of GNRH1 this value was not established since the results of the gene expression in blood of cancer patients and healthy volunteers were overlapping. However one subpopulation consists of cancer patient with much higher GNRH1 expression than in control group was found.

Conclusions

Assessment of CGB and GNRH1 expression level in cancer patients' blood may be useful for indicating metastatic spread of tumor cells.
A strong convergence theorem on solving common solutions for generalized equilibrium problems and fixed-point problems in Banach space
Authors: Qu De-ning , Cheng Cao-zong
Published: August 2011

In this paper, the common solution problem (P1) of generalized equilibrium problems for a system of inverse-strongly monotone mappings "Equation missing" and a system of bifunctions "Equation missing" satisfying certain conditions, and the common fixed-point problem (P2) for a family of uniformly quasi-ϕ-asymptotically nonexpansive and locally uniformly Lipschitz continuous or uniformly Hölder continuous mappings "Equation missing" are proposed. A new iterative sequence is constructed by using the generalized projection and hybrid method, and a strong convergence theorem is proved on approximating a common solution of (P1) and (P2) in Banach space.

2000 MSC: 26B25, 40A05
Another weak convergence theorems for accretive mappings in banach spaces
Authors: Saejung Satit , Wongchan Kanokwan , Yotkaew Pongsakorn
Published: August 2011

We present two weak convergence theorems for inverse strongly accretive mappings in Banach spaces, which are supplements to the recent result of Aoyama et al. [Fixed Point Theory Appl. (2006), Art. ID 35390, 13pp.].

2000 MSC: 47H10; 47J25.
TLR4 mutation reduces microglial activation, increases Aβ deposits and exacerbates cognitive deficits in a mouse model of Alzheimer's disease
Authors: Song Min , Jin JingJi , Lim Jeong-Eun , Kou Jinghong , Pattanayak Abhinandan , Rehman Jamaal A , Kim Hong-Duck , Tahara Kazuki , Lalonde Robert , Fukuchi Ken-ichiro
Published: August 2011

Background

Amyloid plaques, a pathological hallmark of Alzheimer's disease (AD), are accompanied by activated microglia. The role of activated microglia in the pathogenesis of AD remains controversial: either clearing Aβ deposits by phagocytosis or releasing proinflammatory cytokines and cytotoxic substances. Microglia can be activated via toll-like receptors (TLRs), a class of pattern-recognition receptors in the innate immune system. We previously demonstrated that an AD mouse model homozygous for a loss-of-function mutation of TLR4 had increases in Aβ deposits and buffer-soluble Aβ in the brain as compared with a TLR4 wild-type AD mouse model at 14-16 months of age. However, it is unknown if TLR4 signaling is involved in initiation of Aβ deposition as well as activation and recruitment of microglia at the early stage of AD. Here, we investigated the role of TLR4 signaling and microglial activation in early stages using 5-month-old AD mouse models when Aβ deposits start.

Methods

Microglial activation and amyloid deposition in the brain were determined by immunohistochemistry in the AD models. Levels of cerebral soluble Aβ were determined by ELISA. mRNA levels of cytokines and chemokines in the brain and Aβ-stimulated monocytes were quantified by real-time PCR. Cognitive functions were assessed by the Morris water maze.

Results

While no difference was found in cerebral Aβ load between AD mouse models at 5 months with and without TLR4 mutation, microglial activation in a TLR4 mutant AD model (TLR4M Tg) was less than that in a TLR4 wild-type AD model (TLR4W Tg). At 9 months, TLR4M Tg mice had increased Aβ deposition and soluble Aβ42 in the brain, which were associated with decrements in cognitive functions and expression levels of IL-1β, CCL3, and CCL4 in the hippocampus compared to TLR4W Tg mice. TLR4 mutation diminished Aβ-induced IL-1β, CCL3, and CCL4 expression in monocytes.

