Urgent need for consistent standards in functional enrichment analysis

Gene set enrichment tests (a.k.a. functional enrichment analysis) are among the most frequently used methods in computational biology. Despite this popularity, there are concerns that these methods are being applied incorrectly and the results of some peer-reviewed publications are unreliable. These problems include the use of inappropriate background gene lists, lack of false discovery rate correction and lack of methodological detail. To ascertain the frequency of these issues in the literature, we performed a screen of 186 open-access research articles describing functional enrichment results. We find that 95% of analyses using over-representation tests did not implement an appropriate background gene list or did not describe this in the methods. Failure to perform p-value correction for multiple tests was identified in 43% of analyses. Many studies lacked detail in the methods section about the tools and gene sets used. An extension of this survey showed that these problems are not associated with journal or article level bibliometrics. Using seven independent RNA-seq datasets, we show misuse of enrichment tools alters results substantially. In conclusion, most published functional enrichment studies suffered from one or more major flaws, highlighting the need for stronger standards for enrichment analysis.     

Curcumin,its derivatives,and their nanoformulations: Revolutionizing cancer treatment

Curcumin is a natural compound derived from turmeric and can target malignant tumor molecules involved in cancer propagation. It has potent antioxidant activity, but its effectiveness is limited due to poor absorption and rapid elimination from the body. Various curcumin derivatives have also shown anticancer potential in in-vitro and in-vivo models. Curcumin can target multiple signaling pathways involved in cancer development/progression or induce cancer cell death through apoptosis. In addition, curcumin and its derivatives could also enhance the effectiveness of conventional chemotherapy, radiation therapy and reduce their associated side effects. Lately, nanoparticle-based delivery systems are being developed/explored to overcome the challenges associated with curcumin's delivery, increasing its overall efficacy. The use of an imaging system to track these formulations could also give beneficial information about the bioavailability and distribution of the nano-curcumin complex. In conclusion, curcumin holds significant promise in the fight against cancer, especially in its nanoform, and could provide precise delivery to cancer cells without affecting normal healthy cells.     

Management of sternal wounds with bilateral pectoralis major myocutaneous advancement flaps in 114 consecutively treated patients: refinements in technique and outcomes analysis

Because life-threatening sternal wound complications can occur following sternotomy, the optimal management of sternal wound infections remains an important topic. To decrease morbidity following operative treatment of these patients, the authors made a number of refinements in their treatment protocol over the past several years, particularly with regard to the extent of débridement, method of flap apposition, and management of drains. The purpose of this study was to obtain specific outcomes data by reviewing a large series of patients treated by a single surgeon. In this series of 114 consecutive sternal wounds treated by the senior author (Ascherman), patients were managed almost exclusively with débridement and immediate closure with bilateral pectoralis major myocutaneous advancement flaps. There were no intraoperative deaths. The 30-day perioperative mortality rate was 7.9 percent, with only one death directly related to sternal infection. Nineteen patients (16.7 percent) experienced postoperative morbidity, including partial wound dehiscences (5 percent), skin edge necrosis (5 percent), and seromas (3.5 percent). The authors advocate single-stage management of complicated sternal wounds with immediate débridement and bilateral pectoralis major myocutaneous advancement flaps. The procedure is rapid and effective. Refinements in technique have significantly lowered morbidity.     

Exploring fungal biodiversity for the production of water-soluble pigments as potential natural food colorants

The production of many currently authorized natural food colorants has a number of disadvantages, including a dependence on the supply of raw materials and variations in pigment extraction. Fungi provide a readily available alternative source of naturally derived food colorants that could easily be produced in high yields. The recent authorization of a fungal food colorant has fuelled research to explore the extraordinary chemical diversity and biodiversity of fungi for the biotechnological production of pigments as natural food colorants. These studies require an appropriate use of chemotaxonomic tools and a priori knowledge of fungal metabolites to carry out intelligent screening for known or novel colorants as lead compounds. Such screening would result in the preselection of some potential pigment producers and the deselection of pathogenic strains and toxin producers. With advances in gene technology, in the future it should be possible to employ metabolic engineering to create microbial cell factories for the production of food colorants.     

Casein-derived phosphopeptides disrupt tight junction integrity,and precipitously dry up milk secretion in goats

Mammary involution is triggered by local stimuli, but the precise mechanism has not been defined. Milk stasis accumulate local signals, which makes the tight junctions (TJ) leaky. The aim of the study was to check the hypothesis that casein hydrolyzates (CNH) compromise TJ integrity and dry up milk secretion. A single dose of CNH transiently (12 to 24 h) compromised TJ integrity in the treatedudder. This was associated by a transient (12 to 96 h) decline in milk secretion. No such changes were recorded in the contralateral gland that served as a control. Four repeated doses of CNH after each milking caused drastic changes in mammary secretion and composition, which were associated with irreversible cessation of milk secretion within 96 h. No such changes were recorded in goats treated with de-phosphorylated casein (control). We conclude that CNH are the milk-borne factors that cause the disruption of TJ integrity and induction of involution, and that the serine-Ps in the CNHs are essential for the excretion of biological activity.     

Modeling protein-protein,protein-peptide,and protein-oligosaccharide complexes: CAPRI 7th edition

We present the seventh report on the performance of methods for predicting the atomic resolution structures of protein complexes offered as targets to the community-wide initiative on the Critical Assessment of Predicted Interactions. Performance was evaluated on the basis of 36 114 models of protein complexes submitted by 57 groups—including 13 automatic servers—in prediction rounds held during the years 2016 to 2019 for eight protein-protein, three protein-peptide, and five protein-oligosaccharide targets with different length ligands. Six of the protein-protein targets represented challenging hetero-complexes, due to factors such as availability of distantly related templates for the individual subunits, or for the full complex, inter-domain flexibility, conformational adjustments at the binding region, or the multi-component nature of the complex. The main challenge for the protein-peptide and protein-oligosaccharide complexes was to accurately model the ligand conformation and its interactions at the interface. Encouragingly, models of acceptable quality, or better, were obtained for a total of six protein-protein complexes, which included four of the challenging hetero-complexes and a homo-decamer. But fewer of these targets were predicted with medium or higher accuracy. High accuracy models were obtained for two of the three protein-peptide targets, and for one of the protein-oligosaccharide targets. The remaining protein-sugar targets were predicted with medium accuracy. Our analysis indicates that progress in predicting increasingly challenging and diverse types of targets is due to closer integration of template-based modeling techniques with docking, scoring, and model refinement procedures, and to significant incremental improvements in the underlying methodologies.