Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II.

In plants and algae, the primary antenna protein bound to photosystem II is light-harvesting complex II (LHCII), a pigment-protein complex that binds eight chlorophyll (Chl) a molecules and six Chl b molecules. Chl a and Chl b differ only in that Chl a has a methyl group (-CH3) on one of its pyrrole rings, while Chl b has a formyl group (-CHO) at that position. This blue-shifts the Chl b absorbance relative to Chl a. It is not known how the protein selectively binds the right Chl type at each site. Knowing the selection criteria would allow the design of light-harvesting complexes that bind different Chl types, modifying an organism to utilize the light of different wavelengths. The difference in the binding affinity of Chl a and Chl b in pea and spinach LHCII was calculated using multiconformation continuum electrostatics and free energy perturbation. Both methods have identified some Chl sites where the bound Chl type (a or b) has a significantly higher affinity, especially when the protein provides a hydrogen bond for the Chl b formyl group. However, the Chl a sites often have little calculated preference for one Chl type, so they are predicted to bind a mixture of Chl a and b. The electron density of the spinach LHCII was reanalyzed, which, however, confirmed that there is negligible Chl b in the Chl a-binding sites. It is suggested that the protein chooses the correct Chl type during folding, segregating the preferred Chl to the correct binding site.

Identification of a novel quinoline-based UV-protective pigment from a psychrotrophic Arctic bacterium.

AIMS: Psychrotrophs are extremophilic microorganisms that grow optimally in low temperature having many unique bioactive molecules of biotechnological applications. In this study, we characterized a pigment from an arctic bacterium with protective activity towards UV exposure. METHODS AND RESULTS: The present research reports isolation and characterization of a psychrotrophic bacteria, RSAP2, from the soil sample of NyAlesund (78°56"N, 11°54"E), Svalbard, Norway. The strain showed closest 16S rRNA gene sequence similarity (99.9%) with Kocuria indica NIO-1021. RSAP2 is a Gram-positive, coccoid aerobe which produces a yellow pigment. The optimal parameters for pigment production while grown in LB medium were 3% (w/v) NaCl and 4 days of incubation of the culture at 20°C and pH 9 with shaking (180 rpm). The pigment was extracted in methanol and acetone (2:1) and further purified through column chromatography. It was characterized by mass spectrometry, UV-visible, fluorescence, IR, 1 H NMR, 13 C NMR spectroscopy and CHNS/O analysis. The pigment has a molecular weight of about 258 daltons and the molecular formula was determined as C15 H18 N2 O2 and is a quinoline derivative. We show that the pigment can protect Escherichia coli against UV-mediated mutagenesis. We further demonstrate that the pigment displays a significant antimicrobial effect and in sublethal concentrations it impairs biofilm formation ability of the model organism Staphylococcus aureus. CONCLUSIONS: The pigment of a psychrotrophic Arctic bacterium, most likely a strain of K. indica, was purified and its chemical structure was determined. The quinoline-based pigment has the ability to protect live cells from UV induced damage. SIGNIFICANCE AND IMPACT OF STUDY: Analysis and characterization of this newly isolated quinoline-based pigment is a potential candidate for future application in skin care products.

Production of extracellular lipase from psychrotrophic bacterium Oceanisphaera sp. RSAP17 isolated from arctic soil.

Cold-active extracellular lipases produced by different psychrotrophs are important for various industrial applications. We have isolated a Gram-negative, rod-shaped, aerobe, non-pigment producing psychrotrophic bacterial strain RSAP17 (MTCC 12991, MCC 4275) from the unexplored Arctic soil sample of NyAlesund, Svalbard, Norway (78° 55″ N, 11° 54″ E). The detailed morphological, biochemical, and molecular characteristics were investigated to characterize the isolate RSAP17. Analyses of the 16S rDNA sequence of strain RSAP17 (Accession no. MK391379) shows the closest match with Oceanisphaera marina YM319T (99.45%) and Oceanisphaera sediminis TW92 JCM 17329T (97.40%). The isolate is capable of producing extracellular lipase but not amylase, cellulase or urease. The optimal parameters for lipase production have been found in tributyrin based (10 mL/L) agar media supplemented with 3% (w/v) NaCl after 2-3 days of incubation at 20-22 °C temperature and pH 9 at shaking condition. We have purified the extracellular lipase from the RSAP17 grown culture supernatant through 75% ammonium sulfate precipitation followed by dialysis and DEAE cellulose column chromatography. The invitro lipolytic activity of the purified lipase enzymes has been done through zymogram analysis. The molecular weight found for the lipase is 103.8 kD. The optimal activity of the purified lipase has been found at 25 °C and pH 9. MALDI-TOF-MS study of the purified lipase showed the highest match with the sequence of prolipoprotein diacylglyceryl transferase with 44% sequence coverage. Further study on large-scale production, substrate utilization and enzymatic kinetics of this lipase could unravel its possibility in future biotechnological applications.

