Research Perspectives of Microbiology and Biotechnology Vol. 4

Dental caries is a highly prevalent microbial chronic dental disease that affects a greater portion of the world’s population. Saliva surrounding the oral cavity's soft and hard tissues contains both organic and inorganic components, some of which are important contributors to the host's caries development, Saliva has shown great promise as a diagnostic fluid because, unlike blood or other bodily fluids, it contains a large number of diseases indicators. Saliva contains most of the enzymes that aid in metabolism. There are important enzymes associated with cell injury and cell death like salivary enzymes which play an important role in caries demineralization and remineralization. This review highlights the salivary alpha-amylase, alkaline phosphatase, and protease enzyme actions in early childhood caries and prevention.

Cellulose is the largest waste component, thus creating a serious pollution problem. Anaerobic bacteria producing cellulases have not been extensively studied though they are the efficient producers of cellulase. The anaerobic cellulolytic bacterium, Clostridium papyrosolvens was isolated from a consortium developed in the laboratory from the compost sample collected in the surroundings of Mysore, Karnataka, India. Clostridium papyrosolvens CFR-1010, an anaerobic cellulolytic bacterial strain was identified as a potent cellulase producer and selected for the purification and kinetic studies of Exo-\(\beta\)-1,4-glucanase and Endo-\(\beta\)-1,4- glucanase. The molecular masses of the enzymes were 65 and 60 kDa, respectively. The enzymes showed maximum activities at pH 5.0 and at a temperature of 50^oC. The activities increased in the presence of MnCl₂, whereas, N-bromosuccinimide decreased enzyme activities by 68 and 75% respectively, thus suggesting the presence of tryptophan residues at the active sites of enzymes. Exoglucanase had a Km of 20 mg/ml and Vmax of 22 units/min/mg of protein whereas the endoglucanase exhibited a Km of 6.66mg/ml and Vmax of 11.76 units/min/mg of protein. Results of the present studies suggest the use of C. papyrosolvens for cellulase production in shorter periods of time and they also add significance for the exploration of this organism for industrial applications. The exo \(\beta\)-1,4-glucanse and endo-\(\beta\)-1,4-glucanase from C. papyrosolvens CFR-1010 are applicable for the biodegradation of cellulosic wastes which can be used in the biogas digesters and for the commercial production of glucose or various other fermentation products.

The Present study proposes to look for RT-PCR cycle threshold correlation with positive Rapid COVID-19 LFA results and the ability of LFAs to be used as a proxy, inexpensive marker of infectiousness in mass settings given the present global post-pandemic scenario. Lateral flow antigen assays (LFA) are a quick and affordable way to detect COVID-19 in healthcare settings with limited infrastructure. Rapid diagnostic tests are essential for early, timely case identification that allows for supportive care and patient isolation. In light of the COVID-19 pandemic, molecular testing is still an expensive endeavor. Moreover, residual RNA cannot be distinguished from replication-competent viruses using molecular techniques. The present study is a retrospective cross-sectional hospital-based study of 1.25 years duration (September 2020- January 2022). Rapid COVID-19 LFA results were compared with Real-time PCR for detection of SARS-CoV-2 in nasopharyngeal swabs. Two hundred rapid antigen-positive nasopharyngeal swabs obtained from COVID-19 suspects/contacts/preoperative/ screening patients were subjected to RT-PCR to study the correlation with cycle threshold (CT) values obtained for all the antigen-positive cases. 200 Rapid COVID-19 LFA-positive samples were analysed in the present study. Amidst the LFA-positive samples included in the study 187 (93.5%) were found to have concordant results when subjected to the gold-standard Real-time PCR. Discordant results were documented in 13 (6.5%) COVID-19 LFA-positive samples which were found to be negative by RT-PCR. The average Cycle threshold values were found to be 23.75 for the E gene, 25.36 for the N gene and 24.07 for RdRp gene. The average PCR Cycle threshold of LFA positive cases remained significantly undeterred (p<0.5) throughout the time period of the study stipulating the undaunted viral load across the different waves of the pandemic. Maximum association of LFA positivity with symptom manifestation was seen during the 1st wave of COVID-19 (September-December 2020 in India). The association of symptoms with LFA test positivity reduced to a significant extent during the 3rd wave of the pandemic in January 2022 (p<0.5) indicating the reduced clinical severity but not infectivity of the SARS-CoV-2 infection during the 3rd wave of the pandemic. When compared to RT-PCR, lateral flow assay-based diagnostic techniques are more economically and technically convenient while maintaining a high degree of concordance. These tests offer a clear benefit in terms of expediting patient triage and, consequently, improving patient management. RT-PCR being highly sensitive assay can aid diagnosis in patients with low viral load and seems superior than the LFA which requires a higher vial load for positivity. Considering the above factors SARS-CoV-2 LFAs find utility as proxy infectivity indicating modalities for rapid triaging and patient management.

