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The objective of this study is to evaluate the role of miR-137 in low-intensity shear stress–induced endoplasmic reticulum (ER) stress and cell apoptosis in human aortic endothelial cells (HAECs). HAECs were transfected with miR-137 mimic, miR-137 inhibitor, or the corresponding negative control and then exposed to pulsatile shear stress in a parallel-plate flow chamber at 1, 2, 5, 10, and 15 dyn/cm2 for 3 h. Real-time polymerase chain reaction was used to detect mRNA expression of miR-137 and SDS22. A dual-luciferase reporter assay was employed to verify the direct interaction between miR-137 and SDS22. The internal morphology of cells and cell apoptosis was assessed by TUNEL staining observed under a transmission electron microscope. Meanwhile, the protein expression of oxidative stress–related, apoptosis-related, and activated c-Jun N-terminal kinase (JNK)/activator protein-1 (AP-1) signaling–related genes were analyzed by western blotting. Low strength shear stress (0–5 dyn/cm2) caused a negative change of HAEC surface and internal morphology in an intensity-dependent manner, and these changes were gradually weakened when shear stress was increased more than 5 dyn/cm2. Furthermore, low-intensity shear stress promoted oxidative stress response, accelerated cell apoptosis, and upregulated miR-137 expression and JNK/AP-1 signaling in HAECs. MiR-137 directly targets SDS22. Knockdown of miR-137 noticeably reduced activation of JNK/AP-1 signaling, oxidative stress response, and cell apoptosis induced by shear stress. MiR-137 regulated low-intensity shear stress–induced human aortic endothelial cell ER stress and cell apoptosis via JNK/AP-1 signaling.

Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.

Mitochondria are double-membrane-bound organelles involved mainly in supplying cellular energy, but also play roles in signaling, cell differentiation, and cell death. Mitochondria are implicated in carcinogenesis, and therefore dozens of lethal signal transduction pathways converge on these organelles. Accordingly, mitochondria provide an alternative target for cancer management. In this study, F16, a drug that targets mitochondria, and chlorambucil (CBL), which is indicated for the treatment of selected human neoplastic diseases, were covalently linked, resulting in the synthesis of a multi-mitochondrial anticancer agent, FCBL. FCBL can associate with human serum albumin (HSA) to form an HSA-FCBL nanodrug, which selectively recognizes cancer cells, but not normal cells. Systematic investigations show that FCBL partially accumulates in cancer cell mitochondria to depolarize mitochondrial membrane potential (MMP), increase reactive oxygen species (ROS), and attack mitochondrial DNA (mtDNA). With this synergistic effect on multiple mitochondrial components, the nanodrug can effectively kill cancer cells and overcome multiple drug resistance. Furthermore, based on its therapeutic window, HSA-FCBL exhibits clinically significant differential cytotoxicity between normal and malignant cells. Finally, while drug dosage and drug resistance typically limit first-line mono-chemotherapy, HSA-FCBL, with its ability to compromise mitochondrial membrane integrity and damage mtDNA, is expected to overcome those limitations to become an ideal candidate for the treatment of neoplastic disease.

Schisandra chinensis has been used as traditional medicine. The structures of isolate active compounds (schisandrin B, deoxyschisandrin, schisandrin C) from S. chinensis were characterized by physical and spectroscopic analyses. Active compounds were tested for their potential to act as anti-melanogenesis or skin-whitening agents by their abilities to inhibit tyrosinase activity in the cell-free mushroom tyrosinase assay and cellular tyrosinase derived from B16 melanoma cells. The tyrosinase inhibitory activity was correlated to the inhibition of melanin productions in a-MSH-stimulated and unstimulated B16 cells. Cellular tyrosinase kinetics were analyzed and showed by Lineweaver- Burk plot. Schisandrin B was minimally cytotoxic (cell viability: 88.99% at 0.75 µM) and the IC50 value for suppression of mushroom tyrosinase activity was estimated as 0.6 µM. Zymography analysis demonstrated schisandrin B’s concentration-dependent effects and the kinetic analysis indicated schisandrin B’s noncompetitive-inhibitory action.

