Regulation of the clock gene expression in human adipose tissue by weight loss.

BACKGROUND: The circadian clock coordinates numerous metabolic processes to adapt physiological responses to light-dark and feeding regimens and is itself regulated by metabolic cues. The implication of the circadian clock in the regulation of energy balance and body weight is widely studied in rodents but not in humans. Here we investigated (1) whether the expression of clock genes in human adipose tissue is changed by weight loss and (2) whether these alterations are associated with metabolic parameters. SUBJECTS/METHODS: Subcutaneous adipose tissue (SAT) samples were collected before and after 8 weeks of weight loss on an 800 kcal per day hypocaloric diet (plus 200 g per day vegetables) at the same time of the day. Fifty overweight subjects who lost at least 8% weight after 8 weeks were selected for the study. The expression of 10 clock genes and key metabolic and inflammatory genes in adipose tissue was determined by quantitative real-time PCR. RESULTS: The expression of core clock genes PER2 and NR1D1 was increased after the weight loss. Correlations of PERIOD expression with body mass index (BMI) and serum total, high-density lipoprotein and low-density lipoprotein (LDL) cholesterol levels and of NR1D1 expression with total and LDL cholesterol were found that became non-significant after correction for multiple testing. Clock gene expression levels and their weight loss-induced changes tightly correlated with each other and with genes involved in fat metabolism (FASN, CPT1A, LPL, PPARG, PGC1A, ADIPOQ), energy metabolism (SIRT1), autophagy (LC3A, LC3B) and inflammatory response (NFKB1, NFKBIA, NLRP3, EMR1). CONCLUSION: Clock gene expression in human SAT is regulated by body weight changes and associated with BMI, serum cholesterol levels and the expression of metabolic and inflammatory genes. Our data confirm the tight crosstalk between molecular clock and metabolic and inflammatory pathways involved in adapting adipose tissue metabolism to changes of the energy intake in humans.

Evaluation of a pro-active strategy for managing tuberculosis-HIV co-infection in a UK tertiary care setting.

Management of tuberculosis (TB)-HIV co-infection is complicated by interactions between the diseases and their therapies. We developed and evaluated a strategy to (i) treat co-infected patients in a single co-infection clinic, (ii) maximize use of first-line drugs, (iii) delay antiretroviral therapy (ART) until two months post-TB treatment except in severe immunosuppression, (iv) commence efavirenz at 600 mg daily with therapeutic drug monitoring (TDM) and (v) target treatment completion. We conducted a prospective cohort review over 5.5 years in a UK tertiary referral center where 56 HIV-positive patients treated for TB were followed-up for a median 30 months. Main outcome measures were treatment completion, adverse events, immune reconstitution inflammatory syndrome, immunological and virological parameters, and TDM for efavirenz. Treatment completion rates were 88% (49/56); four patients were lost to local follow-up and three (5.4%) died during treatment; no deaths were TB-related. Adverse events were common (55%), but caused no treatment interruptions. Standard doses (600 mg daily) of efavirenz with rifampicin achieved or exceeded therapeutic levels in 25/28 (89%). This study supports combined management for TB-HIV co-infected patients. Delaying ART to two months post-TB treatment did not seem to result in poor clinical outcomes in this well-resourced context. Although efavirenz 600 mg daily usually achieved satisfactory levels, TDM is recommended.

Craniofacial and dental development in cardio-facio-cutaneous syndrome: the importance of Ras signaling homeostasis.

Cardio-facio-cutaneous syndrome (CFC) is a RASopathy that is characterized by craniofacial, dermatologic, gastrointestinal, ocular, cardiac, and neurologic anomalies. CFC is caused by activating mutations in the Ras/mitogen-activated protein kinase (MAPK) signaling pathway that is downstream of receptor tyrosine kinase (RTK) signaling. RTK signaling is known to play a central role in craniofacial and dental development, but to date, no studies have systematically examined individuals with CFC to define key craniofacial and dental features. To fill this critical gap in our knowledge, we evaluated the craniofacial and dental phenotype of a large cohort (n = 32) of CFC individuals who attended the 2009 and 2011 CFC International Family Conferences. We quantified common craniofacial features in CFC which include macrocephaly, bitemporal narrowing, convex facial profile, and hypoplastic supraorbital ridges. In addition, there is a characteristic dental phenotype in CFC syndrome that includes malocclusion with open bite, posterior crossbite, and a high-arched palate. This thorough evaluation of the craniofacial and dental phenotype in CFC individuals provides a step forward in our understanding of the role of RTK/MAPK signaling in human craniofacial development and will aid clinicians who treat patients with CFC.

