bluuebunny/crossref_metadata_2025 huggingface dataset:
Cophenetic metrics for phylogenetic trees, after Sokal and Rohlf
Authors: Cardona Gabriel , Mir Arnau , Rosselló Francesc , Rotger Lucía , Sánchez David
Published: January 2013

Background

Phylogenetic tree comparison metrics are an important tool in the study of evolution, and hence the definition of such metrics is an interesting problem in phylogenetics. In a paper in Taxon fifty years ago, Sokal and Rohlf proposed to measure quantitatively the difference between a pair of phylogenetic trees by first encoding them by means of their half-matrices of cophenetic values, and then comparing these matrices. This idea has been used several times since then to define dissimilarity measures between phylogenetic trees but, to our knowledge, no proper metric on weighted phylogenetic trees with nested taxa based on this idea has been formally defined and studied yet. Actually, the cophenetic values of pairs of different taxa alone are not enough to single out phylogenetic trees with weighted arcs or nested taxa.

Results

For every (rooted) phylogenetic treeT, let itscophenetic vectorφ(T) consist of all pairs of cophenetic values between pairs of taxa inTand all depths of taxa inT. It turns out that these cophenetic vectors single out weighted phylogenetic trees with nested taxa. We then define a family of cophenetic metricsdφ,pby comparing these cophenetic vectors by means ofLpnorms, and we study, either analytically or numerically, some of their basic properties: neighbors, diameter, distribution, and their rank correlation with each other and with other metrics.

Conclusions

The cophenetic metrics can be safely used on weighted phylogenetic trees with nested taxa and no restriction on degrees, and they can be computed inO(n2) time, wherenstands for the number of taxa. The metricsdφ,1anddφ,2have positive skewed distributions, and they show a low rank correlation with the Robinson-Foulds metric and the nodal metrics, and a very high correlation with each other and with the splitted nodal metrics. The diameter ofdφ,p, forp⩾1, is inO(n(p+2)/p), and thus for lowpthey are more discriminative, having a wider range of values.
RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum
Authors: Zhao Chunzhao , Waalwijk Cees , de Wit Pierre J G M , Tang Dingzhong , van der Lee Theo
Published: January 2013

Background

The genome of Fusarium graminearum has been sequenced and annotated previously, but correct gene annotation remains a challenge. In addition, posttranscriptional regulations, such as alternative splicing and RNA editing, are poorly understood in F. graminearum. Here we took advantage of RNA-Seq to improve gene annotations and to identify alternative splicing and RNA editing in F. graminearum.

Results

We identified and revised 655 incorrectly predicted gene models, including revisions of intron predictions, intron splice sites and prediction of novel introns. 231 genes were identified with two or more alternative splice variants, mostly due to intron retention. Interestingly, the expression ratios between different transcript isoforms appeared to be developmentally regulated. Surprisingly, no RNA editing was identified in F. graminearum. Moreover, 2459 novel transcriptionally active regions (nTARs) were identified and our analysis indicates that many of these could be missed genes. Finally, we identified the 5′ UTR and/or 3′ UTR sequences of 7666 genes. A number of representative novel gene models and alternatively spliced genes were validated by reverse transcription polymerase chain reaction and sequencing of the generated amplicons.

Conclusions

We have developed novel and efficient strategies to identify alternatively spliced genes and incorrect gene models based on RNA-Seq data. Our study identified hundreds of alternatively spliced genes in F. graminearum and for the first time indicated that alternative splicing is developmentally regulated in filamentous fungi. In addition, hundreds of incorrect predicted gene models were identified and revised and thousands of nTARs were discovered in our study, which will be helpful for the future genomic and transcriptomic studies in F. graminearum.
Multilevel comparative analysis of the contributions of genome reduction and heat shock to the Escherichia colitranscriptome
Authors: Ying Bei-Wen , Seno Shigeto , Kaneko Fuyuro , Matsuda Hideo , Yomo Tetsuya
Published: January 2013

Background

Both large deletions in genome and heat shock stress would lead to alterations in the gene expression profile; however, whether there is any potential linkage between these disturbances to the transcriptome have not been discovered. Here, the relationship between the genomic and environmental contributions to the transcriptome was analyzed by comparing the transcriptomes of the bacteriumEscherichia coli(strain MG1655 and its extensive genomic deletion derivative, MDS42) grown in regular and transient heat shock conditions.

Results

The transcriptome analysis showed the following: (i) there was a reorganization of the transcriptome in accordance with preferred chromosomal periodicity upon genomic or heat shock perturbation; (ii) there was a considerable overlap between the perturbed regulatory networks and the categories enriched for differentially expressed genes (DEGs) following genome reduction and heat shock; (iii) the genes sensitive to genome reduction tended to be located close to genomic scars, and some were also highly responsive to heat shock; and (iv) the genomic and environmental contributions to the transcriptome displayed not only a positive correlation but also a negatively compensated relationship (i.e., antagonistic epistasis).

