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Nitrification and denitrification are soil biological processes responsible for large nitrogen losses from agricultural soils and generation of the greenhouse gas (GHG) N

Flux balance analysis (FBA) and ordinary differential equation models have been instrumental in depicting the metabolic functioning of a cell. Nevertheless, they demonstrate a population's average behavior (summation of individuals), thereby portraying homogeneity. However, living organisms such as

There are three prominent alcohol dehydrogenases superfamilies: short-chain, medium-chain, and iron-containing alcohol dehydrogenases (FeADHs). Many members are valuable catalysts for producing industrially relevant products such as active pharmaceutical intermediates, chiral synthons, biopolymers, biofuels, and secondary metabolites. However, FeADHs are the least explored enzymes among the superfamilies for commercial tenacities. They portray a conserved structure having a "tunnel-like" cofactor and substrate binding site with particular functions, despite representing high sequence diversity. Interestingly, phylogenetic analysis demarcates enzymes catalyzing distinct native substrates where closely related clades convert similar molecules. Further, homologs from various mesophilic and thermophilic microbes have been explored for designing a solvent and temperature-resistant enzyme for industrial purposes. The review explores different iron-containing alcohol dehydrogenases potential engineering of the enzymes and substrates helpful in manufacturing commercial products.

Legumes are the most important crop plants in agriculture, contributing 27% of the world's primary food production. However, productivity and production of Legumes is reduced due to increasing environmental stress. Hence, there is a pressing need to understand the molecular mechanism involved in stress response and legumes adaptation. Proteomics provides an important molecular approach to investigate proteins involved in stress response. Both the gel-based and gel-free-based techniques have significantly contributed to understanding the proteome regulatory network in leguminous plants. In the present review, we have discussed the role of different proteomic approaches (2-DE, 2 D-DIGE, ICAT, iTRAQ, etc.) in the identification of various stress-responsive proteins in important leguminous crops, including soybean, chickpea, cowpea, pigeon pea, groundnut, and common bean under variable abiotic stresses including heat, drought, salinity, waterlogging, frost, chilling and metal toxicity. The proteomic analysis has revealed that most of the identified differentially expressed proteins in legumes are involved in photosynthesis, carbohydrate metabolism, signal transduction, protein metabolism, defense, and stress adaptation. The proteomic approaches provide insights in understanding the molecular mechanism of stress tolerance in legumes and have resulted in the identification of candidate genes used for the genetic improvement of plants against various environmental stresses. Identifying novel proteins and determining their expression under different stress conditions provide the basis for effective engineering strategies to improve stress tolerance in crop plants through marker-assisted breeding.

Preventing nosocomial infection is a major unmet need of our times. Existing air decontamination technologies suffer from demerits such as toxicity of exposure, species specificity, noxious gas emission, environment-dependent performance and high power consumption. Here, we present a novel technology called “ZeBox” that transcends the conventional limitations and achieves high microbicidal efficiency. In ZeBox, a non-ionizing electric field extracts naturally charged microbes from flowing air and deposits them on engineered microbicidal surfaces. The surface’s three dimensional topography traps the microbes long enough for them to be inactivated. The electric field and chemical surfaces synergistically achieve rapid inactivation of a broad spectrum of microbes. ZeBox achieved near complete kill of airborne microbes in challenge tests (5–9 log reduction) and $$>90\%$$ > 90 % efficiency in a fully functional stem cell research facility in the presence of humans. Thus, ZeBox fulfills the dire need for a real-time, continuous, safe, trap-and-kill air decontamination technology.

