Metabolomic and genomic insights into TMA degradation by a novel halotolerant strain - Paracoccus sp. PS1.

Trimethylamine N-oxide (TMAO) is a gut metabolite that acts as a biomarker for chronic diseases, and is generated by the oxidation of trimethylamine (TMA) produced by gut microflora. Since, microbial degradation of TMA is predicted to be used to restrict the production of TMAO, we aimed to isolate bacterial strains that could effectively degrade TMA before being oxidized to TMAO. As marine fish is considered to have a rich content of TMAO, we have isolated TMA degrading isolates from fish skin. Out of the fourteen isolates, depending on their rapid TMA utilization capability in mineral salt medium supplemented with TMA as a sole carbon and nitrogen source, isolate PS1 was selected as our desired isolate. Its TMA degrading capacity was further confirmed through spectrophotometric, Electrospray Ionization Time-of-Flight Mass Spectrometry (ESI TOF-MS) and High performance liquid chromatography (HPLC) analysis and in silico analysis of whole genome (WG) gave further insights of protein into its TMA degradation pathways. PS1 was taxonomically identified as Paracoccus sp. based on its 16S rRNA and whole genome sequence analysis. As PS1 possesses the enzymes required for degradation of TMA, clinical use of this isolate has the potential to reduce TMAO generation in the human gut.

Biocontrol of biofilm forming Burkholderia cepacia using a quorum quenching crude lactonase enzyme extract from a marine Chromohalobacter sp. strain D23.

Biofilm plays advantageous role in Burkholderia cepacia by exerting multi-drug resistance. As quorum sensing (QS) system regulates biofilm formation and pathogenicity in B. cepacia strains, quorum quenching (QQ) may be a novel strategy to control persistent B. cepacia infections. In these regards, 120 halophilic bacteria were isolated from marine sample and tested using Chromobacterium violaceum and C. violaceum CV026-based bioassays initially, showing reduced violacein synthesis by QQ enzyme by 6 isolates. Among them, Chromohalobacter sp. D23 significantly degraded both C6-homoserine lactone (C6-HSL) and C8-HSL due to potent lactonase activity, which was detected by C. violaceum CV026 biosensor. Further high-performance liquid chromatography (HPLC) study confirmed degradation of N-acyl homoserine lactones (N-AHLs) particularly C6-HSL and C8-HSL by crude lactonase enzyme. Chromohalobacter sp. D23 reduced biofilm formation in terms of decreased total biomass and viability in biofilm-embedded cells in B. cepacia significantly which was also evidenced by fluorescence microscopic images. An increase in antibiotic susceptibility of B. cepacia biofilm was achieved when crude lactonase enzyme of Chromohalobacter sp. strain D23 was combined with chloramphenicol (1-5 × MIC). Chromohalobacter sp. D23 also showed prominent decrease in QS-mediated synthesis of virulence factors such as extracellular polymeric substances (EPS), extracellular protease, and hemolysin in B. cepacia. Again crude lactonase enzyme of Chromohalobacter sp. strain D23 inhibited B. cepacia biofilm formation inside nasal oxygen catheters in vitro. Finally, antibiotic susceptibility test and virulence tests revealed sensitivity of Chromohalobacter sp. strain D23 against a wide range of conventional antibiotics as well as absence of gelatinolytic, hemolytic, and serum coagulating activities. Therefore, the current study shows potential quorum quenching as well as anti-biofilm activity of Chromohalobacter sp. D23 against B. cepacia.

Plant Growth-Promoting Traits of a Thermophilic Strain of the Klebsiella Group with its Effect on Rice Plant Growth.

In agriculture, instead of synthetic fertilizers, natural bio-inoculants can be used to increase growth and yield of crops. For this purpose, we report a thermophilic bacteria Klebsiella sp. strain PMnew, isolated from Paniphala hot spring. The strain was characterized and assessed for plant growth-promoting traits. Oryza sativa L. var Swarna (rice) seeds were inoculated with the strain to study the bacterization effect on vegetative and reproductive growth of rice plants. The results indicate that PMnew produces organic acids to solubilize phosphate (550.16 ± 0.04 µg/ml), fixes nitrogen, produces indole compounds, siderophore, and ACC deaminase, and shows heavy metal resistance to chromium, cobalt, arsenic, cadmium, and mercury. It also possesses the ability to utilize several monomeric and polymeric sugars as sole carbon source including starch, agar, xylan, gelatin, and pectin, and can grow under both nutrient-rich and deficient conditions. Inoculated rice plants grew twice the length of control plants and surpassed the total grain mass yield of control plants by almost 18 times. Thus, this study brings forth a broad spectrum and easy to cultivate bio-inoculant, which can be used to increase rice production.