Prognostic significance of neuron-associated protein expression in non-muscle-invasive urothelial bladder cancer.

BACKGROUND: Numerous novel genes have been identified in urothelial bladder cancer (UBC); genes including ninjurin, synuclein and neuropilin seem to be associated with invasive tumours and aggressive behaviour. AIMS: To define the protein expression of these biomarkers and to reveal their prognostic value in a large series of superficial (pTa) and minimally invasive (pT1) cases of UBC with a long and adequate follow-up. METHODS: Tissue microarray was done on 183 paraffin-embedded tumour tissues (pTa 81, pT1 102). Statistical analysis was performed to define the association between each of these biomarkers, clinical data and tumour outcomes. RESULTS: There was a statistically significant association between synuclein expression and tumour stage (p = 0.029). Ninjurin expression was significantly associated with tumour progression in univariate analysis. Tumour grade seemed to have an independent value in predicting tumour recurrence and progression. CONCLUSION: Tumours with strong synuclein expressions are more likely to be more advanced tumours (pT1). Tumours expressing ninjurin tend to progress slower than those with no ninjurin expressions. Synuclein and neuropilin failed to show any value in predicting tumour behaviour.

Array comparative genomic hybridisation (aCGH) analysis of premenopausal breast cancers from a nuclear fallout area and matched cases from Western New York.

High-resolution array comparative genomic hybridisation (aCGH) analysis of DNA copy number aberrations (CNAs) was performed on breast carcinomas in premenopausal women from Western New York (WNY) and from Gomel, Belarus, an area exposed to fallout from the 1986 Chernobyl nuclear accident. Genomic DNA was isolated from 47 frozen tumour specimens from 42 patients and hybridised to arrays spotted with more than 3000 BAC clones. In all, 20 samples were from WNY and 27 were from Belarus. In total, 34 samples were primary tumours and 13 were lymph node metastases, including five matched pairs from Gomel. The average number of total CNAs per sample was 76 (range 35-134). We identified 152 CNAs (92 gains and 60 losses) occurring in more than 10% of the samples. The most common amplifications included gains at 8q13.2 (49%), at 1p21.1 (36%), and at 8q24.21 (36%). The most common deletions were at 1p36.22 (26%), at 17p13.2 (26%), and at 8p23.3 (23%). Belarussian tumours had more amplifications and fewer deletions than WNY breast cancers. HER2/neu negativity and younger age were also associated with a higher number of gains and fewer losses. In the five paired samples, we observed more discordant than concordant DNA changes. Unsupervised hierarchical cluster analysis revealed two distinct groups of tumours: one comprised predominantly of Belarussian carcinomas and the other largely consisting of WNY cases. In total, 50 CNAs occurred significantly more commonly in one cohort vs the other, and these included some candidate signature amplifications in the breast cancers in women exposed to significant radiation. In conclusion, our high-density aCGH study has revealed a large number of genetic aberrations in individual premenopausal breast cancer specimens, some of which had not been reported before. We identified a distinct CNA profile for carcinomas from a nuclear fallout area, suggesting a possible molecular fingerprint of radiation-associated breast cancer.

Genetic structure, introgression, and a narrow hybrid zone between northern and California spotted owls (Strix occidentalis).