The adaptive radiation of Bromeliaceae (pineapple family) is one of the most diverse among Neotropical flowering plants. Diversification in this group was facilitated by shifts in several adaptive traits or "key innovations" including the transition from C3 to CAM photosynthesis associated with xeric (heat/drought) adaptation. We used phylogenomic approaches, complemented by differential gene expression (RNA-seq) and targeted metabolite profiling, to address the mechanisms of C3 /CAM evolution in the extremely species-rich bromeliad genus, Tillandsia, and related taxa. Evolutionary analyses of whole-genome sequencing and RNA-seq data suggest that evolution of CAM is associated with coincident changes to different pathways mediating xeric adaptation in this group. At the molecular level, C3 /CAM shifts were accompanied by gene expansion of XAP5 CIRCADIAN TIMEKEEPER homologs, a regulator involved in sugar- and light-dependent regulation of growth and development. Our analyses also support the re-programming of abscisic acid-related gene expression via differential expression of ABF2/ABF3 transcription factor homologs, and adaptive sequence evolution of an ENO2/LOS2 enolase homolog, effectively tying carbohydrate flux to abscisic acid-mediated abiotic stress response. By pinpointing different regulators of overlapping molecular responses, our results suggest plausible mechanistic explanations for the repeated evolution of correlated adaptive traits seen in a textbook example of an adaptive radiation.

Summary Genotyping‐by‐sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are emerging providing 1000 and more genotypes and millions of SNPs for one species covering a hitherto inaccessible intraspecific genetic variation. The larger the databases are growing, the better statistical approaches for genomic selection will be available. However, there are clear limitations on the statistical but also on the biological part. Intraspecific genetic variation is able to explain a high proportion of the phenotypes, but a large part of phenotypic plasticity also stems from environmentally driven transcriptional, post‐transcriptional, translational, post‐translational, epigenetic and metabolic regulation. Moreover, regulation of the same gene can have different phenotypic outputs in different environments. Consequently, to explain and understand environment‐dependent phenotypic plasticity based on the available genotype variation we have to integrate the analysis of further molecular levels reflecting the complete information flow from the gene to metabolism to phenotype. Interestingly, metabolomics platforms are already more cost‐effective than NGS platforms and are decisive for the prediction of nutritional value or stress resistance. Here, we propose three fundamental pillars for future breeding strategies in the framework of Green Systems Biology: (i) combining genome selection with environment‐dependent PANOMICS analysis and deep learning to improve prediction accuracy for marker‐dependent trait performance; (ii) PANOMICS resolution at subtissue, cellular and subcellular level provides information about fundamental functions of selected markers; (iii) combining PANOMICS with genome editing and speed breeding tools to accelerate and enhance large‐scale functional validation of trait‐specific precision breeding.

Ramón y Cajal Programme (RYC-2015-17871, Spanish Ministry of Economy and Competitiveness); Programa de Ayudas Predoctorales Severo Ochoa, Autonomous Community of Asturias, Spain; Spanish Ministry of Universities fellowship (FPU19/01142)

BackgroundDespite rigorous disinfection, fumigation and air treatment, infectious microbial load has been found to circulate and survive for significant durations in health care settings. This raises significant concerns for hospital acquired infections. We have developed a novel, hybrid, trap- and-kill airborne-microbicidal technology called “ZeBox” which is efficient in clearing 99.999% of airborne microbial load under controlled lab conditions. In this study we evaluate the clinical performance of the ZeBox in reducing airborne and surface microbial load in two independent hospital settings.MethodsThe studies were conducted in single bed and multi bed ICU of two hospitals. Airborne and surface microbial loads were collected at pre-determined sampling sites pre- and post-deployment of the ZeBox enabled device. The Normality of data distribution was determined using the Shapiro-Wilk test. Statistical significance was determined using Students’ T test and Mann-Whitney’s U test. Pathogenic and opportunistic organisms were characterized using 16S rDNA sequencing. Furthermore, the antibiotic sensitivity of the isolated organisms was tested against current treatments of choice across major antibiotic classes.ResultsPost-deployment, we found statistically significant reductions in both airborne and surface microbial load within the operating range of the ZeBox enabled technology. Across the both hospital ICUs, there was 90% reduction of airborne microbial load on average, and 75% reduction of surface microbial load on average, providing a low bioburden zone of roughly 10-15 feet diameter around the unit. These reduced microbial levels were maintained during the entire duration of device operation over several weeks. Many of the clinical isolates recovered from one of the hospitals were drug resistant, which highlighted the potential ability of ZeBox to eliminate drug-resistant microbes and thereby reduce the frequency of hospital acquired infections.ConclusionsZeBox enabled technology can significantly reduce a broad spectrum of microbial burden in air and on surfaces in clinical settings. It can thereby serve an unmet need in reducing the incidence of hospital acquired infections.

