bluuebunny/crossref_metadata_2025 huggingface dataset:
Cartilage-selective genes identified in genome-scale analysis of non-cartilage and cartilage gene expression
Authors: Funari Vincent A , Day Allen , Krakow Deborah , Cohn Zachary A , Chen Zugen , Nelson Stanley F , Cohn Daniel H
Published: June 2007

Background

Cartilage plays a fundamental role in the development of the human skeleton. Early in embryogenesis, mesenchymal cells condense and differentiate into chondrocytes to shape the early skeleton. Subsequently, the cartilage anlagen differentiate to form the growth plates, which are responsible for linear bone growth, and the articular chondrocytes, which facilitate joint function. However, despite the multiplicity of roles of cartilage during human fetal life, surprisingly little is known about its transcriptome. To address this, a whole genome microarray expression profile was generated using RNA isolated from 18–22 week human distal femur fetal cartilage and compared with a database of control normal human tissues aggregated at UCLA, termed Celsius.

Results

161 cartilage-selective genes were identified, defined as genes significantly expressed in cartilage with low expression and little variation across a panel of 34 non-cartilage tissues. Among these 161 genes were cartilage-specific genes such as cartilage collagen genes and 25 genes which have been associated with skeletal phenotypes in humans and/or mice. Many of the other cartilage-selective genes do not have established roles in cartilage or are novel, unannotated genes. Quantitative RT-PCR confirmed the unique pattern of gene expression observed by microarray analysis.

Conclusion

Defining the gene expression pattern for cartilage has identified new genes that may contribute to human skeletogenesis as well as provided further candidate genes for skeletal dysplasias. The data suggest that fetal cartilage is a complex and transcriptionally active tissue and demonstrate that the set of genes selectively expressed in the tissue has been greatly underestimated.
Large-scale copy number variants (CNVs): Distribution in normal subjects and FISH/real-time qPCR analysis
Authors: Qiao Ying , Liu Xudong , Harvard Chansonette , Nolin Sarah L , Brown W Ted , Koochek Maryam , Holden Jeanette JA , Lewis ME Suzanne , Rajcan-Separovic Evica
Published: June 2007

Background

Genomic copy number variants (CNVs) involving >1 kb of DNA have recently been found to be widely distributed throughout the human genome. They represent a newly recognized form of DNA variation in normal populations, discovered through screening of the human genome using high-throughput and high resolution methods such as array comparative genomic hybridization (array-CGH). In order to understand their potential significance and to facilitate interpretation of array-CGH findings in constitutional disorders and cancers, we studied 27 normal individuals (9 Caucasian; 9 African American; 9 Hispanic) using commercially available 1 Mb resolution BAC array (Spectral Genomics). A selection of CNVs was further analyzed by FISH and real-time quantitative PCR (RT-qPCR).

Results

A total of 42 different CNVs were detected in 27 normal subjects. Sixteen (38%) were not previously reported. Thirteen of the 42 CNVs (31%) contained 28 genes listed in OMIM. FISH analysis of 6 CNVs (4 previously reported and 2 novel CNVs) in normal subjects resulted in the confirmation of copy number changes for 1 of 2 novel CNVs and 2 of 4 known CNVs. Three CNVs tested by FISH were further validated by RT-qPCR and comparable data were obtained. This included the lack of copy number change by both RT-qPCR and FISH for clone RP11-100C24, one of the most common known copy number variants, as well as confirmation of deletions for clones RP11-89M16 and RP5-1011O17.

Conclusion

We have described 16 novel CNVs in 27 individuals. Further study of a small selection of CNVs indicated concordant and discordant array vs. FISH/RT-qPCR results. Although a large number of CNVs has been reported to date, quantification using independent methods and detailed cellular and/or molecular assessment has been performed on a very small number of CNVs. This information is, however, very much needed as it is currently common practice to consider CNVs reported in normal subjects as benign changes when detected in individuals affected with a variety of developmental disorders.
Helicobacter pylori genome variability in a framework of familial transmission
Authors: Kivi Mårten , Rodin Sandra , Kupershmidt Ilya , Lundin Annelie , Tindberg Ylva , Granström Marta , Engstrand Lars
Published: June 2007

Background

Helicobacter pylori infection is exceptionally prevalent and is considered to be acquired primarily early in life through person-to-person transmission within the family. H. pylori is a genetically diverse bacterial species, which may facilitate adaptation to new hosts and persistence for decades. The present study aimed to explore the genetic diversity of clonal isolates from a mother and her three children in order to shed light on H. pylori transmission and host adaptation.

Results

Two different H. pylori strains and strain variants were identified in the family members by PCR-based molecular typing and sequencing of five loci. Genome diversity was further assessed for 15 isolates by comparative microarray hybridizations. The microarray consisted of 1,745 oligonucleotides representing the genes of two previously sequenced H. pylori strains. The microarray analysis detected a limited mean number (± standard error) of divergent genes between clonal isolates from the same and different individuals (1 ± 0.4, 0.1%, and 3 ± 0.3, 0.2%, respectively). There was considerable variability between the two different strains in the family members (147 ± 4, 8%) and for all isolates relative to the two sequenced reference strains (314 ± 16, 18%). The diversity between different strains was associated with gene functional classes related to DNA metabolism and the cell envelope.

