Bioinformatics Analysis of RNA-seq Data Reveals Genes Related to Cancer Stem Cells in Colorectal Cancerogenesis

Cancer stem cells (CSC) play one of the crucial roles in the pathogenesis of various cancers, including colorectal cancer (CRC). Although great efforts have been made regarding our understanding of the cancerogenesis of CRC, CSC involvement in CRC development is still poorly understood. Using bioinformatics and RNA-seq data of normal mucosa, colorectal adenoma, and carcinoma (n = 106) from GEO and TCGA, we identified candidate CSC genes and analyzed pathway enrichment analysis (PEI) and protein–protein interaction analysis (PPI). Identified CSC-related genes were validated using qPCR and tissue samples from 47 patients with adenoma, adenoma with early carcinoma, and carcinoma without and with lymph node metastasis and were compared to normal mucosa. Six CSC-related genes were identified: ANLN, CDK1, ECT2, PDGFD, TNC, and TNXB. ANLN, CDK1, ECT2, and TNC were differentially expressed between adenoma and adenoma with early carcinoma. TNC was differentially expressed in CRC without lymph node metastases whereas ANLN, CDK1, and PDGFD were differentially expressed in CRC with lymph node metastases compared to normal mucosa. ANLN and PDGFD were differentially expressed between carcinoma without and with lymph node metastasis. Our study identified and validated CSC-related genes that might be involved in early stages of CRC development (ANLN, CDK1, ECT2, TNC) and in development of metastasis (ANLN, PDGFD).     

Saliva Proteomics as Fluid Signature of Inflammatory and Immune-Mediated Skin Diseases

Saliva is easy to access, non-invasive and a useful source of information useful for the diagnosis of serval inflammatory and immune-mediated diseases. Following the advent of genomic technologies and -omic research, studies based on saliva testing have rapidly increased and human salivary proteome has been partially characterized. As a proteomic protocol to analyze the whole saliva proteome is not currently available, the most common aim of the proteomic analysis is to discriminate between physiological and pathological conditions. The salivary proteome has been initially investigated in several diseases: oral squamous cell carcinoma and oral leukoplakia, chronic graft-versus-host disease, and Sjögren’s syndrome. Otherwise, salivary proteomics studies in the dermatological field are still in the initial phase, thus the aim of this review is to collect the best research evidence on the role of saliva proteomics analysis in immune-mediated skin diseases to understand the direction of research in this field. The results of PRISMA analysis reported herein suggest that human saliva analysis could provide significant data for the diagnosis and prognosis of several immune-mediated and inflammatory skin diseases in the next future.     

Hyporheic Exchange with Gravel Beds: Basic Hydrodynamic Interactions and Bedform-Induced Advective Flows

Stream-subsurface exchange processes are important because of their role in controlling the transport of contaminants and ecologically relevant substances in streams. Laboratory flume experiments were conducted to examine solute exchange with gravel streambeds. Two morphologies were studied: flat beds and beds covered by dune-shaped bedforms. High rates of exchange were observed with flat beds under a wide range of stream flow conditions, indicating that there was considerable turbulent coupling of stream and pore water flows. The presence of bedforms produced additional exchange under all flow conditions. The exchange with bedforms could be represented well by considering solute flux caused by bedform-induced advective pumping. Pumping exchange was enhanced by inertial effects, including non-Darcy flow and turbulent diffusion. For the flat bed case, dye injections showed that exchange also occurred by a combination of advective pore water flow and turbulent diffusion near the stream–subsurface interface. The relative effects of advective and diffusive transport processes could not be separated due to the complex nature of the induced flows in the gravel bed. However, exchange was found to scale with the square of the stream Reynolds number in all cases. Comparison of these results with those obtained with coarser and finer sediments demonstrated that the exchange rate is also proportional to the square of the characteristic bed sediment size. These scaling relationships can be used to improve interpretation of solute transport observed in natural rivers.     

