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Modulation in growth, biochemical attributes and proteome profile of rice cultivars under salt stress.

One of the major abiotic stresses that affect productivity of rice is salinity. Rice cultivars showed significant genetic variation in response to salt stress. In the present investigation, differential growth pattern and physio-chemical traits-based screening of high yielding rice cultivars of various salt affected areas of India was carried out, and salt-sensitive and salt-tolerant cultivars were identified. Differential responses of antioxidant enzyme activity and tolerance index at maximum level of salt treatment depicted that Jhelum and Vytilla-4 cultivars of rice were sensitive and tolerant to salt stress, respectively. Analysis of growth, morpho-physiological, and biochemical parameters also confirmed the salt-tolerant and salt-sensitive characters of cv. Vytilla-4 and cv. Jhelum, respectively. Nano-LCMS/MS-based proteome profile of these two cultivars was carried out to find out the mechanism lying behind the salt tolerance. A total number of 514 and 770 protein spots were reported in the most salt-tolerant (cv. Vytilla-4) and salt-sensitive (cv. Jhelum) cultivars, respectively. The differentially expressed proteins (DEPs) were found associated with major metabolic pathways including photosynthesis, energy metabolism, amino acid metabolism, nitrogen assimilation and stress and signalling pathways. The changes in the major proteins like Ribulose bisphosphate carboxylase small chain, chlorophyll a-b binding protein, phosphoglycerate kinase, cytochrome c oxidase subunit 5C, glutamine synthetase, glutathione S-transferase, peroxidase, and thioredoxin elucidated the mechanism activated by salt-tolerant cv. Vytilla-4. The transcriptional validation of some of the differentially expressed proteins through real-time quantitative PCR analysis further validated the proteomic results. Outcomes of this work could help in finding out the potential cross-links of different pathways involved in salt-tolerance mechanisms operating in the studied here rice cultivars under salt stress.

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Comprehensive evaluation of the effects of climate change and land use and land cover change variables on runoff and sediment discharge.

Climate change and various human activities have resulted in noticeable changes in watershed hydrological and soil erosion regimes. In this study, a comprehensive investigation was conducted to distinguish between the effects of climate variables and those of land use and land cover change (LUCC) variables on runoff and sediment discharge in the Zhenjiangguan watershed, which is located at the headstream basin of the Minjiang River in southwest China. Statistical analysis results revealed significant and slight decreasing trends in runoff and sediment discharge, respectively. Abrupt changes occurred in 1974 and 1995, which divided the entire time series into a decrease-increase-decrease tendency pattern; this pattern was the response to climate changes and the Reforestation and Returning Farmland to Forest project in China. In addition, redundancy analysis was used for partition statistical analyses, and the contributions of climate change and LUCC to runoff and sediment discharge were at the ratio of 4:1. Since 1990, the effect of LUCC has increased notably and its relationship with hydrological variables changed from positive to negative in approximately 1995. Finally, simulations performed using the distributed Basic Pollution Calculation Center (BPCC) model confirmed that climate and LUCC variables reduced the runoff depth and sediment load between 1980 and 2003. The contributions of climate fluctuation and LUCC to runoff depth were at the ratio of 5:1, and those to sediment load were at the ratio of 3:1, which exhibited the dominant role of climate change and the high sensitivity of sediment load to human interference. Overall, the results of distributed hydrological modeling were consistent with those of statistical analyses. The results provided detailed information and explained the mechanics underlying hydrological processes and soil erosion.

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Impact of forest cover and conservation agriculture on sediment export: A case study in a montane reserve, south-western China.

