Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source "Turkish DeLight".

X-ray crystallography is a robust and powerful structural biology technique that provides high-resolution atomic structures of biomacromolecules. Scientists use this technique to unravel mechanistic and structural details of biological macromolecules (e.g., proteins, nucleic acids, protein complexes, protein-nucleic acid complexes, or large biological compartments). Since its inception, single-crystal cryocrystallography has never been performed in Türkiye due to the lack of a single-crystal X-ray diffractometer. The X-ray diffraction facility recently established at the University of Health Sciences, Istanbul, Türkiye will enable Turkish and international researchers to easily perform high-resolution structural analysis of biomacromolecules from single crystals. Here, we describe the technical and practical outlook of a state-of-the-art home-source X-ray, using lysozyme as a model protein. The methods and practice described in this article can be applied to any biological sample for structural studies. Therefore, this article will be a valuable practical guide from sample preparation to data analysis.

Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source.

High-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish light source (Turkish DeLight). The complete dataset was collected in 18.5 min with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.

Study on active capacity and detergent application potential of low-temperature alkaline serine protease produced by new strain Exiguobacterium indicum 1.2.3.

Microorganisms have long captivated researchers for their potential to produce enzymes with diverse industrial applications. Efficient production of proteases from new strains is crucial as these enzymes play a vital role in breaking down protein bonds, enabling their use in industrial applications. Therefore, a novel Exiguobacterium indicum 1.2.3 was isolated (Istanbul, Turkiye) and characterized in this study. This strain produced alkaline serine protease, which works in lower temperatures (20-40 °C) with casein as a specific substrate. The protease was utterly stable for 3 h at 30 °C. The enzyme was also highly stable in the pH range of 8-11. The optimum activity was obtained at pH 10. The crude enzyme activity was enhanced by various metal ions and retained 147%, 125%, 124%, and 117% of its activity within 1 mM Ca2+, Mn2+, Cu2+, and Mg2+, respectively. The crude enzyme was inactive with phenylmethylsulfonyl fluoride, indicating a serine residue on the active side. The enzyme exhibited a significant proteolytic effect in the presence of surfactants and oxidizing agents. The addition of Tween 80, Triton X-100, and sodium perborate improved enzymatic activity up to 135%, 109%, and 105%, respectively. According to the washing results, the crude enzyme effectively removed the blood on different types of standard pre-stained textiles at 30 °C. In conclusion, Exiguobacterium indicum 1.2.3 is a promising candidate for protease production, with its diverse applications spanning various industrial sectors, particularly detergents.

Potential of nanobiosensor in sustainable agriculture: the state-of-art.

A rapid surge in world population leads to an increase in worldwide demand for agricultural products. Nanotechnology and its applications in agriculture have appeared as a boon to civilization with enormous potential in transforming conventional farming practices into redefined farming activities. Low-cost portable nanobiosensors are the most effective diagnostic tool for the rapid on-site assessment of plant and soil health including plant biotic and abiotic stress level, nutritional status, presence of hazardous chemicals in soil, etc. to maintain proper farming and crop productivity. Nanobiosensors detect physiological signals and convert them into standardized detectable signals. In order to achieve a reliable sensing analysis, nanoparticles can aid in signal amplification and sensor sensitivity by lowering the detection limit. The high selectivity and sensitivity of nanobiosensors enable early detection and management of targeted abnormalities. This study identifies the types of nanobiosensors according to the target application in agriculture sector.

Draft Genome Sequence of an Endophytic Micromonospora sp. Strain, ANENR4, Isolated from the Root of a Peanut Plant (Arachis hypogaea).

The genus Micromonospora was found to occur in a diverse range of habitats. Here, we report the genome sequence of an endophytic strain of Micromonospora sp., ANENR4. ANENR4 was isolated from the healthy roots of a peanut (Arachis hypogaea) plant from Egra, West Bengal, India.

Antimicrobial potential of a ponericin-like peptide isolated from Bombyx mori L. hemolymph in response to Pseudomonas aeruginosa infection.