Conclusion

The contributions of genome reduction and heat shock to theEscherichia colitranscriptome were evaluated at multiple levels. The observations of overlapping perturbed networks, directional similarity in transcriptional changes, positive correlation and epistatic nature linked the two contributions and suggest somehow a crosstalk guiding transcriptional reorganization in response to both genetic and environmental disturbances in bacteriumE.coli.
Adjustment method for microarray data generated using two-cycle RNA labeling protocol
Authors: Wang Fugui , Chen Rui , Ji Dong , Bai Shunong , Qian Minping , Deng Minghua
Published: January 2013

Background

Microarray technology is widely utilized for monitoring the expression changes of thousands of genes simultaneously. However, the requirement of relatively large amount of RNA for labeling and hybridization makes it difficult to perform microarray experiments with limited biological materials, thus leads to the development of many methods for preparing and amplifying mRNA. It is addressed that amplification methods usually bring bias, which may strongly hamper the following interpretation of the results. A big challenge is how to correct for the bias before further analysis.

Results

In this article, we observed the bias in rice gene expression microarray data generated with the Affymetrix one-cycle, two-cycle RNA labeling protocols, followed by validation with Real Time PCR. Based on these data, we proposed a statistical framework to model the processes of mRNA two-cycle linear amplification, and established a linear model for probe level correction. Maximum Likelihood Estimation (MLE) was applied to perform robust estimation of the Retaining Rate for each probe. After bias correction, some known pre-processing methods, such as PDNN, could be combined to finish preprocessing. Then, we evaluated our model and the results suggest that our model can effectively increase the quality of the microarray raw data: (i) Decrease the Coefficient of Variation for PM intensities of probe sets; (ii) Distinguish the microarray samples of five stages for rice stamen development more clearly; (iii) Improve the correlation coefficients among stamen microarray samples. We also discussed the necessity of model adjustment by comparing with another simple adjustment method.

Conclusion

We conclude that the adjustment model is necessary and could effectively increase the quality of estimation for gene expression from the microarray raw data.
RNAi phenotypes are influenced by the genetic background of the injected strain
Authors: Kitzmann Peter , Schwirz Jonas , Schmitt-Engel Christian , Bucher Gregor
Published: January 2013

Background

RNA interference (RNAi) is a powerful tool to study gene function in organisms that are not amenable to classical forward genetics. Hence, together with the ease of comprehensively identifying genes by new generation sequencing, RNAi is expanding the scope of animal species and questions that can be addressed in terms of gene function. In the case of genetic mutants, the genetic background of the strains used is known to influence the phenotype while this has not been described for RNAi experiments.

Results

Here we show in the red flour beetle Tribolium castaneum that RNAi against Tc-importin α1 leads to different phenotypes depending on the injected strain. We rule out off target effects and show that sequence divergence does not account for this difference. By quantitatively comparing phenotypes elicited by RNAi knockdown of four different genes we show that there is no general difference in RNAi sensitivity between these strains. Finally, we show that in case of Tc-importin α1 the difference depends on the maternal genotype.

Conclusions

These results show that in RNAi experiments strain specific differences have to be considered and that a proper documentation of the injected strain is required. This is especially important for the increasing number of emerging model organisms that are being functionally investigated using RNAi. In addition, our work shows that RNAi is suitable to systematically identify the differences in the gene regulatory networks present in populations of the same species, which will allow novel insights into the evolution of animal diversity.
Functional analysis of the ATP-binding cassette (ABC) transporter gene family of Tribolium castaneum
Authors: Broehan Gunnar , Kroeger Tobias , Lorenzen Marcé , Merzendorfer Hans
Published: January 2013

Background

The ATP-binding cassette (ABC) transporters belong to a large superfamily of proteins that have important physiological functions in all living organisms. Most are integral membrane proteins that transport a broad spectrum of substrates across lipid membranes. In insects, ABC transporters are of special interest because of their role in insecticide resistance.

Results

We have identified 73 ABC transporter genes in the genome ofT. castaneum, which group into eight subfamilies (ABCA-H). This coleopteran ABC family is significantly larger than those reported for insects in other taxonomic groups. Phylogenetic analysis revealed that this increase is due to gene expansion within a single clade of subfamily ABCC. We performed an RNA interference (RNAi) screen to study the function of ABC transporters during development. In ten cases, injection of double-stranded RNA (dsRNA) into larvae caused developmental phenotypes, which included growth arrest and localized melanization, eye pigmentation defects, abnormal cuticle formation, egg-laying and egg-hatching defects, and mortality due to abortive molting and desiccation. Some of the ABC transporters we studied in closer detail to examine their role in lipid, ecdysteroid and eye pigment transport.

Conclusions

The results from our study provide new insights into the physiological function of ABC transporters inT. castaneum,and may help to establish new target sites for insect control.
A new computational approach redefines the subtelomeric vir superfamily of Plasmodium vivax
Authors: Lopez Francisco Javier , Bernabeu Maria , Fernandez-Becerra Carmen , del Portillo Hernando A
Published: January 2013

Background

Subtelomeric multigene families of malaria parasites encode virulent determinants. The published genome sequence of Plasmodium vivax revealed the largest subtelomeric multigene family of human malaria parasites, the vir super-family, presently composed of 346 vir genes subdivided into 12 different subfamilies based on sequence homologies detected by BLAST.

