Abiotic stress conditions adversely affect plant growth, resulting in significant decline in crop productivity. To mitigate and recover from the damaging effects of such adverse environmental conditions, plants have evolved various adaptive strategies at cellular and metabolic levels. Most of these strategies involve dynamic changes in protein abundance that can be best explored through proteomics. This review summarizes comparative proteomic studies conducted with roots of various plant species subjected to different abiotic stresses especially drought, salinity, flood, and cold. The main purpose of this article is to highlight and classify the protein level changes in abiotic stress response pathways specifically in plant roots. Shared as well as stressor-specific proteome signatures and adaptive mechanism(s) are simultaneously described. Such a comprehensive account will facilitate the design of genetic engineering strategies that enable the development of broad-spectrum abiotic stress-tolerant crops.

Drug target identification is a critical step toward understanding the mechanism of action of a drug, which can help one improve the drug's current therapeutic regime and expand the drug's therapeutic potential. However, current in vitro affinity-chromatography-based and in vivo activity-based protein profiling approaches generally face difficulties in discriminating specific drug targets from nonspecific ones. Here we describe a novel approach combining isobaric tags for relative and absolute quantitation with clickable activity-based protein profiling to specifically and comprehensively identify the protein targets of andrographolide (Andro), a natural product with known anti-inflammation and anti-cancer effects, in live cancer cells. We identified a spectrum of specific targets of Andro, which furthered our understanding of the mechanism of action of the drug. Our findings, validated through cell migration and invasion assays, showed that Andro has a potential novel application as a tumor metastasis inhibitor. Moreover, we have unveiled the target binding mechanism of Andro with a combination of drug analog synthesis, protein engineering, and mass-spectrometry-based approaches and determined the drugbinding sites of two protein targets, NF-B and actin. Molecular & Cellular Proteomics 13: 10.1074/mcp. M113.029793, 876-886, 2014.As most drugs exert pharmacological effects by interacting with their target proteins, the identification of these target proteins is a critical step in unraveling the mechanisms of drug action. It is also imperative for our understanding of the pharmacodynamics of a known drug, suggesting potentially unrevealed actions and thus refining future clinical applications of the substance. Traditional approaches used to identify protein targets of a drug typically utilize immobilized drug affinity chromatography coupled with mass spectrometry (MS) 1 (1, 2). These methods can be applied to cell lysates, but not in an in vivo setting, because of the requirement of a solid support. In vitro target profiling might not accurately reflect the drug's actions in the in vivo physiological environment. To overcome this limitation, several groups have used activity-based protein profiling (ABPP) combined with bio-orthogonal click chemistry to identify drug targets both in vitro and in vivo (supplemental Fig. S1) (3-15). ABPP probes exert their functions via covalent reactions with the target proteins or photoaffinity-based labeling via the incorporation of photoreactive groups. With the increasing sensitivity of modern MS platforms, low-abundance protein targets can be successfully identified. Although both conventional affinity chromatography and recent ABPP-based methods allow us to detect a set of candidate protein targets for a drug, it remains difficult to 1 The abbreviations used are: MS, mass spectrometry; ABPP, activity-based protein profiling; ICABPP, clickable activity-based protein profiling; iTRAQ, isobaric tags for relative and absolute quantitation; DMSO, dimethyl sulfoxide; Andro, androgr...