The northern spotted owl (Strix occidentalis caurina) is a threatened subspecies and the California spotted owl (Strix occidentalis occidentalis) is a subspecies of special concern in the western United States. Concern for their continued viability has arisen because of habitat loss caused by timber harvesting. The taxonomic status of the northern subspecies has been the subject of continuing controversy. We investigated the phylogeographical and population genetic structure of northern and California spotted owls with special reference to their region of contact. Mitochondrial DNA (mtDNA) control region sequences confirmed the existence of two well-differentiated lineages connected by a narrow hybrid zone in a region of low population density in north central California. Maximum-likelihood estimates indicated bidirectional gene flow between the lineages but limited introgression outside the region of contact. The lengths of both the mtDNA hybrid zone and the reduced density patch were similar and slightly exceeded estimates of natal dispersal distances. This suggests that the two subspecies were in secondary contact in a hybrid zone trapped by a population density trough. Consequently, the zone of interaction is expected to be geographically stable. We discovered a third, rare clade of haplotypes, which we interpreted to be a result of incomplete lineage sorting; those haplotypes result in a paraphyletic northern spotted owl with respect to the California spotted owl. A congeneric species, the barred owl (Strix varia), occasionally hybridizes with spotted owls; our results indicated an upper bound for the frequency of barred owl mtDNA haplotypes in northern spotted owl populations of 3%.

Nonrandom Distribution of Virulences Within Two Field Collections of Uromyces appendiculatus.

ABSTRACT Two collections of urediniospores of Uromyces appendiculatus, each from a different commercial bean field, were characterized for associations of virulence among individuals within each collection. Four bean (Phaseolus vulgaris) lines with distinct, race-specific resistance to which virulence in each population was polymorphic were used to obtain measures of all six possible pairwise virulence associations for each collection. We inoculated one of the lines and collected urediniospores only from the segment of the population that was virulent on that line. This segment, when compared with nonselected collections from susceptible Pinto 111, gave a direct measure of degree of association as the change in frequency of virulence observed. Plants of the second bean line were inoculated in separate sets with both selected and unselected collections. Frequencies of virulence were estimated from the numbers of susceptible-type and resistant-type infections. Reciprocals of each pairing also were made. For collection P21, all virulences were significantly associated, either positively or negatively, except one pair (in one direction of selection only); whereas, for collection M5, all virulences were significantly associated. Virulence association in P21 was shown to be the result of predominance of phenotypes with certain combinations of virulence by inoculation of the four bean lines with 10 randomly chosen single-uredinial individuals. In support of this, a large random-mated F1 population derived from each collection showed much less virulence association, with the majority of pairs of virulences showing nonsignificant changes in virulence frequency after passage through the first line. Random mating also significantly changed virulence frequency from that of the original population in all instances. Changes were in both directions, suggesting either that virulences were not all recessive, or that heterozygote frequency was sometimes above and sometimes below the Hardy-Weinberg expectation in the field populations.

Variability of repeated coronary artery calcium measurements by electron beam tomography.

In 120 patients, the mean interscan variability of coronary calcium quantification by electron beam tomography was 19.9% (median 7.8%) for the traditional calcium score, and 16.2% (median 5.7%) for volumetric scoring. Although this difference was not significant, there was a significant influence of the total amount of calcium, number of acquired images, and image noise on interscan reproducibility.

Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene.

The single-copy RAG-1 gene is found throughout higher vertebrates and consists of a single 3.1-kb exon without intervening introns. A 2.9-kb region of the RAG-1 locus was sequenced for 14 basal taxa of birds plus the crocodylian outgroups Alligator and Gavialis. Phylogenetic analysis of the sequences supported the hypothesis that the deepest evolutionary split in extant birds separates paleognaths from neognaths. A deep division among neognaths separates the chicken- and duck-like birds ("galloanserines") from a clade consisting of all other birds ("plethornithines"). The relationships of these three basal clades in Aves were supported by high bootstrap (98 to 100%) and large decay index values (above 14). Additionally, the plethornithine clade is characterized by a 15-bp (five-codon) synapomorphic deletion relative to all other birds. RAG-1 evolves slowly, with a number of properties favoring its phylogenetic utility, including rarity of indels, minimal saturation of transition changes at 3rd positions of codons, nearly constant base composition across taxa, and no asymmetry in directional patterns of reconstructed change. However, RAG-1 does not evolve in a clocklike manner, suggesting that this gene cannot easily be used for estimating ages of ancient lineages.