Results

A novel computational approach was used to redefine vir genes. First, a protein-weighted graph was built based on BLAST alignments. This graph was processed to ensure that edge weights are not exclusively based on the BLAST score between the two corresponding proteins, but strongly dependant on their graph neighbours and their associations. Then the Markov Clustering Algorithm was applied to the protein graph. Next, the Homology Block concept was used to further validate this clustering approach. Finally, proteome-wide analysis was carried out to predict new VIR members. Results showed that (i) three previous subfamilies cannot longer be classified as vir genes; (ii) most previously unclustered vir genes were clustered into vir subfamilies; (iii) 39 hypothetical proteins were predicted as VIR proteins; (iv) many of these findings are supported by a number of structural and functional evidences, sub-cellular localization studies, gene expression analysis and chromosome localization (v) this approach can be used to study other multigene families in malaria.

Conclusions

This methodology, resource and new classification of vir genes will contribute to a new structural framing of this multigene family and other multigene families of malaria parasites, facilitating the design of experiments to understand their role in pathology, which in turn may help furthering vaccine development.
Identification of miRNAs and their targets using high-throughput sequencing and degradome analysis in cytoplasmic male-sterile and its maintainer fertile lines of Brassica juncea
Authors: Yang Jinghua , Liu Xunyan , Xu Baochen , Zhao Na , Yang Xiaodong , Zhang Mingfang
Published: January 2013

Background

Regulatory network of cytoplasmic male sterility (CMS) occurrence is still largely unknown in plants, although numerous researches have been attempted to isolate genes involved in CMS. Here, we employed high-throughput sequencing and degradome analysis to identify microRNAs and their targets using high-throughput sequencing in CMS and its maintainer fertile (MF) lines of Brassica juncea.

Results

We identified 197 known and 78 new candidate microRNAs during reproductive development of B. juncea. A total of 47 differentially expressed microRNAs between CMS and its MF lines were discovered, according to their sequencing reads number. Different expression levels of selected microRNAs were confirmed by using real-time quantitative PCR between CMS and MF lines. Furthermore, we observed that the transcriptional patterns of these microRNAs could be mimicked by artificially inhibiting mitochondrial F1F0-ATPase activity and its function in MF line by using treatment with oligomycin. Targeted genes of the microRNAs were identified by high-throughput sequencing and degradome approaches, including auxin response factor, NAC (No Apical Meristem) domain transcription factor, GRAS family transcription factor, MYB transcription factor, squamosa promoter binding protein, AP2-type transcription factor, homeobox/homeobox-leucine zipper family and TCP family transcription factors, which were observed to be differentially expressed between CMS and MF.

Conclusion

Taken together, from these findings we suggested microRNA might participate in the regulatory network of CMS by tuning fork in gene expressions in CMS B. juncea. The differential expression of miRNAs observed between CMS and MF lines suggested that biogenesis of miRNAs could be influenced in the CMS.
The impact of MFG-E8 in chronic pancreatitis: potential for future immunotherapy?
Authors: D’Haese Jan G , Demir Ihsan Ekin , Kehl Timo , Winckler Jannik , Giese Nathalia A , Bergmann Frank , Giese Thomas , Büchler Markus W , Friess Helmut , Hartel Mark , Ceyhan Güralp O
Published: January 2013

Background

The glycoprotein MFG-E8 mediates phagocytic clearance of apoptotic cells and influences the pathogenesis and progression of inflammatory diseases. MFG-E8 was shown to attenuate the progression of inflammation and to improve survival in septic rats. Accumulating evidence suggests an immunomodulatory link between MFG-E8 and the pro-inflammatory chemokine fractalkine, which may determine the severity of pain, fibrosis, and inflammation in chronic pancreatitis (CP).

Methods

The expression and localization of MFG-E8 was investigated in CP (n = 62), and normal pancreas (NP; n = 34) by QRT-PCR, Western-blot and immunohistochemistry analyses. Results were correlated with mRNA expression of fractalkine, CX3CR1, and with the presence and degree of pain and fibrosis. Human pancreatic stellate cells (hPSCs) were isolated from CP tissues and evaluated for MFG-E8 mRNA expression after fractalkine stimulation.

Results

MFG-E8-mRNA was significantly overexpressed in CP and isolated hPSCs when compared to NP. Western-blot and immunohistochemistry analysis confirmed accumulation of MFG-E8 in CP, with noticeably increased MFG-E8 immunoreactivity in tubular complexes. MFG-E8 expression correlated significantly with fractalkine expression, severe fibrosis, and the presence of pain in CP patients. Stimulation of hPSCs with fractalkine led to a significant increase in MFG-E8 expression.

Conclusions

In the present study, we demonstrated for the first time that MFG-E8 is significantly up-regulated in CP patients and together with fractalkine correlated noticeably with severe fibrosis and the presence of pain. hPSCs overexpress MFG-E8 upon fractalkine stimulation in vitro, which underlines the suggested immunmodulatory link in CP and may be a key mechanism in CP fibrogenesis and pain generation. Taken together, these novel findings suggest that MFG-E8 blockade may be a promising tool for future immunotherapy in CP to attenuate both fibrosis and pain sensation.
Radiofrequency ablation of liver tumors: quantitative assessment of tumor coverage through CT image processing
Authors: Passera Katia , Selvaggi Sabrina , Scaramuzza Davide , Garbagnati Francesco , Vergnaghi Daniele , Mainardi Luca
Published: January 2013

Background

Radiofrequency ablation (RFA) is one of the most promising non-surgical treatments for hepatic tumors. The assessment of the therapeutic efficacy of RFA is usually obtained by visual comparison of pre- and post-treatment CT images, but no numerical quantification is performed.