Preventing nosocomial infection is a major unmet need of our times. Existing air decontamination technologies suffer from demerits such as toxicity of exposure, species specificity, noxious gas emission, environment-dependent performance and high power consumption. Here, we present a novel technology called “ZeBox” that transcends the conventional limitations and achieves high microbicidal efficiency. In ZeBox, a non-ionizing electric field extracts naturally charged microbes from flowing air and deposits them on engineered microbicidal surfaces. The surface’s three dimensional topography traps the microbes long enough for them to be inactivated. The electric field and chemical surfaces synergistically achieve rapid inactivation of a broad spectrum of microbes. ZeBox achieved near complete kill of airborne microbes in challenge tests (5-9 log reduction) and >90% efficiency in a fully functional stem cell research facility in the presence of humans. Thus, ZeBox fulfills the dire need for a real-time, continuous, safe, trap-and-kill air decontamination technology.

Short-chain dehydrogenases/reductases (SDRs) are a convenient class of enzymes used to synthesize enantiopure alcohols. Several studies describe native or engineered SDRs for converting substrates of interest using cost and time-intensive high-throughput approaches. The classification of SDRs is based on chain length and cofactor binding site. Of these, the shorter ‘Classical’ and the longer ‘Extended’ enzymes participate in ketoreduction. However, comparative analysis of various modelled SDRs reveals a length independent conserved N-terminal Rossmann fold and a variable C-terminus region for both types. The general hypothesis is that the latter domain influences the enzyme’s flexibility that may affect the observed promiscuity of the enzyme. We have used a machine learning algorithm on this flexible domain to build a rationale to screen promiscuous candidates. We have built a data set consisting of physicochemical properties derived from the amino-acid composition of enzymes to select closely associated promiscuous mesophilic enzymes. The resulting in vitro studies on pro-pharmaceutical substrates illustrate a direct correlation between the C-terminal lid-loop structure, enzyme melting temperature and the turnover number. We present a walkthrough for exploring promiscuous SDRs for catalyzing enantiopure alcohols of industrial importance.

Grain filling and grain development are essential biological processes in the plant’s life cycle, eventually contributing to the final seed yield and quality in all cereal crops. Studies of how the different wheat (Triticum aestivum L.) grain components contribute to the overall development of the seed are very scarce. We performed a proteomics and metabolomics analysis in four different developing components of the wheat grain (seed coat, embryo, endosperm, and cavity fluid) to characterize molecular processes during early and late grain development. In-gel shotgun proteomics analysis at 12, 15, 20, and 26 days after anthesis (DAA) revealed 15 484 identified and quantified proteins, out of which 410 differentially expressed proteins were identified in the seed coat, 815 in the embryo, 372 in the endosperm, and 492 in the cavity fluid. The abundance of selected protein candidates revealed spatially and temporally resolved protein functions associated with development and grain filling. Multiple wheat protein isoforms involved in starch synthesis such as sucrose synthases, starch phosphorylase, granule-bound and soluble starch synthase, pyruvate phosphate dikinase, 14-3-3 proteins as well as sugar precursors undergo a major tissue-dependent change in abundance during wheat grain development suggesting an intimate interplay of starch biosynthesis control. Different isoforms of the protein disulfide isomerase family as well as glutamine levels, both involved in the glutenin macropolymer pattern, showed distinct spatial and temporal abundance, revealing their specific role as indicators of wheat gluten quality. Proteins binned into the functional category of cell growth/division and protein synthesis/degradation were more abundant in the early stages (12 and 15 DAA). At the metabolome level all tissues and especially the cavity fluid showed highly distinct metabolite profiles. The tissue-specific data are integrated with biochemical networks to generate a comprehensive map of molecular processes during grain filling and developmental processes.