Reforestation and agricultural conservation have long been recognized as important in reducing on-site soil loss and off-site sediment export. Quantitative assessment of their effectiveness is critical, and assists cost-benefit analysis and decision-making in land management and landscape planning. We applied a paired watershed approach to monitor 1-year sediment export in two watersheds with forest-dominated (reference) and mosaic (target) land use in the Naban River Watershed National Natural Reserve (NRWNNR) in Xishuangbanna, south-western China. Analysis of land-use change in the target watersheds showed decreasing total forest cover (FC) (from 57% to 47%), but increasing FC in steep areas (from 54% to 59%) from 2007 to 2012. A distributed hydrological model (Land-Use Change Impact Assessment, LUCIA) was well calibrated and validated through field data from the two watersheds. Scenarios were created representing different FCs (from 31% to 83%) and agricultural management (as-usual and conservation). Simulation results quantified the relation between FC and sediment export as a logarithmic or logit model, indicating at least one turning point of FC, beyond which further forest reduction should significantly increase sediment export. This point was identified in the range between 57% and 61% of the target watershed under as-usual management; it was shifted to 47%-53% by conservation agriculture. Compared with the reference (with 83% FC), conservation agriculture was able to almost fully compensate for increased sediment export by forest reduction to 57% in 2007. However, when forest was reduced further to 47% in 2012, sediment export increased significantly. We concluded that total FC was as important as FC in montane watershed management in steep areas; and crop type conversion, such as rubber to maize in this study, and on-site agriculture management affect more to sediment export than agricultural expansion. We recommend conservation agriculture as an efficient tool for reducing sediment export on a watershed scale.

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Quantitative Proteome Landscape of the NCI-60 Cancer Cell Lines.

Here we describe a proteomic data resource for the NCI-60 cell lines generated by pressure cycling technology and SWATH mass spectrometry. We developed the DIA-expert software to curate and visualize the SWATH data, leading to reproducible detection of over 3,100 SwissProt proteotypic proteins and systematic quantification of pathway activities. Stoichiometric relationships of interacting proteins for DNA replication, repair, the chromatin remodeling NuRD complex, β-catenin, RNA metabolism, and prefoldins are more evident than that at the mRNA level. The data are available in CellMiner (discover.nci.nih.gov/cellminercdb and discover.nci.nih.gov/cellminer), allowing casual users to test hypotheses and perform integrative, cross-database analyses of multi-omic drug response correlations for over 20,000 drugs. We demonstrate the value of proteome data in predicting drug response for over 240 clinically relevant chemotherapeutic and targeted therapies. In summary, we present a novel proteome resource for the NCI-60, together with relevant software tools, and demonstrate the benefit of proteome analyses.

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Mini-pillar microarray for individually electrochemical sensing in microdroplets.

High throughput and high sensitivity are two important aspects in multiple biomarker recognition, drug discovery and relevant biochemical sensing. Here, we integrate mini-pillar microarray with the circuit components toward high-throughput individual electrochemical sensing in microdroplets. On such droplet-microarray-based electrochemical platform, the high adhesion of the mini-pillar can hold a microdroplet (hundreds nanoliter to a few microliter) regardless of rotation and deformation. Each pillar as a unit has a three-electrode to achieve individual electrochemical sensing, and electrodes are integrated on one side to achieve the sequential electrochemical read-out. Qualitative and quantitative electrochemical assessments of multiple glucose concentrations in individual microdroplets are also achieved. Such mini-pillar-based individual electrochemical platform shows great potential in high-throughput and high-sensitive biomolecular recognitions, provides an opportunity to develop miniaturized sensing platform for emerging biological and pathological applications.

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Optical and electrochemical-based nano-aptasensing approaches for the detection of circulating tumor cells (CTCs).

More recently, detection of circulating tumor cells (CTCs) has been considered as an appealing prognostic and diagnostic approach for cancer patients. CTCs as a type of tumor-derived cells are secreted by the tumor and released into the blood circulation. Since the migration of CTCs is an early event in cancer progression, patients who still have tumor-free lymph nodes have to be well examined for the CTCs presence in their blood circulation. Nowadays, there is a broad range of detection methods available to identify CTCs. As artificial RNA oligonucleotides or single-stranded DNA with receptor and catalytic characteristics, aptamers have been standing out, owing to their target-induced conformational modifications, elevated stability, and target specificity to be implemented in biosensing techniques. To date, several sensitivity-enhancement methods alongside smart nanomaterials have been used for the creation of new aptasensors to address the limit of detection (LOD), and improve the sensitivity of numerous analyte identification methods. The present review article supports a focused overview of the recent studies in the identification and quantitative determination of CTCs by aptamer-based biosensors and nanobiosensors.

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In vivo analysis of subchondral trabecular bone in patients with osteoarthritis of the knee using second-generation high-resolution peripheral quantitative computed tomography (HR-pQCT).