The present study evaluates the prevalence and trends of Achromobacter xylosoxidans in clinical specimens and the trend in its sensitivity pattern. Achromobacter xylosoxidans is an emerging nosocomial pathogen that is commonly found in the environment. It may lead to nosocomial infections in hospital settings, particularly in the intensive care unit. It is frequently identified in humidifiers in intensive care units and is also frequently linked to patients who have several comorbidities and are immunocompromised. The Retrospective analysis was done of the culture reports positive for Achromobacter xylosoxidans by VITEK 2 method and its Antimicrobial sensitivity pattern was analysed from period of September 2021 to February 2023. The maximum (54.54%) infection was seen in the age group >50 years. The maximum number (66.2%) of Achromobacter xylosoxidans were isolated from the Suction tip, followed by blood (8%) and the Tracheal Tip (5%). Surgical ICU contributed to the maximum number of infections i.e. 40.2%, followed by Respiratory ICU (22.1%). Maximum sensitivity was seen for Cotrimoxazole and Meropenem (around 80%), followed by Cefoperazone-Sulbactam (74%), Imipenem, Levofloxacin, Ceftazidime (around 65%). The sensitivity was minimal for Ceftriaxone (0%), Aztreonam (1.3%), and Gentamicin (5.2%). The most common risk factors/comorbidities associated with Achromobacter infections was recent ICU admission (87.01%). The variation in antibiotic sensitivity or resistance can be due to the various factors like antibiotics used in patients in primary treatment, the immune status of the patients from which the sample was collected, overuse or misuse of antibiotics, availability of antibiotics, etc. The antibiotic of choice in our conclusion is Cotrimoxazole, followed by Piperacillin-Tazobactam. Colistin should be kept as a reserve drug for the last resort treatment.

Serendipita indica is a cultivable endophyte that holds a broad host spectrum and possesses exceptional multifunctional capabilities to promote plant performance by enhancing growth, protection and stress tolerance. S. indica confers resistance to heavy metals, toxins and pathogens, it acts as a biopesticide, bioprotectant and biofertilizer by enhancing secondary metabolite production which results in early seed germination and flowering. This easily cultivable fungus shows beneficial plant-microbe interaction and acts as a powerful tool in improving plant growth by combatting environmental stresses. Symbiotic association of S. indica, with cereal crops helps plants to develop a variety of defence mechanisms by causing major morphological and physiological changes which promote plant growth and confers resistance to biotic and abiotic stresses. Heavy metal, drought, and salinity stress are among the severe environmental constraints to our modern agriculture which badly affect crop productivity in terms of growth and yield. To deal with such abiotic stress, this fungus helps plants to undergo host-specific modulations including gene alteration, activation of antioxidant activities, changes in photosynthetic activities, formation of rhizosheath, etc. for an enhancement in yield and growth of the plant. The current study exploited the effectiveness of S. indica against abiotic stress to ameliorate tolerance in plants.