Conclusion

The present data from clonal H. pylori isolates of family members do not support that transmission and host adaptation are associated with substantial sequence diversity in the bacterial genome. However, important phenotypic modifications may be determined by additional genetic mechanisms, such as phase-variation. Our findings can aid further exploration of H. pylori genetic diversity and adaptation.
QTL mapping of agronomic traits in tef [Eragrostis tef(Zucc) Trotter]
Authors: Yu Ju-Kyung , Graznak Elizabeth , Breseghello Flavio , Tefera Hailu , Sorrells Mark E
Published: June 2007

Background

Tef [Eragrostis tef (Zucc.) Trotter] is the major cereal crop in Ethiopia. Tef is an allotetraploid with a base chromosome number of 10 (2n = 4× = 40) and a genome size of 730 Mbp. The goal of this study was to identify agronomically important quantitative trait loci (QTL) using recombinant inbred lines (RIL) derived from an inter-specific cross between E. tef and E. pilosa (30-5).

Results

Twenty-two yield-related and morphological traits were assessed across eight different locations in Ethiopia during the growing seasons of 1999 and 2000. Using composite interval mapping and a linkage map incorporating 192 loci, 99 QTLs were identified on 15 of the 21 linkage groups for 19 traits. Twelve QTLs on nine linkage groups were identified for grain yield. Clusters of more than five QTLs for various traits were identified on seven linkage groups. The largest cluster (10 QTLs) was identified on linkage group 8; eight of these QTLs were for yield or yield components, suggesting linkage or pleotrophic effects of loci. There were 15 two-way interactions of loci to detect potential epistasis identified and 75% of the interactions were derived from yield and shoot biomass. Thirty-one percent of the QTLs were observed in multiple environments; two yield QTLs were consistent across all agro-ecology zones. For 29.3% of the QTLs, the alleles from E. pilosa (30-5) had a beneficial effect.

Conclusion

The extensive QTL data generated for tef in this study will provide a basis for initiating molecular breeding to improve agronomic traits in this staple food crop for the people of Ethiopia.
Modulation of RANTES expression by HCV core protein in liver derived cell lines
Authors: Ruggieri Anna , Franco Marina , Gatto Ilaria , Kumar Ajit , Rapicetta Maria
Published: June 2007

Background

Hepatitis C virus (HCV) infection is associated with high percentage of chronicity which implies the ability of the virus to evade or modulate host cell immune system. Modulation of chemokines, such as RANTES may be part of the virus induced pathogenicity. We examined the effect of core and structural proteins of HCV on RANTES expression in two liver derived cell lines, HepG2 and Chang Liver (CHL).

Methods

HepG2 and Chang Liver (CHL) cell lines were established and selected for constitutive expression of HCV core and structural genes. Flow cytometry and quantitative RT-PCR analysis were performed to examine the effect of HCV core protein on RANTES expression. Luciferase analysis after RANTES-Luc-promoter transfection of established cell lines was assayed by luminometer measurements (RLU) of RANTES promoter activity. IRF-1 and IRF-7 expression was then examined by immunoblotting analysis.

Results

Results of flow cytometry and RT-PCR analysis indicated that RANTES is differentially regulated by HCV core protein in the two cell lines examined as its expression was inhibited in HepG2 cells, by a reduction of RANTES promoter activity. Conversely, RANTES protein and mRNA were induced by the core protein in CHL cells, through the induction of the promoter.

Since HCV genome modulates IRF-1 and IRF-7 in replicon system and IRF-1, IRF-3 and IRF-7 have been reported to regulate RANTES promoter in various cell systems, analysis of the mechanism underlying RANTES modulation by the core protein revealed that IRF-1 expression was induced in HepG2 cells by the core protein, whereas in CHL cells it was expressed at a very low level that was not influenced by transfection with the core protein construct. This suggested that IRF-1 level may mediate the expression of RANTES in cell lines of liver origin. The effect of the core protein on RANTES promoter was countered by co-transfection with NF90, a double-stranded-RNA binding protein that activates some interferon response genes and acts as a component of cell defense against viral infection.

Conclusion

HCV core protein have opposite effects on the expression of RANTES in different cell types in vitro, possibly reflecting a similar scenario in different microenvironments in vivo.
Innate immunity glycoprotein gp-340 variants may modulate human susceptibility to dental caries
Authors: Jonasson Anette , Eriksson Christer , Jenkinson Howard F , Källestål Carina , Johansson Ingegerd , Strömberg Nicklas
Published: June 2007

Background

Bacterial adhesion is an important determinant of colonization and infection, including dental caries. The salivary scavenger receptor cysteine-rich glycoprotein gp-340, which mediates adhesion of Streptococcus mutans (implicated in caries), harbours three major size variants, designated gp-340 I to III, each specific to an individual saliva. Here we have examined the association of the gp-340 I to III polymorphisms with caries experience and adhesion of S. mutans.

Methods

A case-referent study was performed in 12-year-old Swedish children with high (n = 19) or low (n = 19) caries experiences. We measured the gp-340 I to III saliva phenotypes and correlated those with multiple outcome measures for caries experience and saliva adhesion of S. mutans using the partial least squares (PLS) multivariate projection technique. In addition, we used traditional statistics and 2-year caries increment to verify the established PLS associations, and bacterial adhesion to purified gp-340 I to III proteins to support possible mechanisms.