Using a priori information to improve soil moisture retrieval from ENVISAT ASAR AP data in semiarid regions

This paper presents a retrieval algorithm that estimates spatial and temporal distribution of volumetric soil moisture content, at an approximate depth of 5 cm, using multitemporal ENVISAT Advanced Synthetic Aperture Radar (ASAR) alternating polarization images, acquired at low incidence angles (i.e., from 15/spl deg/ to 31/spl deg/). The algorithm appropriately assimilates a priori information on soil moisture content and surface roughness in order to constrain the inversion of theoretical direct models, such as the integral equation method model and the geometric optics model. The a priori information on soil moisture content is obtained through simple lumped water balance models, whereas that on soil roughness is derived by means of an empirical approach. To update prior estimates of surface parameters, when no reliable a priori information is available, a technique based solely on the use of multitemporal SAR information is proposed. The developed retrieval algorithm is assessed on the Matera site (Italy) where multitemporal ground and ASAR data were simultaneously acquired in 2003. Simulated and experimental results indicate the possibility of attaining an accuracy of approximately 5% in the retrieved volumetric soil moisture content, provided that sufficiently accurate a priori information on surface parameters (i.e., within 20% of their whole variability range) is available. As an example, multitemporal soil moisture maps at watershed scale, characterized by a spatial resolution of approximately 150 m, are derived and illustrated in the paper.     

Thromboembolic events in beta thalassemia major: an Italian multicenter study

Oxidation of cholesterol (1a) or pregnenolone (1b) with pyridinium dichromate (PDC) in dimethylformamide (DMF) or in dichloromethane (DCM) and pyridinium chlorochromate (PCC) in DCM provided cholest-4-en-3,6-dione (2a) or pregn-4-en-3,6,20-trione (2b). TLC monitoration of the reactions implied that cholest-5-en-3-one (3a) or pregn-5-en-3,20-dione (3b) and cholest-4-en-3-one (4a) or pregn-4-en-3,20-dione (4b) might be intermediates. Individual oxidation of 3a or 3b with PDC and PCC could give 2a or 2b, but 4a or 4b remained unchanged. Further investigation indicated that 4a or 4b was an isomerization product of 3a or 3b on silica gel TLC plate rather than really existence in the reaction mixture. These results shown steroidal 5-en-3-ones were intermediates of the transformation of steroidal 5-en-3 beta-ols to steroidal 4-en-3,6-diones oxidized by PDC and PCC.     

Effect of aldose reductase inhibition on glutathione redox status in erythrocytes of diabetic patients

Diabetic patients undergo a chronic oxidative stress. This phenomenon is demonstrated by low levels of reduced glutathione (GSH) levels. The NADPH used by glutathione reductase for the reduction of oxidized glutathione (GSSG) to GSH is also used by aldose reductase for the reduction of glucose to sorbitol through the polyol pathway. The competition for NADPH could be responsible for the decreased glutathione levels found in non-insulin-dependent diabetic patients. For this purpose, we investigated the effect of polyol pathway inhibition on the glutathione redox status in these patients. We measured GSH and GSSG levels in erythrocytes of non-insulin-dependent diabetic patients (n = 15) before and after 1 week of treatment with placebo, followed by 1 week of treatment with an aldose reductase inhibitor (tolrestat 200 mg/dl). We found lower GSH levels (7.7 +/- 1.4 mumol/g hemoglobin [Hb]), higher GSSG levels (0.35 +/- 0.09 mumol/g Hb), and lower GSH/GSSG ratios (23.9 +/- 7.7) in diabetics compared with controls (n = 15; 9.8 +/- 0.8 mumol/g Hb, P < .001; 0.17 +/- 0.02, P < .001; and 58.3 +/- 9.1, P < .001, respectively). We did not demonstrate any statistical difference after 1 week of treatment with placebo. In contrast, the treatment with tolrestat induced a significant increase in GSH (8.9 +/- 0.7 mumol/g Hb, P < .01), a decrease in GSSG (0.25 +/- 0.06 mumol/g Hb, P < .02), and an increase in the GSH/GSSG ratio (37.3 +/- 8.4, P < .01). These data strongly support the hypothesis that the polyol pathway plays an important role in the impairment of the glutathione redox status in diabetic patients.     

Disease mapping in veterinary epidemiology: a Bayesian geostatistical approach

Model-based geostatistics and Bayesian approaches are useful in the context of veterinary epidemiology when point data have been collected by appropriate study design. We take advantage of an example of Epidemiological Surveillance on urban settings where a two-stage sampling design with first stage transects is applied to study the risk of dog parasite infection in the city of Naples, 2004-2005. We specified Bayesian Gaussian spatial exponential models and Bayesian kriging were performed to predict the continuous risk surface of parasite infection on the study region. We compared the results with those obtained by the application of hierarchical Bayesian models on areal data (proportion of positive specimens by transect). The models results were consistent with each other and the Bayesian geostatistical approach proved to be more accurate in identifying areas at risk of zoonotic parasitic diseases. In general, larger risk areas were identified at the city border where wild dogs mixed with domestic dogs and human or urban barriers were less present.     