Curcumin, the major pigment of the dietary spice turmeric, has the potential for chemoprevention by promotion of apoptosis. Here, we investigated the molecular mechanisms of curcumin in glycolytic inhibition and apoptotic induction in human colorectal cancer HCT116 and HT29 cells. On the one hand, curcumin downregulated the expression and activity of hexokinase II (HKII) in HCT116 and HT29 cells in a concentration-dependent manner, but had little effect on the other key glycolytic enzymes (PFK, PGM, and LDH). On the other, curcumin induced dissociation of HKII from the mitochondria, resulting in mitochondrial-mediated apoptosis. Furthermore, the phosphorylation of mitochondrial HKII through AKT was responsible for the curcumin-induced dissociation of HKII, which was different from the mechanism of HKII inhibitor 3-BrPA. These results have important implications for the metabolism reprogramming effect and the susceptibility to curcumin-induced mitochondrial cytotoxicity through the regulation of HKII, and provide a molecular basis for the development of naturally compounds as novel anticancer agents for colorectal carcinoma.

The synthesis of 3,5-disubstituted 1,2,4-oxadiazoles by the cyclocondensation of amidoximes with trifluoroacetic anhydride or benzoic acid derivatives in moderate to high yields is described. The study on the phase transition behavior has disclosed that some of the synthesized oxadiazoles show smectic or nematic phases depending on their structures, which have the high potential application as liquid crystalline monomers.

Patients with reflux esophagitis experience an increased incidence of esophageal cancer. In China, this may be the result of contamination of the food supply by Aspergillus fungi, which is known to harbor sterigmatocystin, a carcinogenic mycotoxin. To delineate the potential link between sterigmatocystin and esophageal cancer, an experimental model of reflux esophagitis was developed in rats that had undergone a cardiectomy and partial pylorus ligation. The rats were treated with sterigmatocystin or saline, and esophageal squamous cell hyperplasia was assessed based on the pathological evaluation. The expression of proliferating cell nuclear antigen (PCNA), transporter associated with antigen processing 1 (TAP1) and low molecular weight protein 2 (LMP2) was determined by immunohistochemistry. Intraperitoneal administration of sterigmatocystin promoted the proliferation of squamous epithelium. In addition, it also increased the expression of PCNA in esophageal epithelial cells in rats with reflux esophagitis and was correlated with the increased severity of epithelial hyperplasia. The expression levels of TAP1 and LMP2, which are located in the cytoplasm of esophageal epithelial cells, were reduced in rats with reflux esophagitis, and sterigmatocystin exposure further decreased the expression. Thus, the downregulation of TAP1 and LMP2 proteins by sterigmatocystin may directly affect tumor immunity by allowing transformed cells to escape the host immune surveillance, thereby promoting esophageal cancer.

The present study aimed to construct a lentiviral RNA interference (RNAi) vector targeting the transforming growth factor β1 (TGFβ1) gene of rats, in order to examine its effect on silencing of the TGFβ1 gene and on the expression of collagen type 1 α1 (Col1a1) in HSC‑T6 rat hepatic stellate cells. Three RNAi sites of the TGFβ1 gene were selected according to its CDs sequence. Three pairs of small interfering RNA (siRNA) of these RNAi sites were synthesized and then transfected into HSC‑T6 cells, respectively, to confirm the optimal siRNA sequence via reverse transcription‑polymerase chain reaction analysis. Subsequently, shRNA targeting the sequence of the optimal siRNA was designed, synthesized and annealed to form a double‑stranded structure. The annealed oligonucleotide fragment was cloned into pGreenPuro plasmids to establish the pGreenPuro/TGFβ1 shRNA lentiviral vector, which was then transfected into 293T cells, following identification by restriction enzyme digestion and sequencing for the production of lentiviral particles exhibiting high reactivity. These particles were used to infect HSC‑T6 cells, following which the expression of GFP in the transfected cells was observed under an inverted microscope. The effects on TGFβ1 gene silencing and the expression levels of Colla1 were detected at the mRNA and protein levels. The results provided confirmation of the optimal siRNA sequence. Enzyme digestion and sequencing verified successful construction of the pGreenPuro/TGFβ1 shRNA lentiviral vector. This lentiviral vector effectively silenced the TGFβ1 gene in the HSC‑T6 cells, and inhibited the expression of Col1a1 at the mRNA and protein levels. Taken together, the lentiviral RNAi vector targeting the TGFβ1 gene of rats was successfully constructed, which effectively silenced the TGFβ1 gene of the HSC‑T6 cells and inhibited the expression of Col1a1.

