Effect of complex nutrients, amino acids, vitamins on Ni(II) biosorption from aqueous solution by Ni(II) resistant Saccharomyces cerevisiae AJ208.

The paper aims to establish and enhance the microorganism's successful growth, proper activity, and biosorption potency for Ni(II) biosorption from an aqueous solution using 5,000 mg/l Ni(II) resistant Saccharomyces cerevisiae AJ208. Complex nutrients, amino acids, and vitamins were added to the specifically optimized fermentation media as essential growth factors. Amino acids such as L-cysteine (0.0002 g/ml), L-Proline (0.0002 g/ml), L-Lysine (0.0002 g/ml), L-tryptophan (0.0001 g/ml) and L-Histidine (0.0003 g/ml) led to an increase of more than 87% biosorption. Vitamins such as, Ascorbic acids (0.01 × 10-8 g/ml), folic acids (0.01 × 10-8 g/ml), pyridoxine-HCl (0.01 × 10-8 g/ml),Thiamin-HCl (0.05 × 10-8 g/ml) promotes biosorption more than 91%. The Ni(II) bio-removal increased with complex nutrients like soybean meal, malt extract, and yeast extract at the concentration of 0.03, 0.4, 0.05 in g/ml, and nickel removal reached more than 85%. The multiple linear regression (MLR) and ANN application of the experimental data have predicted Ni(II) percentage removal well. This adsorption shows that the proposed Ni(II) removal process using complex nutrients is environmentally friendly and economically feasible.Novelty statement: This study evaluates a cost-effective approach to bioremediation of Ni(II) by using complex nutrients as a growth factor. Media enriched with complex nutrients is cheap than chemical media. Ni(II) Removal significant increased up to 87%, 88.34%, 96% with soybean meal, L-proline, and L-ascorbic acids at 3,000 mg/l initial Ni(II) concentration using newly developed 5,000 mg/l Ni(II) resistant Saccharomyces cerevisiae AJ208 and their NCBI accession number: MZ027228 (AJ208 ITS 1) and MZ027229 (AJ208 ITS 2).

Flower bud proteome reveals modulation of sex-biased proteins potentially associated with sex expression and modification in dioecious Coccinia grandis.

BACKGROUND: Dioecy is an important sexual system wherein, male and female flowers are borne on separate unisexual plants. Knowledge of sex-related differences can enhance our understanding in molecular and developmental processes leading to unisexual flower development. Coccinia grandis is a dioecious species belonging to Cucurbitaceae, a family well-known for diverse sexual forms. Male and female plants have 22A + XY and 22A + XX chromosomes, respectively. Previously, we have reported a gynomonoecious form (22A + XX) of C. grandis bearing morphologically hermaphrodite flowers (GyM-H) and female flowers (GyM-F). Also, we have showed that foliar spray of AgNO3 on female plant induces morphologically hermaphrodite bud development (Ag-H) despite the absence of Y-chromosome. RESULTS: To identify sex-related differences, total proteomes from male, female, GyM-H and Ag-H flower buds at early and middle stages of development were analysed by label-free proteomics. Protein search against the cucumber protein sequences (Phytozome) as well as in silico translated C. grandis flower bud transcriptome database, resulted in the identification of 2426 and 3385 proteins (FDR ≤ 1%), respectively. The latter database was chosen for further analysis as it led to the detection of higher number of proteins. Identified proteins were annotated using BLAST2GO pipeline. SWATH-MS-based comparative abundance analysis between Female_Early_vs_Male_Early, Ag_Early_vs_Female_Early, GyM-H_Middle_vs_Male_Middle and Ag_Middle_vs_ Male_Middle led to the identification of 650, 1108, 905 and 805 differentially expressed proteins, respectively, at fold change ≥1.5 and P ≤ 0.05. Ethylene biosynthesis-related candidates as highlighted in protein interaction network were upregulated in female buds compared to male buds. AgNO3 treatment on female plant induced proteins related to pollen development in Ag-H buds. Additionally, a few proteins governing pollen germination and tube growth were highly enriched in male buds compared to Ag-H and GyM-H buds. CONCLUSION: Overall, current proteomic analysis provides insights in the identification of key proteins governing dioecy and unisexual flower development in cucurbitaceae, the second largest horticultural family in terms of economic importance. Also, our results suggest that the ethylene-mediated stamen inhibition might be conserved in dioecious C. grandis similar to its monoecious cucurbit relatives. Further, male-biased proteins associated with pollen germination and tube growth identified here can help in understanding pollen fertility.