Retraction: Differential detection and quantification of cyclic AMP and other adenosine phosphates in live cells.

Retraction of 'Differential detection and quantification of cyclic AMP and other adenosine phosphates in live cells' by Sujoy Das et al., Chem. Commun., 2017, 53, 7600-7603.

Elucidating the chemical and biochemical applications of Citrus sinensis-mediated silver nanocrystal.

Synthesis of nanoparticles using biodegradable source is safer and echo-friendly. Here, we describe the synthesis of polycrystalline silver nanocrystals using Citrus sinensis acting as both reducing and capping agents. After exposing the silver ions to orange extract, rapid reduction of silver ions led to the formation of stable silver nanocrystals due to the reducing and stabilizing properties of orange fruit juice. The synthesized silver nanocrystals were characterized using various analytical techniques like UV-vis spectroscopy, X-ray diffraction (XRD), dynamic light scattering (DLS), scanning electron microscope (SEM) and transmission electron microscopy (TEM). The biochemical activity of the synthesized nanocrystals was studied in the light of affinity to bovine serum albumin using several biophysical methods like absorbance, fluorescence and circular dichroism spectroscopy. Cytotoxic activity of these nanocrystals was also studied against Hep-2 cell line using fluorescence microscopy. It was also found that the synthesized nanocrystals can sense mercuric ion down to 50 µM in the presence of a number of cations. Furthermore, we established that the silver nanoparticles can effectively catalyse the reduction of methylene blue by ascorbic acid. The present study will enrich our knowledge on the chemical and biochemical activities of green-synthesized silver nanocrystals.

EvoStruct-Sub: An accurate Gram-positive protein subcellular localization predictor using evolutionary and structural features.

Determining subcellular localization of proteins is considered as an important step towards understanding their functions. Previous studies have mainly focused solely on Gene Ontology (GO) as the main feature to tackle this problem. However, it was shown that features extracted based on GO is hard to be used for new proteins with unknown GO. At the same time, evolutionary information extracted from Position Specific Scoring Matrix (PSSM) have been shown as another effective features to tackle this problem. Despite tremendous advancement using these sources for feature extraction, this problem still remains unsolved. In this study we propose EvoStruct-Sub which employs predicted structural information in conjunction with evolutionary information extracted directly from the protein sequence to tackle this problem. To do this we use several different feature extraction method that have been shown promising in subcellular localization as well as similar studies to extract effective local and global discriminatory information. We then use Support Vector Machine (SVM) as our classification technique to build EvoStruct-Sub. As a result, we are able to enhance Gram-positive subcellular localization prediction accuracies by up to 5.6% better than previous studies including the studies that used GO for feature extraction.

A chromogenic and ratiometric fluorogenic probe for rapid detection of a nerve agent simulant DCP based on a hybrid hydroxynaphthalene-hemicyanine dye.

A new cyanine dye (CYD) based on hybrid hydroxynaphthalene-hemicyanine has been synthesized and characterized. The chromogenic and ratiometric fluorogenic probe (CYD) enables a fast and highly sensitive response to an OP nerve agent mimic diethyl chlorophosphate (DCP) through tandem phosphorylation and intramolecular cyclization reaction within 1 min and with the detection limit as low as 18.86 nM. To our knowledge this is the first report of a hydroxyl assisted bathochromic shift in a selective chemodosimeter for DCP exhibiting a ratiometric response. TDDFT calculations were performed in order to demonstrate the electronic properties of the probe and the cyclized product. Moreover, the utility of the probe CYD for the detection of DCP in live cells, in the gas phase and in a spiked soil sample has also been demonstrated.

Differential detection and quantification of cyclic AMP and other adenosine phosphates in live cells.

A new naphthol-based rhodamine derivative (NpRD) has been developed for the selective and differential detection of adenosine 3',5'-cyclic monophosphate (cAMP) and adenosine phosphates (APs) (ATP, ADP, and AMP) from other nucleotides. The simple detection and quantification of cAMP in human blood cells and in other samples based on the 'turn on' fluorescence properties of this chemosensor through colorimetry or fluorometry makes it unique for probable application in high throughput screening.

Selective fluorescence sensing and quantification of uric acid by naphthyridine-based receptor in biological sample.

Naphthyridine-based fluorescent probe H1 was synthesized and characterized for the quantification and selective detection of Uric Acid (UA) in live cell. In presence of UA, H1 forms the specific host-guest complex mainly through intermolecular hydrogen bonding and aromatic stacking which produces "turn-off" fluorescence. The probe and UA is found to be 1:1 stoichiometry on the basis of absorption and fluorescence titrations. The probe H1 has been shown to detect UA up to 0.6µM at pH 7.4. DFT-TDDFT calculations were performed in order to demonstrate the sensing mechanism and the electronic properties of the receptor-donor complex. The selectivity was evaluated in Vero cells in the presence of UA with other purine derivatives, structurally similar to UA. It was found to exhibit no cytotoxicity effect in tested concentration of H1 and good membrane permeability for the detection of UA in living cell system. The unknown concentration of UA in serum and urine can be measured easily using the fluorescence property of probe H1.