Roots secrete a vast array of low molecular weight compounds into the soil broadly referred to as root exudates. It is a key mechanism by which plants and soil microbes interact in the rhizosphere. The effect of drought stress on the exudation process and composition is rarely studied, especially in cereal crops. This study focuses on comparative metabolic profiling of the exudates from sensitive and tolerant genotypes of pearl millet after a period of drought stress. We employed a combined platform of gas and liquid chromatography coupled to mass spectrometry to cover both primary and secondary metabolites. The results obtained demonstrate that both genotype and drought stress have a significant impact on the concentration and composition of root exudates. The complexity and function of these differential root exudates are discussed. To reveal the potential effect of root exudates on the soil microbial community after a period of drought stress, we also tested for biological nitrification inhibition (BNI) activity. The analysis revealed a genotype-dependent enhancement of BNI activity after a defined period of drought stress. In parallel, we observed a genotype-specific relation of elongated root growth and root exudation under drought stress. These data suggest that the drought stress-dependent change in root exudation can manipulate the microbial soil communities to adapt and survive under harsh conditions.The online version contains supplementary material available at 10.1007/s00374-021-01578-w.

Being rooted in place, plants are faced with the challenge of responding to unfavourable local conditions. One such condition, heat stress, contributes massively to crop losses globally. Heatwaves are predicted to increase, and it is of vital importance to generate crops that are tolerant to not only heat stress but also to several other abiotic stresses (e.g. drought stress, salinity stress) to ensure that global food security is protected. A better understanding of the molecular mechanisms that underlie the temperature stress response in pollen will be a significant step towards developing effective breeding strategies for high and stable production in crop plants. While most studies have focused on the vegetative phase of plant growth to understand heat stress tolerance, it is the reproductive phase that requires more attention as it is more sensitive to elevated temperatures. Every phase of reproductive development is affected by environmental challenges, including pollen and ovule development, pollen tube growth, male-female cross-talk, fertilization, and embryo development. In this review we summarize how pollen is affected by heat stress and the molecular mechanisms employed during the stress period, as revealed by classical and -omics experiments.

Nosocomial infections, also known as hospital-acquired infections (HAI), appear 48 hours or more after hospital admission and are independent of the original infirmity of the patient. To prevent or to reduce HAI, the central paradigm is to construct protective barriers between the large number of people who are sick and whose immune systems are compromised in the precincts of the hospital. Microbes that result in HAI do so by two routes of infection: touch and aerosol. We describe here ZeBox technology, a voltage induced synergistic killing of the microbe on designed surfaces, as a game-changer in this domain. Its kill rate is hitherto unmatched by any known chemical or non-chemical (viz; UV, ionisation) technology. In an enclosed test chamber, under challenge conditions, ZeBox technology can kill about a billion microbes in 10 minutes. When tested under clinical settings, the device could effectively reduce microbes, both from air and surfaces with more than 90% efficiency. The optimum requirement to reduce HAI would be to construct an online microbicidal device that operates in a continuous trap and kill mode in the background of people and patient movement, and decontaminates air and surfaces. We present unequivocal data to fortify our claims of online, continuous, safe, trap and kill mechanism of ZeBox technology.

Pigeonpea [Cajanus cajan (L.) Millsp.] is a pulse crop cultivated in the semi‐arid regions of Asia and Africa. It is a rich source of protein and capable of alleviating malnutrition, improving soil health and the livelihoods of small‐holder farmers. Hybrid breeding has provided remarkable improvements for pigeonpea productivity, but owing to a tedious and costly seed production system, an alternative two‐line hybrid technology is being explored. In this regard, an environment‐sensitive male sterile line has been characterized as a thermosensitive male sterile line in pigeonpea precisely responding to day temperature. The male sterile and fertile anthers from five developmental stages were studied by integrating transcriptomics, proteomics and metabolomics supported by precise phenotyping and scanning electron microscopic study. Spatio‐temporal analysis of anther transcriptome and proteome revealed 17 repressed DEGs/DEPs in sterile anthers that play a critical role in normal cell wall morphogenesis and tapetal cell development. The male fertility to sterility transition was mainly due to a perturbation in auxin homeostasis, leading to impaired cell wall modification and sugar transport. Limited nutrient utilization thus leads to microspore starvation in response to moderately elevated day temperature which could be restored with auxin‐treatment in the male sterile line. Our findings outline a molecular mechanism that underpins fertility transition responses thereby providing a process‐oriented two‐line hybrid breeding framework for pigeonpea.