Methods

In this work, a novel method aiming at providing a more objective tool for the evaluation of RFA coverage is described. Image registration and segmentation techniques were applied to enable the visualization of the tumor and the corresponding post-RFA necrosis in the same framework. In addition, a set of numerical indexes describing tumor/necrosis overlap and their mutual position were computed.

Results

After validation of segmentation step, the method was applied on a dataset composed by 10 tumors, suspected not to be completed treated. Numerical indexes showed that only two tumors were totally treated and the percentage of a residual tumor was in the range of 5.12%-35.92%.

Conclusions

This work represents a first attempt to obtain a quantitative tool aimed to assess the accuracy of RFA treatment. The possibility to visualize the tumor and the correspondent post-RFA necrosis in the same framework and the definition of some synthetic numerical indexes could help clinicians in ameliorating RFA treatment.
Jugular venous reflux and plasma endothelin-1 are associated with cough syncope: a case control pilot study
Authors: Chung Chih-Ping , Cheng Chun-Yu , Zivadinov Robert , Chen Wei-Chih , Sheng Wen-Yung , Lee Yu-Chin , Hu Han-Hwa , Hsu Hung-Yi , Yang Kuang-Yao
Published: January 2013

Background

Jugular venous reflux (JVR) has been reported to cause cough syncope via retrograde-transmitted venous hypertension and consequently decreased cerebral blood flow (CBF). Unmatched frequencies of JVR and cough syncope led us to postulate that there should be additional factors combined with JVR to exaggerate CBF decrement during cough, leading to syncope. The present pilot study tested the hypothesis that JVR, in addition to an increased level of plasma endothelin-1 (ET-1), a potent vasoconstrictor, is involved in the pathophysiology of cough syncope.

Methods

Seventeen patients with cough syncope or pre-syncope (Mean[SD] = 74.63(12.37) years; 15 males) and 51 age/gender-matched controls received color-coded duplex ultrasonography for JVR determination and plasma ET-1 level measurements.

Results

Multivariate logistic analysis showed that the presence of both-side JVR (odds ratio [OR] = 10.77, 95% confident interval [CI] = 2.40-48.35, p = 0.0019) and plasma ET-1 > 3.43 pg/ml (OR = 14.57, 95% CI = 2.95-71.59, p = 0.001) were independently associated with the presence of cough syncope/ pre-syncope respectively. There was less incidence of cough syncope/ pre-syncope in subjects with the absence of both-side JVR and a plasma ET-1 ≦3.43 pg/ml. Presence of both side JVR and plasma ET-1 level of > 3.43 pg/ml, increased risk for cough syncope/pre-syncope (p < 0.001).

Conclusions

JVR and higher plasma levels of ET-1 are associated with cough syncope/ pre-syncope. Although sample size of this study was small, we showed a synergistic effect between JVR and plasma ET-1 levels on the occurrence of cough syncope/pre-syncope. Future studies should confirm our pilot findings.
Maternal near miss and quality of maternal health care in Baghdad, Iraq
Authors: Jabir Maysoon , Abdul-Salam Imad , Suheil Dhikra M , Al-Hilli Wafa , Abul-Hassan Sana , Al-Zuheiri Amal , Al-Ba'aj Rasha , Dekan Abeer , Tunçalp Özge , Souza Joao Paulo
Published: January 2013

Background

The maternal near-miss concept has been developed as an instrument for assisting health systems to evaluate and improve their quality of care. Our study aimed at studying the characteristics and quality of care provided to women with severe complications in Baghdad through the use of the World Health Organization (WHO) near-miss approach for maternal health.

Methods

This is a facility-based, cross-sectional study conducted in 6 public hospitals in Baghdad between March 1, 2010 and the June 30, 2010. WHO near-miss approach was utilized to analyze the data in terms of indicators of maternal near miss and access to and quality of maternal care.

Results

The maternal near-miss rate was low at 5.06 per 1,000 live births, while the overall maternal near miss: mortality ratio was 9:1. One third of the near-miss cases were referred from other facilities and the mortality index was the same for referred women and for in-hospital women (11%). The intensive care unit (ICU) admission rate was 37% for women with severe maternal outcomes (SMO), while the overall admission rate was 0.28%. Anemia (55%) and previous cesarean section (45%) were the most common associated conditions with severe maternal morbidity. The use of magnesium sulfate for treatment of eclampsia, oxytocin for prevention and treatment of postpartum hemorrhage, prophylactic antibiotics during caesarean section, and corticosteroids for inducing fetal lung maturation in preterm birth is suboptimum.

