Partha Sarathi Das

Bio: Partha Sarathi Das is an academic researcher from Vidyasagar University. The author has contributed to research in topics: Gene & Synonymous substitution. The author has an hindex of 3, co-authored 8 publications receiving 95 citations.

Exploitation of chicken feather waste as a plant growth promoting agent using keratinase producing novel isolate Paenibacillus woosongensis TKB2

Abstract: A potent feather degrading bacterium was isolated from soil and it was identified as Paenibacillus woosongensis TKB2 on the basis of morphological, biochemical and as well as 16S rDNA sequence characteristics. The physico-chemical cultural condition for keratinase (principal feather degrading enzyme) production by the isolate was optimized following OVAT (one variable at a time) protocol. It was found that the bacterium produced highest amount of keratinase at 0.75% (w/v) raw feather as sole substrate, 2% (v/v) inoculums, pH 8.5, incubation temperature 30 °C, 5% (w/v) sodium chloride and other mineral components like 0.05% K 2 HPO 4 , 0.025% MgSO 4 and 0.02% CaCO 3 (w/v). The filter sterilized fermented hydrolysate has the ability to promote significantly the germination of seeds (germination rate 87.5%) and growth of Bengal gram ( Cicer arietinum ) seedlings. It induces the nodule formation (3 fold) and increased soil fertility by altering N, P, K and the C/N ratio by 1.2 fold. This also enhanced the quantity of free living nitrogen fixers (2 fold) and phosphate solubilizers (5.8 fold) in comparison to the control soil. Thus the enzymatic feather hydrolysate can be exploited as a useful biological fertilizer in future.

A model to predict the function of hypothetical proteins through a nine-point classification scoring schema.

Abstract: Hypothetical proteins [HP] are those that are predicted to be expressed in an organism, but no evidence of their existence is known. In the recent past, annotation and curation efforts have helped overcome the challenge in understanding their diverse functions. Techniques to decipher sequence-structure-function relationship, especially in terms of functional modelling of the HPs have been developed by researchers, but using the features as classifiers for HPs has not been attempted. With the rise in number of annotation strategies, next-generation sequencing methods have provided further understanding the functions of HPs. In our previous work, we developed a six-point classification scoring schema with annotation pertaining to protein family scores, orthology, protein interaction/association studies, bidirectional best BLAST hits, sorting signals, known databases and visualizers which were used to validate protein interactions. In this study, we introduced three more classifiers to our annotation system, viz. pseudogenes linked to HPs, homology modelling and non-coding RNAs associated to HPs. We discuss the challenges and performance of these classifiers using machine learning heuristics with an improved accuracy from Perceptron (81.08 to 97.67), Naive Bayes (54.05 to 96.67), Decision tree J48 (67.57 to 97.00), and SMO_npolyk (59.46 to 96.67). With the introduction of three new classification features, the performance of the nine-point classification scoring schema has an improved accuracy to functionally annotate the HPs.

Systems Challenges of Hepatic Carcinomas: A Review

Abstract: Hepatocellular Carcinoma (HCC) is ubiquitous in its prevalence in most of the developing countries. In the era of systems biology, multi-omics has evinced an extensive approach to define the underlying mechanism of disease progression. HCC is a multifactorial disease and the investigation of progression of liver cirrhosis becomes much extensive with cultivating omics approaches. We have performed a comprehensive review about such challenges in multi-omics approaches that are concerned to identify the immunological, genetics and epidemiological factors associated with HCC.

Data Mining and Pattern Recognition Models for Identifying Inherited Diseases: Challenges and Implications.

Abstract: Data mining and pattern recognition methods reveal interesting findings in genetic studies, especially on how the genetic makeup is associated with inherited diseases. Although researchers have proposed various data mining models for biomedical approaches, there remains a challenge in accurately prioritizing the single nucleotide polymorphisms (SNP) associated with the disease. In this commentary, we review the state-of-art data mining and pattern recognition models for identifying inherited diseases and deliberate the need of binary classification- and scoring-based prioritization methods in determining causal variants. While we discuss the pros and cons associated with these methods known, we argue that the gene prioritization methods and the protein interaction (PPI) methods in conjunction with the K nearest neighbors' could be used in accurately categorizing the genetic factors in disease causation.