De novo transcriptome assembly from flower buds of dioecious, gynomonoecious and chemically masculinized female Coccinia grandis reveals genes associated with sex expression and modification.

BACKGROUND: Coccinia grandis (ivy gourd), is a dioecious member of Cucurbitaceae having heteromorphic sex chromosomes. Chromosome constitution of male and female plants of C. grandis is 22A + XY and 22A + XX respectively. Earlier we showed that a unique gynomonoecious form of C. grandis (22A + XX) also exists in nature bearing morphologically hermaphrodite flowers (GyM-H). Additionally, application of silver nitrate (AgNO3) on female plants induces stamen development leading to the formation of morphologically hermaphrodite flowers (Ag-H) despite the absence of Y-chromosome. Due to the unavailability of genome sequence and the slow pace at which sex-linked genes are identified, sex expression and modification in C. grandis are not well understood. RESULTS: We have carried out a comprehensive RNA-Seq study from early-staged male, female, GyM-H, and Ag-H as well as middle-staged male and GyM-H flower buds. A de novo transcriptome was assembled using Trinity and annotated by BLAST2GO and Trinotate pipelines. The assembled transcriptome consisted of 467,233 'Trinity Transcripts' clustering into 378,860 'Trinity Genes'. Female_Early_vs_Male_Early, Ag_Early_vs_Female_Early, and GyM-H_Middle_vs_Male_Middle comparisons exhibited 35,694, 3574, and 14,954 differentially expressed transcripts respectively. Further, qRT-PCR analysis of selected candidate genes validated digital gene expression profiling results. Interestingly, ethylene response-related genes were found to be upregulated in female buds compared to male buds. Also, we observed that AgNO3 treatment suppressed ethylene responses in Ag-H flowers by downregulation of ethylene-responsive transcription factors leading to stamen development. Further, GO terms related to stamen development were enriched in early-staged male, GyM-H, and Ag-H buds compared to female buds supporting the fact that stamen growth gets arrested in female flowers. CONCLUSIONS: Suppression of ethylene responses in both male and Ag-H compared to female buds suggests a probable role of ethylene in stamen suppression similar to monoecious cucurbits such as melon and cucumber. Also, pollen fertility associated GO terms were depleted in middle-staged GyM-H buds compared to male buds indicating the necessity of Y-chromosome for pollen fertility. Overall, this study would enable identification of new sex-biased genes for further investigation of stamen arrest, pollen fertility, and AgNO3-mediated sex modification.

Flower development, pollen fertility and sex expression analyses of three sexual phenotypes of Coccinia grandis.