Results

All except one subject were typed as gp-340 I to III (10, 23 and 4, respectively). The gp-340 I phenotype correlated positively with caries experience (VIP = 1.37) and saliva adhesion of S. mutans Ingbritt (VIP = 1.47). The gp-340 II and III phenotypes tended to behave in the opposite way. Moreover, the gp-340 I phenotype tended to show an increased 2-year caries increment compared to phenotypes II/III. Purified gp-340 I protein mediated markedly higher adhesion of S. mutans strains Ingbritt and NG8 and Lactococcus lactis expressing AgI/II adhesins (SpaP or PAc) compared to gp-340 II and III proteins. In addition, the gp-340 I protein appeared over represented in subjects positive for Db, an allelic acidic PRP variant associated with caries, and subjects positive for both gp-340 I and Db tended to experience more caries than those negative for both proteins.

Conclusion

Gp-340 I behaves as a caries susceptibility protein.
Fibrinogen gamma-A chain precursor in CSF: a candidate biomarker for Alzheimer's disease
Authors: Lee Joung Wook , Namkoong Hong , Kim Hyun Kee , Kim Sanghee , Hwang Dong Whi , Na Hae Ri , Ha Seon-Ah , Kim Jae-Ryong , Kim Jin Woo
Published: June 2007

Background

Cerebrospinal fluid (CSF) may be valuable for exploring protein markers for the diagnosis of Alzheimer's disease (AD). The prospect of early detection and treatment, to slow progression, holds hope for aging populations with increased average lifespan. The aim of the present study was to investigate candidate CSF biological markers in patients with mild cognitive impairment (MCI) and AD and compare them with age-matched normal control subjects.

Methods

We applied proteomics approaches to analyze CSF samples derived from 27 patients with AD, 3 subjects with MCI and 30 controls. The AD group was subdivided into three groups by clinical severity according to clinical dementia rating (CDR), a well known clinical scale for dementia.

Results

We demonstrated an elevated level of fibrinogen gamma-A chain precursor protein in CSF from patients with mild cognitive impairment and AD compared to the age-matched normal subjects. Moreover, its expression was more prominent in the AD group than in the MCI and correlated with disease severity and progression. In contrast, fibrinogen gamma-A chain precursor protein was detected very low in the age-matched normal group.

Conclusion

These findings suggest that the CSF level of fibrinogen gamma-A chain precursor may be a candidate biomarker for AD.
Variations of care quality for infectious pulmonary tuberculosis in Taiwan: a population based cohort study
Authors: Chung Wei-Sheng , Chang Ray-E , Guo How-Ran
Published: June 2007

Background

Effective and efficient care is required to prevent the spread of infectious pulmonary tuberculosis (PTB). We attempted to compare care quality among different healthcare institutions in Southern Taiwan.

Methods

This study conducted population-based retrospective cohort design. One tuberculosis sanatorium, 2 medical centers, 11 regional hospitals, and 15 district hospitals and primary practitioners in the study area had reported tuberculosis cases, registered from January 1 to June 30 2003. Those cases with sputum positive PTB were followed 15 months after anti-tuberculosis treatment initiation. Meanwhile, Level of conformance with diagnostic guidelines, efficiency of diagnostic and treatment process, and treatment were measured as main outcome. Association was investigated using Chi-square tests, Kruskal Wallis tests, Mann-Whiteney U tests, and multiple logistic regression analysis to evaluate outcome differences among different levels of institutions.

Results

The analyses included 421 patients. In comparison with patients receiving treatment at medical centers, regional hospitals, and district hospitals/primary practitioners, patients at the Chest Specialty Hospital were more likely to provide at least three sputum specimens (74.1% vs. 48.2%, 36.8%, and 50.0%), shorter workdays examining sputum smears (2.4 ± 2.4 days vs. 2.6 ± 2.1, 4.5 ± 3.1, and 3.5 ± 2.6 days), shorter interval between the first consultation and treatment (10.1 ± 18.3 days vs. 31.0 ± 53.6, 31.2 ± 70.4, and 25.4 ± 37.6 days), and a higher successful treatment rate (92.6% vs. 65.2%, 63.9%, and 68.0%). Furthermore, after adjusting age and gender, the patients treated by the pulmonologists and treated at Chest Specialty Hospital had significantly more successful treatment rate, of which odds ratios were 1.74 and 4.58 respectively.

Conclusion

Differences in care quality exist among different types of healthcare institutions and among individual physicians. The implementation of practice guidelines should contribute to an improvement in the care quality of the treatment and diagnosis of PTB.
Bladder sensory desensitization decreases urinary urgency
Authors: Silva Carlos , Silva João , Castro Helder , Reis Frederico , Dinis Paulo , Avelino António , Cruz Francisco
Published: June 2007

Background

Bladder desensitization has been investigated as an alternative treatment for refractory detrusor overactivity. Most open and controlled clinical trials conducted with intravesical RTX showed that desensitization delays the appearance of involuntary detrusor contractions during bladder filling and decreases the number of episodes of urgency incontinence.

Urgency is being recognised as the fundamental symptom of overactive bladder (OAB), a symptomatic complex which recent epidemiological studies have shown to affect more than 10% of the Western population. As anti-muscarinic drugs, the first line treatment for OAB, are far from being able to fully control urgency, the opportunity to test other therapeutic approaches is created. The present work was, therefore, designed as an exploratory investigation to evaluate the effect of bladder desensitization on urinary urgency.