Conclusions

The WHO near-miss approach allowed systematic identification of the roadblocks to improve quality of care and then monitoring the progress. Critical evidence-based practices, relevant to the management of women experiencing life-threatening conditions, are underused. In addition, possible limitations in the referral system result in a very high proportion of women presenting at the hospital already in a severe health condition (i.e. with organ dysfunction). A shortage of ICU beds leading to women taken care of without admission to ICU may also contribute to a high proportion of maternal deaths and organ dysfunction.
Development and validation of a pregnancy symptoms inventory
Authors: Foxcroft Katie F , Callaway Leonie K , Byrne Nuala M , Webster Joan
Published: January 2013

Background

Physical symptoms are common in pregnancy and are predominantly associated with normal physiological changes. These symptoms have a social and economic cost, leading to absenteeism from work and additional medical interventions. There is currently no simple method for identifying common pregnancy related problems in the antenatal period. A validated tool, for use by pregnancy care providers would be useful. The aim of this study was to develop and validate a Pregnancy Symptoms Inventory for use by health professionals.

Methods

A list of symptoms was generated via expert consultation with health professionals. Focus groups were conducted with pregnant women. The inventory was tested for face validity and piloted for readability and comprehension. For test-re-test reliability, the tool was administered to the same women 2 to 3 days apart. Finally, midwives trialled the inventory for 1 month and rated its usefulness on a 10cm visual analogue scale (VAS).

Results

A 41-item Likert inventory assessing how often symptoms occurred and what effect they had, was developed. Individual item test re-test reliability was between .51 to 1, the majority (34 items) scoring ≥0.70. The top four “often” reported symptoms were urinary frequency (52.2%), tiredness (45.5%), poor sleep (27.5%) and back pain (19.5%). Among the women surveyed, 16.2% claimed to sometimes or often be incontinent. Referrals to the incontinence nurse increased > 8 fold during the study period.

Conclusions

The PSI provides a comprehensive inventory of pregnancy related symptoms, with a mechanism for assessing their effect on function. It was robustly developed, with good test re-test reliability, face validity, comprehension and readability. This provides a validated tool for assessing the impact of interventions in pregnancy.
Level of awareness of mammography among women attending outpatient clinics in a teaching hospital in Ibadan, South-West Nigeria
Authors: Obajimi Millicent O , Ajayi Ikeoluwapo O , Oluwasola Abideen O , Adedokun Babatunde O , Adeniji-Sofoluwe Adenike T , Mosuro Olushola A , Akingbola Titilola S , Bassey Oku S , Umeh Eric , Soyemi Temitope O , Adegoke Folasade , Ogungbade Idiat , Ukaigwe Chinwe , Olopade Olufunmilayo I
Published: January 2013

Background

Mammography has been used in developed countries with considerable success but very little is known about this imaging modality in low resource settings. This study examined the level of awareness of mammography and determined factors influencing the level of awareness.

Methods

We conducted a hospital based cross sectional study to investigate the level of awareness of mammography among 818 randomly selected women attending the General Outpatient clinics (GOP) of the University College Hospital (UCH), Ibadan, Nigeria. Independent predictors of level of awareness of mammography were identified using multiple logistic regression analysis.

Results

The proportion of women who ever heard of mammography was 5%, and they demonstrated poor knowledge of the procedure. Those with primary or secondary levels of education were about three times less likely to be aware of mammography when compared with those with tertiary level of education (OR = 0.3, 95% CI, 0.12 – 0.73). Also, participation in community breast cancer prevention activities (OR = 3.4, 95% CI, 1.39 – 8.36), and previous clinical breast examination (OR = 2.34, 95% CI, 1.10 – 4.96) independently predicted mammography awareness. Newspapers and magazines appeared to be the most important sources of information about mammography screening.

Conclusion

The level of awareness of mammography is poor among women attending outpatient clinics in the studied population. Interventions promoting awareness of this screening procedure should give particular attention to the illiterate and older women while clinicians performing breast examinations should utilize the opportunity to inform women about the mammography procedure. Promotion of educational articles on breast cancer and its screening methods via media remains vital for the literate.
Cloning, overexpression, purification, and characterization of a polyextremophilic β-galactosidase from the Antarctic haloarchaeon Halorubrum lacusprofundi
Authors: Karan Ram , Capes Melinda D , DasSarma Priya , DasSarma Shiladitya
Published: January 2013

Background

Halorubrum lacusprofundi is a cold-adapted halophilic archaeon isolated from Deep Lake, a perennially cold and hypersaline lake in Antarctica. Its genome sequencing project was recently completed, providing access to many genes predicted to encode polyextremophilic enzymes active in both extremely high salinity and cold temperatures.

Results

Analysis of the genome sequence of H. lacusprofundi showed a gene cluster for carbohydrate utilization containing a glycoside hydrolase family 42 β-galactosidase gene, named bga. In order to study the biochemical properties of the β-galactosidase enzyme, the bga gene was PCR amplified, cloned, and expressed in the genetically tractable haloarchaeon Halobacterium sp. NRC-1 under the control of a cold shock protein (cspD2) gene promoter. The recombinant β-galactosidase protein was produced at 20-fold higher levels compared to H. lacusprofundi, purified using gel filtration and hydrophobic interaction chromatography, and identified by SDS-PAGE, LC-MS/MS, and ONPG hydrolysis activity. The purified enzyme was found to be active over a wide temperature range (−5 to 60°C) with an optimum of 50°C, and 10% of its maximum activity at 4°C. The enzyme also exhibited extremely halophilic character, with maximal activity in either 4 M NaCl or KCl. The polyextremophilic β-galactosidase was also stable and active in 10–20% alcohol-aqueous solutions, containing methanol, ethanol, n-butanol, or isoamyl alcohol.