Conclusion

This is the first demonstration of TLR4-dependent activation of microglia at the early stage of β-amyloidosis. Our results indicate that TLR4 is not involved in the initiation of Aβ deposition and that, as Aβ deposits start, microglia are activated via TLR4 signaling to reduce Aβ deposits and preserve cognitive functions from Aβ-mediated neurotoxicity.
Immunomodulator expression in trophoblasts from the feline immunodeficiency virus (FIV)-infected cat
Authors: Scott Veronica L , Shack Leslie A , Eells Jeffrey B , Ryan Peter L , Donaldson Janet R , Coats Karen S
Published: August 2011

Background

FIV infection frequently compromises pregnancy under experimental conditions and is accompanied by aberrant expression of some placental cytokines. Trophoblasts produce numerous immunomodulators that play a role in placental development and pregnancy maintenance. We hypothesized that FIV infection may cause dysregulation of trophoblast immunomodulator expression, and aberrant expression of these molecules may potentiate inflammation and compromise pregnancy. The purpose of this project was to evaluate the expression of representative pro-(TNF-α, IFN-γ, IL-1β, IL-2, IL-6, IL-12p35, IL-12p40, IL-18, and GM-CSF) and anti-inflammatory cytokines (IL-4, IL-5, and IL-10); CD134, a secondary co-stimulatory molecule expressed on activated T cells (FIV primary receptor); the chemokine receptor CXCR4 (FIV co-receptor); SDF-1α, the chemokine ligand to CXCR4; and FIV gag in trophoblasts from early-and late-term pregnancy.

Methods

We used an anti-cytokeratin antibody in immunohistochemistry to identify trophoblasts selectively, collected these cells using laser capture microdissection, and extracted total RNA from the captured cell populations. Real time, reverse transcription-PCR was used to quantify gene expression.

Results

We detected IL-4, IL-5, IL-6, IL-1β, IL-12p35, IL-12p40, and CXCR4 in trophoblasts from early-and late-term pregnancy. Expression of cytokines increased from early to late pregnancy in normal tissues. A clear, pro-inflammatory microenvironment was not evident in trophoblasts from FIV-infected queens at either stage of pregnancy. Reproductive failure was accompanied by down-regulation of both pro-and anti-inflammatory cytokines. CD134 was not detected in trophoblasts, and FIV gag was detected in only one of ten trophoblast specimens collected from FIV-infected queens.

Conclusion

Feline trophoblasts express an array of pro-and anti-inflammatory immunomodulators whose expression increases from early to late pregnancy in normal tissues. Non-viable pregnancies were associated with decreased expression of immunomodulators which regulate trophoblast invasion in other species. The detection of FIV RNA in trophoblasts was rare, suggesting that the high rate of reproductive failure in FIV-infected queens was not a direct result of viral replication in trophoblasts. The influence of placental immune cells on trophoblast function and pregnancy maintenance in the FIV-infected cat requires additional study.
Ambient particulate air pollution induces oxidative stress and alterations of mitochondria and gene expression in brown and white adipose tissues
Authors: Xu Zhaobin , Xu Xiaohua , Zhong Mianhua , Hotchkiss Ian P , Lewandowski Ryan P , Wagner James G , Bramble Lori A , Yang Yifeng , Wang Aixia , Harkema Jack R , Lippmann Morton , Rajagopalan Sanjay , Chen Lung-Chi , Sun Qinghua
Published: August 2011

Background

Prior studies have demonstrated a link between air pollution and metabolic diseases such as type II diabetes. Changes in adipose tissue and its mitochondrial content/function are closely associated with the development of insulin resistance and attendant metabolic complications. We investigated changes in adipose tissue structure and function in brown and white adipose depots in response to chronic ambient air pollutant exposure in a rodent model.

Methods

Male ApoE knockout (ApoE-/-) mice inhaled concentrated fine ambient PM (PM < 2.5 μm in aerodynamic diameter; PM2.5) or filtered air (FA) for 6 hours/day, 5 days/week, for 2 months. We examined superoxide production by dihydroethidium staining; inflammatory responses by immunohistochemistry; and changes in white and brown adipocyte-specific gene profiles by real-time PCR and mitochondria by transmission electron microscopy in response to PM2.5 exposure in different adipose depots of ApoE-/- mice to understand responses to chronic inhalational stimuli.

Results

Exposure to PM2.5 induced an increase in the production of reactive oxygen species (ROS) in brown adipose depots. Additionally, exposure to PM2.5 decreased expression of uncoupling protein 1 in brown adipose tissue as measured by immunohistochemistry and Western blot. Mitochondrial number was significantly reduced in white (WAT) and brown adipose tissues (BAT), while mitochondrial size was also reduced in BAT. In BAT, PM2.5 exposure down-regulated brown adipocyte-specific genes, while white adipocyte-specific genes were differentially up-regulated.

