Gene structure prediction using information on homologous protein sequence

In this paper a new approach for the prediction of protein coding gene structures is described. The principal scheme of prediction is as follows: first, the exons with the best potential are predicted in a sequence with unknown functions and a list of potential amino acid fragments coded by these exons is formed. Second, testing the homology between each amino acid fragment from the list and proteins from the SWISS-PROT database of amino acid sequences. One protein with the best homology is chosen out of all the homologous sequences. Third, reconstruction of the exon-intron structure, basing it on its homology with the chosen protein sequences. The method was tested on an independent control set (20 genes). The results were as follows: 21% of real exons were lost and 3% of non-real exons were found. This system can be used to refine the results of gene prediction systems, especially if highly homologous proteins are found in the amino acid sequence database.     

Effects of different particle deposition parameters on adhesion of resin cement to zirconium dioxide and phase transformation

This study evaluated the effect of air-abrasion parameters such as particle size, distance, and time on adhesion of resin cement to zirconium dioxide (Y-TZP) and t→m phase transformation. Y-TZP blocks (N = 80) (In-Ceram YZ, Vita) (4 mm^3?×?4 mm^3?×?3 mm³) were assigned into eight groups (n = 10): air-abrasion with 30 μm (CoJet Sand, S30) and 110 μm (Rocatec-Plus, S110) silica-coated alumina particles, applied for either for 10–20 s (T = time), from a distance of 10–20 mm (D = distance), composing the following groups: S₃₀T₁₀D₁₀, S₃₀T₁₀D₂₀, S₃₀T₂₀D₁₀, S₃₀T₂₀D₂₀, S₁₁₀T₁₀D₁₀, S₁₁₀T₁₀D₂₀, S₁₁₀T₂₀D₁₀, and S₁₁₀T₂₀D₂₀. Resin composite (RelyX ARC) was bonded to Y-TZP blocks in polyethylene molds. The specimens were aged (10,000 thermal cycles and water storage for 90 days) prior to shear bond test. Failure types were analyzed under stereomicroscope and SEM, and phase transformation was calculated. Data (MPa) were analyzed using 3-way ANOVA and Tukey’s tests. Air-abrasion with 110 μm silica particles (10.96) presented significantly higher bond strength (p = 0.0149) compared to 30 μm (8.96). Time (p = 0.403) and distance (p = 0.179) parameters did not affect the results significantly. Air-abrasion with 110 μm particles (12.3) promoted higher bond strength than that of 30 μm (6.4) when applied for 10 s from a distance of 10 mm (Tukey’s). Failure types were predominantly adhesive. Phase transformation ranged between 30.3 and 35.9% for 30 μm particles and 23.8–43.7% for 110 μm particles. While the size of silica-coated alumina particles were more relevant parameter for resin cement adhesion to Y-TZP, time (up to 20 s) and distance (up to 20 mm) appear to be less pertinent.     

Environmental impact of castor oil catalytic transfer hydrogenation

In the vegetable oil chemical industry, hydrogenation is one of the most important processes. An alternative method for vegetable oil hydrogenation is the use of catalytic transfer hydrogenation (CTH), which can utilize organic molecules as hydrogen donors at ambient pressure. These alternative processes should be optimized in relation to the variables required for a good conversion and impacts should also be known to be minimized. An assessment of the environmental impact of laboratory scale chemical processes is an important tool to improve the technological aspects of a process (increased yields, reduced production times, lower costs) and it can also lead to the creation of a cleaner technology. Using the Leopold Matrix, we have succeeded in developing a more efficient and cleaner process for the CTH of castor oil using Raney Ni as a catalyst and cyclohexene or isopropanol as a hydrogen donor solvent. The results of the technical and environmental assessments showed that the extent of conversion for the unsaturation reaction was high (>99 %), and the environmental impact of the process could be significantly reduced to create a cleaner technology. It was found, after process optimization, that the remaining environmental impacts were negative (67.48 %), local (78.95 %), temporary (95.33 %), direct (80.12 %), and reversible (95.32 %).     

Polo-like kinase 1 as a target for human cytomegalovirus pp65 lower matrix protein

Human cytomegalovirus (HCMV) pp65 protein is the major constituent of viral dense bodies but is dispensable for viral growth in vitro. pp65 copurifies with a S/T kinase activity and has been implicated in phosphorylation of HCMV IE1 immediate-early protein and its escape from major histocompatibility complex 1 presentation. Furthermore, the presence of pp65 correlates with a virion-associated kinase activity. To clarify the role of pp65, yeast two-hybrid system (THS) screening was performed to identify pp65 cellular partners. A total of 18 out of 48 yeast clones harboring cDNAs for putative pp65 binding proteins encoded the Polo-like kinase 1 (Plk1) C-terminal domain. Plk1 behaved as a bona fide pp65 partner in THS control crosses, and the interaction was confirmed by in vitro binding experiments. Endogenous Plk1 was coimmunoprecipitated with pp65 from transiently transfected COS7 cells. In infected fibroblasts, Plk1 was coimmunoprecipitated with pp65 at late infection stages. Furthermore, Plk1 was detected within wild-type HCMV particles but not within the particles of a pp65-negative mutant (RVAd65). The hydrophilic region of pp65 was phosphorylated in vitro by Plk1. These results suggest that one function of pp65 may be to capture a cell kinase, perhaps in order to alter its activity, nucleotide preference, substrate specificity, or subcellular localization to the advantage of HCMV.     