BACKGROUND: Coccinia grandis is a dioecious species of Cucurbitaceae having heteromorphic sex chromosomes. The chromosome constitution of male and female plants is 22 + XY and 22 + XX respectively. Y chromosome of male sex is conspicuously large and plays a decisive role in determining maleness. Sex modification has been studied in hypogynous Silene latifolia (Caryophyllaceae) but there is no such report in epigynous Coccinia grandis. Moreover, the role of organ identity genes during sex expression in Coccinia has not been evaluated earlier. Investigations on sexual phenotypes of C. grandis including a rare gynomonoecious (GyM) form and AgNO3 mediated sex modification have added a new dimension to the understanding of sex expression in dioecious flowering plants. RESULTS: Morphometric analysis showed the presence of staminodes in pistillate flowers and histological study revealed the absence of carpel initials in male flowers. Though GyM plant had XX sex chromosomes, the development of stamens occurred in hermaphrodite flowers but the pollens were not fertile. Silver nitrate (AgNO3) application enhanced stamen growth in wild type female flowers like that of GyM plant but here also the pollens were sterile. Differential expression of CgPI could be involved in the development of different floral phenotypes. CONCLUSIONS: The three principle factors, Gynoecium Suppression (SuF), Stamen Promoting Factor (SPF) and Male Fertility (mF) that control sex expression in dioecious C. grandis assumed to be located on Y chromosome, play a decisive role in determining maleness. However, the characteristic development of stamens in hermaphrodite flowers of GyM plant having XX sex chromosomes indicates that Y-linked SPF regulatory pathway is somehow bypassed. Our experimental findings together with all other previous chromosomal and molecular cytogenetical data strongly support the view that C. grandis could be used as a potential model system to study sex expression in dioecious flowering plant.

Conversion of viable but nonculturable enteric bacteria to culturable by co-culture with eukaryotic cells.

Viable but nonculturable (VBNC) Vibrio cholerae non-O1/non-O139, V. parahaemolyticus, enterohemorrhagic Escherichia coli, enterotoxigenic E. coli, enteropathogenic E. coli, Shigella flexneri, and Salmonella enterica were converted to the culturable state by co-culture with selected eukaryotic cells, e.g., HT-29, Caco-2, T84, HeLa, Intestine 407, and CHO cells.

Development of Ni(II) resistant S. cerevisiae and its application: Adsorption study and modeling.

The study aims to develop Ni(II) resistant Saccharomyces cerevisiae to decontaminate high Ni(II) concentrations from an aqueous system. Initially, two different microorganisms were taken: Bacillus circulans MTCC 3161, Saccharomyces cerevisiae. For these two strains, the experiments were carried out for successive screening for survival/tolerance, minimum inhibitory concentration (MIC), and biosorption capacity for Ni(II) from an aqueous solution. Ni(II) resistant Saccharomyces cerevisiae AJ208 showed a MIC of 5500 mg/L for Ni(II). Nucleotide sequences of Saccharomyces cerevisiae AJ208 were deposited in the Gene bank. All experiments were conducted to determine the effects of various physical conditions, such as pH, age and volume of inoculum, temperature, and incubation time, the volume of fermentation medium. The characterization of the Saccharomyces cerevisiae AJ208 was carried out using SEM-EDAX, FTIR. The Langmuir isotherm and pseudo-second-order kinetic models are well fitted with the experimental data. The Langmuir maximum adsorption capacity is 170.06 mg/g. The thermodynamic studies showed the mechanism of Ni(II) removal is an endothermic and spontaneous reaction. The experimental data have been analyzed using statistical method (MLR) and Genetic algorithm (GA). This study reports the highest Ni(II) resistant Saccharomyces cerevisiae AJ208 (5000 mg/L) and also the feasibility of Ni(II) removal from 3000 mg/L initial Ni(II) concentration into an aqueous solution, which could be of great interest as a potential reference strain for Ni(II) removal.

Fluorinated analogs of malachite green: synthesis and toxicity.

A series of fluorinated analogs of malachite green (MG) have been synthesized and their toxicity to Saccharomyces cerevisiae and a human ovarian epithelial cell line examined. The toxicity profiles were found to be different for these two species. Two analogs, one with 2,4-difluoro substitution and the other with 2-fluoro substitution seem to be the most promising analogs because they showed the lowest toxicity to the human cells.

Isolation of viable but nonculturable Vibrio cholerae O1 from environmental water samples in Kolkata, India, in a culturable state.

