A workflow for mutation extraction and structure annotation

Rich information on point mutation studies is scattered across heterogeneous data sources. This paper presents an automated workflow for mining mutation annotations from full-text biomedical literature using natural language processing (NLP) techniques as well as for their subsequent reuse in protein structure annotation and visualization. This system, called mSTRAP (Mutation extraction and STRucture Annotation Pipeline), is designed for both information aggregation and subsequent brokerage of the mutation annotations. It facilitates the coordination of semantically related information from a series of text mining and sequence analysis steps into a formal OWL-DL ontology. The ontology is designed to support application-specific data management of sequence, structure, and literature annotations that are populated as instances of object and data type properties. mSTRAPviz is a subsystem that facilitates the brokerage of structure information and the associated mutations for visualization. For mutated sequences without any corresponding structure available in the Protein Data Bank (PDB), an automated pipeline for homology modeling is developed to generate the theoretical model. With mSTRAP, we demonstrate a workable system that can facilitate automation of the workflow for the retrieval, extraction, processing, and visualization of mutation annotations -- tasks which are well known to be tedious, time-consuming, complex, and error-prone. The ontology and visualization tool are available at (http://datam.i2r.a-star.edu.sg/mstrap).     

Cytotoxic activity and mechanism of action of metabolites from the Goniothalamus genus

The World Health Organization estimates that 4 billion people or 80 % of the population use plants for curative purposes or for their natural health benefits. Accordingly, biodiversity is an important source of active natural products especially used in traditional medicine as healers transmitted knowledge of traditional usage of medicinal plants from generation to generation whereas pharmacologically active compounds within remained obscure. The present review documents cytotoxicity and anti-cancer potential of known compounds of the Goniothalamus species from the Annonaceae family existing in tropical and subtropical Asia and being intensively used for medicinal purposes.     

Generation of novel monoclonal antibodies for the enrichment and characterization of human corneal endothelial cells (hCENC) necessary for the treatment of corneal endothelial blindness

Corneal transplantation is the primary treatment option to restore vision for patients with corneal endothelial blindness. Although the success rate of treatment is high, limited availability of transplant grade corneas is a major obstacle. Tissue-engineered corneal endothelial grafts constructed using cultivated human corneal endothelial cells (hCENC) isolated from cadaveric corneas may serve as a potential graft source. Currently, tools for the characterization of cultured hCENC and enrichment of hCENC from potential contaminating cells such as stromal fibroblasts are lacking. In this study, we describe the generation and characterization of novel cell surface monoclonal antibodies (mAbs) specific for hCENC. These mAbs could be used for enrichment and characterization of hCENC. Out of a total of 389 hybridomas, TAG-1A3 and TAG-2A12 were found to be specific to the corneal endothelial monolayer by immunostaining of frozen tissue sections. Both mAbs were able to clearly identify hCENC with good ‘cobblestone-like’ morphology from multiple donors. The antigen targets for TAG-1A3 and TAG-2A12 were found to be CD166/ALCAM and Peroxiredoxin-6 (Prdx-6), respectively, both of which have not been previously described as markers of hCENC. Additionally, unlike other Prdx-6 mAbs, TAG-2A12 was found to specifically bind cell surface Prdx-6, which was only expressed on hCENC and not on other cell types screened such as human corneal stromal fibroblasts (hCSF) and human pluripotent stem cells (hPSC). From our studies, we conclude that TAG-1A3 and TAG-2A12 are promising tools to quantitatively assess hCENC quality. It is also noteworthy that the binding specificity of TAG-2A12 could be used for the enrichment of hCENC from cell mixtures of hCSF and hPSC.     

Island Waste Management Systems

Island waste management professionals are faced with limited land resources, high energy costs, large seasonal fluctuations in waste volumes, and complex social and political dynamics that stem from their often closely knit societies. These and other factors can discourage typical waste management practices, but they also provide opportunities for island governments and businesses to explore alternative technologies and policies that suit their particular circumstances and that might be environmentally preferable. This critical review discusses the waste management literature on islands to date, including several industrial ecology (IE) studies. Common advantages and disadvantages faced by island waste management challenges are presented from the perspectives of business and municipal management. Waste generation data are presented from more than 40 islands around the world and tested for correlation with economic and geographic parameters and using cluster analysis, with the aim of identifying trends among island types. Poor data quality and comparability are ongoing challenges that underscore the potential benefits of a consistent program of island waste management data collection. Finally, the review explores opportunities for applying IE research to generate useful insights and policies in the areas of material flow analysis, industrial symbiosis, life cycle assessment, and social ecology.     

