Large-scale protein quantification has become a major proteomics application in many areas of biological and medical research. During the past years, different techniques have been developed, including gel-based such as differential in-gel electrophoresis (DIGE) and liquid chromatography-based such as isotope labeling and label-free quantification. These quantitative proteomics tools hold significant promise for biomarker discovery, diagnostic and therapeutic applications. They are also important for research in functional genomics and systems biology towards basic understanding of molecular networks and pathway interactions. In this review, we summarize current technologies in quantitative proteomics and discuss recent applications of the technologies.

Myosin VI is the only known molecular motor for the transportation of cargo vesicles from the plus end to the minus end of actin filaments. Thus, myosin VI possesses several unique features to distinguish it from other myosin family motors, such as the ability to move in a reverse direction, the unusual large walking step size, and the cargo-mediated dimerization. Recent structural studies of myosin VI have provided mechanistic insights into these unique features. On the basis of the resolved structures of myosin VI each domains (i.e., the structures of the N-terminal motor domain, the C-terminal cargo binding domain, and the region in the middle), the unique features of myosin VI will be reviewed here from a structural perspective. The structural studies of myosin VI definitely provide some answers about the unique features of myosin VI, but also raise significant questions on how myosin VI functions as a special motor both for directional cargo transport and for structural anchoring.

Protein misfolding is a general causation of classical conformational diseases and many pathogenic changes that are the result of structural conversion. Here I review recent progress in clinical and computational approaches for each stage of the misfolding process, aiming to present readers an outline for swift comprehension of this field.

Precise spatio-temporal control of gene expression at transcriptional and translational levels is required for both of proper developmental programming of the central nervous system and the performing of normal brain functions. Many studies have demonstrated that microRNAs (miRNAs), a class of endogenous small RNAs, participate in post-transcriptional regulation of gene expression, and thus execute regulatory functions in various biologic processes. Emerging evidence indicates that miRNAs participate in gene regulatory networks during the developmental, physiologic, and pathological processes of the brain. In this review, we attempt to summarize some of the recent advances in research on the involvement of miRNAs in the regulation of neuronal development, neuroplasticity, and brain diseases, revealing their indispensable roles in neural functions.

The TAM family of receptors is preferentially expressed by professional and non-professional phagocytes, including macrophages, dendritic cells and natural killer cells in the immune system, osteoclasts in bone, Sertoli cells in testis, and retinal pigmental epithelium cells in the retina. Mutations in the Mertk single gene or in different combinations of the double or triple gene mutations in the same cell cause complete or partial impairment in phagocytosis of their preys; and as a result, either the normal apoptotic cells cannot be efficiently removed or the tissue neighbor cells die by apoptosis. This scenario of TAM regulation represents a widely adapted model system used by phagocytes in all different tissues. The present review will summarize current known functional roles of TAM receptors and their ligands, Gas 6 and protein S, in the regulation of phagocytosis.

Functional biological research has benefited tremendously by analyses of the phenotypes of mutant organisms which can be generated through targeted mutation of genes. In Drosophila, compared with random mutagenesis methods gene targeting has gained its popularity because it can introduce any desired mutation into a gene of interest. However, applications of gene targeting have been limited because the targeting efficiency varies with different genes, and the time and labor of targeting procedure are intensive. Nevertheless, improvement of gene targeting and development of its variant technologies have received much attention of scientists. Here we review recent progress that has been made in expanding the applications of gene targeting, which include the ФC31 integration system and zinc-finger nucleases induced gene targeting, and new strategies that generate more efficient and reliable gene targeting.

Rice is an important food crop worldwide. Its productivity has been influenced by various abiotic and biotic factors including temperature, drought, salt, microbe, ozone, hormone and glyphosate. The responses of plants to stress are regulated by multiple signaling pathways, and the mechanisms of leaf growth and development in response to stress remain unclear to date. Recently, proteomics studies have provided new evidence for better understanding the mechanisms. The proteins in response to different stress conditions are mainly involved in photosynthesis, signal transduction, transcription, protein synthesis and destination, defense response, cytoskeleton, energy, cell wall and other metabolism. In addition, some stress type-specific proteins have been identified, such as small heat shock proteins under temperature stress, S-like RNase homolog and actin depolymerizing factor under drought stress, ascorbate peroxidase and lipid peroxidation under salt stress, probenazole-inducible protein and rice pathogenesis-related proteins under blast fungus. Many of the proteins including ribulose-1, 5-bisphosphate carboxylase/oxygenase (RuBisCO), molecular chaperones, antioxidases and S-adenosylmethionine synthetase play very important roles in leaves. This paper reviews the proteomic characterization of rice leaves in response to various environmental factors.

