Institute of Microbial Technology

Klionsky D.J., Abdel-Aziz A.K., Abdelfatah S., Abdellatif M., Abdoli A., Abel S., Abeliovich H., Abildgaard M.H., Abudu Y.P., Acevedo-Arozena A., Adamopoulos I.E., Adeli K., Adolph T.E., Adornetto A., Aflaki E., et. al.

ABSTRACT In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Johnson R., Vishwakarma K., Hossen M.S., Kumar V., Shackira A.M., Puthur J.T., Abdi G., Sarraf M., Hasanuzzaman M.

Potassium (K) is an essential element for the growth and development of plants; however, its scarcity or excessive level leads to distortion of numerous functions in plants. It takes part in the control of various significant functions in plant advancement. Because of the importance index, K is regarded second after nitrogen for whole plant growth. Approximately, higher than 60 enzymes are reliant on K for activation within the plant system, in which K plays a vital function as a regulator. Potassium provides assistance in plants against abiotic stress conditions in the environment. With this background, the present paper reviews the physiological functions of K in plants like stomatal regulation, photosynthesis and water uptake. The article also focuses upon the uptake and transport mechanisms of K along with its role in detoxification of reactive oxygen species and in conferring tolerance to plants against abiotic stresses. It also highlights the research progress made in the direction of K mediated signaling cascades.

Vishwakarma K., Kumar N., Shandilya C., Mohapatra S., Bhayana S., Varma A.

The present scenario of agricultural sector is dependent hugely on the use of chemical-based fertilizers and pesticides that impact the nutritional quality, health status, and productivity of the crops. Moreover, continuous release of these chemical inputs causes toxic compounds such as metals to accumulate in the soil and move to the plants with prolonged exposure, which ultimately impact the human health. Hence, it becomes necessary to bring out the alternatives to chemical pesticides/fertilizers for improvement of agricultural outputs. The rhizosphere of plant is an important niche with abundant microorganisms residing in it. They possess the properties of plant growth promotion, disease suppression, removal of toxic compounds, and assimilating nutrients to plants. Utilizing such beneficial microbes for crop productivity presents an efficient way to modulate the crop yield and productivity by maintaining healthy status and quality of the plants through bioformulations. To understand these microbial formulation compositions, it becomes essential to understand the processes going on in the rhizosphere as well as their concrete identification for better utilization of the microbial diversity such as plant growth–promoting bacteria and arbuscular mycorrhizal fungi. Hence, with this background, the present review article highlights the plant microbiome aboveground and belowground, importance of microbial inoculants in various plant species, and their subsequent interactive mechanisms for sustainable agriculture.

Ali E.S., Sharker S.M., Islam M.T., Khan I.N., Shaw S., Rahman M.A., Uddin S.J., Shill M.C., Rehman S., Das N., Ahmad S., Shilpi J.A., Tripathi S., Mishra S.K., Mubarak M.S.

Nanotechnology is reshaping health care strategies and is expected to exert a tremendous impact in the coming years offering better healthcare facilities. It has led to not only therapeutic drug delivery feasibility but also to diagnostics. Materials in the size of nano range (1-100 nm) used in the design, fabrication, regulation, and application of therapeutic drugs or devices are classified as medical nanotechnology and nanopharmacology. Delivery of more complex molecules to the specific site of action as well as gene therapy has pushed forward the nanoparticle-based drug delivery to its maximum. Areas that benefit from nano-based drug delivery systems are cancer, diabetes, infectious diseases, neurodegenerative diseases, blood disorders and orthopedic-related ailments. Moreover, development of nanotherapeutics with multi-functionalities has a considerable potential to fill the gaps that exist in the present therapeutic domain. In cancer treatment, nanomedicines have superiority over current therapeutic practices as they can effectively deliver the drug to the affected tissues, thus reducing drug toxicities. Along this line, polymeric conjugates of asparaginase and polymeric micelles of paclitaxel have recently been recommended for the treatment of various types of cancers. Nanotechnology-based therapeutics and diagnostics provide greater effectiveness with less or no toxicity concerns. Similarly, diagnostic imaging holds promising future applications with newer nano-level imaging elements. Advancements in nanotechnology have emerged to a newer direction which use nanorobotics for various applications in healthcare. Accordingly, this review comprehensively highlights the potentialities of various nanocarriers and nanomedicines for multifaceted applications in diagnostics and drug delivery, especially the potentialities of polymeric nanoparticle, nanoemulsion, solid-lipid nanoparticle, nanostructured lipid carrier, self-micellizing anticancer lipids, dendrimer, nanocapsule and nanosponge-based therapeutic approaches in the field of cancer. Furthermore, this article summarizes the most recent literature pertaining to the use of nano-technology in the field of medicine, particularly in treating cancer patients.

