The Effect of Cumulative Length of Hospital Stay on the Antifungal Resistance of <Emphasis Type="Italic">Candida</Emphasis> Strains Isolated from Critically Ill Surgical Patients

Fluconazole is the first line of therapy for the management of candidiasis. However, fluconazole-resistant strains pose an emerging challenge in everyday clinical practice. In this study, we sought to determine whether cumulative length of hospital stay (CLOS) is a predictive factor for the acquisition of non-susceptible Candida strains to fluconazole. Thirty-three critically ill emergency surgery patients with 56 Candida isolates were enrolled in this prospective study. We divided our isolates according to their minimum inhibitory concentration (MIC) to fluconazole using 8 mcg/ml as a cutoff. We then compared the two groups with respect to basic demographics, antifungal agents prescribed, number of wide-spectrum antibiotics, duration of central venous catheter placement, elapsed time to positive culture, duration of prior hospital stay, and length of hospital stay. Non-susceptible fluconazole samples belonged to patients with a significantly longer prior hospital stay and a longer CLOS (P = 0.02 and 0.01, respectively). The difference between the 2 groups regarding non-albicans strains was statistically significant (P < 0.001). By fitting a non-parametric receiver-operating characteristics (ROC) curve into our analysis, a CLOS ≥ 29 days predicted the occurrence of non-susceptible strains with 90% sensitivity and 79.6% specificity (correct classification 81.5%). A CLOS ≥ 29 days is a strong predictor for the isolation of non-susceptible Candida isolates to fluconazole among critically ill emergency surgery patients. Clinicians should consider the duration of previous hospital stay when deciding on empiric antifungal therapy.     

Rare and common regulatory variation in population-scale sequenced human genomes

Population-scale genome sequencing allows the characterization of functional effects of a broad spectrum of genetic variants underlying human phenotypic variation. Here, we investigate the influence of rare and common genetic variants on gene expression patterns, using variants identified from sequencing data from the 1000 genomes project in an African and European population sample and gene expression data from lymphoblastoid cell lines. We detect comparable numbers of expression quantitative trait loci (eQTLs) when compared to genotypes obtained from HapMap 3, but as many as 80% of the top expression quantitative trait variants (eQTVs) discovered from 1000 genomes data are novel. The properties of the newly discovered variants suggest that mapping common causal regulatory variants is challenging even with full resequencing data; however, we observe significant enrichment of regulatory effects in splice-site and nonsense variants. Using RNA sequencing data, we show that 46.2% of nonsynonymous variants are differentially expressed in at least one individual in our sample, creating widespread potential for interactions between functional protein-coding and regulatory variants. We also use allele-specific expression to identify putative rare causal regulatory variants. Furthermore, we demonstrate that outlier expression values can be due to rare variant effects, and we approximate the number of such effects harboured in an individual by effect size. Our results demonstrate that integration of genomic and RNA sequencing analyses allows for the joint assessment of genome sequence and genome function.     

A guide and guard: The many faces of T-cadherin

Cadherins are a superfamily of transmembrane proteins that mediate calcium-dependent intercellular adhesion. T-cadherin (T-cad, H-cadherin or cadherin-13) is an atypical member, lacking transmembrane and cytosolic domains and possessing a glycosylphosphatidylinositol moiety that anchors T-cadherin to the plasma membrane. This article reviews current knowledge on the biomolecular characteristics of T-cadherin, its expression and function in different tissues in health and disease and its mechanisms of signal transduction. The structural characteristics of T-cadherin protein predict that it is unlikely to function as a “true” adhesion molecule in vivo. Studies from different fields suggest that it may act rather as a signalling receptor participating in recognition of the environment and regulation of cell motility, proliferation and phenotype. Cellular expression levels of T-cadherin in various tissues frequently correlate (be it negatively or positively) with the proliferative potential of the cells. Loss- and gain-of-function studies demonstrate the ability of T-cadherin to modulate cell motility and growth. Gathering evidence suggests that the “functional predestination” of T-cadherin is in control of tissue architecture through “guiding” navigation of moving structures, segregating functional tissue compartments and “guarding” integrity of functionally connected tissue layers.     

Overlapping protective roles for glutathione transferase gene family members in chemical and oxidative stress response in Agrobacterium tumefaciens

In the present work, we describe the characterisation of the glutathione transferase (GST) gene family from Agrobacterium tumefaciens C58. A genome survey revealed the presence of eight GST-like proteins in A. tumefaciens (AtuGSTs). Comparison by multiple sequence alignment generated a dendrogram revealing the phylogenetic relationships of AtuGSTs-like proteins. The beta and theta classes identified in other bacterial species are represented by five members in A. tumefaciens C58. In addition, there are three “orphan” sequences that do not fit into any previously recognised GST classes. The eight GST-like genes were cloned, expressed in Escherichia coli and their substrate specificity was determined towards 17 different substrates. The results showed that AtuGSTs catalyse a broad range of reactions, with different members of the family exhibiting quite varied substrate specificity. The 3D structures of AtuGSTs were predicted using molecular modelling. The use of comparative sequence and structural analysis of the AtuGST isoenzymes allowed us to identify local sequence and structural characteristics between different GST isoenzymes and classes. Gene expression profiling was conducted under normal culture conditions as well as under abiotic stress conditions (addition of xenobiotics, osmotic stress and cold and heat shock) to induce and monitor early stress-response mechanisms. The results reveal the constitutive expression of GSTs in A. tumefaciens and a modulation of GST activity after treatments, indicating that AtuGSTs presumably participate in a wide range of functions, many of which are important in counteracting stress conditions. These functions may be relevant to maintaining cellular homeostasis as well as in the direct detoxification of toxic compounds.     

Lycopene recovery from tomato peel under mild conditions assisted by enzymatic pre-treatment and non-ionic surfactants

The tomato processing industry generates large quantities of tomato peel residues, usually creating environmental problems. These residues are a significant source of lycopene, thus providing an attractive alternative for profitable handling of these otherwise problematic by-products. The enzymatic pretreatment of these residues for lycopene recovery has already been employed, although the use of surfactants for enhancing the recovery has not been examined so far. The enzymatic pretreatment of tomato peels, using two commercially available pectinolytic enzyme preparations, was evaluated suggesting that there is an optimum pretreatment time of about 1 h, enzyme amount 250 Units/mL and no significant pH influence. Lycopene surfactant - assisted extraction was further investigated, showing that, among eight surfactants used, the most suitable was "Span 20", with an optimum ratio of 6-7 surfactant molecules per lycopene molecule. Sequential enzymatic pretreatment and surfactant-assisted extraction (30 min for each step) was evaluated leading to an improved lycopene extraction yield, with a somewhat smaller surfactant molar ratio (i.e. 4-5). In the latter case, the yield of lycopene recovery was almost four times greater compared to just 1 hr enzymatic pretreatment, and was approximately ten times greater compared to the recovery from untreated peels. Furthermore, such lipophilic compound recovery, avoiding the use of organic solvents, is environmentally attractive and ensures direct lycopene use in the food and cosmetics industries.