The main effectors in the innate immune system of Bombyx mori L. are antimicrobial peptides (AMPs). Here, we infected B. mori with varied inoculum sizes of Pseudomonas aeruginosa ATCC 25668 cells to investigate changes in morpho-anatomical responses, physiological processes and AMP production. Ultraviolet-visible spectra revealed a sharp change in λmax from 278 to 285 nm (bathochromic shift) in the hemolymph of infected B. mori incubated for 24 h. Further, Fourier Transform InfraRed studies on the hemolymph extracted from the infected B. mori showed a peak at 1550 cm-1, indicating the presence of α-helical peptides. The peptide fraction was obtained through methanol, acetic acid and water mixture (90:1:9) extraction, followed by peptide purification using Reverse Phase High Performance Liquid Chromatography. The fraction exhibiting antibacterial properties was collected and characterized by Matrix-Assisted Laser Desorption/Ionization-Time of Flight. A linear α-helical peptide with flexible termini (LLKELWTKMKGAGKAVLGKIKGLL) was found, corresponding to a previously described peptide from ant venom and here denominated as Bm-ponericin-L1. The antibacterial activity of Bm-ponericin-L1 was determined against ESKAPE pathogens. Scanning electron microscopy confirmed the membrane disruption potential of Bm-ponericin-L1. Moreover, this peptide also showed promising antibiofilm activity. Finally, cell viability and hemolytic assays revealed that Bm-ponericin-L1 is non-toxic toward primary fibroblasts cell lines and red blood cells, respectively. This study opens up new perspectives toward an alternative approach to overcoming multiple-antibiotic-resistance by means of AMPs through invertebrates' infection with human pathogenic bacteria.

Draft Genome Sequence of Streptomyces sp. Strain PSAA01, Isolated from the Soil of Eastern Himalayan Foothills.

Streptomyces strains are powerhouses for a diverse range of secondary metabolites, including antibiotics, anticancer and immunosuppressive agents, and enzymes. Here, we report the genome sequence of Streptomyces sp. strain PSAA01, which was isolated from a soil sample taken in Manas National Park, Assam, India, in the eastern Himalayan foothills of India.

Whole-Genome Shotgun (WGS) Sequence of cis-Isoprene Polymer-Degrading Nocardia sp. strain BSTN01.

Species belonging to the genus Nocardia are known to be facultative human pathogens. There are also reports of Nocardia species capable of degrading various forms of rubber. Here, we report the whole-genome shotgun (WGS) sequence of Nocardia sp. strain BSTN01, isolated from stored water in latex-collecting cups thrown away near a local rubber processing unit in Tripura, India.

Study of epidemiological behaviour of malaria and its control in the Purulia district of West Bengal, India (2016-2020).

Purulia is a malaria-prone district in West Bengal, India, with approximately half of the blocks defined as malaria endemic. We analyzed the malaria case in each block of the Purulia district from January 1, 2016, to December 31, 2020. As per the API, 20 blocks of Purulia were assigned to four different categories (0-3) and mapped using ArcGIS software. An exponential decay model was fitted to forecast the trend of malaria cases for each block of Purulia (2021-2025). There was a sharp decrease in total malaria cases and API from 2016 to 2020 due to the mass distribution of LLINs. The majority of cases (72.63%) were found in ≥ 15-year age group. Males were more prone to malaria (60.09%). Malaria was highly prevalent among Scheduled Tribes (48.44%). Six blocks were reported in Category 3 (high risk) and none in Category 0 (no risk) in 2016, while no blocks were determined to be in Category 3, and three blocks were in Category 0 in 2020. The exponential decay model prediction is oriented towards gaining malaria-free status in thirteen blocks of Purulia by 2025. This study will incite the government to uphold and strengthen the current efforts to meet the malaria elimination goals.

Exogenous pulmonary surfactant: A review focused on adjunctive therapy for severe acute respiratory syndrome coronavirus 2 including SP-A and SP-D as added clinical marker.