The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries) is not well understood, and little is known about this species' genetic diversity. This knowledge gap is partly due to the difficulty of sample collection. This is the first work to address this question. Here, the genetic diversity and phylogenetic relationship of 636 individual Tibetan sheep from fifteen populations were assessed using 642 complete sequences of the mitochondrial DNA D-loop. Samples were collected from the Qinghai-Tibetan Plateau area in China, and reference data were obtained from the six reference breed sequences available in GenBank. The length of the sequences varied considerably, between 1031 and 1259 bp. The haplotype diversity and nucleotide diversity were 0.992±0.010 and 0.019±0.001, respectively. The average number of nucleotide differences was 19.635. The mean nucleotide composition of the 350 haplotypes was 32.961% A, 29.708% T, 22.892% C, 14.439% G, 62.669% A+T, and 37.331% G+C. Phylogenetic analysis showed that all four previously defined haplogroups (A, B, C, and D) were found in the 636 individuals of the fifteen Tibetan sheep populations but that only the D haplogroup was found in Linzhou sheep. Further, the clustering analysis divided the fifteen Tibetan sheep populations into at least two clusters. The estimation of the demographic parameters from the mismatch analyses showed that haplogroups A, B, and C had at least one demographic expansion in Tibetan sheep. These results contribute to the knowledge of Tibetan sheep populations and will help inform future conservation programs about the Tibetan sheep native to the Qinghai-Tibetan Plateau.

Initiation of hair follicle (HF) is the first and most important stage of HF morphogenesis. However the precise molecular mechanism of initiation of hair follicle remains elusive. Meanwhile, in previous study, the more attentions had been paid to the function of genes, while the roles of non-coding RNAs (such as long noncoding RNA and microRNA) had not been described. Therefore, the roles of long noncoding RNA(LncRNA) and coding RNA in sheep skin during the initiation of sheep secondary HF were integrated and analyzed, by using strand-specific RNA sequencing (ssRNA-seq).A total of 192 significant differentially expressed genes were detected, including 67 up-regulated genes and 125 down-regulated genes between stage 0 and stage 1 of HF morphogenesis during HF initiation. Only Wnt2, FGF20 were just significant differentially expressed among Wnt, Shh, Notch and BMP signaling pathways. Further expression profile analysis of lncRNAs showed that 884 novel lncRNAs were discovered in sheep skin expression profiles. A total of 15 lncRNAs with significant differential expression were detected, 6 up-regulated and 9 down-regulated. Among of differentially expressed genes and LncRNA, XLOC002437 lncRNA and potential target gene COL6A6 were all significantly down-regulated in stage 1. Furthermore, by using RNAhybrid, XLOC005698 may be as a competing endogenous RNA ‘‘sponges” oar-miR-3955-5p activity. Gene Ontology and KEGG pathway analyses indicated that the significantly enriched pathway was peroxisome proliferator-activated receptors (PPARs) pathway (corrected P-value < 0.05), indicating that PPAR pathway is likely to play significant roles during the initiation of secondary HF.Results suggest that the key differentially expressed genes and LncRNAs may be considered as potential candidate genes for further study on the molecular mechanisms of HF initiation, as well as supplying some potential values for understanding human hair disorders.

Building ontology is a fundamental but also hard work. Collaborative ontology editing tools can make ontology development more efficiently. In this paper, the important features of collaborative ontology development were analyzed, and several tools such as AGROVOC Concept Server Workbench (ACSW), Collaborative Protege and WebProtege were studied. Besides, some comparisons among them from several aspects were made and some prospects for the further improvement of these tools were given. Finally, we show it is a good way to build agricultural ontology with these tools collaboratively and simultaneously.