Conclusions

PM2.5 exposure triggers oxidative stress in BAT, and results in key alterations in mitochondrial gene expression and mitochondrial alterations that are pronounced in BAT. We postulate that exposure to PM2.5 may induce imbalance between white and brown adipose tissue functionality and thereby predispose to metabolic dysfunction.
Differential expression of HIF-1α in CD44+CD24-/low breast ductal carcinomas
Authors: Oliveira-Costa João Paulo , Zanetti Juliana S , Silveira Giórgia G , Soave Danilo F , Oliveira Lucinei R , Zorgetto Verônica A , Soares Fernando A , Zucoloto Sérgio , Ribeiro-Silva Alfredo
Published: August 2011

Background

Cancer stem cell (CSC) hypothesis postulates that tumors are maintained by a self-renewing CSC population that is also capable of differentiating into non-self-renewing cell populations that constitute the bulk of tumor. Stem cells renewal and differentiation can be directly influenced by the oxygen levels of determined tissues, probably by the reduction of oxidative DNA damage in hypoxic regions, thus leading to a friendlier microenvironment, regarding to clonal expansion and for resistance to chemotherapeutic regimens. Furthermore, there have been strong data indicating a pivotal role of hypoxic niche in cancer stem cells development. There are evidence that hypoxia could drive the maintenance of CSC, via HIF-1α expression, but it still to be determined whether hypoxia markers are expressed in breast tumors presenting CD44+CD24-/lowimmunophenotype.

Methods

Immunohistochemical analysis of CD44+CD24-/lowexpression and its relationship with hypoxia markers and clinical outcome were evaluated in 253 samples of breast ductal carcinomas. Double-immunolabeling was performed using EnVision Doublestain System (Dako, Carpinteria, CA, USA). Slides were then scanned into high-resolution images using Aperio ScanScope XT and then, visualized in the software Image Scope (Aperio, Vista, CA, USA).

Results

In univariate analysis, CD44+CD24-/lowexpression showed association with death due to breast cancer (p = 0.035). Breast tumors expressing CD44+CD24-/lowimmunophenotype showed relationship with HIF-1α (p = 0.039) and negativity for HER-2 (p = 0.013).

Conclusion

Considering that there are strong evidences that the fraction of a tumour considered to be cancer stem cells is plastic depending upon microenvironmental signals, our findings provide further evidence that hypoxia might be related to the worse prognosis found in CD44+CD24-/low positive breast tumors.
Understanding the impact of 1q21.1 copy number variant
Authors: Harvard Chansonette , Strong Emma , Mercier Eloi , Colnaghi Rita , Alcantara Diana , Chow Eva , Martell Sally , Tyson Christine , Hrynchak Monica , McGillivray Barbara , Hamilton Sara , Marles Sandra , Mhanni Aziz , Dawson Angelika J , Pavlidis Paul , Qiao Ying , Holden Jeanette J , Lewis Suzanne ME , O'Driscoll Mark , Rajcan-Separovic Evica
Published: August 2011

Background

1q21.1 Copy Number Variant (CNV) is associated with a highly variable phenotype ranging from congenital anomalies, learning deficits/intellectual disability (ID), to a normal phenotype. Hence, the clinical significance of this CNV can be difficult to evaluate. Here we described the consequences of the 1q21.1 CNV on genome-wide gene expression and function of selected candidate genes within 1q21.1 using cell lines from clinically well described subjects.

Methods and Results

Eight subjects from 3 families were included in the study: six with a 1q21.1 deletion and two with a 1q21.1 duplication. High resolution Affymetrix 2.7M array was used to refine the 1q21.1 CNV breakpoints and exclude the presence of secondary CNVs of pathogenic relevance. Whole genome expression profiling, studied in lymphoblast cell lines (LBCs) from 5 subjects, showed enrichment of genes from 1q21.1 in the top 100 genes ranked based on correlation of expression with 1q21.1 copy number. The function of two top genes from 1q21.1, CHD1L/ALC1 and PRKAB2, was studied in detail in LBCs from a deletion and a duplication carrier. CHD1L/ALC1 is an enzyme with a role in chromatin modification and DNA damage response while PRKAB2 is a member of the AMP kinase complex, which senses and maintains systemic and cellular energy balance. The protein levels for CHD1L/ALC1 and PRKAB2 were changed in concordance with their copy number in both LBCs. A defect in chromatin remodeling was documented based on impaired decatenation (chromatid untangling) checkpoint (DCC) in both LBCs. This defect, reproduced by CHD1L/ALC1 siRNA, identifies a new role of CHD1L/ALC1 in DCC. Both LBCs also showed elevated levels of micronuclei following treatment with a Topoisomerase II inhibitor suggesting increased DNA breaks. AMP kinase function, specifically in the deletion containing LBCs, was attenuated.