Pyridine Based Fluorescence Probe: Simultaneous Detection and Removal of Arsenate from Real Samples with Living Cell Imaging Properties.

Pyridine based fluorescence probe, DFPPIC and its functionalized Merrifield polymer has been synthesized, characterized and used as an arsenate selective fluorescence sensor. Arsenate induced fluorescence enhancement is attributed to inter-molecular H-bonding assisted CHEF process. The detection limit for arsenate is 0.001 µM, much below the WHO recommended tolerance level in drinking water. DFPPIC can detect intracellular arsenate in drinking water of Purbasthali, West Bengal, India efficiently. Graphical Abstract DFPPIC and its Merrifield conjugate polymer are used for selective determination and removal of arsenate from real drinking water samples of Purbasthali, a highly arsenic contaminated region of West Bengal, India. DFPPIC is very promising to imaging arsenate in living cells.

Colorimetric and fluorimetric response of Schiff base molecules towards fluoride anion, solution test kit fabrication, logical interpretations and DFT-D3 study.

Two newly synthesized Schiff base molecules are herein reported as anion sensors. -NO2 substituted receptor (P1) is comparatively more acidic and can sense F(-), OAc(-) and H2PO4(-), whereas -CN substituted receptor (P2) is less acidic and is selective for F(-) only. Reversible UV-Vis response for both receptors with F(-) can mimic multiple logic gate functions, and several complex electronic circuits based on XNOR, XOR, OR, AND, NOT and NOR logic operations with 'Write-Read-Erase-Read' options have been executed. Interesting 'turn on and off' fluorescence responses were noticed for the receptors with F(-). Intracellular F(-) detection as a diagnosis of non-skeletal fluorosis was successful using a fluorescence microscope with Candida albicans (prokaryotic cell, a diploid fungus) and pollen grains of Tecoma stans (eukaryotic cell) incubated in 10(-6) M fluoride-contaminated hand-pump water collected from Bankura, West Bengal, India. Furthermore, a solution test kit was fabricated for easy and selective detection of F(-) in an aqueous solvent.

A new pyrene based highly sensitive fluorescence probe for copper(II) and fluoride with living cell application.

A new pyrene based fluorescence probe has been synthesized for fluorogenic detection of Cu(2+) in acetonitrile-aqueous media (7 : 3 CH3CN-HEPES buffer, v/v, at pH 7.5) with bioimaging in both prokaryotic (Candida albicans cells) and eukaryotic (Tecoma stans pollen cells) living cells. The anion recognition properties of the sensor have also been studied in acetonitrile by fluorescence methods which show remarkable sensitivity toward fluoride over other anions examined.

Antipyrine based arsenate selective fluorescent probe for living cell imaging.

Condensation of salicylaldehyde and 4-aminoantipyrine has yielded a new fluorescent probe (APSAL) capable of detecting intracellular arsenate at the micromolar level for the first time. The structure of the probe has been established by different spectroscopic techniques and confirmed from X-ray crystallography. Common anions, viz., F(-), Cl(-), Br(-), I(-), N(3)(-), NCO(-), NO(2)(-), NO(3)(-), SCN(-), CN(-), CH(3)COO(-), SO(4)(2-), ClO(4)(-), and HPO(4)(2-) do not interfere. The binding constant of APSAL for H(2)AsO(4)(-) has been determined using the Benesi-Hildebrand equation as 8.9 × 10(3) M(-1). Fluorescence quantum yield of APSAL (0.016) increases more than 12 times upon binding arsenate ion.

Rhodamine-based fluorescent probe for Al3+ through time-dependent PET-CHEF-FRET processes and its cell staining application.