A Beckwith–Wiedemann-Associated CDKN1C Mutation Allows the Identification of a Novel Nuclear Localization Signal in Human p57Kip2

p57^Kip2 protein is a member of the CIP/Kip family, mainly localized in the nucleus where it exerts its Cyclin/CDKs inhibitory function. In addition, the protein plays key roles in embryogenesis, differentiation, and carcinogenesis depending on its cellular localization and interactors. Mutations of CDKN1C, the gene encoding human p57^Kip2, result in the development of different genetic diseases, including Beckwith–Wiedemann, IMAGe and Silver–Russell syndromes. We investigated a specific Beckwith–Wiedemann associated CDKN1C change (c.946 C>T) that results in the substitution of the C-terminal amino acid (arginine 316) with a tryptophan (R316W-p57^Kip2). We found a clear redistribution of R316W-p57^Kip2, in that while the wild-type p57^Kip2 mostly occurs in the nucleus, the mutant form is also distributed in the cytoplasm. Transfection of two expression constructs encoding the p57^Kip2 N- and C-terminal domain, respectively, allows the mapping of the nuclear localization signal(s) (NLSs) between residues 220–316. Moreover, by removing the basic RKRLR sequence at the protein C-terminus (from 312 to 316 residue), p57^Kip2 was confined in the cytosol, implying that this sequence is absolutely required for nuclear entry. In conclusion, we identified an unreported p57^Kip2 NLS and suggest that its absence or mutation might be of relevance in CDKN1C-associated human diseases determining significant changes of p57^Kip2 localization/regulatory roles.     

Extension of Collagen Deposition in COVID-19 Post Mortem Lung Samples and Computed Tomography Analysis Findings

Lung fibrosis has specific computed tomography (CT) findings and represents a common finding in advanced COVID-19 pneumonia whose reversibility has been poorly investigated. The aim of this study was to quantify the extension of collagen deposition and aeration in postmortem cryobiopsies of critically ill COVID-19 patients and to describe the correlations with qualitative and quantitative analyses of lung CT. Postmortem transbronchial cryobiopsy samples were obtained, formalin fixed, paraffin embedded and stained with Sirius red to quantify collagen deposition, defining fibrotic samples as those with collagen deposition above 10%. Lung CT images were analyzed qualitatively with a radiographic score and quantitatively with computer-based analysis at the lobe level. Thirty samples from 10 patients with COVID-19 pneumonia deceased during invasive mechanical ventilation were included in this study. The median [interquartile range] percent collagen extension was 6.8% (4.6–16.2%). In fibrotic compared to nonfibrotic samples, the qualitative score was higher (260 (250–290) vs. 190 (120–270), p = 0.036) while the gas fraction was lower (0.46 (0.32–0.47) vs. 0.59 (0.37–0.68), p = 0.047). A radiographic score above 230 had 100% sensitivity (95% confidence interval, CI: 66.4% to 100%) and 66.7% specificity (95% CI: 41.0% to 92.3%) to detect fibrotic samples, while a gas fraction below 0.57 had 100% sensitivity (95% CI: 66.4% to 100%) and 57.1% specificity (95% CI: 26.3% to 88.0%). In COVID-19 pneumonia, qualitative and quantitative analyses of lung CT images have high sensitivity but moderate to low specificity to detect histopathological fibrosis. Pseudofibrotic CT findings do not always correspond to increased collagen deposition.     

Interactive Multi‐objective Dynamic Optimization of Bioreactors under Parametric Uncertainty

Model‐based optimization techniques play a key role in achieving a sustainable operation of biochemical processes. Models are an approximation of the real process under study, hence, uncertainty is inherently present and for a sustainable process operation this uncertainty should be accounted for. In practice, optimality with respect to different conflicting objectives is required and multi‐objective optimization is a valuable tool. In this article the sigma point approach is applied to account for parametric uncertainty in the frame of interactive multi‐objective bioprocess optimization.