Repeatability and Relationship of Incidence and Severity Measures of Scab of Wheat Caused by Fusarium graminearum in Inoculated Nurseries.

Breeders of hard red spring wheat (Triticum aestivum) are attempting to incorporate resistance to scab, caused by Fusarium graminearum. In artificially inoculated, replicated field plots, 37 wheat entries (inbred lines or cultivars) were evaluated for 3 years and an additional 60 entries for 2 of the 3 years for incidence (percent spikes infected), severity (percent infected spikelets within infected spikes), and disease index (percent infected spikelets in 50-spike sample). From year to year, entries had similar index values, with coefficients of determination (r 2) ranging from 0.59 to 0.78, with a mean of 0.73. Entries appeared slightly more similar from year to year for incidence than for severity, although both measures of disease had highly significant r 2 values. Incidence and severity were highly correlated in the wheat germ plasm examined; r 2 values in single years ranged from 0.51 to 0.67, with a mean of 0.64. A representative subset of 22 entries was included for a fourth year. None of the measures of disease in year 4 correlated with their counterparts in any of the first 3 years. This loss of repeatability may have been caused by severe lodging or by high temperatures during the evaluation period that accelerated disease progress and wheat maturity during year 4. Incidence and severity remained correlated in year 4 (r 2 = 0.60).

Effects of plant species richness on invasion dynamics, disease outbreaks, insect abundances and diversity.

Declining biodiversity represents one of the most dramatic and irreversible aspects of anthropogenic global change, yet the ecological implications of this change are poorly understood. Recent studies have shown that biodiversity loss of basal species, such as autotrophs or plants, affects fundamental ecosystem processes such as nutrient dynamics and autotrophic production. Ecological theory predicts that changes induced by the loss of biodiversity at the base of an ecosystem should impact the entire system. Here we show that experimental reductions in grassland plant richness increase ecosystem vulnerability to invasions by plant species, enhance the spread of plant fungal diseases, and alter the richness and structure of insect communities. These results suggest that the loss of basal species may have profound effects on the integrity and functioning of ecosystems.

HLA class I and class II antibodies: monitoring before and after kidney transplantation and their clinical relevance.

BACKGROUND: In search of an alternative screening technique, we compared complement-dependent cytotoxicity (CDC) with PRA-STAT, a commercially available enzyme-linked immunosorbent assay (ELISA). METHODS: A total of 188 pre- and posttransplant sera from 50 renal allograft recipients were tested with both methods. RESULTS: A significant correlation was found between both methods. Discrepant results could be explained by the fact that PRA-STAT detects both HLA class I and II antibodies (while CDC with peripheral blood lymphocytes as target cell detects mainly HLA class I reactivity), by the presence of IgM antibodies (which are not detected by the IgG-specific ELISA test), and by CDC "false-positive" results due to antibody rejection treatment. The clinical relevance of antibodies detected by PRA-STAT is suggested by the following. (a) In eight patients, donor-specific HLA antibodies detected by PRA-STAT (but not seen by CDC) resulted in severe rejection episodes, which led to graft loss in four cases. In all but one patient, antibodies were directed against class II or mixtures of class I and H antigens. Six patients with complications were shown to have developed de novo antibodies against DQ incompatibilities. (b) Half of the patients with a positive ELISA test at the moment of crossmatch experienced complications. Such patients are at a threefold higher risk of suffering from rejection episodes and/or graft loss than patients who are not sensitized (P<0.05, Fisher exact test). CONCLUSIONS: Because PRA-STAT is very reproducible, detects both HLA class I and II antibodies, and is not influenced by rejection therapy, we consider it an additional tool for pre- and posttransplant monitoring of kidney allograft recipients.

Role of protein tyrosine kinase on regulation of trabecular meshwork and ciliary muscle contractility.