Slit homolog 2 (Slit2) is distributed in various tissues and participates in numerous cellular processes; however, the role of Slit2 in the regulation of angiogenesis remains controversial, since it has previously been reported to exert proangiogenic and antiangiogenic activities. The present study aimed to investigate the effects of Slit2 on vascular endothelial cell proliferation and migration in vitro, and to reveal the possible underlying signaling pathway. Aortic endothelial cells were isolated from Sprague Dawley rats and cultured. Cell proliferation assay, cell migration assay, immunocytochemistry and small interfering RNA transfection were subsequently performed. The results demonstrated that exogenous Slit2 administration markedly suppressed TNF‑α‑induced endothelial cell proliferation and migration in vitro. In addition, TNF‑α application upregulated the protein expression levels of vascular endothelial growth factor (VEGF) and Notch in RAECs, whereas Slit2 administration downregulated VEGF and Notch expression in RAECs cultured in TNF‑α conditioned medium. Further studies indicated that knockdown of VEGF suppressed the effects of TNF‑α on the induction of RAEC proliferation and migration. VEGF knockdown‑induced inhibition of RAEC proliferation and migration in TNF‑α conditioned medium was also achieved without Slit2 administration. Furthermore, VEGF knockdown markedly decreased Notch1 and Notch2 expression. These results indicated that Slit2 suppresses TNF‑α‑induced vascular endothelial cell proliferation and migration in vitro by inhibiting the VEGF‑Notch signaling pathway. Therefore, Slit2 may inhibit the proliferation and migration of endothelial cells during vascular development.

Treatment of Spicaria elegans with cytochrome P-450 inhibitor resulted in two new deoxy-cytochalasins, 7-deoxy-cytochalasin Z7 (1) and 7-deoxy-cytochalasin Z9 (2), which were recognized as plausible precursors of cytochalasins Z7 and Z9, respectively. Their structures were elucidated by spectroscopic methods and the absolute configuration of 1 was determined by the conventional Mosher ester method. Their cytotoxicities against two cancer cell lines were evaluated.

The target of rapamycin (TOR) signaling regulates the nucleocytoplasmic shuttling of transcription factors in yeast. Whether the mammalian counterpart of TOR (mTOR) also regulates nucleocytoplasmic shuttling is not known. Using a phospho-specific monoclonal antibody, we demonstrate that mTOR phosphorylates Ser(168,170) of endogenous NFATc4, which are conserved gate-keeping Ser residues that control NFAT subcellular distribution. The mTOR acts as a basal kinase during the resting state to maintain NFATc4 in the cytosol. Inactivation and nuclear export of NFATc4 are mediated by rephosphorylation of Ser(168,170), which can be a nuclear event. Kinetic analyses demonstrate that rephosphorylation of Ser(168,170) of endogenous NFATc4 is mediated by mTOR and, surprisingly, by extracellular signal-regulated kinase 5 (ERK5) mitogen-activated protein kinase as well. Ablation of ERK5 in the Erk5(-/-) cells ascertains defects in NFATc4 rephosphorylation and nucleocytoplasmic shuttling. In addition, phosphorylation of NFATc4 by ERK5 primes subsequent phosphorylation mediated by CK1alpha. These results demonstrate that distinct protein kinases are integrated to phosphorylate the gate-keeping residues Ser(168,170) of NFATc4, to regulate subcellular distribution. These data also expand the repertoire of physiological substrates of mTOR and ERK5.

The geometries of the lowest-lying isomers of Au n Pt 2 , ( n =1–4), clusters are determined using the density functional method B3LYP with relativistic effective core potentials (RECP) and LANL2DZ basis set. Several low-lying isomers were determined, and many of them in electronic configurations with a high spin multiplicity. The stability trend of Pt-doped Au n clusters are compared to that of pure Au n clusters. Our results show that the gold–platinum interaction is strong enough to improve the cluster stability, and indicate that the larger the Au n cluster is, smaller the distortions by substitution of the two Pt atoms are.