Conclusion

Our studies are unique as they show for the first time that the 1q21.1 CNV not only causes changes in the expression of its key integral genes, associated with changes at the protein level, but also results in changes in their known function, in the case of AMPK, and newly identified function such as DCC activation in the case of CHD1L/ALC1. Our results support the use of patient lymphoblasts for dissecting the functional sequelae of genes integral to CNVs in carrier cell lines, ultimately enhancing understanding of biological processes which may contribute to the clinical phenotype.
Integrating multiple types of data to predict novel cell cycle-related genes
Authors: Wang Lin , Hou Lin , Qian Minping , Li Fangting , Deng Minghua
Published: August 2011

Background

Cellular functions depend on genetic, physical and other types of interactions. As such, derived interaction networks can be utilized to discover novel genes involved in specific biological processes. Epistatic Miniarray Profile, or E-MAP, which is an experimental platform that measures genetic interactions on a genome-wide scale, has successfully recovered known pathways and revealed novel protein complexes in Saccharomyces cerevisiae (budding yeast).

Results

By combining E-MAP data with co-expression data, we first predicted a potential cell cycle related gene set. Using Gene Ontology (GO) function annotation as a benchmark, we demonstrated that the prediction by combining microarray and E-MAP data is generally >50% more accurate in identifying co-functional gene pairs than the prediction using either data source alone. We also used transcription factor (TF)–DNA binding data (Chip-chip) and protein phosphorylation data to construct a local cell cycle regulation network based on potential cell cycle related gene set we predicted. Finally, based on the E-MAP screening with 48 cell cycle genes crossing 1536 library strains, we predicted four unknown genes (YPL158C, YPR174C, YJR054W, and YPR045C) as potential cell cycle genes, and analyzed them in detail.

Conclusion

By integrating E-MAP and DNA microarray data, potential cell cycle-related genes were detected in budding yeast. This integrative method significantly improves the reliability of identifying co-functional gene pairs. In addition, the reconstructed network sheds light on both the function of known and predicted genes in the cell cycle process. Finally, our strategy can be applied to other biological processes and species, given the availability of relevant data.
A 64-year old man presenting with carotid artery occlusion and corticobasal syndrome: a case report
Authors: Engelen Marc , Westhoff Dunja , de Gans Jan , Nederkoorn Paul J
Published: August 2011

Introduction

Magnetic resonance imaging of the brain in patients with corticobasal degeneration typically shows focal or asymmetric atrophy, usually maximal in the frontoparietal cortex. Many patients who are diagnosed with corticobasal degeneration using current diagnostic criteria do not have classical corticobasal degeneration pathology. Our case is remarkable for the fact that the symptoms and the characteristic magnetic resonance imaging appearance were typical for corticobasal degeneration. However, we were quite convinced that the clinical picture had a vascular etiology. Only a few cases have been reported where the presumed cause for the corticobasal syndrome was multiple brain infarctions bilaterally.

Case presentation

A 64-year-old Caucasian man visited a neurologist because of profound asymmetric sensory and motor disturbances. A magnetic resonance imaging scan of his brain revealed occlusion of his internal carotid artery on the left side with multiple vascular lesions in his left hemisphere and notable atrophy of mainly the left parietal and frontal cortex.

Conclusion

We describe a patient with corticobasal syndrome caused by multiple infarctions, probably caused by emboli of the carotid stenosis. This patient illustrates the fact that the word 'syndrome' should be preferred above 'degeneration' in the name of this disease.
Integrative network analysis identifies key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma
Authors: Zheng Siyuan , Tansey William P , Hiebert Scott W , Zhao Zhongming
Published: August 2011

Background

Incidence of hepatitis C virus (HCV) induced hepatocellular carcinoma (HCC) has been increasing in the United States and Europe during recent years. Although HCV-associated HCC shares many pathological characteristics with other types of HCC, its molecular mechanisms of progression remain elusive.

Methods

To investigate the underlying pathology, we developed a systematic approach to identify deregulated biological networks in HCC by integrating gene expression profiles with high-throughput protein-protein interaction data. We examined five stages including normal (control) liver, cirrhotic liver, dysplasia, early HCC and advanced HCC.