Expression of recombinant anti‐breast cancer immunotherapeutic monoclonal antibody in baculovirus–insect cell system

The anti‐breast cancer monoclonal antibody (mAb) BR55 was expressed in the baculovirus–insect cell expression system, which is advantageous because of its high production capacity, cell culture flexibility and glycosylation capability. The baculovirus–insect cell expression system was successfully established for production of mAb BR55 and mAb BR55 fused with the KDEL (Lys–Asp–Glu–Leu) endoplasmic reticulum (ER) retention signal (mAb BR55K). The heavy chain (HC) and light chain (LC) genes of mAb BR55 were cloned under the control of the polyhedrin (P_PH) and P₁₀ promoters, respectively, in the pFastBacDual vector. The antibody gene‐expression cassettes carrying both the HC and LC genes were transferred into a bacmid in Escherichia coli (DH10Bac). The bacmid carrying the expression cassettes was transfected into Sf9 insect cells to generate baculovirus expressing mAb BR55 and BR55K. Western blot analysis confirmed the expression of mAb BR55 and BR55K in baculovirus‐infected insect cells. Cell direct enzyme linked immunosorbent assay (ELISA) showed that both mAbs from insect cell lysates or cell culture medium bound to MCF‐7 human breast cancer cells. Both mAb BR55 and BR55K were successfully purified using a Protein A affinity column. Collectively, these results suggest that the anti‐breast cancer mAb BR55 can be expressed, properly assembled and purified from the baculovirus expression system, which can serve as an alternative system for antibody production.     

Cumulative Sum Analysis for Experiences of a Single-Session Retrograde Intrarenal Stone Surgery and Analysis of Predictors for Stone-Free Status

Introduction

This study investigated the learning curve of a single-session retrograde intrarenal surgery (RIRS) in patients with mid-sized stones. Competence and trainee proficiency for RIRS was assessed using cumulative sum analysis (CUSUM).

Materials and Methods

The study design and the use of patients'' information stored in the hospital database were approved by the Institutional Review Board of our institution. A retrospective review was performed for 100 patients who underwent a single-session RIRS. Patients were included if the main stone had a maximal diameter between 10 and 30 mm. The presence of a residual stone was checked on postoperative day 1 and at one-month follow-up visit. Fragmentation efficacy was calculated “removed stone volume (mm³) divided by operative time (min)”. CUSUM analysis was used for monitoring change in fragmentation efficacy, and we tested whether or not acceptable surgical outcomes were achieved.

Results

The mean age was 54.7±14.8 years. Serum creatinine level did not change significantly. Estimated GFR and hemoglobin were within normal limits postoperatively. The CUSUM curve tended to be flat until the 25th case and showed a rising pattern but declined again until the 56th case. After that point, the fragmentation efficacy reached a plateau. The acceptable level of fragmentation efficacy was 25 ml/min. Multivariate logistic regression analyses showed that stone-free rate was significantly lower for cases with multiple stones than those with a single stone (OR = 0.147, CI 0.032 – 0.674, P value  = 0.005) and for cases with higher number of sites (OR = 0.676, CI 0.517 – 0.882, P value  = 0.004).

Conclusions

The statistical analysis of RIRS learning experience revealed that 56 cases were required for reaching a plateau in the learning curve. The number of stones and the number of sites were significant predictors for stone-free status.     

Effects of age,replicative lifespan and growth rate of human nucleus pulposus cells on selecting age range for cell-based biological therapies for degenerative disc diseases

Autologous disc cell implantation, growth factors and gene therapy appear to be promising therapies for disc regeneration. Unfortunately, the replicative lifespan and growth kinetics of human nucleus pulposus (NP) cells related to host age are unclear. We investigated the potential relations among age, replicative lifespan and growth rate of NP cells, and determined the age range that is suitable for cell-based biological therapies for degenerative disc diseases. We used NP tissues classified by decade into five age groups: 30s, 40s, 50s, 60s and 70s. The mean cumulative population doubling level (PDL) and population doubling rate (PDR) of NP cells were assessed by decade. We also investigated correlations between cumulative PDL and age, and between PDR and age. The mean cumulative PDL and PDR decreased significantly in patients in their 60s. The mean cumulative PDL and PDR in the younger groups (30s, 40s and 50s) were significantly higher than those in the older groups (60s and 70s). There also were significant negative correlations between cumulative PDL and age, and between PDR and age. We found that the replicative lifespan and growth rate of human NP cells decreased with age. The replicative potential of NP cells decreased significantly in patients 60 years old and older. Young individuals less than 60 years old may be suitable candidates for NP cell-based biological therapies for treating degenerative disc diseases.     

Molecular modeling of cornulin (CRNN) for docking with phytocompounds from Justicia adhatoda L.

Cornulin (CRNN) is linked with tumour progression. Therefore, it is of interest to document data on the molecular modeling of cornulin (CRNN) for docking with phytocompounds (Pyrazinamide, Anisotine, Vasicinone, Vasicoline) from Justicia adhatoda L. Thus, we document the optimal binding features of these compounds with the cornulin model for further consideration.     

Molecular docking analysis of SARS-CoV-2 linked RNA dependent RNA polymerase (RdRp) with compounds from Plectranthus amboinicus

It is of interest to document the moelcular docking analysis of SARS-CoV-2 linked RNA dependent RNA polymerase (RdRp) with compounds from Plectranthus amboinicus. Hence, we report the binding features of rutin, Luteolin, Salvianolic acid A, Rosmarinic acid and p-Coumaric acid with the target protein SARS-CoV-2 linked RNA dependent RNA polymerase (RdRp) for further consideration.