Subchondral bone plays an important role in the pathological mechanisms of knee osteoarthritis (OA). High-resolution peripheral quantitative computed tomography (HR-pQCT) is an imaging modality allowing noninvasive microstructural analysis of human bone, and the second generation enables scanning of the knee. The purpose of this study was to perform in vivo analysis of subchondral trabecular bone in patients with medial knee OA, to elucidate features of bone microstructure in medial knee OA, and to investigate relationships between bone microstructure and both stage of disease and lower limb alignment.

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Comparative quantitative proteomics of osmotic signal transduction mutants in Botrytis cinerea explain mutant phenotypes and highlight interaction with cAMP and Ca signalling pathways.

Signal transduction (ST) is essential for rapid adaptive responses to changing environmental conditions. It acts through rapid post-translational modifications of signalling proteins and downstream effectors that regulate the activity and/or subcellular localisation of target proteins, or the expression of downstream genes. We have performed a quantitative, comparative proteomics study of ST mutants in the phytopathogenic fungus Botrytis cinerea during axenic growth under non-stressed conditions to decipher the roles of two kinases of the hyper-osmolarity pathway in B. cinerea physiology. We studied the mutants of the sensor histidine kinase Bos1 and of the MAP kinase Sak1. Label-free shotgun proteomics detected 2425 proteins, 628 differentially abundant between mutants and wild-type, 270 common to both mutants, indicating independent and shared regulatory functions for both kinases. Gene ontology analysis showed significant changes in functional categories that may explain in vitro growth and virulence defects of both mutants (secondary metabolism enzymes, lytic enzymes, proteins linked to osmotic, oxidative and cell wall stress). The proteome data also highlight a new link between Sak1 MAPK, cAMP and Ca signalling. This study reveals the potential of proteomic analyses of signal transduction mutants to decipher their biological functions. TEXTE-VULAGRISATION: The fungus Botrytis cinerea is responsible for grey mold disease of hundreds of plant species. During infection, the fungus has to face important changes of its environment. Adaptation to these changing environmental conditions involves proteins of such called signal transduction pathways that regulate the production, activity or localisation of cellular components, mainly proteins. While the components of such signal transduction pathways are well known, their role globally understood, the precise impact on protein production remains unknown. In this study we have analysed and compared the global protein content of two Botrytis cinerea signal transduction mutants - both avirulent - to the pathogenic parental strain. The data of 628 differential proteins between mutants and wild-type, showed significant changes in proteins related to plant infection (secondary metabolism enzymes, lytic enzymes, proteins linked to osmotic, oxidative and cell wall stress) that may explain the virulence defects of both mutants. Moreover, we observed intracellular accumulation of secreted proteins in one of the mutants suggesting a potential secretion defect. This study reveals the potential of proteomic(global protein content) analyses of signal transduction mutants to decipher their biological functions.

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A study of soil erosion rates using Pu, in the wet-dry tropics of Northern Australia.

The Daly River drains a large (52500 km) and mainly undisturbed catchment in the Australian wet-dry tropics. The basin landscapes are mantled by a thick veneer of kandosol soil which has developed under varying rates of erosion, uplift, bedrock type and climate and has been identified as being suitable for agriculture. Commencement of large scale clearing and cropping since 2002 have raised concerns about the increased loss of top soil from the land clearing and cultivation activities adjacent to the Daly River. This study was undertaken to determine the modern soil loss rates which can be used to develop a sustainable soil conservation strategy for this catchment. Pu, released in the 1950s and 1960s by atmospheric nuclear weapons tests, is used to obtain a quantitative assessment of recent rates of soil loss. Soil cores 30-40 cm deep have been collected from fields with various land uses including peanut and hay cropping and cattle grazing. Cores taken from undisturbed and unburnt areas in open eucalypt woodland have been used as reference sites. The soil loss rates have been established by comparing the excess or deficiency of the Pu tracer over that of the reference sites. Since land use practices in the catchment are similar, it is likely that the measured soil loss rates are indicative of soil loss rates over the Daly Basin as well. The development of Pu as a soil tracer represents a viable alternative to the traditionally used Cs tracer. This also represents a new tool in the quantification of catchment soil loss and the adoption of appropriate soil conservation strategies for the tropical regions and regions where increasing settlement and agriculture are encroaching on catchment slopes.

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