Rhodamine-diformyl p-cresol conjugate (L) has been developed as a novel Al(3+)-selective fluorometric and colorimetric sensor based on the FRET mechanism for the first time. L can selectively detect Al(3+) through time-dependent PET-CHEF and FRET processes. This phenomenon is nicely reflected from (1)H NMR, fluorescence lifetime, and fluorescence cell imaging studies. The probe can detect Al(3+) as low as 5 × 10(-9) M in HEPES-buffered EtOH:water (0.1 M, 4:1, v/v, pH 7.4). The probe shows pH-dependent emission properties viz. an intense red emission (585 nm) at acidic pH and an intense green fluorescence (535 nm) at basic pH. Thus, L can also be used as a pH sensor via tunable wavelength.

Cell permeable fluorescent receptor for detection of H2PO4(-) in aqueous solvent.

A new colorimetric fluorescent receptor for H(2)PO(4)(-) is reported in this communication. The receptor can detect dihydrogen phosphates optically by developing a color change from yellow to green. Acute spectral responses to H(2)PO(4)(-) in HEPES buffer (DMSO-HEPES 1:9) have been observed. The selectivity zone in terms of pH of the receptor for H(2)PO(4)(-) is attributed to the fitness in the acidity (pK(a)) of receptor with H(2)PO(4)(-). Hydrogen bonding plays the key role here which is confirmed by (1)H NMR titration. The receptor also has good potential for bio-imaging. The mode of interaction has also been established by ab initio calculation.

Molecular evidence for the occurrence of Japanese encephalitis virus genotype I and III infection associated with acute encephalitis in patients of West Bengal, India, 2010.

BACKGROUND: Japanese encephalitis virus (JEV), a mosquito-borne zoonotic pathogen, is the sole etiologic agent of Japanese Encephalitis (JE); a neurotropic killer disease which is one of the major causes of viral encephalitis worldwide with prime public health concern. JE was first reported in the state of West Bengal, India in 1973. Since then it is being reported every year from different districts of the state, though the vaccination has already been done. Therefore, it indicates that there might be either partial coverage of the vaccine or the emergence of mutated/new strain of JEV. Considering this fact, to understand the JEV genotype distribution, we conducted a molecular epidemiological study on a total of 135 serum/cerebrospinal fluid (CSF) samples referred and/or collected from the clinically suspected patients with Acute encephalitis syndrome (AES), admitted in different district hospitals of West Bengal, India, 2010. FINDINGS: JEV etiology was confirmed in 36/135 (26.6%) and 13/61 (21.3%) 2-15 days' febrile illness samples from AES cases by analyzing Mac-ELISA followed by RT-PCR test respectively. Phylogenetic analysis based on complete envelope gene sequences of 13 isolates showed the emergence of JEV genotype I (GI), co-circulating with genotype III (GIII). CONCLUSION: This study represents the first report of JEV GI with GIII, co-circulating in West Bengal. The efficacy of the vaccine (derived from JEV GIII strain SA-14-14-2) to protect against emerging JEV GI needs careful evaluation. In future, JE outbreak is quite likely in the state, if this vaccine fails to protect sufficiently against GI of JEV.

Highly selective organic fluorescent probe for azide ion: formation of a "molecular ring".

An indole based naphthalene derivative is reported as a highly selective fluorescent probe for azide ion in aqueous ethanol. The probe is applied for cell imaging of the N(3)(-) ion in contaminated living cells. Both experimental and theoretical studies have been performed to figure out the plausible mechanism of fluorescence enhancement of the probe upon binding with N(3)(-).

Cd(II)-triggered excimer-monomer conversion of a pyrene derivative: time dependent red-shift of monomer emission with cell staining application.

An efficient fluorescent probe (E)-N1-((E)-2-((pyren-7-yl)methyleneamino)ethyl)-N2-((pyren-7-yl)methylene)ethane-1,2-diamine (L) has been synthesized by a facile one-step condensation reaction. L can selectively detect Cd(2+) in presence of other common metal ions in 0.1 M HEPES buffered DMSO-water (4 : 1, v/v) medium. The detection limit of Cd(2+) is 1.8 × 10(-8) M. Cd(2+) can effectively convert the excimer emission of L into its monomer emission which in turn exhibits a time-dependent red-shift.