Methods

Twenty-three OAB patients with refractory urgency entered, after given informed consent, a 30 days run-in period in which medications influencing the bladder function were interrupted. At the end of this period patients filled a seven-day voiding chart where they scored, using a 0–4 scale, the bladder sensations felt before each voiding. Then, patients were instilled with 100 ml of 10% ethanol in saline (vehicle solution) and 30 days later a second seven-day voiding chart was collected. Finally, patients were instilled with 100 ml of 50 nM RTX in 10% ethanol in saline. At 1 and 3 months additional voiding charts were collected.

At the end of the vehicle and 3 months period patients were asked to give their subjective impression about the outcome of the treatment and about the willingness to repeat the previous instillation.

Results

At the end of the run-in period the mean number of episodes of urgency per week was 71 ± 12 (mean ± SEM). After vehicle instillation, the mean number of episodes of urgency was 56 ± 11, but only 4 patients (17%) considered that their urinary condition had improved enough to repeat the treatment. At 1 and 3 months after RTX the number of episodes of urgency decreased to 39 ± 9 (p = 0.002) and 37 ± 6 (p = 0.02), respectively (p indicates statistical differences against vehicle). The percentage of patients with subjective improvement after RTX and willing to repeat the instillation at a later occasion was 69%.

Conclusion

In OAB patients with refractory urgency bladder desensitization should be further investigated as an alternative to the standard management. Additionally, the specific effect of RTX on TRPV1 receptors suggests that urothelium and sub-urothelial C-fibers play an important role to the generation of urgency sensation.
Medicine in words and numbers: a cross-sectional survey comparing probability assessment scales
Authors: Witteman Cilia LM , Renooij Silja , Koele Pieter
Published: June 2007

Background

In the complex domain of medical decision making, reasoning under uncertainty can benefit from supporting tools. Automated decision support tools often build upon mathematical models, such as Bayesian networks. These networks require probabilities which often have to be assessed by experts in the domain of application. Probability response scales can be used to support the assessment process. We compare assessments obtained with different types of response scale.

Methods

General practitioners (GPs) gave assessments on and preferences for three different probability response scales: a numerical scale, a scale with only verbal labels, and a combined verbal-numerical scale we had designed ourselves. Standard analyses of variance were performed.

Results

No differences in assessments over the three response scales were found. Preferences for type of scale differed: the less experienced GPs preferred the verbal scale, the most experienced preferred the numerical scale, with the groups in between having a preference for the combined verbal-numerical scale.

Conclusion

We conclude that all three response scales are equally suitable for supporting probability assessment. The combined verbal-numerical scale is a good choice for aiding the process, since it offers numerical labels to those who prefer numbers and verbal labels to those who prefer words, and accommodates both more and less experienced professionals.
Patients' understanding of genetic susceptibility testing in mainstream medicine: qualitative study on thrombophilia
Authors: Saukko Paula M , Ellard Sian , Richards Suzanne H , Shepherd Maggie H , Campbell John L
Published: June 2007

Background

UK and US policy initiatives have suggested that, in the future, patients and clinicians in mainstream medicine could use genetic information to prevent common illnesses. There are no studies on patients' experience and understanding of the process of testing for common genetic susceptibilities in mainstream medicine.

Methods

Qualitative interviews with 42 individuals who had undergone testing for a genetic susceptibility for deep vein thrombosis in primary and secondary care in the UK.

Results

Some participants, often from higher social classes, had a good understanding of the test and its implications. They had often sought additional information on thrombophilia from relatives and from the Internet. Others, often from less privileged backgrounds, had a poorer understanding of the test – seven individuals were unaware of having had the genetic test. Features of genetic information led to misunderstandings: (i) at referral, (ii) when communicating results, and (iii) when making sense of the implications of testing. Participants' accounts indicated that non-specialist doctors may feel obliged to refer a patient for a genetic test they know little about, because a patient requests it after a relative had tested positive. Sometimes a referral for a genetic test was lost under information overload when multiple tests and issues were considered. The inconsistent and informal ways of communicating test results – for example by phone – in mainstream medicine also led to confusion. Participants did not generally overestimate their risk, but some were uncertain about whether they were taking the right preventive actions and/or whether their children were at risk. Information about genetic susceptibilities was difficult to make sense of, as it related to ambiguous risks for participants and family members, complicated and unfamiliar terminology and multiple genes and preventive strategies.

Conclusion

Policy visions of clinicians and patients in mainstream medicine seeking and using genetic information at their own initiative may not be realistic. Patients need more direct support in making sense of genetic information, if this information is to bring the anticipated health benefits, and not fuel health inequalities or create ethical problems. Clinicians in secondary and primary care need guidance to help them introduce genetic tests, communicate their results and explain their implications.
Do parents who smoke underutilize health care services for their children? A cross sectional study within the longitudinal PIAMA study
Authors: Jacobs-van der Bruggen Monique AM , Wijga Alet H , Brunekreef Bert , de Jongste Johan C , Baan Caroline A , Kerkhof Marjan , Smit Henriette A
Published: June 2007

Background

A higher prevalence of respiratory symptoms and an associated increase in health care utilization among children with parents who smoke is to be expected. From previous studies however, it appears that parents who smoke may underutilize health services for their children, especially with respect to respiratory care. This study explores the validity and generalizability of the previous assumption.