The study presents a comprehensive assessment of plant-sourced natural compounds for wound healing, encompassing their chemical origins and the biological processes involved in their therapeutic effects on wound healing. Wound healing involves multiple stages, and any interruption during this sequence can result in improper wound healing. Restoration of the structure and function of damaged tissues, which is an intricate process, is governed by the discharge of multiple cytokines and growth factors at the site of injury. Wound healing may benefit greatly from a variety of plants or compounds derived from plants with high concentrations of antioxidants as well as anti-inflammatory, immunomodulatory, and antibacterial properties.

2,5-diketocamphane 1,2-monooxygenase (2,5-DKCMO) and 3,6-diketocamphane 1,6-monooxygenase (3,6-DKCMO) isolated from camphor-grown Pseudomonas putida ATCC 17453, are key enantio complementary ketolactonases that promote the initial ring cleavage of the two antipodes of this natural bicyclic terpene. Their initial characterization over sixty years ago represented a seminal discovery, being the first confirmed examples of enzyme-catalysed Baeyer-Villiger oxidations. Interestingly, over the last six decades, the perceived functional nature of these oxygen-dependent biocatalysts has transmogrified significantly. Extensive studies that commenced in the mid-1960s consistently reported that the enzymes were monomeric true flavoproteins dependent on both FMNH₂ and nonheme iron as bound cofactors. The role of the metal ion, in cooperation with the flavin, was considered to be essential for the activation of molecular oxygen. However, all of those criteria have been changed absolutely by subsequent studies, resulting in the enzymes currently being acknowledged to be metal ion-independent homodimeric flavin-dependent two-component monooxygenases deploying FMNH₂ not as a bound cofactor, but rather as a distinct cosubstrate.  That transition is a paradigm that serves to illustrate the constantly evolving nature of scientific knowledge.

Cancer is a major cause of death worldwide and angiogenesis is critical in cancer progression. The development of new blood vessels and the nutrition of tumor cells are heavily dependent on angiogenesis. Angiogenesis is the formation of new blood vessels from existing vasculature. In normal physiology, angiogenesis has a role in embryogenesis, the female reproductive cycle, and wound healing and bone formation [1]. There are several “on” and “off” switches that regulate the process. Decreasing or inhibiting angiogenesis can be therapeutic in cancer and other diseases. Thus, angiogenesis is an important process that occurs both during health and disease. This study was conducted to investigate the anti-angiogenic activity of Carica papaya leaf. Fresh green papaya leaves, were randomly collected from Yadav Nursery, Geeta Colony, East Delhi. The anti-angiogenic activity of papaya leaf was evaluated using the docking behaviour of known bioactive compounds of a leaf as ligands with angiogenic receptors VEGFR1 and VEGFR2 along with their putative binding sites using Swiss Dock Web server (In silico) and further based on docking results leaf aqueous extract was used for implantation in the chorioallantoic membrane (CAM) egg yolk angiogenesis model (in vivo). Docking studies and binding free energy calculations revealed that among known bioactive compounds of leaf Ascorbic acid, quercetin, riboflavin and lycopene have maximum free energy as compared to other investigated ligands. Similarly, CAM assay also showed the inhibitory effect of the Carica papaya leaf with respect to their reduction in length, size and junctions of blood capillaries compared to untreated egg yolk. The results showed that Ascorbic Acid, Quercetin, Riboflavin and, Lycopene (leaf compounds) can attenuate angiogenesis in pathological conditions and can be potent in drug discovery as well as medical science. Further studies need to be conducted to determine anti-angiogenic pathways followed by leaf extract or juice. It can be concluded that administration of Carica papaya leaf juice is safe and does induce anti angiogenic process during disease condition like Cancer.