SRA is a steroid receptor co-activator which acts as a functional RNA and is classified as belonging to the growing family of functional non-coding RNAs. None of the different SRA transcripts described to date encode a detectable SRA protein following in vitro and in vivo translation experiments. We have identified three new SRA-RNA isoforms differing mainly from the originally cloned SRA by an extended 5 ′ extremity. These long SRA isoforms, able to encode a stable protein in vitro, led to the production in vivo of a nuclear protein when transfected into the MCF-7 human breast cancer cell line. Reverse-transcription polymerase chain reaction and Western blot analysis of RNA and protein extracts from different breast cancer cell lines confirmed the presence of endogenous coding SRA isoforms and their corresponding proteins. Our results demonstrate that full-length SRA-RNAs likely to encode stable proteins are widely expressed in breast cancer cell lines.

Following spinal cord trauma, mitochondrial dysfunction associated with increased oxidative stress is a critical event leading to leukocyte inflammatory responses, neuronal cell death and demyelination, contributing to permanent locomotor and neurological disability. The present study demonstrated that the mitochondrial enhancer N-acetylcysteine (NAC) may restore redox balance via enhancement of mitochondrial respiratory activity following traumatic spinal cord injury (SCI). In addition, NAC ameliorates oxidative stress-induced neuronal loss, demyelination, leukocyte infiltration and inflammatory mediator expression and improves long-term locomotor function. Furthermore, neuronal survival and neurological recovery are significantly correlated with increased mitochondrial bioenergetics in SCI following treatment with NAC. Therefore, NAC may represent a potential therapeutic agent for preserving mitochondrial dynamics and integrity following traumatic SCI.

RPM2 is a Saccharomyces cerevisiae nuclear gene that encodes the protein subunit of mitochondrial RNase P and has an unknown function essential for fermentative growth. Cells lacking mitochondrial RNase P cannot respire and accumulate lesions in their mitochondrial DNA. The effects of a new RPM2 allele, rpm2-100, reveal a novel function of RPM2 in mitochondrial biogenesis. Cells with rpm2-100 as their only source of Rpm2p have correctly processed mitochondrial tRNAs but are still respiratory deficient. Mitochondrial mRNA and rRNA levels are reduced in rpm2-100 cells compared to wild type. The general reduction in mRNA is not reflected in a similar reduction in mitochondrial protein synthesis. Incorporation of labeled precursors into mitochondrially encoded Atp6, Atp8, Atp9, and Cytb protein was enhanced in the mutant relative to wild type, while incorporation into Cox1p, Cox2p, Cox3p, and Var1p was reduced. Pulse-chase analysis of mitochondrial translation revealed decreased rates of translation of COX1, COX2, and COX3 mRNAs. This decrease leads to low steady-state levels of Cox1p, Cox2p, and Cox3p, loss of visible spectra of aa3 cytochromes, and low cytochrome c oxidase activity in mutant mitochondria. Thus, RPM2 has a previously unrecognized role in mitochondrial biogenesis, in addition to its role as a subunit of mitochondrial RNase P. Moreover, there is a synthetic lethal interaction between the disruption of this novel respiratory function and the loss of wild-type mtDNA. This synthetic interaction explains why a complete deletion of RPM2 is lethal.

Pyridoxal-specific phosphatase purified from human erythrocytes was inactivated by a variety of thiol-specific reagents in a time- and concentration-dependent manner. The presence of pyridoxal phosphate, a substrate, or inorganic phosphate, a competitive inhibitor, protected the enzyme from inactivation. Phosphatase inactivated by disulfide reagents was reactivated by the addition of excess dithiothreitol, indicating that the inactivation was due to formation of a mixed disulfide between the reagent and a free cysteinyl residue at or near the active site of the enzyme. Incorporation of either 1 mol of 5,5'-dithiobis(2-nitrobenzoic acid) (DTNB), 0.6 mol of iodo[3H]acetate, or 0.6 mol of N-[3H]ethylmaleimide per mol of subunit led to complete inactivation of the enzyme. High concentration of phosphate prevented the incorporation of DTNB and iodo[3H]acetate. Amino acid analysis of carboxymethylated enzyme and DTNB titration of the denatured phosphatase indicated that there may be only 1 cysteinyl residue per subunit. Modification by iodoacetate did not affect the quaternary structure of the enzyme. The phosphatase modified by iodo[3H]acetate was subjected to trypsin digestion, and the resulting peptides were separated on a reverse phase C18 column. Two radioactive peaks were obtained and contained a peptide with the N-terminal sequence of Ala-Gln-Gly-Val-Leu-Phe-Asp-Cys(Cm)-Asp-Gly-Val-Leu-X-Asn-Gly. Most of the radioactivity was released with Cys(Cm). These results indicate that the cysteinyl residue in this sequence is at or near the active site and is essential for activity. Residues 5-12 and 15 of this peptide are identical with a sequence of a yeast alkaline p-nitrophenylphosphatase, and the peptide has little homology with other mammalian phosphatases.