The E. coli metabolome is an interconnected set of enzymes that has measurable kinetic parameters ascribed for the production of most of its metabolites. Flux Balance Analysis (FBA) or Ordinary Differential Equation (ODE) models are used to simulate and increase product yield using defined media. However, such simulations either give a range (min-max) of the metabolite yield for FBA model or tries to enumerate the exact production in the ODE models. The transcriptome expression diversity of the individual cells are not taken into account. We formulate the metabolic behaviour of individual cells by using a robust POpulation SYstem Biology ALgorithm (POSYBAL). This allowed for predicted multiple gene knockouts for increasing homologous metabolite like shikimate and heterologous metabolite like isobutanol. We demonstrate the performance one such triple knockout prediction viz. adhE, ackA and ldhA for isobutanol and aroK, aroA and aroL triple knockout for shikimate. The isobutanol yield increased by 40 times in the knockouts (>2000 ppm) compared to 50ppm produced in the wild-type (BL21) strain, and the shikimate yield was increased to 42 times, i.e. from 58 to ~2100ppm. This formulation was also based on the additional concept of “Nitrogen Swapping” where cells were grown in standard multi-component media during the growth phase and then swapped in low Nitrogen media in the production phase. This swap redistributed the flux distribution such that it flowed primarily through non-nitrogenous pathway such as to maximize the metabolites like shikimate and isobutanol that lack the element Nitrogen in its constituent. Further analysis of various feature of the prediction of the POSYBAL model indicates that even under normal glucose uptake the bacterial cell population diverges into rapidly growing and nearly non-growing cells thus increasing its diversity and hence robustness under any antibacterial attack. This feature is discussed from an evolutionary standpoint.

Draft genome, 994 re-sequenced lines and GWAS for yield-traits provide a resource of genetics and genomics tools for pearl millet researchers and breeders. Supplementary information The online version of this article (doi:10.1038/nbt.3943) contains supplementary material, which is available to authorized users., Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop. Supplementary information The online version of this article (doi:10.1038/nbt.3943) contains supplementary material, which is available to authorized users.

Hand washing is the practice which can save us from a vast spectrum of communicable diseases. The primary schools toilets and community toilets usually have wash basins or platforms built at a particular height. It has been observed that due to the height of these wash basins; it becomes unapproachable for small children. Also, limited numbers of taps discourage children from practising hand washing. Keeping these factors in view and to promote the practice of hand washing among school children, Save the children has come up with a unique design of three stage hand washing platforms. The design of the platform is child friendly and allows children of every age group to wash their hands comfortably irrespective of their height.

The adaptive radiation of Bromeliaceae (pineapple family) is one of the most diverse among Neotropical flowering plants. Diversification in this group was facilitated by several ‘key innovations’ including the transition from C3 to CAM photosynthesis. We used a phylogenomic approach complemented by differential gene expression (RNA-seq) and targeted metabolite profiling to address the patterns and mechanisms of C3/CAM evolution in the extremely species-rich bromeliad genus Tillandsia and related taxa. Evolutionary analyses at a range of different levels (selection on protein-coding genes, gene duplication and loss, regulatory evolution) revealed three common themes driving the evolution of CAM: response to heat and drought, alterations to basic carbohydrate metabolism, and regulation of organic acid storage. At the level of genes and their products, CAM/C3 shifts were accompanied by gene expansion of a circadian regulator, re-programming of ABA-related gene expression, and adaptive sequence evolution of an enolase, effectively linking carbohydrate metabolism to ABA-mediated stress response. These changes include several pleiotropic regulators, which facilitated the evolution of correlated adaptive traits during a textbook adaptive radiation.

