The Promises and the Challenges of Biotransformations in Microflow

The challenges of transition toward the postpetroleum world shed light on the biocatalysis as the most sustainable way for the valorization of biobased raw materials. However, its industrial exploitation strongly relies on integration with innovative technologies such as microscale processing. Microflow devices remarkably accelerate biocatalyst screening and engineering, as well as evaluation of process parameters, and intensify biocatalytic processes in multiphase systems. The inherent feature of microfluidic devices to operate in a continuous mode brings additional interest for their use in chemoenzymatic cascade systems and in connection with the downstream processing units. Further steps toward automation and analytics integration, as well as computer‐assisted process development, will significantly affect the industrial implementation of biocatalysis and fulfill the promises of the bioeconomy. This review provides an overview of recent examples on implementation of microfluidic devices into various stages of biocatalytic process development comprising ultrahigh‐throughput biocatalyst screening, highly efficient biocatalytic process design including specific immobilization techniques for long‐term biocatalyst use, integration with other (bio)chemical steps, and/or downstream processing.     

Applying Imaging Genetics to ADHD: the Promises and the Challenges

Attention deficit/hyperactivity disorder (ADHD) is one of the most prevalent childhood psychiatric disorders. During the past decades, studies have focused on its genetic background and the abnormality of the brain structure and function. Recently, an advanced technique linking these two areas, namely, the imaging genetics emerged and kept growing. Imaging genetics primarily identifies genes that influence the brain variations. There are three main strategies of doing an imaging genetic study: using neuroimaging as endophenotypes to find the associated DNA variants, finding neuroimaging effects of risk genes, and hypothesis-free whole-brain voxelwise genome-wide association study. In this review, we begin with demonstrating the basic principles of imaging genetics precisely, with examples from other psychiatric conditions, and then go on to synthesize the existing imaging genetic studies in ADHD. Finally, we elaborate the challenges of applying imaging genetics to ADHD. We conclude that imaging genetics has somewhat showed its potential to provide a more precise understanding of how the genes shape the brain variations and further the clinical features of ADHD.     

Biomass Yield and Nutrient Responses of Switchgrass to Phosphorus Application

Increasing desire for renewable energy sources has increased research on biomass energy crops in marginal areas with low potential for food and fiber crop production. In this study, experiments were established on low phosphorus (P) soils in southern Oklahoma, USA to determine switchgrass biomass yield, nutrient concentrations, and nutrient removal responses to P and nitrogen (N) fertilizer application. Four P rates (0, 15, 30, and 45?kg?P?ha^?1) and two N fertilizer rates (0 and 135?kg?N?ha^?1) were evaluated at two locations (Ardmore and Waurika) for 3?years. While P fertilization had no effect on yield at Ardmore, application of 45?kg?P?ha^?1 increased yield at Waurika by 17% from 10.5 to 12.3?Mg?ha^?1. Across P fertilizer rates, N fertilizer application increased yields every year at both locations. In Ardmore, non-N-fertilized switchgrass produced 3.9, 6.7, and 8.8?Mg?ha^?1, and N-fertilized produced 6.6, 15.7, and 16.6?Mg?ha^?1 in 2008, 2009, and 2010, respectively. At Waurika, corresponding yields were 7.9, 8.4, and 12.2?Mg?ha^?1 and 10.0, 12.1, and 15.9?Mg?ha^?1. Applying 45?kg?P?ha^?1 increased biomass N, and P concentration and N, P, potassium, and magnesium removal at both locations. Increased removal of nutrients with N fertilization was due to both increased biomass and biomass nutrient concentrations. In soils of generally low fertility and low plant available P, application of P fertilizer at 45?kg?P?ha^?1 was beneficial for increasing biomass yields. Addition of N fertilizer improves stand establishment and biomass production on low P sites.     

Functional Genomics of Drought Tolerance in Bioenergy Crops

With predicted global changes in temperature and precipitation, drought will increasingly impose a challenge to biomass production. Most of the bioenergy crops have some degree of drought susceptibility as revealed for example through measures of low water-use efficiency (WUE). It is imperative to improve drought tolerance and WUE in bioenergy crops for sustainable biomass production in arid and semi-arid regions. Genetics and functional genomics can play critical roles in generating knowledge to inform and aid genetic improvement for drought tolerance in bioenergy crops. The molecular aspects of drought response have been extensively investigated in model plants like Arabidopsis, yet our understanding of the molecular mechanisms underlying drought tolerance in bioenergy crops is limited. Plants in general exhibit various responses to drought stress depending on species and genotype. A rational strategy for studying drought tolerance in bioenergy crops is to translate the knowledge from model plants relative to the unique features associated with individual bioenergy species and genotypes. In this review, we summarize the general knowledge concerning drought responsive pathways, with a focus on the identification of commonality and specialty in drought responsive mechanisms among alternate species and genotypes. We describe the genomic resources developed for bioenergy crops and discuss genetic and epigenetic regulation of drought responses. We also examine comparative and evolutionary genomics as a means to leverage the ever-increasing genomics resources and provide new insights beyond what is known from studies on individual species. Finally, we outline future opportunities for studying drought tolerance using the emerging technologies.     