The specificity and active site properties of vitamin B6 phosphatase purified from human erythrocytes were studied by kinetic analyses with vitamin B6 compounds and derivatives and chemical modification with group-specific reagents. The kinetic constants for pyridoxal phosphate (PLP), 4-pyridoxic acid phosphate, pyridoxine phosphate, and pyridoxamine phosphate were determined from pH 5 to 9. The values of Vmax/Km and pKm were highest for PLP and 4-pyridoxic acid phosphate and lowest for pyridoxamine phosphate. Vmax/Km and pKm for the four substrates were maximum between pH 6 and 8. Ionizable groups with pKa values about 6 and 8 affected substrate binding to the enzyme. Vmax values for all the substrates gradually decreased with increasing pH. The enzyme also catalyzed the dephosphorylation of 4'-secondary amine derivatives of vitamin B6-phosphate. The phosphatase had greatest catalytic efficiency with substrates that contained a negatively charged group on the 4'-position of the pyridine ring. It is concluded that there are one or two positively charged groups at the active site of the enzyme that interact with the substrate's phosphate ester and 4'-substituent. The phosphatase was inactivated by phenylglyoxal, and PLP protected the enzyme against this inactivation. Phenylglyoxal did not modify Lys or Cys residues or an alpha-amino group since the enzyme's NH2 terminus is blocked, and it did not affect the quaternary structure of the phosphatase. The enzyme was inactivated by the incorporation of 1 mol of phenylglyoxal/subunit. Diethylpyrocarbonate inactivated the enzyme by reacting with a group with a pKa of 6.7, and pyridoxine phosphate protected the enzyme against this inactivation. These data suggest that Arg and His residues are at or near the active site and may play roles in substrate binding and/or catalysis.

Bilirubin oxidase was purified from a culture filtrate of Myrothecium verrucaria Mv 2, 1089 by DEAE-cellulose and Sephadex G-100 column chromatographies. The purified enzyme had a specific activity of 30 U/mg protein and showed a single band on polyacrylamide gel electrophoresis. Some of the general properties of this bilirubin oxidase were as follows: the optimum pH for the enzyme reaction was 7.5 and the optimum temperature was 50 degrees C. The enzyme was stable at pH ranging from 9.0 to 9.5. The mol wt was calculated to be 61,900-62,700 by SDS-PAGE and gel-filtration technique. The apparent Km value of the bilirubin oxidase was calculated to be 9.4 x 10(-5) mol/L. The enzyme activity was greatly reduced by incubation of bilirubin oxidase with Fe2+, Hg+, NaN3, NH+4, and Zn2+. The enzyme reaction was inhibited in the presence of Ca2+, Hg+, Zn2+, Fe2+, and BSA.

Graft-versus-host disease (GVHD) is a serious complication of allogeneic bone marrow transplantation, and donor T cells are indispensable for GVHD. Current therapies have limited efficacy, selectivity, and high toxicities. We used a novel flow cytometry technique for the analysis of intracellular phosphorylation events in single cells in murine BMT models to identify and validate novel GVHD drug targets.1-7 This method circumvents the requirement for large numbers of purified cells, unlike western blots. We defined a signaling profile for alloactivated T cells in vivo and identified the phosphorylation of ERK1/2 and STAT-3 as important events during T-cell (allo)activation in GVHD. We establish that interference with STAT-3 phosphorylation can inhibit T-cell activation and proliferation in vitro and GVHD in vivo. This suggests that phospho-specific flow cytometry is useful for the identification of promising drug targets, and ERK1/2 and STAT-3 phosphorylation in alloactivated T cells may be important for GVHD.