Type I and type II pneumocytes are two forms of epithelial cells found lining the alveoli in the lungs. Type II pneumocytes exclusively secrete 'pulmonary surfactants,' a lipoprotein complex made up of 90% lipids (mainly phospholipids) and 10% surfactant proteins (SP-A, SP-B, SP-C, and SP-D). Respiratory diseases such as influenza, severe acute respiratory syndrome coronavirus infection, and severe acute respiratory syndrome coronavirus 2 infection are reported to preferentially attack type II pneumocytes of the lungs. After viral invasion, consequent viral propagation and destruction of type II pneumocytes causes altered surfactant production, resulting in dyspnea and acute respiratory distress syndrome in patients with coronavirus disease 2019. Exogenous animal-derived or synthetic pulmonary surfactant therapy has already shown immense success in the treatment of neonatal respiratory distress syndrome and has the potential to contribute efficiently toward repair of damaged alveoli and preventing severe acute respiratory syndrome coronavirus 2-associated respiratory failure. Furthermore, early detection of surfactant collectins (SP-A and SP-D) in the circulatory system can be a significant clinical marker for disease prognosis in the near future.

Bio-molecule functionalized rapid one-pot green synthesis of silver nanoparticles and their efficacy toward the multidrug resistant (MDR) gut bacteria of silkworms (Bombyx mori).

The present study aimed to synthesise bio-molecule functionalized silver nanoparticles (AgNPs) using leaf extract from mulberry variety S-1635 (Morus alba L.) and to explore its antibacterial efficacy against multidrug resistant (MDR) gut bacteria isolated from natural infection observed from silkworm larvae in rearing conditions. AgNPs formation was established by surface plasmon resonance at 480 nm. The crystallinity of the synthesised AgNPs was checked by HR-TEM and XRD analysis. SEM and TEM characterisation further exhibited the spherical, monodispersed, well scattered nature of the AgNPs with an average particle size of 11.8 nm ± 2.8. The presence of (111), (200), (220) and (311) planes in Bragg's reflections confirmed the face-cantered-cubic crystalline silver. EDX analysis confirmed the presence of elemental silver. FT-IR spectra revealed functional groups were responsible for the reduction of silver ions. The zeta potential value of -17.3 mV and -25.6 mV was recorded in MH and DMEM/F-12 media, respectively. The LC-QTOF/MS and HRMS spectra disclosed the presence of bioactive compounds like flavonoid, gallic acid, and stigmasterol, which are probably involved in the reduction and functionalization of AgNPs. The antibacterial efficacy of bio-molecule functionalized AgNPs and the naked AgNPs was tested on Gram-positive and Gram-negative bacteria isolated from silkworms and characterized by using 16S rDNA and gyrB genes. The cytotoxicity of AgNPs was tested on WRL-68, HEK-293, ACHN, and HUH-7 cell lines using MTT assay. This study provides an insight into the application of bio-molecule functionalized AgNPs for combating various silkworm pathogens which severely affect the agro-rural economy of developing countries.

Synthesis of Long-Term Stable Gold Nanoparticles Benefiting from Red Raspberry (Rubus idaeus), Strawberry (Fragaria ananassa), and Blackberry (Rubus fruticosus) Extracts-Gold Ion Complexation and Investigation of Reaction Conditions.

We report synthesis of monodispersed, stable, and colloidal gold nanoparticles (Au NPs) using anthocyanin-riched red raspberry (Rubus idaeus), strawberry (Fragaria ananassa), and blackberry (Rubus fruticosus) extracts as functions of concentration of HAuCl4·3H2O and berries extract, reaction time, and reaction pH values (pHs) and demonstrate their unique stability in highly concentrated salt (sodium chloride, NaCl) solutions. The catecholamine group of anthocyanin molecules give preferential coordination reaction with gold ions (Au3+) for creating anthocyanin-Au3+ complexes, which may lead to initiation of nucleation for seed formation, and then, oxidation of catecholamine results in a flow of electrons from anthocyanins to Au seeds for anisotropic growth. Finally, the surface of the Au NPs is saturated with anthocyanins, and formation of monodispersed and stable Au NPs with narrow size distribution is completed. We also report the effects of some experimental parameters including concentrations of Au3+ ions and barrier extracts, reaction time, and pHs on formation of the Au NPs with rational explanations. The long-term colloidal stability of the Au NPs in the 400 mM NaCl solution was comparatively studied with commercial Au NPs (citrate capped). As results show that anthocyanin-riched berry extracts directed Au NPs we proposed here can be considered as promising and safe tools for biomedical applications owing to their highly much colloidal dispersibility and salt tolerance properties.