PURPOSE: Trabecular meshwork and ciliary muscle express properties of smooth muscle cells. The contractility of trabecular meshwork and ciliary muscle is differently modulated by various agents. To reveal contractile regulatory processes, the effects of activation and inhibition of protein tyrosine kinases (PTKs) and their interaction with other protein kinases on contractility were measured. METHODS: Measurements of isometric tension were performed on isolated bovine trabecular meshwork and ciliary muscle strips using a custom-built, electromagnetic, force-length transducer. Protein tyrosine kinase (PTK) was stimulated by epidermal growth factor (EGF) and was inhibited by genistein or tyrphostin 51. Protein kinase C (PKC) was inhibited by chelerythrine or NPC-15437 and protein kinases A and G (PKA-PKG) by H8. RESULTS: Isolated strips were precontracted by applying carbachol 10(-6) M for 30 minutes (100% carbachol maximum contraction). Inhibition of PTK evoked a maximum relaxation of 79.2+/-4.2% in trabecular meshwork and of 38.1+/-3.1% in ciliary muscle (n=8). Inhibition of PKC or PKA-PKG induced relaxations only in trabecular meshwork. When PTK and PKC or PKA-PKG were inhibited, the relaxation induced by inhibition of PTK was additive to inhibition of the other protein kinases. Stimulation of a receptor with PTK activity by EGF induced a relaxation in trabecular meshwork and a contraction in ciliary muscle precontracted by carbachol. When trabecular meshwork and ciliary muscle were activated by EGF, inhibition of PTK by genistein relaxed the cell preparations. CONCLUSIONS: Inhibition of PTK induces more prominent relaxation in trabecular meshwork than in ciliary muscle. The effects of inhibition of PTK on relaxation are independent of inhibition of PKC and PKA-PKG. The signaling cascade after activation of a tyrosine kinase receptor by EGF is differently modulated in trabecular meshwork and ciliary muscle. The effect of genistein on relaxation is probably not directly related to the EGF receptor. PTK inhibitors are possible agents for the development of novel antiglaucoma drugs.

Intensified ESWL of gallstones: dissociation of pulverisation, pain relief and stone-clearance.

BACKGROUND/AIMS: Recently, intensified shock wave lithotripsy for gallstone pulverisation and subsequent clearance without bile salt medication has been advocated. We report our first 44 patients treated by this regime: Patients with intact gallbladder function and symptomatic gallstones of any size, number and composition. METHODOLOGY: Forty-four consecutive patients who received intensified shock wave lithotripsy for gallstone pulverisation and clearance were included in this study. The patients all had intact gallbladder function and presented with symptomatic gallstones of any size, number and composition. RESULTS: Pulverisation was achieved in 75% of all cases (12 months), but only 34% were stone free. The proportion of patients with stone pulverisation compared to subsequent complete clearance was 93% versus 60% in small (

Molecular phylogenetics of finches and sparrows: consequences of character state removal in cytochrome b sequences.

The complete mitochondrial cytochrome b genes of 53 genera of oscine passerine birds representing the major groups of finches and some allies were compared. Phylogenetic trees resulting from three levels of character partition removal (no data removed, transitions at third positions of codons removed, and all transitions removed [transversion parsimony]) were generally concordant, and all supported several basic statements regarding relationships of finches and finch-like birds, including: (1) larks (Alaudidae) show no close relationship to any finch group; (2) Peucedramus (olive warbler) is phylogenetically far removed from true wood warblers; (3) a clade consisting of fringillids, passerids, motacillids, and emberizids is supported, and this clade is characterized by evolution of a vestigial 10th wing primary; and (4) Hawaiian honeycreepers are derived from within the cardueline finches. Excluding transition substitutions at third positions of codons resulted in phylogenetic trees similar to, but with greater bootstrap nodal support than, trees derived using either all data (equally weighted) or transversion parsimony. Relative to the shortest trees obtained using all data, the topologies obtained after elimination of third-position transitions showed only slight increases in realized treelength and homoplasy. These increases were negligable compared to increases in overall nodal support; therefore, this partition removal scheme may enhance recovery of deep phylogenetic signal in protein-coding DNA datasets.