Pearl millet is the fifth most important cereal crop worldwide and cultivated especially by small holder farmers in arid and semi-arid regions because of its drought and salt tolerance. The molecular mechanisms of drought stress tolerance in Pennisetum remain elusive. We have used a shotgun proteomics approach to investigate protein signatures from different tissues under drought and control conditions. Drought stressed plants showed significant changes in stomatal conductance and increased root growth compared to the control plants. Root, leaf and seed tissues were harvested and 2281 proteins were identified and quantified in total. Leaf tissue showed the largest number of significant changes (120), followed by roots (25) and seeds (10). Increased levels of root proteins involved in cell wall-, lipid-, secondary- and signaling metabolism and the concomitantly observed increased root length point to an impaired shoot-root communication under drought stress. The harvest index (HI) showed a significant reduction under drought stress. Proteins with a high correlation to the HI were identified using sparse partial least square (sPLS) analysis. Considering the importance of Pearl millet as a stress tolerant food crop, this study provides a first reference data set for future investigations of the underlying molecular mechanisms.Drought stress is the most limiting factor for plant growth and crop production worldwide. At the same time drought susceptible cereal crops are among the largest producers worldwide. In contrast, Pearl millet is a drought and salt tolerant cereal crop especially used in arid and semi-arid regions by small farmers. The multifactorial molecular mechanisms of this unique drought tolerance are not known. Here, we employ shotgun proteomics for a first characterization of the Pearl millet drought stress proteome. The experimental setup and the data set generated from this study reveal comprehensive physiological and proteomic responses of the drought stressed Pearl millet plants. Our study reveals statistically significant tissue-specific protein signatures during the adaptation to drought conditions. Thus, the work provides a first reference study of the drought stress proteome and related drought responsive proteins (DRP's) in Pearl millet.

Key message Pollen development and stress. Abstract In angiosperms, pollen or pollen grain (male gametophyte) is a highly reduced two- or three-cell structure which plays a decisive role in plant reproduction. Male gametophyte development takes place in anther locules where diploid sporophytic cells undergo meiotic division followed by two consecutive mitotic processes. A desiccated and metabolically quiescent form of mature pollen is released from the anther which lands on the stigma. Pollen tube growth takes place followed by double fertilization. Apart from its importance in sexual reproduction, pollen is also an interesting model system which integrates fundamental cellular processes like cell division, differentiation, fate determination, polar establishment, cell to cell recognition and communication. Recently, pollen functionality has been studied by multidisciplinary approaches which also include OMICS analyses like transcriptomics, proteomics and metabolomics. Here, we review recent advances in proteomics of pollen development and propose the process of developmental priming playing a key role to guard highly sensitive developmental processes.

Pollen cells possess specialized cellular compartments separated by membranes. Consequently, mature pollen contains proteinaceous factors for inter- and intracellular transport of metabolites or ions to facilitate the upcoming energy exhausting processes — germination and fertilization. Despite the current advancement in the understanding of pollen development little is known about the role and molecular nature of the membrane proteome that participates in functioning and development of male gametophyte. We dissected the membrane proteome of mature pollen from economically important crop Solanum lycopersicum (tomato). Isolated membrane fractions from mature pollen of two tomato cultivars (cv. Moneymaker and cv. Red setter) were subjected to shotgun proteomics (GEL-LC–Orbitrap-MS). The global tomato protein assignment was achieved by mapping the peptides on reference genome (cv. Heinz 1706) and de novo assembled transcriptome based on mRNA sequencing from the respective cultivar. We identified 687 proteins, where 176 were assigned as putative membrane proteins. About 58% of the identified membrane proteins participate in transport processes. In depth analysis revealed proteins corresponding to energy related pathways (Glycolysis and Krebs cycle) as prerequisite for mature pollen, thereby revealing a reliable model of energy reservoir of the male gametophyte. Biological significance Mature pollen plays an indispensable role in plant fertility and crop production. To decipher the functionality of pollen global proteomics studies have been undertaken. However, these datasets are deficient in membrane proteins due to their low abundance and solubility. The work presented here provides a comprehensive investigation of membrane proteome of male gametophyte of an agriculturally important crop plant tomato. The analysis of membrane enriched fractions from two tomato cultivars ensured an effective profiling of the pollen membrane proteome. Particularly proteins of the Krebs cycle or the glycolysis process have been detected and thus a model for the energy dynamics and preparedness of the male gametophyte for the upcoming events — germination and fertilization is provided.