Dual mode selective chemosensor for copper and fluoride ions: a fluorometric, colorimetric and theoretical investigation.

A pyrene containing chemosensor viz. has been designed for the efficient and selective detection of Cu(2+) and F(-) ions in dual sensing mode which do not interfere with each other. The chemosensing behavior of towards Cu(2+) was demonstrated through fluorescence, time resolved fluorescence spectroscopy, and visual fluorescence colour changes, and towards F(-) through naked-eye colour changes, absorption and (1)H NMR titrations. The chemosensor shows excellent selectivity towards Cu(2+) through an excimer switch-off mechanism. Density Functional Theory (DFT) calculations were performed to show the structure and electronic properties of and its copper complex [-Cu(2+)]. The selectivity and sensitivity towards F(-) were explained in terms of H-bonding interactions between and F(-), then deprotonation of . The biological application of has been evaluated in HEK 293 cells and it exhibits good membrane permeability for the detection of Cu(2+). The sensor also shows appreciable sensitivity towards fluoride in toothpaste.

Segregation of nod-containing and nod-deficient bradyrhizobia as endosymbionts of Arachis hypogaea and as endophytes of Oryza sativa in intercropped fields of Bengal Basin, India.

Bradyrhizobial invasion in dalbergoid legumes like Arachis hypogaea and endophytic bacterial invasions in non-legumes like Oryza sativa occur through epidermal cracks. Here, we show that there is no overlap between the bradyrhizobial consortia that endosymbiotically and endophytically colonise these plants. To minimise contrast due to phylogeographic isolation, strains were collected from Arachis/Oryza intercropped fields and a total of 17 bradyrhizobia from Arachis (WBAH) and 13 from Oryza (WBOS) were investigated. 16SrRNA and concatenated dnaK-glnII-recA phylogeny clustered the nodABC-positive WBAH and nodABC-deficient WBOS strains in two distinct clades. The in-field segregation is reproducible under controlled conditions which limits the factors that influence their competitive exclusion. While WBAH renodulated Arachis successfully, WBOS nodulated in an inefficient manner. Thus, Arachis, like other Aeschynomene legumes support nod-independent symbiosis that was ineffectual in natural fields. In Oryza, WBOS recolonised endophytically and promoted its growth. WBAH however caused severe chlorosis that was completely overcome when coinfected with WBOS. This explains the exclusive recovery of WBOS in Oryza in natural fields and suggests Nod-factors to have a role in counterselection of WBAH. Finally, canonical soxY1 and thiosulphate oxidation could only be detected in WBOS indicating loss of metabolic traits in WBAH with adaptation of symbiotic lifestyle.

A new selective chromogenic and turn-on fluorogenic probe for copper(II) in solution and vero cells: recognition of sulphide by [CuL].

A new coumarin-appended thioimidazole-linked imine conjugate, viz. has been synthesized and characterized. has been found to recognize Cu(2+) selectively among a wide range of biologically relevant metal ions. The chemosensing behavior of has been demonstrated through fluorescence, absorption, visual fluorescence color changes, ESI-MS and (1)H NMR titrations. The chemosensor showed selectivity toward Cu(2+) by switch on fluorescence among the 18 metal ions studied with a detection limit of 1.53 µM. The complex formed between and Cu(2+) is found to be 1 : 1 on the basis of absorption and fluorescence titrations and was confirmed by ESI-MS. DFT and TDDFT calculations were performed in order to demonstrate the structure of and [CuL] and the electronic properties of chemosensor and its copper complex. This highly fluorescent [CuL] complex has been used to recognize sulphide selectively among the other allied anions. Microstructural features of and its Cu(2+) complex have been investigated by SEM imaging (scanning electron microscopy). The biological applications of were evaluated in Vero cells and it was found to exhibit low cytotoxicity and good membrane permeability for the detection of Cu(2+).

An azodye-rhodamine-based fluorescent and colorimetric probe specific for the detection of Pd(2+) in aqueous ethanolic solution: synthesis, XRD characterization, computational studies and imaging in live cells.

Azodye-rhodamine hybrid colorimetric fluorescent probe (L) has been designed and synthesized. The structure of L has been established based on single crystal XRD. It has been shown to act as a selective turn-on fluorescent chemosensor for Pd(2+) with >40 fold enhancement by exhibiting red emission among the other 27 cations studied in aqueous ethanol. The coordination features of the species of recognition have been computationally evaluated by DFT methods and found to have a distorted tetrahedral Pd(2+) center in the binding core. The probe (L) has been shown to detect Pd up to 0.45 µM at pH 7.4. Furthermore, the probe can be used to image Pd(2+) in living cells.