To better understand the mechanisms that regulate p120-catenin (p120) and E-cadherin function, we are systematically generating phospho-specific monoclonal antibodies (MAb) to the major p120 phosphorylation sites. p120 has emerged recently as a master regulator of E-cadherin stability and an important modulator of RhoGTPase activities. A number of phosphorylation sites have been identified, but none have as yet been linked to specific regulatory roles. Here, we describe a novel phospho-specific monoclonal antibody to the major PKC-induced p120 phosphorylation site, phospho-serine 879 (pS879). With a few exceptions, p120 MAb pS879 is remarkably specific for the phosphorylated S879 epitope and works effectively in common applications such as Western blot analysis, immunoprecipitation, and immunofluorescence. p120 MAb pS879 should facilitate efforts to identify the role of S879 phosphorylation and to map signaling pathways that modify p120 function through activation of PKC.

A method for high-throughput cloning and analysis of short hairpin RNAs (shRNAs) is described. Using this approach, 464 shRNAs against 116 different genes were screened for knockdown efficacy, enabling rapid identification of effective shRNAs against 74 genes. Statistical analysis of the effects of various criteria on the activity of the shRNAs confirmed that some of the rules thought to govern small interfering RNA (siRNA) activity also apply to shRNAs. These include moderate GC content, absence of internal hairpins, and asymmetric thermal stability. However, the authors did not find strong support for position specific rules. In addition, analysis of the data suggests that not all genes are equally susceptible to RNA interference (RNAi).

This unit presents protocols for measuring intracellular phosphoepitopes by flow cytometry for biochemical investigations in both human and murine primary cells as well as in cell lines. Conventional methods that require cellular lysis cannot discriminate between proteins from different cellular subsets. Intracellular detection of phosphorylated and nonphosphorylated signaling molecules, on the other hand, has recently exposed the heterogeneity that can be observed upon signal transduction. Although staining methodologies for cytokines and cell cycle antigens have been appreciated for years, detection of phosphorylated molecules presents several new challenges, including generation of reagents and details of the staining technique. As these techniques are adapted to new applications, the protocols continue to be refined. This unit describes signal amplification of intracellular signals upon detergent-based permeabilizations, staining protocol for adherent cells, methodology for whole-blood staining, and multiparameter staining procedures for surface and intracellular antigens.

Rpm2p is a protein subunit of yeast mitochondrial RNase P and is also required for the maturation of Rpm1r, the mitochondrially-encoded RNA subunit of the enzyme. Previous work demonstrated that an insertional disruption of RPM2, which produces the C-terminally truncated protein Rpm2-DeltaCp, supports growth on glucose but cells lose some or all of their mitochondrial genome and become petite. These petites, even if they retain the RPM1 locus, lose their ability to process the 5'-ends of mitochondrial tRNA. We report here that if strains containing the truncated RPM2 allele are created and maintained on respiratory carbon sources they have wild-type mitochondrial genomes, and a significant portion of tRNA transcripts are processed. In contrast, precursor Rpm1r transcripts accumulate and mature Rpm1r is not made. These data show that one function of the deleted C-terminal region is in the maturation of Rpm1r, and that this region and mature Rpm1r are not absolutely required for RNase P activity. Finally, we demonstrate that full activity can be restored if the N-terminal and C-terminal domains of Rpm2p are supplied in trans.

Publisher Summary Yeast mitochondrial RNase P is the endonuclease, which is is composed of both RNA and protein subunits coded by the mitochondrial and nuclear genomes, respectively. This chapter describes the in vivo and in vitro approaches used to understand the nucleocytoplasmic interactions necessary for the biosynthesis of this dually derived complex of yeast mitochondria and to gain insight into RNase P structure and function. Many questions about this enzyme and its biosynthesis remain despite the identification and current characterization of Rpm1r and Rpm2p. First, none of the experiments eliminates the possible presence of a nuclear encoded RNA in this enzyme. Second, although Rpm2p clearly fills all the criteria expected of a protein subunit of the enzyme and is the most abundant protein in near homogeneous preparations, it is possible that other proteins play either essential or stimulatory roles. Successful production of sufficient Rpm2p for in vitro reconstitution studies should determine if Rpm1r and Rpm2p are the only components necessary to support full activity in vitro. If they are, studies on the biochemistry and biogenesis of a well-defined yeast mitochondrial RNase P can be initiated. Immunoprecipitation of complexes or cross-linking between the known RNA and proteins offer other approaches to identify additional components that can be required for in vitro reconstitution or be associated with the enzyme in vivo.