Results

Among the five consecutive pathological stages, we identified four networks including precancerous networks (Normal-Cirrhosis and Cirrhosis-Dysplasia) and cancerous networks (Dysplasia-Early HCC, Early-Advanced HCC). We found little overlap between precancerous and cancerous networks, opposite to a substantial overlap within precancerous or cancerous networks. We further found that the hub proteins interacted with HCV proteins, suggesting direct interventions of these networks by the virus. The functional annotation of each network demonstrates a high degree of consistency with current knowledge in HCC. By assembling these functions into a module map, we could depict the stepwise biological functions that are deregulated in HCV-induced hepatocarcinogenesis. Additionally, these networks enable us to identify important genes and pathways by developmental stage, such asLCKsignalling pathways in cirrhosis,MMPgenes andTIMPgenes in dysplastic liver, andCDC2-mediated cell cycle signalling in early and advanced HCC.CDC2(alternative symbolCDK1), a cell cycle regulatory gene, is particularly interesting due to its topological position in temporally deregulated networks.

Conclusions

Our study uncovers a temporal spectrum of functional deregulation and prioritizes key genes and pathways in the progression of HCV induced HCC. These findings present a wealth of information for further investigation.
Combinations of newly confirmed Glioma-Associated loci link regions on chromosomes 1 and 9 to increased disease risk
Authors: Yang Tun-Hsiang , Kon Mark , Hung Jui-Hung , DeLisi Charles
Published: August 2011

Background

Glioblastoma multiforme (GBM) tends to occur between the ages of 45 and 70. This relatively early onset and its poor prognosis make the impact of GBM on public health far greater than would be suggested by its relatively low frequency. Tissue and blood samples have now been collected for a number of populations, and predisposing alleles have been sought by several different genome-wide association (GWA) studies. The Cancer Genome Atlas (TCGA) at NIH has also collected a considerable amount of data. Because of the low concordance between the results obtained using different populations, only 14 predisposing single nucleotide polymorphism (SNP) candidates in five genomic regions have been replicated in two or more studies. The purpose of this paper is to present an improved approach to biomarker identification.

Methods

Association analysis was performed with control of population stratifications using the EIGENSTRAT package, under the null hypothesis of "no association between GBM and control SNP genotypes," based on an additive inheritance model. Genes that are strongly correlated with identified SNPs were determined by linkage disequilibrium (LD) or expression quantitative trait locus (eQTL) analysis. A new approach that combines meta-analysis and pathway enrichment analysis identified additional genes.

Results

(i) A meta-analysis of SNP data from TCGA and the Adult Glioma Study identifies 12 predisposing SNP candidates, seven of which are reported for the first time. These SNPs fall in five genomic regions (5p15.33, 9p21.3, 1p21.2, 3q26.2 and 7p15.3), three of which have not been previously reported. (ii) 25 genes are strongly correlated with these 12 SNPs, eight of which are known to be cancer-associated. (iii) The relative risk for GBM is highest for risk allele combinations on chromosomes 1 and 9. (iv) A combined meta-analysis/pathway analysis identified an additional four genes. All of these have been identified as cancer-related, but have not been previously associated with glioma. (v) Some SNPs that do not occur reproducibly across populations are in reproducible (invariant) pathways, suggesting that they affect the same biological process, and that population discordance can be partially resolved by evaluating processes rather than genes.

Conclusion

We have uncovered 29 glioma-associated gene candidates; 12 of them known to be cancer related (p= 1. 4 × 10-6), providing additional statistical support for the relevance of the new candidates. This additional information on risk loci is potentially important for identifying Caucasian individuals at risk for glioma, and for assessing relative risk.
Development of a rapid dipstick with latex immunochromatographic assay (DLIA) for diagnosis of schistosomiasis japonica
Authors: Yu Li-Ling , Ding Jian-Zu , Wen Li-Yong , Lou Di , Yan Xiao-Lan , Lin Li-Jun , Lu Shao-Hong , Lin Dan-Dan , Zhou Xiao-Nong
Published: August 2011

Background

Schistosomiasis japonica (schistosomiasis) is a zoonosis that can seriously affect human health. At present, the immunodiagnostic assays for schistosomiasis detection are time-consuming and require well-trained personnel and special instruments, which can limit their use in the field. Thus, there is a pressing need for a simple and rapid immunoassay to screen patients on a large scale. In this study, we developed a novel rapid dipstick with latex immunochromatographic assay (DLIA) to detect anti-Schisaosoma japonicum antibodies in human serum.