Chakraborty P., Bajeli S., Kaushal D., Radotra B.D., Kumar A.

Tuberculosis is a chronic disease that displays several features commonly associated with biofilm-associated infections: immune system evasion, antibiotic treatment failures, and recurrence of infection. However, although Mycobacterium tuberculosis (Mtb) can form cellulose-containing biofilms in vitro, it remains unclear whether biofilms are formed during infection in vivo. Here, we demonstrate the formation of Mtb biofilms in animal models of infection and in patients, and that biofilm formation can contribute to drug tolerance. First, we show that cellulose is also a structural component of the extracellular matrix of in vitro biofilms of fast and slow-growing nontuberculous mycobacteria. Then, we use cellulose as a biomarker to detect Mtb biofilms in the lungs of experimentally infected mice and non-human primates, as well as in lung tissue sections obtained from patients with tuberculosis. Mtb strains defective in biofilm formation are attenuated for survival in mice, suggesting that biofilms protect bacilli from the host immune system. Furthermore, the administration of nebulized cellulase enhances the antimycobacterial activity of isoniazid and rifampicin in infected mice, supporting a role for biofilms in phenotypic drug tolerance. Our findings thus indicate that Mtb biofilms are relevant to human tuberculosis. Mycobacterium tuberculosis forms biofilms in vitro, but it is unclear whether biofilms are also formed during infection in vivo. Here, Chakraborty et al. demonstrate the formation of biofilms in animal models of infection and in patients with tuberculosis, and that biofilm formation can contribute to drug tolerance.

Sarraf M., Vishwakarma K., Kumar V., Arif N., Das S., Johnson R., Janeeshma E., Puthur J.T., Aliniaeifard S., Chauhan D.K., Fujita M., Hasanuzzaman M.

In agriculture, abiotic stress is one of the critical issues impacting the crop productivity and yield. Such stress factors lead to the generation of reactive oxygen species, membrane damage, and other plant metabolic activities. To neutralize the harmful effects of abiotic stress, several strategies have been employed that include the utilization of nanomaterials. Nanomaterials are now gaining attention worldwide to protect plant growth against abiotic stresses such as drought, salinity, heavy metals, extreme temperatures, flooding, etc. However, their behavior is significantly impacted by the dose in which they are being used in agriculture. Furthermore, the action of nanomaterials in plants under various stresses still require understanding. Hence, with this background, the present review envisages to highlight beneficial role of nanomaterials in plants, their mode of action, and their mechanism in overcoming various abiotic stresses. It also emphasizes upon antioxidant activities of different nanomaterials and their dose-dependent variability in plants’ growth under stress. Nevertheless, limitations of using nanomaterials in agriculture are also presented in this review.

McCormick E.M., Lott M.T., Dulik M.C., Shen L., Attimonelli M., Vitale O., Karaa A., Bai R., Pineda‐Alvarez D.E., Singh L.N., Stanley C.M., Wong S., Bhardwaj A., Merkurjev D., Mao R., et. al.

Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently, there are insufficient standardized criteria for mtDNA variant assessment, which leads to inconsistencies in clinical variant pathogenicity reporting. An international working group of mtDNA experts was assembled within the Mitochondrial Disease Sequence Data Resource Consortium and obtained Expert Panel status from ClinGen. This group reviewed the 2015 American College of Medical Genetics and Association of Molecular Pathology standards and guidelines that are widely used for clinical interpretation of DNA sequence variants and provided further specifications for additional and specific guidance related to mtDNA variant classification. These Expert Panel consensus specifications allow for consistent consideration of the unique aspects of the mtDNA genome that directly influence variant assessment, including addressing mtDNA genome composition and structure, haplogroups and phylogeny, maternal inheritance, heteroplasmy, and functional analyses unique to mtDNA, as well as specifications for utilization of mtDNA genomic databases and computational algorithms.

