Background. Next‐generation sequencing methods have been developed and proposed to investigate any query in genomics or clinical activity involving DNA. Technical advancement in these sequencing methods has enhanced sequencing volume to several billion nucleotides within a very short time and low cost. During the last few years, the usage of the latest DNA sequencing platforms in a large number of research projects helped to improve the sequencing methods and technologies, thus enabling a wide variety of research/review publications and applications of sequencing technologies. Objective. The proposed study is aimed at highlighting the most fast and accurate NGS instruments developed by various companies by comparing output per hour, quality of the reads, maximum read length, reads per run, and their applications in various domains. This will help research institutions and biological/clinical laboratories to choose the sequencing instrument best suited to their environment. The end users will have a general overview about the history of the sequencing technologies, latest developments, and improvements made in the sequencing technologies till now. Results. The proposed study, based on previous studies and manufacturers’ descriptions, highlighted that in terms of output per hour, Nanopore PromethION outperformed all sequencers. BGI was on the second position, and Illumina was on the third position. Conclusion. The proposed study investigated various sequencing instruments and highlighted that, overall, Nanopore PromethION is the fastest sequencing approach. BGI and Nanopore can beat Illumina, which is currently the most popular sequencing company. With respect to quality, Ion Torrent NGS instruments are on the top of the list, Illumina is on the second position, and BGI DNB is on the third position. Secondly, memory‐ and time‐saving algorithms and databases need to be developed to analyze data produced by the 3rd‐ and 4th‐generation sequencing methods. This study will help people to adopt the best suited sequencing platform for their research work, clinical or diagnostic activities.
6 October 2021 in IEEE/ACM Transactions on Computational Biology and Bioinformatics
Parkinson's disease is the second most common progressive neurodegenerative movement disorder. Mutations in retromer complex subunit and VPS35 represent the second most common cause of late-onset familial Parkinson's disease. The mutation in VPS35 can disrupt the normal protein functions resulting in Parkinson's disease. The aim of this study was the identification of deleterious missense Single Nucleotide Polymorphisms (nsSNPs) and their structural and functional impact on the VPS35 protein. In this study, several insilico tools were used to identify deleterious and disease-associated nsSNPs. 3D structure of VPS35 protein was constructed through MODELLER 9.2, normalized using FOLDX, and evaluated through RAMPAGE and ERRAT whereas, FOLDX was used for mutagenesis. 25 ligands were obtained from literature and docked using PyRx 0.8 software. Based on the binding affinity, five ligands i.e., PG4, MSE, GOL, EDO, and CAF were further analyzed. Molecular Dynamic simulation analysis was performed using GROMACS 5.1.4, where temperature, pressure, density, RMSD, RMSF, Rg, and SASA graphs were analyzed. The results showed that the mutations Y67H, R524W, and D620N had a structural and functional impact on the VPS35 protein. The current findings will help in appropriate drug design against the disease caused by these mutations in a large population using in-vitro study.pk M. T. Pervaiz is a co-corresponding author. # Authors have an equal contribution.
Parthenium hysterophorus has been used to cure cancer, fever, malaria, diarrhea, dysentery, and neurologic disorders. This study evaluates the anti-diabetic effects of methanolic extract of P. hysterophorus (MEPH) in alloxan-induced diabetic rabbits. Twenty-five rabbits were divided into 5groups (N=5). Group-I served as a negative control. Groups II to V were injected with freshly prepared alloxan solution 150 mg/kg intraperitoneally to induce diabetes. Group II till V received following treatments orally: Group II: Alloxan 150 mg/kg alone; group III: Alloxan + MEPH (50 mg/kg); group IV: Alloxan + MEPH (100 mg/kg); group V: Alloxan +Glucophage (62.5 mg/kg), respectively for 10 days. The body weight of all animals was recorded on the 1st, 4th, 7th and 10th days. Short-term (1st, 3rd, 5th and 7th hour) and long-term (4th, 7th and 10th day) hypoglycemic effects were also recorded. All animals were sacrificed on the 10th day to isolate the pancreas for histopathological examination. The results showed that MPEH reduced the blood glucose levels in all the groups of alloxan-induced diabetic rabbits. The histopathological studies depicted that 100 mg/kg of MEPH most effectively repaired alloxan-induced pancreatic damage. The study showed that the MPEH is useful for developing effective phytomedicine to treat diabetes mellitus.