Effect of feed supplementation with biosynthesized silver nanoparticles using leaf extract of Morus indica L. V1 on Bombyx mori L. (Lepidoptera: Bombycidae).

Herein, we report the synthesis of silver nanoparticles (AgNPs) by a green route using the aqueous leaf extract of Morus indica L. V1. The synthesized AgNPs exhibited maximum UV-Vis absorbance at 460 nm due to surface plasmon resonance. The average diameter (~54 nm) of AgNPs was measured from HR-TEM analysis. EDX spectra also supported the formation of AgNPs, and negative zeta potential value (-14 mV) suggested its stability. Moreover, a shift in the carbonyl stretching (from 1639 cm-1 to 1630 cm-1) was noted in the FT-IR spectra of leaf extract after AgNPs synthesis which confirm the role of natural products present in leaves for the conversion of silver ions to AgNPs. The four bright circular rings (111), (200), (220) and (311) observed in the selected area electron diffraction pattern are the characteristic reflections of face centered cubic crystalline silver. LC-MS/MS study revealed the presence of phytochemicals in the leaf extract which is responsible for the reduction of silver ions. MTT assay was performed to investigate the cytotoxicity of AgNPs against two human cell lines, namely HepG2 and WRL-68. The antibacterial study revealed that MIC value of the synthesized AgNPs was 80 µg/ml against Escherichia coli K12 and Staphylococcus aureus (MTCC 96). Finally, the synthesized AgNPs at 10 µg/ml dosages showed beneficial effects on the survivability, body weights of the Bombyx mori L. larvae, pupae, cocoons and shells weights via enhancing the feed efficacy.

Flocculating, emulsification and metal sorption properties of a partial characterized novel exopolysaccharide produced by Rhizobium tropici SRA1 isolated from Psophocarpus tetragonolobus (L) D.C.

A novel exopolysaccharide (EPS) was produced by a bacterium which was isolated from Psophocarpus tetragonolobus (L) D.C. and identified as 99% Rhizobium tropici SRA1 by 16S rDNA sequencing. The flocculating performances along with emulsifying activity began simultaneously with the growth and the production of EPS and reached its utmost at 28 h. EPS was purified via chilled ethanol precipitation followed by dialysis and lyophilization. The existence of hydroxyl, methoxyl, and carboxylic functional groups were confirmed by Fourier transform infrared (FT-IR) spectrum. EPS was found to be compose of 82.44% neutral sugar and 15.93% uronic acid. The average molecular weight of the exopolysaccharide was estimated as ~ 1.8 × 105. Gas-liquid chromatography indicated the presence of glucose and galactose at a molar ratio of 3:1 in EPS. In the pH range of 3-5 with EPS dosage of 15 mg/l at 30 °C, cation-independent flocculation greater than 90% was observed. Emulsification indices (E24) of EPS were observed as 86.66%, 83.33%, 76.66%, and 73.33% with olive oil, kerosene, toluene, and n-hexane respectively. Biosorption of Cu K [45.69 wt%], Cu L [05.67 wt%], Co K [15.58 wt%], and Co L [11.72 wt%] by EPS was confirmed by energy-dispersive X-ray spectroscopy (EDS). This report on the flocculating, emulsifying, and metal sorption properties of EPS produced by R. tropici SRA1 is unique in the literature.

Antimicrobial peptides from Bombyx mori: a splendid immune defense response in silkworms.

Bombyx mori L., a primary producer of silk, is the main tool in the sericulture industry and provides the means of livelihood to a large number of people. Silk cocoon crop losses due to bacterial infection pose a major threat to the sericulture industry. Bombyx mori L., a silkworm of the mulberry type, has a sophisticated inherent innate immune mechanism to combat such invasive pathogens. Among all the components in this defense system, antimicrobial peptides (AMPs) are notable due to their specificity towards the invading pathogens without harming the normal host cells. Bombyx mori L. so far has had AMPs identified that belong to six different families, namely cecropin, defensin, moricin, gloverin, attacin and lebocin, which are produced by the Toll and immune deficiency (IMD) pathways. Their diverse modes of action depend on microbial pathogens and are still under investigation. This review examines the recent progress in understanding the immune defense mechanism of Bombyx mori based on AMPs.