HYPO: A Database of Hypothetical Human Proteins

Abstract: All annotated genes were once hypothetical or uncharacterized. Keeping this as an epilogue, we have enhanced our former database of hypothetical proteins (HP) in human (HypoDB) with added annotation, application programming interfaces and descriptive features. The database hosts 1000+ manually curated records of the known ‘unknown’ regions in the human genome. The new updated version of HypoDB with functionalities (Blast, Match) is freely accessible at http://www.bioclues.org/hypo2.

Feather degradation by keratinolytic bacteria and biofertilizing potential for sustainable agricultural production.

Abstract: Feathers account for 5-7% of the total weight of chicken have become one of the major pollutants due to their recalcitrant nature. Feather which is constituted of 90% keratin can be a good source of peptides, amino acids, and minerals for use as organic fertilizer. Traditional feather degradation methods consume large amount of energy and reduces the overall quality of the proteins. However, degradation of keratin by keratinolytic bacteria may represent as an alternative for the development of cheap, cost effective, eco-friendly, and easily available nitrogen (N) and minerals rich source as potential organic fertilizers. Keratinase enzymes from bacteria are serine-type proteases showing optimal activity at pH 6 to 9 and 30 to 50 °C. Mechanism of degradation includes, sulfitolysis, proteolysis, followed by deamination. Keratinolytic bacteria showing antagonism against important plant pathogens may act as biocontrol agent. Feather hydrolyzate can also be employed as nitrogenous fertilizers for plant growth. Tryptophan release from the feather degradation can act as precursor for plant phytohormone, indole-3-acetic acid (IAA). Solubilization of inorganic phosphate (P) by keratinolytic bacteria may further elevate the growth of plant. Application of hydrolyzate increases the water holding capacity, N, carbon (C) and mineral content of the soil. It elevates protein, amino acids, and chlorophyll content of plant. Feather hydrolyzate enhances seed germination and growth of plant. Soil application further increases the population of beneficial bacteria. The use of keratinolytic bacteria having antagonistic and plant growth promoting activities, and feather hydrolyzate can emerge as sustainable and alternative tools to promote and improve organic farming, agro-ecosystem, environment, human health, and soil biological activities.

Isolation, characterization and valorizable applications of fish scale collagen in food and agriculture industries

Abstract: Collagen has enormous applications in food, biomedical and pharmaceutical industries; but its high cost severely limits its use. Fish processing waste is a promising and cost efficacious source of collagen, which otherwise stated as an earnest environmental pollutant. Carp (Cyprinus carpio) is one of the main species of freshwater fish consumed in India. Acid-soluble collagen (ASC) was isolated from scales of Cyprinus carpio. Scales were demineralized by EDTA treatment and ASC was extracted from the demineralized scales. The yield of scale ASC was 9.79% (on the wet weight basis). SDS–PAGE and FTIR corroborated the isolated protein as collagen. Denaturation temperature (Td) of isolated collagen was found to be 37 °C. Considering bioactive properties of collagen, a milk based food product – paneer was developed by incorporation of the extracted collagen. Composed paneer was found to be acceptable with good sensorial and textural attributes. Same scales were further treated enzymatically and the released metabolites were tested for their competency to promote the plant growth. Released metabolites showed excellent plant growth promotion and hence could be successfully employed as an economic source of nitrogen fertilizers for plants.

Progress in Microbial Degradation of Feather Waste

Abstract: Feathers are a major by-product of the poultry industry. They are mainly composed of keratins which have wide applications in different fields. Due to the increasing production of feathers from poultry industries, the untreated feathers could become pollutants because of their resistance to protease degradation. Feathers are rich in amino acids, which makes them a valuable source for fertilizer and animal feeds. Numerous bacteria and fungi exhibited capabilities to degrade chicken feathers by secreting enzymes such as keratinases, and accumulated evidence shows that feather-containing wastes can be converted into value-added products. This review summarizes recent progress in microbial degradation of feathers, structures of keratinases, feather application, and microorganisms that are able to secrete keratinase. In addition, the enzymes critical for keratin degradation and their mechanism of action are discussed. We also proposed the strategy that can be utilized for feather degradation. Based on the accumulated studies, microbial degradation of feathers has great potential to convert them into various products such as biofertilizer and animal feeds.