Conclusion

The H. lacusprofundi β-galactosidase is a polyextremophilic enzyme active in high salt concentrations and low and high temperature. The enzyme is also active in aqueous-organic mixed solvents, with potential applications in synthetic chemistry. H. lacuprofundi proteins represent a significant biotechnology resource and for developing insights into enzyme catalysis under water limiting conditions. This study provides a system for better understanding how H. lacusprofundi is successful in a perennially cold, hypersaline environment, with relevance to astrobiology.
Effectiveness of antiviral prophylaxis coupled with contact tracing in reducing the transmission of the influenza A (H1N1-2009): a systematic review
Authors: Mizumoto Kenji , Nishiura Hiroshi , Yamamoto Taro
Published: January 2013

Background

During the very early stage of the 2009 pandemic, mass chemoprophylaxis was implemented as part of containment measure. The purposes of the present study were to systematically review the retrospective studies that investigated the effectiveness of antiviral prophylaxis during the 2009 pandemic, and to explicitly estimate the effectiveness by employing a mathematical model.

Methods

A systematic review identified 17 articles that clearly defined the cases and identified exposed individuals based on contact tracing. Analysing a specific school-driven outbreak, we estimated the effectiveness of antiviral prophylaxis using a renewal equation model. Other parameters, including the reproduction number and the effectiveness of antiviral treatment and school closure, were jointly estimated.

Results

Based on the systematic review, median secondary infection risks (SIRs) among exposed individuals with and without prophylaxis were estimated at 2.1% (quartile: 0, 12.2) and 16.6% (quartile: 8.4, 32.4), respectively. A very high heterogeneity in the SIR was identified with an estimated I
2 statistic at 71.8%. From the outbreak data in Madagascar, the effectiveness of mass chemoprophylaxis in reducing secondary transmissions was estimated to range from 92.8% to 95.4% according to different model assumptions and likelihood functions, not varying substantially as compared to other parameters.

Conclusions

Only based on the meta-analysis of retrospective studies with different study designs and exposure settings, it was not feasible to estimate the effectiveness of antiviral prophylaxis in reducing transmission. However, modelling analysis of a single outbreak successfully yielded an estimate of the effectiveness that appeared to be robust to model assumptions. Future studies should fill the data gap that has existed in observational studies and allow mathematical models to be used for the analysis of meta-data.
Trisomy 8: a common finding in mouse embryonic stem (ES) cell lines
Authors: Kim Young Mi , Lee Ji-Yun , Xia Lijun , Mulvihill John J , Li Shibo
Published: January 2013

Background

Obtaining a germ cell line is one of the most important steps in developing a transgenic or knockout mouse with a targeted mutated gene of interest. A common problem with this technology is that embryonic stem (ES) cells often lack, or are extremely inefficient at, germ line transmission.

Results

To determine whether chromosomal anomalies are correlated with inefficient ES cell germ line transmission, we examined 97 constructed ES cell lines using conventional cytogenetic analysis, and fluorescence in situ hybridization (FISH). Chromosomal abnormalities occurred in 44 (45%) out of the 97 specimens analyzed: 31 specimens had trisomy 8 or mosaic trisomy 8, eight specimens had partial trisomy 8 resulting from unbalanced translocations, and five specimens had other chromosomal anomalies.

Conclusions

Our data suggest that chromosomal analysis is an important tool for improving the yield and quality of gene targeting experiments.
Response of Anopheles gambiae s.l. (Diptera: Culicidae) to larval habitat age in western Kenya highlands
Authors: Munga Stephen , Vulule John , Kweka Eliningaya J
Published: January 2013

Background

Larval control is of paramount importance in the reduction of vector populations. Previous observations have suggested that, larvae of Anopheles gambiae s.l occur more often in small temporary habitats while other studies showed that long-lasting stable habitats are more productive than unstable habitats. In addition, the physical and biological conditions and stability of larval habitats can change rapidly in natural conditions. Therefore, we examined the effect of larval habitat age on productivity, larval survival and oviposition preference of Anopheles gambiae.

Methods

We sampled the three different habitat ages (10, 20 and 30 days) on a daily basis for a period of six months to determine mosquito larval abundance. In addition, we tested the effect of age of water (habitat age) on the oviposition choice preference of An. gambiae, larval development time and survivorship, and wing lengths of emerging adults. Additionally, chlorophyll a and abundance of mosquito larval predators in these habitats were monitored.

Results

Anopheles gambiae s.l. larvae were significantly more abundant (P=0.0002) in habitats that were cleared every 10 days compared to the other habitats. In particular, there were 1.7 times more larvae in this habitat age compared to the ones that were cleared every 30 days. There were significantly (P<0.001) more mosquito larval predators in the ‘30 day’ habitats compared to the other habitats. Oviposition experiments revealed that significantly more eggs (P<0.05) were laid in fresh water and water that was 5 days old compared to water that was 10 and 15 days old. However, pupation rate, development times and wing lengths of male and female An. gambiae in the different habitat ages was statistically insignificant (P>0.05).