Genome-Scale Identification of Cell-Wall-Related Genes in Switchgrass through Comparative Genomics and Computational Analyses of Transcriptomic Data

Large numbers of plant cell-wall (CW)-related genes have been identified or predicted in several plant genomes such as Arabidopsis thaliana, Oryza sativa (rice), and Zea mays (maize), as results of intensive studies of these organisms in the past 2 decades. However, no such gene list has been identified in switchgrass (Panicum virgatum), a key bioenergy crop. Here, we present a computational study for prediction of CW genes in switchgrass using a two-step procedure: (i) homology mapping of all annotated CW genes in the fore-mentioned species to switchgrass, giving rise to a total of 991 genes, and (ii) candidate prediction of CW genes based on switchgrass genes co-expressed with the 991 genes under a large number of experimental conditions. Specifically, our co-expression analyses using the 991 genes as seeds led to the identification of 104 large clusters of co-expressed genes, each referred to as a co-expression module (CEM), covering 830 of the 991 genes plus 823 additional genes that are strongly co-expressed with some of the 104 CEMs. These 1653 genes represent our prediction of CW genes in switchgrass, 112 of which are homologous to predicted CW genes in Arabidopsis. Functional inference of these genes is conducted to derive the possible functional relations among these predicted CW genes. Overall, these data may offer a highly useful information source for cell-wall biologists of switchgrass as well as plants in general.     

Drought Stress and Preharvest Aflatoxin Contamination in Agricultural Commodity: Genetics, Genomics and Proteomics

Throughout the world, aflatoxin contamination is considered one of the most serious food safety issues concerning health. Chronic problems with preharvest aflatoxin contamination occur in the southern US, and are particularly troublesome in corn, peanut, cottonseed, and tree nuts. Drought stress is a major factor to contribute to preharvest afiatoxin contamination. Recent studies have demonstrated higher concentration of defense or stress-related proteins in corn kernels of resistant genotypes compared with susceptible genotypes, suggesting that preharvest field condition (drought or not drought) influences gene expression differently In different genotypes resulting in different levels of "end products": PR(pathogenesis-related) proteins in the mature kernels. Because of the complexity of Aspergillus-plant interactions, better understanding of the mechanisms of genetic resistance will be needed using genomics and proteomics for crop improvement. Genetic Improvement of crop resistance to drought stress is one component and will provide a good perspective on the efficacy of control strategy. Proteomic comparisons of corn kernel proteins between resistant or susceptible genotypes to Aspergillus flavus infection have identified stress-related proteins along with antifungal proteins as associated with kernel resistance. Gene expression studies in developing corn kernels are In agreement with the proteomic studies that defense-related genes could be upregulated or downregulated by abiotic stresses.     

Soil Carbon and Nitrogen Responses to Nitrogen Fertilizer and Harvesting Rates in Switchgrass Cropping Systems

The environmental sustainability of bioenergy cropping systems depends upon multiple factors such as crop selection, agricultural practices, and the management of carbon (C), nitrogen (N), and water resources. Perennial grasses, such as switchgrass (Panicum virgatum L.), show potential as a sustainable bioenergy source due to high yields on marginal lands with low fertilizer inputs and an extensive root system that may increase sequestration of C and N in subsurface soil horizons. We quantified the C and N stocks in roots, free particulate, and mineral-associated soil organic matter pools in a 4-year-old switchgrass system following conversion from row crop agriculture at the W.K. Kellogg Biological Station in southwest Michigan. Crops were fertilized with nitrogen at either 0, 84, or 196 kg N ha^?1 and harvested either once or twice annually. Twice-annual harvesting caused a reduction of C and N stocks in the relatively labile roots and free-particulate organic matter pools. Nitrogen fertilizer significantly reduced total soil organic C and N stocks, particularly in the stable, mineral-associated C and N pools at depths greater than 15 cm. The largest total belowground C stocks in biomass and soil occurred in unfertilized plots with annual harvesting. These findings suggest that fertilization in switchgrass agriculture moderates the sequestration potential of the soil C pool.     