Results

Using latex microspheres as a color probe, DLIA was established to test standard positive and negative sera, in comparison with the classical enzyme-linked immunosorbent assay (ELISA). The sensitivity and specificity of DLIA were 95.10% (97/102) and 94.91% (261/275), respectively. The cross-reaction rates with clonorchiosis, intestinal nematodes, Angiostrongylus cantonensis and paragonimiasis were 0, 0, 0 and 42.11% respectively. All the results showed no significant difference to the ELISA. In field tests, 333 human serum samples from an endemic area were tested with DLIA, and compared with ELISA and Kato-Katz method. There was no significant difference between DLIA and ELISA on positive and negative rates of detection; however, significant differences existed between DLIA and Kato-Katz method, and between ELISA and Kato-Katz method. The kappa value between DLIA and ELISA was 0.90.

Conclusions

This is the first study in which DLIA was used to detect anti-Schistosoma japonicum antibody. The results show that DLIA is a simple, rapid, convenient, sensitive and specific assay for the diagnosis of schistosomiasis and is therefore very suitable for large-scale field applications and clinical detection.
Prevalence of aac(6')-Ib-cr plasmid-mediated and chromosome-encoded fluoroquinolone resistance in Enterobacteriaceae in Italy
Authors: Frasson Ilaria , Cavallaro Antonietta , Bergo Cristina , Richter Sara N , Palù Giorgio
Published: August 2011

The spread of aac(6')-Ib-cr plasmid-mediated quinolone resistance determinants was evaluated in 197 enterobacterial isolates recovered in an Italian teaching hospital. The aac(6')-Ib-cr gene was found exclusively in Escherichia coli strains. The gene was located on a plasmid which presented additional ESBL genes. Most of the clinical strains were clonally related and displayed three point mutations at the topoisomerase level which conferred high resistance to fluoroquinolones.
Regulation of DMD pathology by an ankyrin-encoded miRNA
Authors: Alexander Matthew S , Casar Juan Carlos , Motohashi Norio , Myers Jennifer A , Eisenberg Iris , Gonzalez Robert T , Estrella Elicia A , Kang Peter B , Kawahara Genri , Kunkel Louis M
Published: August 2011

Background

Duchenne muscular dystrophy (DMD) is an X-linked myopathy resulting from the production of a nonfunctional dystrophin protein. MicroRNA (miRNA) are small 21- to 24-nucleotide RNA that can regulate both individual genes and entire cell signaling pathways. Previously, we identified several mRNA, both muscle-enriched and inflammation-induced, that are dysregulated in the skeletal muscles of DMD patients. One particularly muscle-enriched miRNA, miR-486, is significantly downregulated in dystrophin-deficient mouse and human skeletal muscles. miR-486 is embedded within the ANKYRIN1(ANK1) gene locus, which is transcribed as either a long (erythroid-enriched) or a short (heart muscle- and skeletal muscle-enriched) isoform, depending on the cell and tissue types.

Results

Inhibition of miR-486 in normal muscle myoblasts results in inhibited migration and failure to repair a wound in primary myoblast cell cultures. Conversely, overexpression of miR-486 in primary myoblast cell cultures results in increased proliferation with no changes in cellular apoptosis. Using bioinformatics and miRNA reporter assays, we have identified platelet-derived growth factor receptor β, along with several other downstream targets of the phosphatase and tensin homolog deleted on chromosome 10/AKT (PTEN/AKT) pathway, as being modulated by miR-486. The generation of muscle-specific transgenic mice that overexpress miR-486 revealed that miR-486 alters the cell cycle kinetics of regenerated myofibers in vivo, as these mice had impaired muscle regeneration.

Conclusions

These studies demonstrate a link for miR-486 as a regulator of the PTEN/AKT pathway in dystrophin-deficient muscle and an important factor in the regulation of DMD muscle pathology.
Probabilistic modeling and analysis of the effects of extra-cellular matrix density on the sizes, shapes, and locations of integrin clusters in adherent cells
Authors: Welf Erik S , Naik Ulhas P , Ogunnaike Babatunde A
Published: August 2011

Background

Regulation of integrin binding to the specific complementary sites on extra-cellular matrix (ECM) proteins plays a major role in cell adhesion and migration. In addition to regulating single integrin-ligand bonds by affinity modulation, cells regulate their adhesiveness by forming integrin clusters. Although it is clear that cells exhibit different adhesion and migration behaviors on surfaces coated with different concentrations of ECM proteins, it is not clear if this response is mediated by changes in the availability of integrin binding sites or by differential intracellular signaling that may affect integrin binding and clustering.