Crop allelopathy is a promising and environmentally friendly method in weed control; however, the inducible genetic trait for allelopathy in the suppression of weeds needs to be overcome for practical use. Further study needs to be directed to this end to elucidate the molecular genetics and its physiologic mechanism. In this paper, the authors review recent advances in the investigation of rice allelopathy and its molecular regulatory mechanism, especially in responses to stressful conditions including biotic and abiotic factors in China. Previous studies show that rice allelopathy could be enhanced when the rice accession was exposed to stressful conditions, and further analysis by the transcriptomics and proteomics approaches conducted in our laboratory indicated that the increase in allelopathic potential of rice, when exposed to the stresses, was attributed to increased expression level of genes involved in phenolic synthetic metabolism. The increasing phenolic compounds have been confirmed as the main allelochemicals and they jointly act to suppress the target, especially in responses to stressful condition, but it seems to be the primary effect in phenolic allelopathy. We still wonder how the exudates from rice root, which were released into rhizosphere soil, are transformed by soil microorganism to produce the higher secondary effect of phenolic allelopathy in the suppression of weeds. Therefore, the authors suggest that rhizosphere biologic properties of allelopathy in rice and its mechanism are being the key research areas worldwide, and systems biology and its approaches, such as metagenomics and metaproteomics, would be helpful to reveal the process and its molecular ecological mechanism regarding rhizospheric biology of rice allelopathy.

NF-kappaB plays a critical role in cell survival, apoptosis, and inflammatory responses. Serine/threonine-specific phosphatases (PPs) represent the second major class of enzymes that catalyze the dephosphorylation of proteins. The roles of PPs regulating NF-kappaB activities are poorly understood. Here we describe an RNAi-based screen to identify the PPs that involve in regulating NF-kappaB signaling. Thirty-four candidate PPs siRNAs were synthesized and primarily screened by NF-kappaB reporter gene assay in HeLa cells. PHLPP, one of the protein phosphatase type 2C family members (PP2C), was identified as a positive regulator of NF-kappaB signaling. Knock-down of PHLPP dramatically attenuated TNFα-stimulated NF-kappaB transcriptional activation. Knock-down of PHLPP led to enhancement of NF-kappaB/p65 nuclear import and retention, but decreased TNFα-induced phosphorylation at Ser276 on p65. This critical phosphorylation was also drastically reduced by knock-down of PKCalpha and Akt1, two important serine/threonine kinases dephosphorylated by PHLPP. The results together suggest that PHLPP-Akt-PKC may represent an important signaling loop that activates NF-kappaB/p65 signaling through critical serine phosphorylation.

To modulate gene expression in research studies or in potential clinical therapies, transfection of exogenous nucleic acids including plasmid DNA and small interference RNA (siRNA) are generally performed. However, the cellular processing and the fate of these nucleic acids remain elusive. By investigating the cellular behavior of transfected nucleic acids using confocal imaging, here we show that when siRNA was co-transfected into cultured cells with other nucleic acids, including single-stranded RNA oligonucleotides, single and double-stranded DNA oligonucleotides, as well as long double-stranded plasmid DNA, they all aggregate in the same cytoplasmic granules. Interestingly, the amount of siRNA aggregating in granules was found not to correlate with the gene silencing activity, suggesting that assembly of cytoplasmic granules triggered by siRNA transfection may be separable from the siRNA silencing event. Our results argue against the claim that the siRNA-aggregating granules are the functional site of RNA interference (RNAi). Taken together, our studies suggest that, independent of their types or forms, extraneously transfected nucleic acids are processed through a common cytoplasmic pathway and trigger the formation of a new type of cytoplasmic granules “ transfection granules” .