Time Course Field Analysis of COMT-Downregulated Switchgrass: Lignification,Recalcitrance, and Rust Susceptibility

Modifying plant cell walls by manipulating lignin biosynthesis can improve biofuel yields from lignocellulosic crops. For example, transgenic switchgrass lines with downregulated expression of caffeic acid O-methyltransferase, a lignin biosynthetic enzyme, produce up to 38 % more ethanol than controls. The aim of the present study was to understand cell wall lignification over the second and third growing seasons of COMT-downregulated field-grown switchgrass. COMT gene expression, lignification, and cell wall recalcitrance were assayed for two independent transgenic lines at monthly intervals. Switchgrass rust (Puccinia emaculata) incidence was also tracked across the seasons. Trends in lignification over time differed between the 2 years. In 2012, sampling was initiated in mid-growing season on reproductive-stage plants and there was little variation in the lignin content of all lines (COMT-downregulated and control) over time. COMT-downregulated lines maintained 11–16 % less lignin, 33–40 % lower S/G (syringyl-to-guaiacyl) ratios, and 15–42 % higher sugar release relative to controls for all time points. In 2013, sampling was initiated earlier in the season on elongation-stage plants and the lignin content of all lines steadily increased over time, while sugar release expectedly decreased. S/G ratios increased in non-transgenic control plants as biomass accumulated over the season, while remaining relatively stable across the season in the COMT-downregulated lines. Differences in cell wall chemistry between transgenic and non-transgenic lines were not apparent until plants transitioned to reproductive growth in mid-season, after which the cell walls of COMT-downregulated plants exhibited phenotypes consistent with what was observed in 2012. There were no differences in rust damage between transgenics and controls at any time point. These results provide relevant fundamental insights into the process of lignification in a maturing field-grown biofuel feedstock with downregulated lignin biosynthesis.     

Responses of Camellia sinensis to Drought and Rehydration

The effects of drought and rehydration on tea seedlings were significant. After five days of drought imposition the contents of chlorophylls, carotenoids, ascorbate and glutathione, and activities of guaiacol peroxidase and glutathione reductase decreased. Simultaneously, contents of proline, H₂O₂ and superoxide anion, lipid peroxidation and activities of catalase and superoxide dismutase increased. These parameters recovered to different degrees during subsequent rehydration.     

Biomarkers for Bone Tumors: Discovery from Genomics and Proteomics Studies and Their Challenges

Diagnosis of bone tumor currently relies on imaging and biopsy, and hence, the need to find less invasive ways for its accurate detection. More recently, numerous promising deoxyribonucleic acid (DNA) and protein biomarkers with significant prognostic, diagnostic and/or predictive abilities for various types of bone tumors have been identified from genomics and proteomics studies. This article reviewed the putative biomarkers for the more common types of bone tumors (that is, osteosarcoma, Ewing sarcoma, chondrosarcoma [malignant] and giant cell tumor [benign]) that were unveiled from the studies. The benefits and drawbacks of these biomarkers, as well as the technology platforms involved in the research, were also discussed. Challenges faced in the biomarker discovery studies and the problems in their translation from the bench to the clinical settings were also addressed.     

小麦根系特征对干旱胁迫的响应

干旱胁迫时, 小麦(Triticum aestivum)根系率先产生应激响应, 同时向地上部发出信号, 诱导地上部发生生理反应, 从而提高植株抗旱能力。根系构型包括平面几何性状和立体几何结构(即拓扑构型), 具有遗传稳定性和可塑性。干旱胁迫影响根系理化特性, 如根源化学信号、根系细胞酶类和根系渗透作用的响应。根系通过调整其解剖学结构和水分吸收动力等来适应干旱胁迫。该文从根系构型、理化特性和解剖学结构3个方面, 系统阐述了小麦根系特征对干旱胁迫的响应, 并探讨了其与干旱胁迫的关系和当前研究中存在的问题, 以期为相关研究提供参考。     

小麦根系特征对干旱胁迫的响应

干旱胁迫时, 小麦(Triticum aestivum)根系率先产生应激响应, 同时向地上部发出信号, 诱导地上部发生生理反应, 从而提高植株抗旱能力。根系构型包括平面几何性状和立体几何结构(即拓扑构型), 具有遗传稳定性和可塑性。干旱胁迫影响根系理化特性, 如根源化学信号、根系细胞酶类和根系渗透作用的响应。根系通过调整其解剖学结构和水分吸收动力等来适应干旱胁迫。该文从根系构型、理化特性和解剖学结构3个方面, 系统阐述了小麦根系特征对干旱胁迫的响应, 并探讨了其与干旱胁迫的关系和当前研究中存在的问题, 以期为相关研究提供参考。     