RPM2 is identified here as a high-copy suppressor of isp42-3, a temperature-sensitive mutant allele of the mitochondrial protein import channel component, Isp42p. RPM2 already has an established role as a protein component of yeast mitochondrial RNase P, a ribonucleoprotein enzyme required for the 5' processing of mitochondrial precursor tRNAs. A relationship between mitochondrial tRNA processing and protein import is not readily apparent, and, indeed, the two functions can be separated. Truncation mutants lacking detectable RNase P activity still suppress the isp42-3 growth defect. Moreover, RPM2 is required for normal fermentative yeast growth, even though mitochondrial RNase P activity is not. The portion of RPM2 required for normal growth and suppression of isp42-3 is the same. We conclude that RPM2 is a multifunctional gene. We find Rpm2p to be a soluble protein of the mitochondrial matrix and discuss models to explain its suppression of isp42-3.

Pyridoxal phosphatase purified from human erythrocytes catalyzes the dephosphorylation of pyridoxal phosphate (PLP) and pyridoxine phosphate. The enzyme had phosphotransferase activity and transferred 20-25% of the phosphoryl group from either substrate to ethanol. Incubation of the enzyme with [32P]PLP, followed by quenching in acid, resulted in trapping 0.14-0.24 mol of 32P per mol of subunit. The incorporation of 32P was not due to Schiff base formation. Phosphorylation of the enzyme by [32P]PLP required catalysis by the enzyme and did not occur in the presence of excess pyridoxine phosphate or with denatured enzyme. The phosphoenzyme intermediate was relatively acid stable and very labile at high pH or in the presence of hydroxylamine. Woodward′s reagent K, which specifically modifies acidic amino acid residues, inactivated the phosphatase in a concentration- and time-dependent manner which followed pseudo-first-order kinetics. Substrates or Pi protected the enzyme from inactivation. It is concluded that PLP phosphatase catalyzes the hydrolysis of PLP by forming a covalent phosphoenzyme intermediate and the intermediate may be an acylphosphate. The 32P-labeled phosphatase was digested with pepsin, and two radioactive peaks were isolated by reversed-phase chromatography. However, definitive sequences were not obtained.

Graft-versus-host-disease (GVHD) is a serious complication of allogeneic bone marrow transplantation (allo-BMT). The physiology of GVHD is dominated by alloactivated donor T cells, yet current treatments are often nonspecific and offer limited efficacy with relatively high toxicities. We screened for novel drug targets in alloactivated T cells in a murine allo-BMT model using a flow cytometric technique for the in vivo analysis of intracellular signaling. We defined the signaling profile of normal T cells and alloreactive T cells during GVHD, focusing on pathways involved in T cell receptor (TCR), costimulatory, and cytokine signaling. This analysis revealed that although proteins in multiple pathways (MAP kinases, PI3K, Jak/STAT signaling) were all heavily phosphorylated in alloactivated T cells, phosphorylation of STAT-3 and ERK1/2 were particularly prominently increased in donor alloactivated CD4 T cells. We further analyzed the importance of STAT-3 and ERK1/2 signaling in alloactivated T cells via the use of small-molecule inhibitors of STAT-3 (curcurbitacin E/I) and ERK1/2 phosphorylation (SL327). Treatment with these inhibitors attenuated T cell proliferation in response to anti-CD3+CD28 stimulation and in mixed leukocyte reactions in vitro in a dose-dependent fashion (figure 1). Figure 1 Figure 1. Pre-incubation of donor splenocytes with cucurbitacin E significanly reduced T cell activation (CD25, CD69) at 24 hours in adoptive transfer experiments in vivo (p Figure 2 Figure 2. We conclude that flow cytometric analysis of signaling pathways in single cells represents a novel methodology to assess the in vivo signaling profiles of specific cell populations in order to select drug targets for further study. STAT-3 and ERK1/2 phosphorylation may also represent potential targets to selectively inhibit donor T cell alloactivation and proliferation in GVHD.