Formation of functional nanobiocatalysts with a novel and encouraging immobilization approach and their versatile bioanalytical applications.

The discovery of functional organic-inorganic hybrid nanoflowers (FNFs) consisting of proteins/enzymes as the organic components and Cu(ii) ion as the inorganic component has made an enormous impact on enzyme immobilization studies. The FNFs synthesized by an encouraging and novel approach not only showed high stabilities but also much enhanced catalytic activities as compared to free and conventionally immobilized enzymes. A recent development demonstrated that FNF formation has moved beyond the initial discovery in which enzymes and Cu2+ ions used as the organic and inorganic parts, respectively, are replaced with new organic (chitosan, amino acid and plant extracts) and inorganic (Cu2+ and Fe2+) materials. The new organic materials incorporated into FNFs act as Fenton-like agents and then show peroxidase-like activity owing to the metal ions and the porous structure of FNFs in the presence of hydrogen peroxide (H2O2). All FNFs have been widely utilized in many different scientific and industrial fields due to their greatly enhanced activities and stabilities. This review focuses primarily on the preparation, characterization, and bioanalytical applications of FNFs and explains the mechanisms of their formation and enhanced activities and stabilities.

Enzymatic hydrolyzed feather peptide, a welcoming drug for multiple-antibiotic-resistant Staphylococcus aureus: structural analysis and characterization.

This study aimed to explore the bactericidal activity of a feather-degraded active peptide against multiple-antibiotic-resistant (MAR) Staphylococcus aureus. An antibacterial peptide (ABP) was isolated from the chicken feathers containing fermented media of Paenibacillus woosongensis TKB2, a keratinolytic soil isolate. It was purified by HPLC, and its mass was found to be 4666.87 Da using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) spectroscopy. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values of this peptide were 22.5 and 90 µg/ml, respectively. SEM study revealed the distorted cell wall of the test strain along with pore formation. The possible reason for bactericidal activity of the peptide is due to generation of reactive oxygen species (ROS), resulting in membrane damage and leakage of intracellular protein. Complete sequence of the peptide was predicted and retrieved from the sequence database of chicken feather keratin after in silico trypsin digestion using ExPASy tools. Further, net charge, hydrophobicity (77.7 %) and molecular modelling of the peptide were evaluated for better understanding of its mode of action. The hydrophobic region (17 to 27) of the peptide may facilitate for initial attachment on the bacterial membrane. The ABP exhibited no adverse effects on RBC membrane and HT-29 human cell line. This cytosafe peptide can be exploited as an effective therapeutic agent to combat Staphylococcal infections.

Brevibacterium siliguriense sp. nov., a facultatively oligotrophic bacterium isolated from river water.

A Gram-positive-staining, rod-shaped, facultatively oligotrophic bacterial strain, designated MB18(T), was isolated from a water sample collected from the River Mahananda at Siliguri (26° 44' 23.20' N, 88° 25' 22.89' E), West-Bengal, India. On the basis of 16S rRNA gene sequence similarity, the closest relative of this strain was Brevibacterium epidermidis NCDO 2286(T) (96 % similarity). The DNA G+C content of strain MB18(T) was 64.6 mol%. Chemotaxonomic data [MK-8(H(2)) as the major menaquinone, galactose as the sole cell-wall sugar, meso-diaminopimelic acid as the diagnostic cell-wall diamino acid, phosphatidylglycerol and diphosphatidylglycerol as constituents of the polar lipids, anteiso-C(15 : 0), anteiso-C(17 : 0) and iso-C(15 : 0) as the major fatty acids] supported the affiliation of strain MB18(T) to the genus Brevibacterium. The results of DNA G+C content, 16S rRNA gene sequence analysis and biochemical and physiological analyses allowed genotypic and phenotypic differentiation of strain MB18(T) from its nearest neighbour B. epidermidis. The isolate therefore represents a novel species, for which the name Brevibacterium siliguriense sp. nov. is proposed; the type strain is MB18(T) ( = DSM 23676(T) = LMG 25772(T)).