Previously, we reported that viable but nonculturable (VBNC) Vibrio cholerae was converted into a culturable state by coculture with several eukaryotic cell lines including HT-29 cells. In this study, we found that a factor converting VBNC V. cholerae into a culturable state (FCVC) existed in cell extracts of eukaryotic cells. FCVC was nondialyzable, proteinase K-sensitive, and stable to heating at <60°C for 5 min. We prepared thiosulfate citrate bile salts sucrose (TCBS) plates with FCVC (F-TCBS plates). After confirming that VBNC V. cholerae O1 and O139 formed typical yellow colonies on F-TCBS plates, we tried to isolate cholera toxin gene-positive VBNC V. cholerae from environmental water samples collected in urban slum areas of Kolkata, India and succeeded in isolating V. cholerae O1 El Tor variant strains harboring a gene for the cholera toxin. The possible importance of VBNC V. cholerae O1 as a source of cholera outbreaks is discussed.

Aptamers: multifunctional molecules for biomedical research.

Aptamers are single-stranded oligonucleotides that fold into well-defined three-dimensional shapes, allowing them to bind their targets with high affinity and specificity. They can be generated through an in vitro process called "Systemic Evolution of Ligands by Exponential Enrichment" and applied for specific detection, inhibition, and characterization of various targets like small organic and inorganic molecules, proteins, and whole cells. Aptamers have also been called chemical antibodies because of their synthetic origin and their similar modes of action to antibodies. They exhibit significant advantages over antibodies in terms of their small size, synthetic accessibility, and ability to be chemically modified and thus endowed with new properties. The first generation of aptamer drug "Macugen" was available for public use within 25 years of the discovery of aptamers. With others in the pipeline for clinical trials, this emerging field of medical biotechnology is raising significant interest. However, aptamers pose different problems for their development than for antibodies that need to be addressed to achieve practical applications. It is likely that current developments in aptamer engineering will be the basis for the evolution of improved future bioanalytical and biomedical applications. The present review discusses the development of aptamers for therapeutics, drug delivery, target validation and imaging, and reviews some of the challenges to fully realizing the promise of aptamers in biomedical applications.

Selection of the optimum font type and size interface for on screen continuous reading by young adults: an ergonomic approach.

There is a rapid shifting of media: from printed paper to computer screens. This transition is modifying the process of how we read and understand text. The efficiency of reading is dependent on how ergonomically the visual information is presented. Font types and size characteristics have been shown to affect reading. A detailed investigation of the effect of the font type and size on reading on computer screens has been carried out by using subjective, objective and physiological evaluation methods on young adults. A group of young participants volunteered for this study. Two types of fonts were used: Serif fonts (Times New Roman, Georgia, Courier New) and Sans serif fonts (Verdana, Arial, Tahoma). All fonts were presented in 10, 12 and 14 point sizes. This study used a 6 X 3 (font type X size) design matrix. Participants read 18 passages of approximately the same length and reading level on a computer monitor. Reading time, ranking and overall mental workload were measured. Eye movements were recorded by a binocular eye movement recorder. Reading time was minimum for Courier New l4 point. The participants' ranking was highest and mental workload was least for Verdana 14 point. The pupil diameter, fixation duration and gaze duration were least for Courier New 14 point. The present study recommends using 14 point sized fonts for reading on computer screen. Courier New is recommended for fast reading while for on screen presentation Verdana is recommended. The outcome of this study will help as a guideline to all the PC users, software developers, web page designers and computer industry as a whole.

Antibodies are challenged.

Studies on antibody were documented as early as in 1890. They are proteins found in blood or other body fluid of vertebrates, and are used by the immune system to identify and neutralize antigens (like foreign objects, pathogens like bacteria and virus etc). Antibodies are dominating the biomedical research field especially detection, imaging and inhibition of biological target molecules, and therapeutics so far. However, recently aptamer has been seen to compete with antibodies in all the above areas. Aptamers are single stranded oligonucleotides or peptides that fold into well defined three dimensional shapes, allowing them to bind their targets with high affinity and specificity. Aptamer technology is relatively new and discovered only in 1990. Because of synthetic origin and similar function as antibodies, they are often termed as chemical antibody. Within 25 years of discovery, the first generation of aptamer drug "Macugen" is already marketed and available for public use. The Global market for aptamer was $236 million in 2010 and is expected to be valued at nearly $1.8 billion by 2014, with a growing compound annual growth rate of 67.5%. Various drugs being on the pipeline for clinical trials this emerging field of medical biotechnology is raising significant interest. This article gives an overview how aptamers are similar yet distinctly different from antibodies in terms of synthesis, handling, and applicability.