Tumour-localising and -photosensitising properties of a novel zinc(II) octadecylphthalocyanine

1,4,8,11,15,18,22,25-Octadecylphthalocyaninato zinc(II), ZnODPc, incorporated into a Cremophor emulsion, was assayed for its pharmacokinetic and phototherapeutic properties in Balb/c mice bearing an intramuscularly transplanted MS-2 fibrosarcoma. The phthalocyanine was injected intravenously (i.v.) in three doses, i.e. 1.46, 0.73 and 0.37 mumol kg-1 body weight. In all cases, the octadecyl-substituted phthalocyanine showed an unusually high affinity for serum low-density lipoproteins (LDLs) and a high efficiency and selectivity of tumour targeting: the maximum accumulation in the tumour occurred at 24 h after injection, whereas no detectable amount of phthalocyanine was recovered from the muscle, i.e. the peritumoral tissue, between 1 h and 1 week after injection. At the same time, low amounts of phthalocyanine were recovered from skin and then only at short times after injection, with skin photosensitivity rapidly disappearing and the phthalocyanine present in the serum only. Tumour photosensitisation studies were carried out at 24 h after administration of 1.46 mumol kg-1 ZnODPc and showed that this phthalocyanine has a very high phototherapeutic efficiency; this is probably a consequence of the multiple mechanisms by which the phthalocyanine induces tumour damage, involving both direct modification of malignant cells and impairment of blood flow, as well as the alteration of a variety of subcellular components, such as mitochondria, the rough endoplasmic reticulum, the perinuclear membrane and, occasionally, cell nuclei. Tumour necrosis appears to be the consequence of both random cell death and apoptosis.     

Whey filtration: a review of products,application, and pretreatment with transglutaminase enzyme

In the cheese industry, whey, which is rich in lactose and proteins, is underutilized, causing adverse environmental impacts. The fractionation of its components, typically carried out through filtration membranes, faces operational challenges such as membrane fouling, significant protein loss during the process, and extended operating times. These challenges require attention and specific methods for optimization and to increase efficiency. A promising strategy to enhance industry efficiency and sustainability is the use of enzymatic pre-treatment with the enzyme transglutaminase (TGase). This enzyme plays a crucial role in protein modification, catalyzing covalent cross-links between lysine and glutamine residues, increasing the molecular weight of proteins, facilitating their retention on membranes, and contributing to the improvement of the quality of the final products. The aim of this study is to review the application of the enzyme TGase as a pretreatment in whey protein filtration. The scope involves assessing the enzyme's impact on whey protein properties and its relationship with process performance. It also aims to identify both the optimization of operational parameters and the enhancement of product characteristics. This study demonstrates that the application of TGase leads to improved performance in protein concentration, lactose permeation, and permeate flux rate during the filtration process. It also has the capacity to enhance protein solubility, viscosity, thermal stability, and protein gelation in whey. In this context, it is relevant for enhancing the characteristics of whey, thereby contributing to the production of higher quality final products in the food industry. © 2023 Society of Chemical Industry.     

A fast job scheduling system for a wide range of bioinformatic applications

Bioinformatic tools are often used by researchers through interactive Web interfaces, resulting in a strong demand for computational resources. The tools are of different kind and range from simple, quick tasks, to complex analyses requiring minutes to hours of processing time and often longer than that. Batteries of computational nodes, such as those found in parallel clusters, provide a platform of choice for this application, especially when a relatively large number of concurrent requests is expected. Here, we describe a scheduling architecture operating at the application level, able to distribute jobs over a large number of hierarchically organized nodes. While not contrasting and peacefully living together with low-level scheduling software, the system takes advantage of tools, such as SQL servers, commonly used in Web applications, to produce low latency and performance which compares well and often surpasses that of more traditional, dedicated schedulers. The system provides the basic functionality necessary to node selection, task execution and service management and monitoring, and may combine loosely linked computational resources, such as those located in geographically distinct sites.     

Genome-wide association study of milk fatty acid composition in Italian Simmental and Italian Holstein cows using single nucleotide polymorphism arrays

Bovine milk is important for human nutrition, but its fat content is often criticized as a risk factor in cardiovascular disease. Selective breeding programs could be used to alter the fatty acid (FA) composition of bovine milk to improve the healthiness of dairy products for human consumption. Here, we performed a genome-wide association study (GWAS) on bovine milk to identify genomic regions or specific genes associated with FA profile and to investigate genetic differences between the Italian Simmental (IS) and Italian Holstein (IH) breeds. To achieve this, we first characterized milk samples from 416 IS cows and 436 IH cows for their fat profile by gas chromatography. Subjects were genotyped with single nucleotide polymorphism array and a single-marker regression model for GWAS was performed. Our findings confirm previously reported quantitative trait loci strongly associated with bovine milk fat composition. More specifically, our GWAS results revealed significant signals on chromosomes Bos taurus autosome 19 and 26 for milk FA. Further analysis using a gene-centric approach and pathway meta-analysis identified not only some well-known genes underlying quantitative trait loci for milk FA components, such as FASN, SCD, and DGAT1, but also other significant candidate genes, including some with functional roles in pathways related to “Lipid metabolism.” Highlighted genes related to FA profile include ECI2, PCYT2, DCXR, G6PC3, PYCR1, and ALG12 in IS, and CYP17A1, ACO2, PI4K2A, GOT1, GPT, NT5C2, PDE6G, POLR3H, and COX15 in IH. Overall, the breed-specific association outcomes reflect differences in the genetic backgrounds of the IS and IH breeds and their selective breeding histories.     

Medical informatics and bioinformatics: a bibliometric study.

This paper reports on an analysis of the bioinformatics and medical informatics literature with the objective to identify upcoming trends that are shared among both research fields to derive benefits from potential collaborative initiatives for their future. Our results present the main characteristics of the two fields and show that these domains are still relatively separated.