Conclusion

The current study confirmed that age of the habitat significantly influences the productivity of malaria vectors in western Kenya highlands. Given that malaria vectors were found in all habitats with varying ages of water, simple environmental methods of maintaining the drainage ditches in the valley bottoms can help reduce larval abundance of malaria vectors. Such inexpensive methods of controlling mosquito breeding could be promoted to supplement other vector control methods, especially in areas where scarce resources are available for intensive mosquito control.
Dysregulation of JAK-STAT pathway in hematological malignancies and JAK inhibitors for clinical application
Authors: Furqan Muhammad , Mukhi Nikhil , Lee Byung , Liu Delong
Published: January 2013

JAK-STAT (Janus associated kinase-signal transducer and activator of transcription) pathway plays a critical role in transduction of extracellular signals from cytokines and growth factors involved in hematopoiesis, immune regulation, fertility, lactation, growth and embryogenesis. JAK family contains four cytoplasmic tyrosine kinases, JAK1-3 and Tyk2. Seven STAT proteins have been identified in human cells, STAT1-6, including STAT5a and STAT5b. Negative regulators of JAK–STAT pathways include tyrosine phosphatases (SHP1 and 2, CD45), protein inhibitors of activated STATs (PIAS), suppressors of cytokine signaling (SOCS) proteins, and cytokine-inducible SH2-containing protein (CIS). Dysregulation of JAK-STAT pathway have been found to be key events in a variety of hematological malignancies. JAK inhibitors are among the first successful agents reaching clinical application. Ruxolitinib (Jakafi), a non-selective inhibitor of JAK1 & 2, has been approved by FDA for patients with intermediate to high risk primary or secondary myelofibrosis. This review will also summarize early data on selective JAK inhibitors, including SAR302503 (TG101348), lestaurtinib (CEP701), CYT387, SB1518 (pacritinib), LY2784544, XL019, BMS-911543, NS-018, and AZD1480.
Overexpression of Bcl-2 promotes survival and differentiation of neuroepithelial stem cells after transplantation into rat aganglionic colon
Authors: Liu Wei , Yue Weiming , Wu Rongde
Published: January 2013

Introduction

Neural stem cell transplantation is a promising tool for the restoration of the enteric nervous system in a variety of motility disorders. However, limited cell viability after transplantation has restricted its regenerative capacity. The aim of this study was to evaluate the effect of transplantation of neuroepithelial stem cell (NESC) overexpressing anti-apoptotic gene Bcl-2 on the survival, differentiation and function of grafted cells in rat aganglionic colon.

Methods

NESCs were isolated from neural tube of embryonic rat (embryonic day 11.5) and manipulated to overexpress the Bcl-2 gene. After transplantation into the benzalkonium chloride-induced rat aganglionic colon, grafted cells were visualized in colonic sections. Apoptosis and differentiation of the implanted cells were assessed 1, 4 and 8 weeks post transplantation, respectively. Eight weeks post transplantation, neuronal function of the colon was assessed by measuring the response of muscle strips to electrical field stimulation.

Results

Transplantation with Bcl-2-NESCs reduced apoptosis within the transplant at 1 week compared with the vector-NESC grafted group. Our findings also indicated that overexpression of Bcl-2 in the transplanted NESCs enhanced differentiation into PGP9.5-positive and neuronal nitric oxide synthase-positive neurons at 8-week assessment. Moreover, electrical field stimulation-induced relaxation of colonic strips was also significantly increased in the Bcl-2-NESC grafted group.

Conclusion

Transplantation of NESCs genetically modified to overexpress Bcl-2 may have value for enhancing survival and neurogenesis of grafted cells in the adult gut environment and for improving the efficacy of stem cell therapy following a broad range of gastrointestinal motility disorders.
Effects of Estrogen with Micronized Progesterone on Cortical and Trabecular Bone Mass and Microstructure in Recently Postmenopausal Women
Authors: Farr Joshua N. , Khosla Sundeep , Miyabara Yuko , Miller Virginia M. , Kearns Ann E.
Published: January 2013

Context:

In women, cortical bone mass decreases significantly at menopause. By contrast, loss of trabecular bone begins in the third decade and accelerates after menopause.

Objective:

The aim of the study was to investigate the effects of estrogen on cortical and trabecular bone.

Design:

The Kronos Early Estrogen Prevention Study is a double-blind, randomized, placebo-controlled trial of menopausal hormone treatment (MHT) in women, enrolled within 6–36 months of their final menstrual period.

Setting:

The study was conducted at the Mayo Clinic, Rochester, Minnesota.

Intervention:

Subjects were treated with placebo (n = 31), or .45 mg/d conjugated equine estrogens (n = 20), or transdermal 50 μg/d 17β-estradiol (n = 25) with pulsed micronized progesterone.

Main Outcome Measures:

Cortical and trabecular microarchitecture at the distal radius was assessed by high-resolution peripheral quantitative computed tomography.

Results:

At the distal radius, cortical volumetric bone mineral density (vBMD) decreased, and cortical porosity increased in the placebo group; MHT prevented these changes. By contrast, MHT did not prevent decreases in trabecular microarchitecture at the radius. However, MHT prevented decreases in trabecular vBMD at the thoracic spine (assessed in a subset of subjects; n = 51). These results indicate that MHT prevents deterioration in radial cortical vBMD and porosity in recently menopausal women.