Sharma R., Mishra A., Pant D., Malaviya P.

The ability of microalgae to grow in a broad spectrum of wastewaters manifests great potentials for removing contaminants from effluents of industries and urban areas. Since the post-treatment microalgae biomass is also a significant source of high-value products, microalgae-based wastewater treatment is an economical and sustainable solution to wastewater management. Adding more value, the integration of microalgae with living/non-living materials looks more promising. Microalgae-based treatment technology has certain limitations like high operational costs, problematic harvesting, large land requirements, and hindrance in photosynthesis due to turbid wastewater. These challenges need to be essentially addressed to achieve enhanced wastewater remediation. This review has highlighted the potential applications of microalgae in contaminant removal from wastewaters, simultaneous resource recovery, efficient microalgae-based hybrid systems along with bottlenecks and prospects. This state-of-the-art article will edify the role of microalgae in wastewater remediation, biomass valorization for bio-based products, and present numerous possibilities in strengthening the circular bioeconomy.

Gupta R., Kumar A., Kumar S., Pinnaka A.K., Singhal N.K.

• Successfully generated aptamers against E. coli bacterial cells through Cell-SELEX. • Aptamer-nanoprobe based sensitive and selective visual detection assay for E. coli was developed. • Graphene oxide enhances the loading capacity of aptamer on nanoprobe making it more sensitive. • Limit of detection using this nanoprobe was 10 2 cells/mL in Mili Q water and spiked coconut water. • The proposed detection assay was performed in glass capillary to mimic microfluidic channel. E. coli is the most common foodborne bacteria causing illnesses including diarrhea, fever, and death if left undiagnosed and untreated, which makes its detection most important. Traditional detection methods such as culture methods, PCR, or ELISA are time-consuming and require skilled manpower. To overcome the disadvantages of traditional detection methods, a fast, easy, and cost-effective platform is required. ssDNA aptamer is a stable, sensitive, and selective biomolecule used extensively for detection. To provide naked eye visible detection, gold nanoparticles (AuNPs) were used, and to increase the aptamer conjugation, AuNPs were covered with Graphene Oxide. Thus, the overall sensitivity of the designed nanoprobe was also augmented. Therefore, exploiting the properties of gold nanoparticles and graphene oxide, a detection platform with aptamer conjugation has been developed in this study. In the manifestation of E. coli cells, the visible color change was observed from red to blue within an hour incubation. The limit of detection observed visually was 10 2 cells/mL with GO coating and 10 3 cells/mL without GO. The detection limit in real time coconut water samples was also 10 2 cells/mL. This platform was found to be applicable in glass capillary which provides opportunities for making a point of care detection device.

Tripathi D.K., Vishwakarma K., Singh V.P., Prakash V., Sharma S., Muneer S., Nikolic M., Deshmukh R., Vaculík M., Corpas F.J.

Exogenous applications of silicon (Si) can initiate cellular defence pathways to enhance plant resistance to abiotic and biotic stresses. Plant Si accumulation is regulated by several transporters of silicic acid (e.g. Lsi1, Lsi2, and Lsi6), but the precise mechanisms involved in overall Si transport and its beneficial effects remains unclear. In stressed plants, the accumulation of Si leads to a defence mechanism involving the formation of amorphous or hydrated silicic acid caused by their polymerization and interaction with other organic substances. Silicon also regulates plant ionic homeostasis, which involves the nutrient acquisition, availability, and replenishment in the soil through biogeochemical cycles. Furthermore, Si is implicated in modulating ethylene-dependent and jasmonate pathways, as well as other phytohormones, particularly under stress conditions. Crosstalk between Si and phytohormones could lead to improvements in Si-mediated crop growth, especially when plants are exposed to stress. The integration of Si with reactive oxygen species (ROS) metabolism appears to be a part of the signaling cascade that regulates plant phytohormone homeostasis, as well as morphological, biochemical, and molecular responses. This review aims to provide an update on Si interplays with ROS, phytohormones, and other signaling molecules that regulate plant development under stress conditions. • Silicon is beneficial for the plants. • Silicon (Si) can mediate plant growth and development under stress conditions. • Si interplays with reactive oxygen species of plants under stress. • Signaling molecules underpins the beneficial impact of silicon in plants.