A naphthalene exciplex based Al3+ selective on-type fluorescent probe for living cells at the physiological pH range: experimental and computational studies.

2-((Naphthalen-6-yl)methylthio)ethanol (HL) was prepared by one pot synthesis using 2-mercaptoethanol and 2-bromomethylnaphthalene. It was found to be a highly selective fluorescent sensor for Al(3+) in the physiological pH (pH 7.0-8.0). It could sense Al(3+) bound to cells through fluorescence microscopy. Metal ions like Mn(2+), Fe(3+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Ag(+), Cd(2+), Hg(2+), Cr(3+) and Pb(2+) did not interfere. No interference was also observed with anions like Cl(-), Br(-), F(-), SO(4)(2-), NO(3)(-), CO(3)(2-), HPO(4)(2-) and SCN(-). Experimentally observed structural and spectroscopic features of HL and its Al(3+) complex have been substantiated by computational calculations using density functional theory (DFT) and time dependent density functional theory (TDDFT).

Fluorescence sensing of caffeine in aqueous solution with carbazole-based probe and imaging application in live cells.

The host-guest interaction of caffeine in aqueous solutions has been achieved by using carbazole based imino-phenol receptors with oxopurines influences their fluorescence properties and can be exploited for 'turn-ON' fluorescence sensing of caffeine. This new fluorescent probe with high sensitivity and selectivity for detection and first time imaging of caffeine in living cells was developed in aqueous media.

Nickel(II)-induced excimer formation of a naphthalene-based fluorescent probe for living cell imaging.

Ni(2+)-induced intramolecular excimer formation of a naphthalene-based novel fluorescent probe, 1-[(naphthalen-3-yl)methylthio]-2-[(naphthalen-6-yl)methylthio]ethane (L), has been investigated for the first time and nicely demonstrated by excitation spectra, a fluorescence lifetime experiment, and (1)H NMR titration. The addition of Ni(2+) to a solution of L (DMSO:water = 1:1, v/v; λ(em) = 345 nm, λ(ex) = 280 nm) quenched its monomer emission, with subsequent enhancement of the excimer intensity (at 430 nm) with an isoemissive point at 381 nm. The fluorescence lifetime of free L (0.3912 ns) is much lower than that of the nickel(2+) complex (1.1329 ns). L could detect Ni(2+) as low as 1 × 10(-6) M with a fairly strong binding constant, 2.0 × 10(4) M(-1). Ni(2+)-contaminated living cells of plant origin could be imaged using a fluorescence microscope.

Carbazole-thiosemicarbazone-Hg(II) ensemble-based colorimetric and fluorescence turn-on toward iodide in aqueous media and its application in live cell imaging.

A carbazole-thiosemicarbazone-Hg(2+) ensemble-based fluorogenic probe for detection of iodide in aqueous media is reported. The first fluorescent sensor for iodide anions was constructed based on the displacement approach. An 'ensemble' is able to selectively sense iodide over other anions followed by the release of 9-(butane-1-yl)-9H-carbazole-3,6-dihydrazinecarbothioamide to give a remarkable change of fluorescence turn-on signal at pH 7.4 under aqueous media. The practical use of an 'ensemble' was demonstrated by its application to the detection of iodide in the living cells.

Development of a highly selective cell-permeable ratiometric fluorescent chemosensor for oxorhenium(V) ion.

A novel 6-(2-pyridinyl)-5,6-dihydrobenzimidazo[1,2-c]quinazoline (HL) serves as a first-time highly selective and sensitive ratiometric fluorescent chemosensor probe for oxorhenium (ReO(V)) ion in acetonitrile : water = 9 : 1 (v/v) at 25 °C. The decrease in fluorescence at 410 nm and increase in fluorescence at 478 nm with an isoemissive point at 444 nm in the presence of ReO(V) ion is accounted for by the formation of mononuclear [ReOL(2)Cl] complex, characterized by physico-chemical and spectroscopic tools. The fluorescence quantum yield of the chemosensor (HL) was only 0.198 at 410 nm, and it increased more than 3-fold in the presence of 2 equiv. of the ReO(V) ion at 478 nm. Interestingly, the introduction of other metal ions and relevant anions caused the fluorescence intensity at 478 nm to be either unchanged or weakened. The fluorescence-response fits a Hill coefficient of 2.088 indicates the formation of a 1 : 2 stoichiometry for the L-ReO(V) complex. In the concentration range of 0-20 µM of oxorhenium(V) species calibration graph was linear with correlation coefficient (R) of 0.99994 and the calibration sensitivity was found to be 4.0 × 10(-7) M. The cellular image in the confocal microscope clearly indicated the presence of ReO(V) in Candida albicans cells using this chemosensor (HL).