Methods

Data were obtained from a Dutch birth-cohort study; the Prevention and Incidence of Asthma and Mite Allergy (PIAMA) project. Information regarding parental smoking, the child's respiratory symptoms and health care use and potential confounders were obtained by postal questionnaires. Multivariate logistic models were used to relate parental smoking to the child's respiratory symptoms and health care use.

Results

The study comprised 3,564, 4-year old children. In the crude analysis, respiratory symptoms were more frequent among children with a parent who smoked, while health care utilization for respiratory symptoms was not significantly different between children with or without a parent who smoked. In the multivariate analyses, maternal smoking had a larger impact on the child's respiratory symptoms and health care use as compared to paternal smoking. Maternal smoking was positively associated with mild respiratory symptoms of the child, adjusted odds ratio [AOR] 1.50 (1.19–1.91), but not with severe respiratory symptoms AOR 1.03 (0.75–1.40). Among children with mild respiratory symptoms, children with a mother who smoked were less likely to be taken to the general practitioner (GP) for respiratory symptoms, than children with mothers who did not smoke, AOR 0.58 (0.33–1.01). This finding was less pronounced among children with severe respiratory symptoms AOR 0.86 (0.49–1.52). Neither GP visits for non-respiratory symptoms nor specialized care for respiratory disease were significantly associated with parental smoking.

Conclusion

Mothers who smoke appear to underutilize health care for their children with mild respiratory symptoms. Health care workers should be informed about this phenomenon. Inquiring after the respiratory health of the children during regular visits to healthy baby clinics may help to track potential underutilization of care.
Priority setting in the provincial health services authority: survey of key decision makers
Authors: Teng Flora , Mitton Craig , MacKenzie Jennifer
Published: June 2007

Background

In recent years, decision makers in Canada and elsewhere have expressed a desire for more explicit, evidence-based approaches to priority setting. To achieve this aim within health care organizations, knowledge of both the organizational context and stakeholder attitudes towards priority setting are required. The current work adds to a limited yet growing body of international literature describing priority setting practices in health organizations.

Methods

A qualitative study was conducted using in-depth, face-to-face interviews with 25 key decision makers of the Provincial Health Services Authority (PHSA) of British Columbia. Major themes and sub-themes were identified through content analysis.

Results

Priorities were described by decision makers as being set in an ad hoc manner, with resources generally allocated along historical lines. Participants identified the Strategic Plan and a strong research base as strengths of the organization. The main areas for improvement were a desire to have a more transparent process for priority setting, a need to develop a culture which supports explicit priority setting, and a focus on fairness in decision making. Barriers to an explicit allocation process included the challenge of providing specialized services for disparate patient groups, and a lack of formal training in priority setting amongst decision makers.

Conclusion

This study identified factors important to understanding organizational context and informed next steps for explicit priority setting for a provincial health authority. While the PHSA is unique in its organizational structure in Canada, lessons about priority setting should be transferable to other contexts.
Differential expression and role of p21cip/waf1 and p27kip1 in TNF-α-induced inhibition of proliferation in human glioma cells
Authors: Kumar Pabbisetty Sudheer , Shiras Anjali , Das Gowry , Jagtap Jayashree C , Prasad Vandna , Shastry Padma
Published: June 2007

Background

The role of TNF-α in affecting the fate of tumors is controversial, while some studies have reported apoptotic or necrotic effects of TNF-α, others provide evidence that endogenous TNF-α promotes growth and development of tumors. Understanding the mechanism(s) of TNF-α mediated growth arrest will be important in unraveling the contribution of tissue associated macrophages in tumor resistance. The aim of this study was to investigate the role of Cyclin Dependent Kinase Inhibitors (CDKI) – p21cip/waf1and p27kip1in TNF-α mediated responses in context with p53 and activation of NF-κB and Akt pathways. The study was done with human glioma cell lines -LN-18 and LN-229 cells, using monolayer cultures and Multicellular Spheroids (MCS) asin vitromodels.

Results

TNF-α induced inhibition of proliferation and enhanced the expression of p21cip/waf1and p27kip1in LN-18 cells. p21 was induced on exposure to TNF-α, localized exclusively in the nucleus and functioned as an inhibitor of cell cycle but not as an antiapoptotic protein. In contrast, p27 was constitutively expressed, localized predominantly in the cytoplasm and was not involved in arrest of proliferation. Our data using IκBα mutant LN-18 cells and PI3K/Akt inhibitor-LY294002 revealed that the expression of p21 is regulated by NF-κB. Loss of IκBα function in LN-229 cells (p53 positive) did not influence TNF-α induced accumulation of pp53 (Ser-20 p53) suggesting that p53 was not down stream of NF-κB. Spheroidogenesis enhanced p27 expression and p21 induced by TNF-α was significantly increased in the MCS compared to monolayers.