An eye movement study for identification of suitable font characters for presentation on a computer screen.

We are experiencing a shifting of media: from the printed paper to the computer screen. This transition is modifying the process of how we read and understand a text. It is very difficult to conclude on suitability of font characters based upon subjective evaluation method only. Present study evaluates the effect of font type on human cognitive workload during perception of individual alphabets on a computer screen. Twenty six young subjects volunteered for this study. Here, subjects have been shown individual characters of different font types and their eye movements have been recorded. A binocular eye movement recorder was used for eye movement recording. The results showed that different eye movement parameters such as pupil diameter, number of fixations, fixation duration were less for font type Verdana. The present study recommends the use of font type Verdana for presentation of individual alphabets on various electronic displays in order to reduce cognitive workload.

Conversion of viable but nonculturable Vibrio cholerae to the culturable state by co-culture with eukaryotic cells.

VBNC Vibrio cholerae O139 VC-280 obtained by incubation in 1% solution of artificial sea water IO at 4°C for 74 days converted to the culturable state when co-cultured with CHO cells. Other eukaryotic cell lines, including HT-29, Caco-2, T84, HeLa, and Intestine 407, also supported conversion of VBNC cells to the culturable state. Conversion of VBNC V. cholerae O1 N16961 and V. cholerae O139 VC-280/pG13 to the culturable state, under the same conditions, was also confirmed. When VBNC V. cholerae O139 VC-280 was incubated in 1% IO at 4°C for up to 91 days, the number of cells converted by co-culture with CHO cells declined with each additional day of incubation and after 91 days conversion was not observed.

Effects of luteinizing hormone on peroxisome proliferator-activated receptor gamma in the rat ovary before and after the gonadotropin surge.

We have shown previously that mRNA for peroxisome proliferator-activated receptor gamma (PPARgamma) is expressed in granulosa cells and downregulated by the luteinizing hormone (LH) surge. The current studies were undertaken to test the hypothesis that LH stimulates a decrease in the expression of PPARgamma, as well as its activity, in granulosa cells. Ovaries were collected from immature rats 0 and 48 h after they received pregnant mares' serum gonadotropin (PMSG), and 4 and 24 h after administration of human chorionic gonadotropin (hCG), and used for protein isolation or processed for immunolocalization of PPARgamma. The amount of phosphorylated PPARgamma was measured by immunoblot analysis to determine how LH affects the phosphorylation status, and therefore the activity, of PPARgamma. Granulosa cells were also collected from immature rats 48 h after PMSG. Cells were cultured with LH in the absence and presence of H89 and cycloheximide to investigate the role of PKA and protein synthesis in the LH-mediated decline in mRNA for PPARgamma respectively. Protein corresponding to PPARgamma was localized to nuclei of granulosa cells 0 and 48 h after PMSG. Expression was greatly reduced by 4 h after hCG, with expression in mural granulosa cells lost before that in cumulus cells. The amount of phosphorylated PPARgamma did not change during the periovulatory period. Blocking PKA activity had no effect on levels of mRNA for PPARgamma. However, levels of mRNA for PPARgamma were significantly increased in cells treated with cycloheximide (P < 0.05, ANOVA followed by Tukey's HSD). These data suggest that PPARgamma is tightly regulated in the ovary and that its expression is the primary mechanism by which LH influences the activity of PPARgamma. In addition, protein synthesis may be involved in modulating levels of PPARgamma in granulosa cells.