Conclusion:

The maintenance of cortical bone in response to estrogen likely has important clinical implications because cortical bone morphology plays an important role in bone strength. However, effects of MHT on trabecular bone at the radius differ from those at the thoracic spine. Underlying mechanisms for these site-specific effects of MHT on cortical vs trabecular bone require further investigation.
FOXO1/3 Depletion in Granulosa Cells Alters Follicle Growth, Death and Regulation of Pituitary FSH
Authors: Liu Zhilin , Castrillon Diego H. , Zhou Wei , Richards JoAnne S.
Published: January 2013

The Forkhead boxO (FOXO) transcription factors regulate multiple cellular functions. FOXO1 and FOXO3 are highly expressed in granulosa cells of ovarian follicles. Selective depletion of the Foxo1 and Foxo3 genes in granulosa cells of mice reveals a novel ovarian-pituitary endocrine feedback loop characterized by: 1) undetectable levels of serum FSH but not LH, 2) reduced expression of the pituitary Fshb gene and its transcriptional regulators, and 3) ovarian production of a factor(s) that suppresses pituitary cell Fshb expression. Equally notable, and independent of FSH, microarray analyses and quantitative PCR document that depletion of Foxo1/3 alters the expression of specific genes associated with follicle growth vs. apoptosis by disrupting critical and selective regulatory interactions of FOXO1/3 with the activin or bone morphogenetic protein 2 (BMP2) pathways, respectively. As a consequence, both granulosa cell proliferation and apoptosis were decreased. These data provide the first evidence that FOXO1/3 divergently regulate follicle growth or death by interacting with the activin or BMP pathways in granulosa cells and by modulating pituitary FSH production.
Gliotactin and Discs large are co-regulated to maintain epithelial integrity
Authors: Padash-Barmchi Mojgan , Charish Kristi , Que Jammie , Auld Vanessa J.
Published: January 2013

Establishment and maintenance of permeability barriers is one of the most important functions of epithelial cells. Tricellular junctions (TCJs) maintain the permeability barriers at the contact site of three epithelial cells. Gliotactin, a member of the Neuroligin family, is the only known Drosophila protein exclusively localized to the TCJ and is necessary for maintenance of the permeability barrier. Overexpression triggers the spread of Gliotactin away from the TCJ and causes epithelial cells to delaminate, migrate and die. Furthermore, excess Gliotactin at the cell membrane results in an extensive downregulation of Discs large (Dlg) at the septate junctions. The intracellular domain of Gliotactin contains two highly conserved tyrosine residues and a PDZ binding motif. We previously found that phosphorylation of the tyrosine residues is necessary to control the level of Gliotactin at the TCJ. In this study we demonstrate that the phenotypes associated with excess Gliotactin are due to a functional interaction between Gliotactin and Dlg that is dependent on both tyrosine phosphorylation as well as the PDZ binding motif. We further show that elevated levels of Dlg strongly enhance Gliotactin overexpression phenotypes to the point where tissue over-growth is observed. The exhibition of these phenotypes require phosphorylation of Dlg on serine 797, a known Par1 phosphorylation target. Blocking this phosphorylation completely suppresses the cell invasiveness and apoptotic phenotypes associated with Gliotactin overexpression. Additionally, we show that Drosophila JNK acts downstream of Gliotactin and Dlg to mediate the overgrowth and apoptosis caused by the functional interaction of Gliotactin and Dlg.
Cav1.1 controls frequency-dependent events regulating adult skeletal muscle plasticity
Authors: Jorquera Gonzalo , Altamirano Francisco , Contreras-Ferrat Ariel , Almarza Gonzalo , Buvinic Sonja , Jacquemond Vincent , Jaimovich Enrique , Casas Mariana
Published: January 2013

An important pending question in neuromuscular biology is how skeletal muscle cells decipher the stimulation pattern coming from motoneurons to define their phenotype as slow or fast twitch muscle fibers. We have previously shown that voltage-gated L-type calcium channel (Cav1.1) acts as a voltage sensor for activation of inositol (1,4,5)-trisphosphate [Ins(1,4,5)P3]-dependent Ca2+ signals that regulates gene expression. ATP released by muscle cells after electrical stimulation through pannexin-1 channels plays a key role in this process. We show now that stimulation frequency determines both ATP release and Ins(1,4,5)P3 production in adult skeletal muscle and that Cav1.1 and pannexin-1 colocalize in the transverse tubules. Both ATP release and increased Ins(1,4,5)P3 was seen in flexor digitorum brevis fibers stimulated with 270 pulses at 20 Hz, but not at 90 Hz. 20 Hz stimulation induced transcriptional changes related to fast-to-slow muscle fiber phenotype transition that required ATP release. Addition of 30 µM ATP to fibers induced the same transcriptional changes observed after 20 Hz stimulation. Myotubes lacking the Cav1.1-α1 subunit released almost no ATP after electrical stimulation, showing that Cav1.1 has a central role in this process. In adult muscle fibers, ATP release and the transcriptional changes produced by 20 Hz stimulation were blocked by both the Cav1.1 antagonist nifedipine (25 µM) and by the Cav1.1 agonist (-)S-BayK 8644 (10 µM). We propose a new role for Cav1.1, independent of its calcium channel activity, in the activation of signaling pathways allowing muscle fibers to decipher the frequency of electrical stimulation and to activate specific transcriptional programs that define their phenotype.