This study compared the whole cell proteome profiles of two isogenic colorectal cancer (CRC) cell lines (primary SW480 cell line and its lymph node metastatic variant SW620), as an in vitro metastatic model, to gain an insight into the molecular events of CRC metastasis. Using iTRAQ (isobaric tags for relative and absolute quantitation) based shotgun proteomics approach, we identified 1140 unique proteins, out of which 147 were found to be significantly altered in the metastatic cell. Ingenuity pathway analysis with those significantly altered proteins, revealed cellular organization and assembly as the top-ranked altered biological function. Differential expression pattern of 6 candidate proteins were validated by Western blot. Among these, the low expression level of β-catenin combined with the up-regulation of CacyBP (Calcyclin binding Protein), a β-catenin degrading protein, in the metastatic cell provided a rational guide for the downstream functional assays. The relative expression pattern of these two proteins was further validated in three other CRC cells by Western blot and quantitative immunofluorescence studies. Overexpression of CacyBP in three different primary CRC cell lines showed significant reduction in adhesion characteristics as well as cellular β-catenin level as confirmed by our experiments, indicating the possible involvement of CacyBP in CRC metastasis. In short, this study demonstrates successful application of a quantitative proteomics approach to identify novel key players for CRC metastasis, which may serve as biomarkers and/or drug targets to improve CRC therapy.

Keeping continuity with our previous study that revealed direct correlations between CRC metastasis and enhanced CacyBP protein levels, here we attempt to improve our understanding of the mechanisms involved within this enigmatic process. Overexpression of CacyBP (CacyBP-OE) in primary CRC cell and its knock down (CacyBP-KD) in the metastatic CRC cells revealed (through phenotypic studies) the positive impact of the protein on metastasis. Additionally, two individual 4-plex iTRAQ based comparative proteomics experiments were carried out on the CacyBP-OE and CacyBP-KD cells, each with two biological replicates. Mining of proteomics data identified total 279 (63.80% up-regulated and 36.20% down-regulated) proteins to be significantly altered in expression level for the OE set and in the KD set, this number was 328 (48.78% up-regulated and 51.22% downregulated). Functional implications of these significantly regulated proteins were related to metastatic phenotypes such as cell migration, invasion, adhesion and proliferation. Gene ontology analysis identified integrin signaling as the topmost network regulated within CacyBP-OE. Further detection of caveolar mediated endocytosis in the top hit list correlated this phenomenon with the dissociation of integrins from the focal adhesion complex which are known to provide the traction force for cell movement when transported back to the leading edge. This finding was further supported by the data obtained from CacyBP-KD data set showing down-regulation of proteins necessary for integrin endocytosis. Furthermore, intracellular calcium levels (known to influence integrin mediated cell migration) were found to be lowered in CacyBP-KD cells indicating decreased cell motility and vice versa for the CacyBP-OE cells. Actin nucleation by ARP-WASP complex, known to promote cell migration, was also identified as one of the top regulated pathways in CacyBP-OE cells.

The Lugol’s staining method has been widely used to detect changes in the maintenance of stem cell fate in the columella root cap of Arabidopsis roots since the late 1990s. However, various limitations of this method demand for additional or complementary new approaches. For instance, it is unable to reveal the division rate of columella root cap stem cells. Here we report that, by labeling dividing stem cells with 5-ethynyl-2′-deoxyuridine (EdU), the number and distribution of their labeled progeny can be studied so that the division rate of stem cells can be measured quantitatively and in addition, that the progression of stem cell progeny differentiation can be assessed in combination with Lugol’s staining. EdU staining takes few hours and visualization of the stain characteristics of columella root cap can be performed easily under confocal microscopes. This simple technology, when used together with Lugol’s staining, provides a novel quantitative method to study the dynamics of stem cell behavior that govern homeostasis in the Arabidopsis columella root cap.

A study has been conducted to evaluate the virtual reality technology and online teaching system among medical students of Bogomolets National Medical University, Ukraine during COVID-19 pandemic. The final questionnaire contained the 15 questions with 5 options to comprehensively evaluate the virtual reality technology and online teaching system. The feedback of the survey was analyzed to find effectiveness of virtual reality technology and online teaching in medical education in Ukraine. Data of survey reflected that mostly students adopted and agreed on virtual reality technology and online teaching and admitted that these technologies are best alternatives to physical learning with the 65.79% an agreement with the user-friendly interface for virtual reality and online teaching system, while, 64.03% showed an agreement that virtual reality and online teaching system compensated the suspension of face-to-face medical education during the COVID-19. During online learning, there was ample time for educational activities as depicted from their response of 36.84% as strongly agree, 35.96% as agree, 6.14% as disagree, 4.39% as strongly disagree and 16.67% as neither agree nor disagree. Tutors/teachers also enjoyed virtual reality and online learning through their experience and flexibility in time management. Likewise, the results of all questions showed positive reviews and encouraged virtual reality and online teaching in academic continuity and stability in medical education in Ukraine. It can be concluded that digital learning environments are extremely effective in terms of medical students and staff satisfaction, accomplishment, and technical learning skill growth.