Neisseria cinerea is a commensal which usually resides in the human respiratory tract. Very rarely, the organism finds its way into the bloodstream causing severe bacteremia. So far, very few cases of Neisseria bacteremia have been reported. We report a case of a 78-year-old male, post-splenectomy, who presented with high fever, cough and shortness of breath. The patient was initially managed for septic shock with fluid resuscitations, vasopressors and broad-spectrum antibiotics. Later, the blood cultures grew gram-negative coccobacilli, Neisseria cinerea. The patient was successfully treated with intravenous ceftriaxone. This is the first case ever of Neisseria cinerea bacteremia in a post-splenectomy patient and ninth case overall. This case illustrates that the physicians should maintain heightened awareness for Neisseria cinerea bacteremia in post-splenectomy patients.

Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics. It also describes the workflow of measuring metabolites in plants. Metabolomic studies in plant responses to stress are a key research topic in many laboratories worldwide. We summarize different approaches and provide a generic overview of stress responsive metabolite markers and processes compiled from a broad range of different studies. Graphical Abstract.

Recently, we have developed a quantitative shotgun proteomics strategy called mass accuracy precursor alignment (MAPA). The MAPA algorithm uses high mass accuracy to bin mass-to-charge (m/z) ratios of precursor ions from LC-MS analyses, determines their intensities, and extracts a quantitative sample versus m/z ratio data alignment matrix from a multitude of samples. Here, we introduce a novel feature of this algorithm that allows the extraction and alignment of proteotypic peptide precursor ions or any other target peptide from complex shotgun proteomics data for accurate quantification of unique proteins. This strategy circumvents the problem of confusing the quantification of proteins due to indistinguishable protein isoforms by a typical shotgun proteomics approach. We applied this strategy to a comparison of control and heat-treated tomato pollen grains at two developmental stages, post-meiotic and mature. Pollen is a temperature-sensitive tissue involved in the reproductive cycle of plants and plays a major role in fruit setting and yield. By LC-MS-based shotgun proteomics, we identified more than 2000 proteins in total for all different tissues. By applying the targeted MAPA data-processing strategy, 51 unique proteins were identified as heat-treatment-responsive protein candidates. The potential function of the identified candidates in a specific developmental stage is discussed.

We established and elaborated on a method to enrich the membrane proteome of mature pollen from economically relevant crop using the example of Solanum lycopersicum (tomato). To isolate the pollen protein fraction enriched in membrane proteins, a high salt concentration (750 mM of sodium chloride) was used. The membrane protein-enriched fraction was then subjected to shotgun proteomics for identification of proteins, followed by in silico analysis to annotate and classify the detected proteins.

The metabolome of an organism represents the readout of its biochemistry comprising numerous and tightly regulated metabolic pathways. Experimental analysis of the metabolome and its interpretation in a biochemically and physiologically meaningful context is focused by the research field of metabolomics which has become an integral part of many systems biological studies. Pollen development, germination and tube growth comprise numerous steps of metabolic regulation resulting in significant metabolome dynamics. To unravel involved regulatory molecular processes and to promote the understanding of developmental reprogramming and stress tolerance mechanisms in pollen, it is crucial to quantitatively resolve dynamics in the pollen metabolome. Since these dynamics affect various substance groups with different physico-chemical properties, different experimental platforms are needed for robust compound identification and quantification. It has been shown that developmentally and stress-induced metabolic reprogramming in pollen significantly affects the redox homeostasis as well as metabolism of carbohydrates, amino acids, lipids, polyamines, flavonoids and phytohormones. In this chapter, mechanisms of metabolic reprogramming are summarized and discussed in the context of pollen development and stress exposure. Finally, it is discussed how these metabolome dynamics can be resolved methodologically in order to unravel molecular physiological mechanisms of pollen development.