Results

To quantify how the concentration of ECM affects integrin clustering, we seeded cells expressing the integrin αIIbβ3 on different concentrations of the complementary ECM protein fibrinogen (Fg) and measured the resulting integrin cluster properties. We observed heterogeneity in the properties of integrin clusters, and to characterize this population heterogeneity we use a probabilistic modeling approach to quantify changes to the distributions of integrin cluster size, shape, and location.

Conclusions

Our results indicate that in response to increasing ECM density cells form smaller integrin clusters that are less elongated and closer to the cell periphery. These results suggest that cells can sense the availability of ECM binding sites and consequently regulate integrin clustering as a function of ECM density.
Harnessing the self-harvesting capability of benthic cyanobacteria for use in benthic photobioreactors
Authors: Esson Diane , Wood Susanna A , Packer Michael A
Published: August 2011

Benthic species of algae and cyanobacteria (i.e., those that grow on surfaces), may provide potential advantages over planktonic species for some commercial-scale biotechnological applications. A multitude of different designs of photobioreactor (PBR) are available for growing planktonic species but to date there has been little research on PBR for benthic algae or cyanobacteria. One notable advantage of some benthic cyanobacterial species is that during their growth cycle they become positively buoyant, detach from the growth surface and form floating mats. This 'self-harvesting' capability could be advantageous in commercial PBRs as it would greatly reduce dewatering costs. In this study we compared the growth rates and efficiency of 'self-harvesting' among three species of benthic cyanobacteria; Phormidium autumnale; Phormidium murrayi and Planktothrix sp.. Phormidium autumnale produced the greatest biomass and formed cohesive mats once detached. Using this strain and an optimised MLA media, a variety of geometries of benthic PBRs (bPBRs) were trialed. The geometry and composition of growth surface had a marked effect on cyanobacterial growth. The highest biomass was achieved in a bPBR comprising of a vertical polyethylene bag with loops of silicone tubing to provide additional growth surfaces. The productivity achieved in this bPBR was a similar order of magnitude as planktonic species, with the additional advantage that towards the end of the exponential phase the bulk of the biomass detached forming a dense mat at the surface of the medium.
Decreased catalytic function with altered sumoylation of DNA topoisomerase I in the nuclei of scleroderma fibroblasts
Authors: Zhou Xiaodong , Lin Wei , Tan Filemon K , Assassi Shervin , Fritzler Mavin J , Guo Xinjian , Sharif Roozbeh , Xia Tom , Lai Syeling , Arnett Frank C
Published: August 2011

Introduction

Sumoylation is involved in nucleolus-nucleoplasm transport of DNA topoisomerase I (topo I), which may associate with changes of cellular and topo I functions. Skin fibroblasts of patients with systemic sclerosis (SSc) exhibit profibrotic cellular changes. The aims of this study were to examine the catalytic function and sumoylation of topo I in the nuclei of SSc fibroblasts, a major cell type involved in the fibrotic process.

Methods

Eleven pairs of fibroblast strains obtained from nonlesional skin biopsies of SSc patients and age/sex/ethnicity-matched normal controls were examined for catalytic function of nuclear topo I. Immunoprecipitation (IP)-Western blots were used to examine sumoylation of fibroblast topo I. Real-time quantitative RT-PCR was used to measure transcript levels of SUMO1 and COL1A2 in the fibroblasts.

Results

Topo I in nuclear extracts of SSc fibroblasts generally showed a significantly lower efficiency than that of normal fibroblasts in relaxing equivalent amounts of supercoiled DNA. Increased sumoylation of topo I was clearly observed in 7 of 11 SSc fibroblast strains. Inhibition of SUMO1 with SUMO1 siRNA improved the catalytic efficiency of topo I in the SSc fibroblasts. In contrast, sumoylation of recombinant topo I proteins reduced their catalytic function.

Conclusions

The catalytic function of topo I was decreased in SSc fibroblasts, to which increased sumoylation of topo I may contribute.