A naphthalene-based Al3+ selective fluorescent sensor for living cell imaging.

An efficient fluorescent Al(3+) receptor, N-(2-hydroxy-1-naphthalene)-N'-(2-(2-hydroxy-1-naphthalene)amino-ethyl)-ethane-1,2-diamine (L) has been synthesized by the condensation reaction between 2-hydroxy naphthaldehyde and diethylenetriamine. High selectivity and affinity of L towards Al(3+) in ethanol (EtOH) as well as in HEPES buffer at pH 7.4, makes it suitable to detect intracellular Al(3+) with fluorescence microscopy. Metal ions, viz. Li(+), Na(+), K(+), Mg(2+), Ca(2+), Mn(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Ag(+), Cd(2+), Hg(2+) and Pb(2+) do not interfere. The lowest detection limit for Al(3+) is 3.0 × 10(-7) M and 1.0 × 10(-7) M in EtOH and HEPES buffer respectively.

Study of antimicrobial activity and root symbionts of Hemionitis arifolia.

Antibacterial and antifungal activity of crude extract, alcoholic extract and extracted phenol from various parts of tropical pteridophyta, Hemionitis arifolia were tested by agar diffusion and tube dilution assay. Both the crude and alcoholic extracts of vegetative and reproductive leaves of H. arifolia showed considerable antibacterial activity against Gram negative test strain of Escherichia coli (MTCC-739). Extract from reproductive leaves also showed moderate antibacterial activity against Bacillus subtilis (MTCC-441) (Gram positive test strain) but didn't show any antifungal activity against Candida albicans (MTCC-7353). Mycorrhizal and other symbiotic association with the root system of H. arifolia was studied and it is revealed that a number of mycorrhizal strains were present in both vegetative and reproductive form. Presence of Dark Septate Endophytic Fungi (DSF) was also detected.

Metaproteomic Discovery and Characterization of a Novel Lipolytic Enzyme From an Indian Hot Spring.

Lipolytic enzymes are produced by animals, plants and microorganisms. With their chemo-, regio-, and enantio-specific characteristics, lipolytic enzymes are important biocatalysts useful in several industrial applications. They are widely used in the processing of fats and oils, detergents, food processing, paper and cosmetics production. In this work, we used a new functional metaproteomics approach to screen sediment samples of the Indian Bakreshwar hot spring for novel thermo- and solvent-stable lipolytic enzymes. We were able to identify an enzyme showing favorable characteristics. DS-007 showed high hydrolytic activity with substrates with shorter chain length (C10, significantly less hydrolytic activity was observed. A preference for short chain acyl groups is characteristic for esterases, suggesting that DS-007 is an esterase. Consistent with the high temperature at its site of isolation, DS-007 showed a temperature optimum at 55°C and retained 80% activity even after prolonged exposure to temperatures as high as 60°C. The enzyme showed optimum activity at pH 9.5, with more than 50% of its optimum activity between pH 8.0 and pH 9.5. DS-007 also exhibited tolerance toward organic solvents at a concentration of 1% (v/v). One percent of methanol increased the activity of DS-007 by 40% in comparison to the optimum conditions without solvent. In the presence of 10% methanol, DMSO or isopropanol DS-007 still showed around 50% activity. This data indicates that DS-007 is a temperature- and solvent-stable thermophilic enzyme with reasonable activity even at lower temperatures as well as a catalyst that can be used at a broad range of pH values with an optimum in the alkaline range, showing the adaptation to the habitat's temperature and alkaline pH.