This study aimed to analyze the amino acid of OmpA and Rz/Rz1 of lytic bacteriophage from Surabaya, Indonesia. Porines are a type of \(\beta\)-barrel proteins with diffuse channels and OmpA, which has a role in hydrophilic transport, is the most frequent porin in E. coli, it was also chosen as the potential receptor of the phage. Some bacteriophages pierce the bacterial cell wall with their "needles" by a mechanical mechanism, like a syringe, to facilitate their entry. Without endangering the cell's ability to survive, bacteriophages employ the enzymes in their tails. On the other hand, the Rz/Rz1 protein frequently causes significant bacterial cell wall disintegration as part of the mechanism for the release of progeny virions from infected bacteria, which results in host cell lysis. This study employed a sample of 8 bacteriophages from the previous study. The OmpA analysis method was Mass Spectrometry. Analyzed Rz/Rz1 using PCR, DNA sequencing, Expasy Translation, and Expasy Protparam. The result obtained 10% to 29% sequence coverage of OmpA, carrying the ligand binding site. The Rz/Rz1 gene shares a high percentage of 97.04% to 98.89% identities with the Siphoviridae isolate ctTwQ4, partial genome, and Myoviridae isolate cthRA4, partial genome. The Mann Whitney statistical tests indicate the significant differences between Alanine, Aspartate, Glycine, Proline, Serine (p = 0.011), Asparagine, Cysteine (p = 0.009), Isoleucine (p = 0.043), Lysine (p = 0.034), Methionine (p = 0.001), Threonine (p = 0.018), and Tryptophane (p = 0.007) of OmpA and Rz/Rz1. The conclusion obtained from this study is OmpA acts as Phage 1, Phage 2, Phage 3, Phage 5, and Phage 6 receptor for its peptide composition comprising the ligand binding site, and Rz/Rz1 participate in host bacteria lysis. The Rz/Rz1 specialized machinery is triggered to break down the cell walls of bacteria in order to achieve this goal. This mixture may have the ability to lyse and eradicate bacterial strains, which could result in the creation of novel narrow- spectrum antibiotics.

Understanding the process of formation of the complexes between Spike protein variants that make up the structure of the SARS-CoV2 virus and human antibodies, brings light into how variations have an impact on this complex formation. In this work, databases such as CoV3D, PDB and pyDockWEB were used to collect sequencing results and structures of SARS-CoV2 variants. Finally, molecular docking was also used in order to predict the interaction between the virus' Spike protein and antibodies. These results were then made available on a website produced exclusively for public dissemination of these analyses. Among other answers, this work serves as a guideline for molecular docking studies of the interaction between Spike protein variants and human antibodies.

Blue-green algae (cyanobacteria) are considered the most primitive photosynthetic prokaryotes which appeared on this planet during the Precambrian period. The application of cyanobacteria showed immense potential in wastewater and industrial effluent treatment, bioremediation of aquatic and terrestrial habitats,  chemical industries,  biofertilizers, food, feed, and fuel, etc. Spanish local fishermen collected blue-green masses from the lakes that were prepared as a dry cake, known as ‘tecuitlatl’. Spirulina, chlorella and Noctoc cyanobacterial species are being used as food supplements which are full of nutrients such as protein, and vitamins, and also have medicinal values like antiviral, antibacterial, anti-cancerous ECT. Besides, several Cyanobacterial species are also being used as biofertilizers in agriculture, and also for chelating toxic heavy metal ions for removing them from soil which is commonly known as bioremediation of soil pollutants. In viewing the “one platform” solution, nature has provided for all the environmental and medical problems in Cyanobacteria, there is a need to practically implement the use of cyanobacteria in the lives of common man. This chapter not only shades lite on the nutritional but also medicinal values of different species of cyanobacteria but also briefly discussed the new discovery of Exo-polysaccharides (metabolites) of cyanobacteria which are considered as one of the important group of biopolymers having significant ecological, industrial and biotechnological importance. Due to their structural complexity, versatility and valuable biological properties, they are now emerging as high-value compounds. However,  poor understanding of their complex structural properties, and lack of concrete information regarding the genes encoding the proteins involved in the EPS biosynthetic pathways, their process of production and the associated factors controlling their structural stability, strongly limit their commercialization and applications in the various fields of biotechnology.