Short-chain dehydrogenase reductases (SDRs) have been utilized for catalyzing the reduction of many aromatic/aliphatic prochiral ketones to their respective alcohols. However, there is a paucity of data that elucidates their innate biological role and diverse substrate space. In this study, we executed an in-depth biochemical characterization and substrate space mapping (with 278 prochiral ketones) of an unannotated SDR (DHK) from Debaryomyces hansenii and compared it with structurally and functionally characterized SDR Synechococcus elongatus. PCC 7942 FabG to delineate its industrial significance. It was observed that DHK was significantly more efficient than FabG, reducing a diverse set of ketones albeit at higher conversion rates. Comparison of the FabG structure with a homology model of DHK and a docking of substrate to both structures revealed the presence of additional flexible loops near the substrate binding site of DHK. The comparative elasticity of the cofactor and substrate binding site of FabG and DHK was experimentally substantiated using differential scanning fluorimetry. It is postulated that the loop flexibility may account for the superior catalytic efficiency of DHK although the positioning of the catalytic triad is conserved.

Indian grape wines are analyzed for total phenolic content and antioxidant activity along with other parameters, such as pH, alcohol content, and reducing sugars. Concentration of polyphenols, like tannic acid, catechol, vanillin, caeffic acid, ferullic acid, and resveratrol, was quantified using reverse phase-high performance liquid chromatography and ultra high performance liquid chromatography. The red wines showed the highest concentration of phenolic content (6.5 ± 0.1 mg/ml) and antioxidant activity (84.60 ± 1%) as compared to white and port wines, while red wine R2 showed the highest radical scavenging activity among red wines and R4 showed the lowest total phenolic content. The white wine W3 showed less total phenolic content and antioxidant activity. Further, a positive correlation between phenolic content and antioxidant activity was observed.

Black gram (Vigna mungo L. Hepper), is an extensively studied food crop which is affected by many abiotic and biotic factors, especially diseases. The yield potential of Black gram is shallow due to lack of genetic variability and biotic stress susceptibility. Core biotic stress factors include mung bean yellow mosaic virus (MYMV), urdbean leaf crinkle virus (UCLV), wilt (Fusarium oxysporum) and powdery mildew (Erysiphe polygoni DC). Although many studies determine resistant varieties to a particular disease, however, it is often complimented by low yield and susceptibility to other diseases. Hence, this study focuses on investigating the genetic relationships among three varieties and nine accessions of black gram having disease resistance to previously described diseases and susceptibility using random amplified polymorphic deoxyribonucleic acid (RAPD) markers. A total of 33 RAPD primers were used for diversity analysis and yielded 206 fragments. Number of amplified fragments ranged from two (OPN-1) to 13 (OPF-1). The highest similarity coefficient was observed between IC-145202 and IC-164118 (0.921), while lowest similarity was between PU-31 and IC-145202 (0.572). The genetic diversity obtained in this study along with disease analysis suggests PU31as a useful variety for the development of markers linked to MYMV, UCLV, wilt and powdery mildew resistance by marker-assisted back cross breeding and facilitates the production of crosses with multiple disease resistance.

Woodfordia fruticosa Kurz is a member of family Lythraceae, commonly used in the treatment of diseases like leucorrhoea, dysentery, leprosy and menorrhagia. The plant material such as leaves, bark and flowers were collected from three different (200, 402 and 600 m) altitudes of Khandala (M.S. India) and the extracts were prepared in solvents like methanol, ethanol and distilled water. The radical scavenging potential and total phenolic content of the extracts were evaluated. The methanol extract of bark collected from the location one (200 m) showed high radical scavenging activity (96.52 ± 0.02) than distilled water and ethanol extracts (57.80 ± 0.2 and 86.52 ± 0.03). The bark of the plant showed highest (663 ± 37.85) total phenolic content that of flowers and leaves. The methanol extracts of leaves, bark and flowers showed high tannic acid content, while TBARS assay of ethanol extract of flowers showed maximum protection (27.65). It was observed that there is no significant difference in percent scavenging activity in different plant parts collected from three different altitudes but showed difference in the solvent system used. The results obtained are in support of extensive use of Woodfordia fruticosa in traditional medicine and endorses the use of bark, while it needs further investigations on the plants growing in different geographic areas.