Antioxidant Responses of Lentil to Cold and Drought Stress

The effects of cold and drought stress on antioxidant responses and growth parameters in shoots and roots of lentil (Lens culinaris M cv Sultan 1) seedlings were investigated. Ten-day-old hydroponically grown seedlings were subjected to drought and cold (4°C) stress for 5 days. The length and fresh weight of shoots decreased significantly under both stress conditions, contrary to the increase in these growth parameters for roots under the same conditions. The oxidative damage as generation of malondialdehyde and hydrogen peroxide, was markedly higher in shoots under cold. Both stress conditions caused a significant increase in malondialdehyde levels in root tissues. The increase in proline levels was more pronounced under cold stress in shoots and roots. The tested stress conditions had no significant effect on chlorophyll contents. Superoxide dismutase activity was differentially altered in shoot and root tissues under drought and cold stress. The catalase activity was higher in roots under drought stress. On the other hand, ascorbate peroxidase activity increased in root tissues under cold stress. The results indicate that improved tolerance to cold and drought stress in root and shoot tissues of lentil might be correlated to the increased capacity of antioxidative defense system.     

Genomics: Applications,Challenges, and Opportunities for the U.S. Environmental Protection Agency

Genomics information has great potential to enhance assessment of risks to human health and the environment. Although understanding genomic responses with respect to adverse ecological and human health outcomes is not, as yet, established, it is important to consider the likely future impacts of genomics technologies on risk assessment and decision-making. Four areas are identified as those likely to be influenced by the generation of genomics information within, and the submission of such information to, the U.S. Environmental Protection Agency (USEPA): risk assessment, prioritization of contaminants and contaminated sites, monitoring, and reporting provisions. For each of these risk assessment and regulatory applications, representative activities are presented to illustrate the application. Three major challenges for the USEPA associated with genomics are also identified in the areas of research, technical development, and capacity. The USEPA's initial activities to address these challenges are discussed. The Agency recognizes it must be prepared to use genomics information, and that many scientific, policy, ethical, and legal concerns will need to be addressed. The USEPA also recognizes it is essential to continue to collaborate with other federal agencies, academia, the regulated community, and other stakeholders in order to benefit from ongoing advances in genomics in the wider scientific and regulatory communities.     

Autoethnographic Challenges: Confronting Self,Field and Home

Anthropologists working at ‘home’ or in realms of the familiar often share a considerable sense of connection with participants. In these contexts, the researcher's potential position as an ‘insider’ offers particular opportunities for utilising self as a key resource. Through my own fieldwork at ‘home’ in Melbourne as an ‘insider’ among Bosnian migrants, I was confronted with the challenge of using my self to understand others' experiences. In this paper I discuss the autoethnographic process and consider how its application enabled me to consciously understand my own experiences and utilise my experiential self to inform my study.     

干旱胁迫下杨树嫩茎质外体内源激素的响应

质外体与植物细胞有着不可分割的联系,其内发生的干旱胁迫响应鲜见报道,因此本文采用MD HPLC联用技术对3种杨树嫩茎质外体内源激素在干旱胁迫胁迫下的变化进行研究。结果表明: 随着干旱胁迫程度的加剧和时间的延长,3种杨树质外体GA₃、6-BA和3-IAA含量明显减少,而ABA含量极显著增加且GA₃、6-BA、3-IAA和ABA含量的变化品种间差异显著。该研究为植物干旱胁迫生理响应机制研究提供新依据,为活体、动态地定量分析质外体内源激素提供了新方法。     

Infestation Rates and Tiller Morphology Effects by the Switchgrass Moth on Six Cultivars of Switchgrass

Switchgrass (Panicum virgatum L.) is a potential biomass crop for native species-based biofuel systems in North America. A recently identified pest of switchgrass, the switchgrass moth, Blastobasis repartella (Dietz) (Lepidoptera: Coleophoridae), feeds in the basal above-ground internodes and below-ground in the proaxis and rhizomes, causing premature tiller and rhizome loss. Our goal was to determine genetic and temporal variation among six upland cultivars for frequency of tiller infestation by larvae of the switchgrass moth in mature stands in the northern Great Plains and if variation in biomass production was associated with variation in frequency of infestation. Data were collected in 2011 and 2012 for tiller density, biomass, frequency of infestation, number of leaves per healthy and infested tiller, and weights of healthy and infested tillers. Differences were found among cultivars for tiller density, biomass yield, and numbers of leaves per healthy and infested tillers. ‘Summer’, ‘Sunburst’, ‘Pathfinder’, and ‘Cave-In-Rock’ were the highest yielding cultivars. Mean frequency of infestation was different between 2011 (6.7 %) and 2012 (9.6 %). Infested tillers had one less collared leaf than healthy tillers. The weights of healthy tillers were ca. 3× those of infested tillers in both years, suggesting an impact on biomass accumulation and economic value. Levels of infestation were similar for all six cultivars, indicating no feeding preference by the switchgrass moth larva among genetically diverse cultivars of switchgrass. Regression of biomass yield on frequency of infestation showed negative linear relationships for ‘Carthage’ and ‘Kentucky 1625’.