Conclusion

This study demarcates the functional roles for CDKIs-p21cip/waf1and p27kip1during TNF-α stimulated responses in LN-18 glioma cells. Our findings provide evidence that TNF-α-induced p21 might be regulated by NF-κB or p53 independently. p21 functions as an inhibitor of cell proliferation and does not have a direct role in rendering the cells resistant to TNF-α mediated cytotoxicity.
Differential in vitro inhibitory activity against HIV-1 of alpha-(1-3)- and alpha-(1-6)-D-mannose specific plant lectins : Implication for microbicide development
Authors: Saïdi Hela , Nasreddine Nadine , Jenabian Mohammad-Ali , Lecerf Maxime , Schols Dominique , Krief Corinne , Balzarini Jan , Bélec Laurent
Published: June 2007

Background

Plant lectins such as Galanthus nivalis agglutinin (GNA) and Hippeastrum hybrid agglutinin (HHA) are natural proteins able to link mannose residues, and therefore inhibit HIV-target cell interactions. Plant lectins are candidate for microbicide development.

Objective

To evaluate the activity against HIV of the mannose-specific plant lectins HHA and GNA at the cellular membrane level of epithelial cells and monocyte-derived dendritic cells (MDDC), two potential target cells of HIV at the genital mucosal level.

Methods

The inhibitory effects of HHA and GNA were evaluated on HIV adsorption to genital epithelial HEC-1A cell line, on HIV transcytosis throughout a monolayer of polarized epithelial HEC-1A cells, on HIV adsorption to MDDC and on transfer of HIV from MDDC to autologous T lymphocytes.

Results

HHA faintly inhibited attachment to HEC-1A cells of the R5-tropic HIV-1Ba-L strain, in a dose-dependent manner, whereas GNA moderately inhibited HIV adsorption in the same context, but only at high drug doses. Only HHA, but not GNA, inhibited HIV-1JR-CSF transcytosis in a dose-dependent manner. By confocal microscopy, HHA, but not GNA, was adsorbed at the epithelial cell surface, suggesting that HHA interacts specifically with receptors mediating HIV-1 transcytosis. Both plant lectins partially inhibited HIV attachment to MDDC. HHA inhibited more efficiently the transfer of HIV from MDDC to T cell, than GNA. Both HHA and GNA lacked toxicity below 200 μg/ml irrespective the cellular system used and do not disturb the monolayer integrity of epithelial cells.

Conclusion

These observations demonstrate higher inhibitory activities of the lectin plant HHA by comparison to GNA, on HIV adsorption to HEC-1A cell line, HIV transcytosis through HEC-1A cell line monolayer, HIV adsorption to MDDC and HIV transfer from MDDC to T cells, highlighting the potential interest of HHA as effective microbicide against HIV.
Large-scale identification of human genes implicated in epidermal barrier function
Authors: Toulza Eve , Mattiuzzo Nicolas R , Galliano Marie-Florence , Jonca Nathalie , Dossat Carole , Jacob Daniel , de Daruvar Antoine , Wincker Patrick , Serre Guy , Guerrin Marina
Published: June 2007

Background

During epidermal differentiation, keratinocytes progressing through the suprabasal layers undergo complex and tightly regulated biochemical modifications leading to cornification and desquamation. The last living cells, the granular keratinocytes (GKs), produce almost all of the proteins and lipids required for the protective barrier function before their programmed cell death gives rise to corneocytes. We present here the first analysis of the transcriptome of human GKs, purified from healthy epidermis by an original approach.

Results

Using the ORESTES method, 22,585 expressed sequence tags (ESTs) were produced that matched 3,387 genes. Despite normalization provided by this method (mean 4.6 ORESTES per gene), some highly transcribed genes, including that encoding dermokine, were overrepresented. About 330 expressed genes displayed less than 100 ESTs in UniGene clusters and are most likely to be specific for GKs and potentially involved in barrier function. This hypothesis was tested by comparing the relative expression of 73 genes in the basal and granular layers of epidermis by quantitative RT-PCR. Among these, 33 were identified as new, highly specific markers of GKs, including those encoding a protease, protease inhibitors and proteins involved in lipid metabolism and transport. We identified filaggrin 2 (also called ifapsoriasin), a poorly characterized member of the epidermal differentiation complex, as well as three new lipase genes clustered with paralogous genes on chromosome 10q23.31. A new gene of unknown function, C1orf81, is specifically disrupted in the human genome by a frameshift mutation.

Conclusion

These data increase the present knowledge of genes responsible for the formation of the skin barrier and suggest new candidates for genodermatoses of unknown origin.
Quantitative Gene Expression Deregulation in Mantle-Cell Lymphoma: Correlation With Clinical and Biologic Factors
Authors: Kienle Dirk , Katzenberger Tiemo , Ott German , Saupe Doreen , Benner Axel , Kohlhammer Holger , Barth Thomas F.E. , Höller Sylvia , Kalla Jörg , Rosenwald Andreas , Müller-Hermelink Hans Konrad , Möller Peter , Lichter Peter , Döhner Hartmut , Stilgenbauer Stephan
Published: June 2007

Purpose

There is evidence for a direct role of quantitative gene expression deregulation in mantle-cell lymphoma (MCL) pathogenesis. Our aim was to investigate gene expression associations with other pathogenic factors and the significance of gene expression in a multivariate survival analysis.

Patients and Methods

Quantitative expression of 20 genes of potential relevance for MCL prognosis and pathogenesis were analyzed using real-time reverse transcriptase polymerase chain reaction and correlated with clinical and genetic factors, tumor morphology, and Ki-67 index in 65 MCL samples.