Collective cell migration (CCM), where cell-cell integrity remained preserved during the movement, plays an important role in the progression of cancer. However, studies describing CCM in cancer progression are majorly focused on the effect of extracellular tissue components on moving cell plasticity. The molecular and cellular mechanisms of CCM during cancer progression remained poorly explored. Here we report that proteolipid protein 2 (PLP2), a colonic epithelium enriched transmembrane protein, plays a vital role in the CCM of invasive colorectal cancer (CRC) epithelium by modulating leading-edge cell dynamics in 2D (two-dimension). The extracellular pool of PLP2, secreted via exosomes was also found to contribute to the event. During CCM, the protein was found to exist in association with ZO-1 and involved in the positioning of the latter at the migrating edge. PLP2 mediated positioning of ZO-1 at the leading-edge further alters actin cytoskeletal organization that involves Rac1 activation. Together our findings demonstrate that PLP2, via its association with ZO-1, drives the collective cell migration in CRC epithelium by modulating leading-edge actin cytoskeleton and thereby opened up new avenues of cancer research.

Editorial on the Research Topic How Plants Deal with Stress: Exploration through Proteome InvestigationBiotic and abiotic stress factors serve as consistent threats to a plant's life cycle. Biotic stress factors such as damage through pathogens or herbivore attack as well as abiotic stress factors like variation in temperature, rainfall, and salinity, have placed the members of the plant kingdom under constant challenges for their survival. As a consequence, global agricultural and horticultural productivity has always been below its optimal capacity.Being sessile in nature, plants cannot escape from the stress, instead they acclimatize to adverse condition by adopting certain systemic changes. These changes include developmental and physiological alterations which influence the genome, proteome, and metabolome of the plant. Since proteins are key regulators of cellular responses, investigations into proteome alterations during stress induction as well as recovery, can provide important information on how plants cope with stress factors. The process has been widely discussed in this Research Topic which comprises nineteen research articles, two reviews, one mini review, and one opinion article.A significant portion of the research articles included in this Research Topic investigated proteome level alterations in diverse organ parts of the plant body upon exposure to abiotic stress factors such as drought, salinity, and submergence. Comparative proteomic investigations between drought and submergence stress showed that bermudagrass adopt a quiescence strategy in a prolonged submerged state by declining metabolic activities, whereas in a drought environment plants increase their tolerance level through higher levels of photosynthesis and redox potential (Ye et al.). Enhanced levels of molecular chaperones were found to be associated with drought tolerance in multiple studies (Ye et al.; Zhao et al.; Chmielewska et al.) performed on different plant species (bermudagrass, corn, and barley, respectively). Interestingly, when maize plants were challenged by the combination of both drought and heat, up-regulation of a specific set of ethylene-responsive, and ABA-, stress-, and ripening-inducible-like proteins was observed. However, individual exposure to drought or heat stress did not show the above proteome alterations, indicating that these proteins are specifically required to resist the combinatorial effects of the above two stresses (Zhao et al.). Consistently, over-expression of glycolate oxidase (GLO) was found during adaptation of rice plants to both high-light intensity and high temperature but not to high-light intensity alone, with H 2 O 2 and salicylic acid being the signaling molecules that mediate the adaptive responses (Cui et al.). Studies on salt stress reported the up-regulation of mainly defense-related proteins and proteins related to enhanced energy metabolism (Maršálová et al.; Long et al.). In addition, a quantitative proteomics study explored that vacuolar ATPase AVP1 and sugar transporters o...