Results

Genomic losses at the loci of TP53, RB1, and P16 were associated with reduced transcript levels of the respective genes, indicating a gene-dosage effect as the pathomechanism. Analysis of gene expression correlations between the candidate genes revealed a separation into two clusters, one dominated by proliferation activators, another by proliferation inhibitors and regulators of apoptosis. Whereas only weak associations were identified between gene expression and clinical parameters or blastoid morphology, several genes were correlated closely with the Ki-67 index, including the short CCND1 variant (positive correlation) and RB1, ATM, P27, and BMI (negative correlation). In multivariate survival analysis, expression levels of MYC, MDM2, EZH2, and CCND1 were the strongest prognostic factors independently of tumor proliferation and clinical factors.

Conclusion

These results indicate a pathogenic contribution of several gene transcript levels to the biology and clinical course of MCL. Genes can be differentiated into factors contributing to proliferation deregulation, either by enhancement or loss of inhibition, and proliferation-independent factors potentially contributing to MCL pathogenesis by apoptosis impairment.
Cigarette Smoking and Irinotecan Treatment: Pharmacokinetic Interaction and Effects on Neutropenia
Authors: van der Bol Jessica M. , Mathijssen Ron H.J. , Loos Walter J. , Friberg Lena E. , van Schaik Ron H.N. , de Jonge Maja J.A. , Planting André S.Th. , Verweij Jaap , Sparreboom Alex , de Jong Floris A.
Published: June 2007

Purpose

Several constituents of cigarette smoke are known to interact with drug metabolizing enzymes and potentially affect treatment outcome with substrate drugs. The purpose of this study was to determine the effects of cigarette smoking on the pharmacokinetics and adverse effects of irinotecan.

Patients and Methods

A total of 190 patients (49 smokers, 141 nonsmokers) treated with irinotecan (90-minute intravenous administration on a 3-week schedule) were evaluated for pharmacokinetics. Complete toxicity data were available in a subset of 134 patients receiving 350 mg/m2or 600 mg flat-fixed dose irinotecan.

Results

In smokers, the dose-normalized area under the plasma concentration-time curve of irinotecan was significantly lower (median, 28.7 v 33.9 ng · h/mL/mg; P = .001) compared with nonsmokers. In addition, smokers showed an almost 40% lower exposure to SN-38 (median, 0.54 v 0.87 ng · h/mL/mg; P < .001) and a higher relative extent of glucuronidation of SN-38 into SN-38G (median, 6.6 v 4.5; P = .006). Smokers experienced considerably less hematologic toxicity. In particular, the incidence of grade 3 to 4 neutropenia was 6% in smokers versus 38% in nonsmokers (odds ratio [OR], 0.10; 95% CI, 0.02 to 0.43; P < .001). There was no significant difference in incidence of delayed-onset diarrhea (6% v 15%; OR, 0.34; 95% CI, 0.07 to 1.57; P = .149).

Conclusion

This study indicates that smoking significantly lowers both the exposure to irinotecan and treatment-induced neutropenia, indicating a potential risk of treatment failure. Although the underlying mechanism is not entirely clear, modulation of CYP3A and uridine diphosphate glucuronosyltransferase isoform 1A1 may be part of the explanation. The data suggest that additional investigation is warranted to determine whether smokers are at increased risk for treatment failure.
Participation of Geminal Bonds in Organic Reactions
Authors: Naruse Yuji , Inagaki Satoshi
Published: June 2007

The σ-bonds geminal to the π-reacting center have been proposed to participate in the organic reactions via the cyclic transition states and to control the reactivity and the selectivity. An electron-donating geminal σ bond at the Z position enhances the reactivity of the olefins. An electron-donating σ bond prefers the Z position of the π bond in the products of the reverse reactions. The effects of the geminal bond participation come from the orbital phase properties of the cyclic interactions including the geminal σ bonds.
Structural Implication of Oxoammonium Cations for Reversible Organic One-electron Redox Reaction to Nitroxide Radicals
Authors: Yonekuta Yasunori , Oyaizu Kenichi , Nishide Hiroyuki
Published: June 2007

Structures and electrochemical behaviors of nitroxide radicals reveal that their rapid and reversible redox reactions are based not only on their chemical stability but also on the increased sp2 character of nitrogens which is intermediate between the purely sp2 and sp3 nitrogens in oxoammonium cations and amines, respectively.
Decomposition of Toluene by Liquid-phase Atmospheric-pressure Microwave Plasma Generated Using Carbon Felt Pieces Impregnated with NaCl
Authors: Kurihara Hideki , Yajima Tatuhiko
Published: June 2007

Atmospheric-pressure microwave plasma (APMP) was generated in the liquid phase (LPAPMP) using carbon felt pieces impregnated with NaCl. The decomposition reaction of liquid toluene was examined as an application of LPAPMP. The reaction was divided into three periods: in the first period, faint spark discharges were observed in liquid toluene (LPSD) and toluene began to boil; in the second period, LPAPMP was generated and toluene was decomposed rapidly; in the final period, APMP was generated, but toluene had already been evaporated off.
Rhenium-catalyzed Amidation of Heteroaromatic Compounds via C–H Bond Activation
Authors: Kuninobu Yoichiro , Tokunaga Yukimi , Takai Kazuhiko
Published: June 2007

Regioselective insertion of isocyanates into a C–H bond of heteroaromatic compounds took place using a rhenium catalyst, [ReBr(CO)3(thf)]2.
Controlling Infiltration Pressure of a Nanoporous Silica Gel via Surface Treatment
Authors: Han Aijie , Qiao Yu
Published: June 2007

Energy absorption behaviors of a surface-treated nanoporous silica gel are investigated through a pressure-induced infiltration experiment. The results show that the infiltration pressure is dominated by the surface coverage, and thus by controlling the surface treatment time the system performance can be adjusted quite conveniently.
Imaging Mass Spectrometry in Biological Tissues by Laser Ablation Inductively Coupled Plasma Mass Spectrometry
Authors: Becker J.S. , Becker J.Su. , Zoriy M.V. , Dobrowolska J. , Matusch A.
Published: June 2007

Of all the inorganic mass spectrometric techniques, laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) plays a key role as a powerful and sensitive microanalytical technique enabling multi-element trace analysis and isotope ratio measurements at trace and ultratrace level. LA-ICP-MS was used to produce images of detailed regionally-specific element distribution in 20 μm thin sections of different parts of the human brain. The quantitative determination of copper, zinc, lead and uranium distribution in thin slices of human brain samples was performed using matrix-matched laboratory standards via external calibration procedures. Imaging mass spectrometry provides new information on the spatially inhomogeneous element distribution in thin sections of human tissues, for example, of different brain regions (the insular region) or brain tumor tissues. The detection limits obtained for Cu, Zn, Pb and U were in the ng g−1 range. Possible strategies of LA-ICP-MS in brain research and life sciences include the elemental imaging of thin slices of brain tissue or applications in proteome analysis by combination with matrix-assisted laser desorption/ionization MS to study phospho- and metal-containing proteins will be discussed.
Electrospray Ionization Mass Spectrometry: A Major Tool to Investigate Reaction Mechanisms in Both Solution and the Gas Phase
Authors: Eberlin Marcos N.
Published: June 2007

Electrospray ionization mass spectrometry (ESI-MS), in conjunction with its tandem version ESI-MS/MS, is now established as a major tool to study reaction mechanisms in solution. This suitability results mainly from the ability of ESI to “fish” ions directly from solution to the gas phase environment of mass spectrometers. In this review, we summarize recent studies from our laboratory on the use of on-line monitoring by ESI-MS ion fishing of several types of reactions that permitted us to follow how these reactions progress as a function of both time and conditions using the ultra-high sensitivity and speed of ESI-MS to detect and even characterize transient reaction intermediates. We also show that the intrinsic reactivity of each key gaseous species fished by ESI can be further investigated via ESI-tandem mass spectrometry experiments, searching for the most active species via gas-phase ion/molecule reactions. In the gas-phase, solvent and counter-ion effects are absent. These studies often permit a detailed overview of major steps via the interception, characterization and reactivity investigation of key reaction players.
Functional Investigations of Retroviral Protein—Ribonucleic Acid Complexes by Nanospray Fourier Transform Ion Cyclotron Resonance Mass Spectrometry
Authors: Fabris Daniele , Chaudhari Prajakta , Hagan Nathan , Turner Kevin
Published: June 2007

Nanospray-FT-ICR has been employed to investigate the processes of genome dimerization, selection, and packaging in human immunodifficiency virus type 1, which are mediated by specific interactions between the nucleocapsid protein (NC) and the structural elements formed by the genome's packaging signal [ψ-ribonucleic acid (RNA)]. This analytical platform allowed for the unambiguous characterization of all the non-covalent complexes formed in vitro by simultaneous RNA–RNA and protein–RNA binding equilibria. Competitive binding experiments involving the isolated RNA elements were completed to evaluate their ability to sustain specific protein interactions. In similar fashion, ad hoc RNA mutants were used to locate two distinct binding sites on the apical loop and stem-bulge of the monomeric stemloop 1 (SL1) domain, which is responsible for initiating the dimerization process. The stem-bulge motifs provided viable binding sites in both the kissing-loop (KL) and the extended duplex forms of dimeric SL1, whereas the latter included additional sites corresponding to the A-bulge motifs that flank the annealed palindromes. A cross-linking approach using pre-derivatized, photo-cross-linkable NC demonstrated that the SL3 domain was the preferred site for protein binding in the context of full-length ψ-RNA. This concerted strategy is expected to provide new valuable insight into the effects induced by the global folding of ψ-RNA on its ability to interact with the NC protein during genome dimerization, selection and packaging.
Recent Advances in Cluster Science
Authors: Castleman A. Welford
Published: June 2007

Small clusters are entities comprised of assemblies of atoms or molecules which often display properties that differ from the individual components and the bulk and, hence, are considered a unique state of matter. Investigating ones of differing sizes provides information that serves to bridge states of matter and, as recently shown, cluster research bridges many disciplines of science. This plenary lecture focused on the varying properties of matter of restricted size, the ability to produce clusters that mimic elements of the periodic table and, hence, behave as super-atoms that can serve as building blocks for new nanoscale matter with designed properties. Mass spectrometry has in the past, and continues in the future, to play a central role in this field.
Fourier Transform Ion Cyclotron Resonance: State of the Art
Authors: Marshall A.G. , Hendrickson C.L. , Emmett M.R. , Rodgers R.P. , Blakney G.T. , Nilsson C.L.
Published: June 2007

This short review summarizes recent and projected advances in Fourier transform ion cyclotron resonance mass spectrometry instrumentation and applications, ranging from petroleomics to proteomics. More details are available from the cited primary literature and topical reviews.