Proteomic and phosphoproteomic landscape of salivary extracellular vesicles to assess OSCC therapeutical outcomes

Circulating extracellular vesicles (EVs) have emerged as an appealing source for surrogates to evaluate the disease status. Herein, we present a novel proteomic strategy to identify proteins and phosphoproteins from salivary EVs to distinguish oral squamous cell carcinoma (OSCC) patients from healthy individuals and explore the feasibility to evaluate therapeutical outcomes. Bi-functionalized magnetic beads (BiMBs) with Ti (IV) ions and a lipid analog, 1,2-Distearoyl-3-sn-glycerophosphoethanolamine (DSPE) are developed to efficiently isolate EVs from small volume of saliva. In the discovery stage, label-free proteomics and phosphoproteomics quantification showed 315 upregulated proteins and 132 upregulated phosphoproteins in OSCC patients among more than 2500 EV proteins and 1000 EV phosphoproteins, respectively. We further applied targeted proteomics by coupling parallel reaction monitoring with parallel accumulation-serial fragmentation (prm-PASEF) to measure panels of proteins and phosphoproteins from salivary EVs collected before and after surgical resection. A panel of three total proteins and three phosphoproteins, most of which have previously been associated with OSCC and other cancer types, show sensitive response to the therapy in individual patients. Our study presents a novel strategy to the discovery of effective biomarkers for non-invasive assessment of OSCC surgical outcomes with small amount of saliva.     

A MODIFIED PROCEDURE FOR ISOLATION OF ASTROCYTE- AND NEURON-ENRICHED FRACTIONS FROM RAT BRAIN

Our previously published method for isolation of neurons with extensive processes (Farooq et al., 1977) has been modified to permit the isolation of both astrocyte- and neuron-enriched fractions. Rat cerebral tissue is incubated with acetylated trypsin and disrupted. The cell suspension is separated first by differential centrifugation and then by gradient centrifugation on discontinuous Ficoll gradients. The method is reproducible and is applicable equally well to immature and adult animals. The yield of astrocytes of 57% particle purity, and higher weight purity, is 4–7 × 10⁶ cells/brain, amounting to 1.5–2.0 mg of protein. The astrocytes appear to be a mixture of fibrous and protoplasmic types. The yield of neurons of 90% particle purity is 10–14 × 10⁶ cells/brain, amounting to 2.4–3.0 mg of protein. A total yield of neurons of 28–37 × 10⁶ cells/brain can be obtained at 70% purity. These preparations have been characterized by light microscopy and protein, RNA and DNA content.     

Widespread differentiation stage-specific expression of the gene encoding phosphoprotein p19 (metablastin) in mammalian cells

p19 is a highly conserved 19 kD cytosolic protein that undergoes phosphorylation in response to diverse extracellular factors in mammalian cells. Its expression is abundant in brain and testis and is developmentally regulated. To gain insights regarding its function, we analyzed the expression of p19 mRNA in a variety of cell types during induction of differentiation. Murine erythroleukemia cells showed a moderate increase followed by a marked decrease in the abundance of p19 mRNA during induction of differentiation. In murine C2 myoblasts and primary fetal rat osteoblasts, p19 mRNA was abundant in replicating cells and decreased to undetectable levels during differentiation. In resting human peripheral blood lymphocytes, p19 mRNA was virtually undetectable but was strongly induced during blast transformation of both B and T cells. In rat liver, p19 mRNA was abundant on embryonic day 17 and decreased during early postnatal development. Upon fractionation of adult rat liver cells by centrifugal elutriation, p19 mRNA was not detected in hepatocytes while a low level was observed in a fraction enriched in non-parenchymal epithelial cells. CCl4-induced liver regeneration resulted in induction of p19 mRNA in hepatocytes. Primary cultures of embryonic and neonatal rat brain were analyzed by indirect immunofluorescence using co-staining with stage-specific markers. p19 expression was restricted to immature neurons and oligodendrocyte precursors. In contrast to the other cell types examined, the neuronal and glial precursors that express p19 were shown, using BrdU labeling, to be postmitotic both in primary culture and in vivo. The data demonstrate widespread, stage-specific expression of p19 and suggest that the protein exerts a general, lineage-independent function during induction of differentiation of mammalian cells. In view of the available evidence on the stimulation of serine phosphorylation of p19 by several growth factors, our working hypothesis is that phosphorylation of p19 may be involved in the mechanism by which growth factors control cell differentiation.     

Comparative Kinetics and Reciprocal Inhibition of Nitrate and Nitrite Uptake in Roots of Uninduced and Induced Barley (Hordeum vulgare L.) Seedlings

Nitrate and NO₂⁻ transport by roots of 8-day-old uninduced and induced intact barley (Hordeum vulgare L. var CM 72) seedlings were compared to kinetic patterns, reciprocal inhibition of the transport systems, and the effect of the inhibitor, p-hydroxymercuribenzoate. Net uptake of NO₃⁻ and NO₂⁻ was measured by following the depletion of the ions from the uptake solutions. The roots of uninduced seedlings possessed a low concentration, saturable, low K_m, possibly a constitutive uptake system, and a linear system for both NO₃⁻ and NO₂⁻. The low K_m system followed Michaelis-Menten kinetics and approached saturation between 40 and 100 micromolar, whereas the linear system was detected between 100 and 500 micromolar. In roots of induced seedlings, rates for both NO₃⁻ and NO₂⁻ uptake followed Michaelis-Menten kinetics and approached saturation at about 200 micromolar. In induced roots, two kinetically identifiable transport systems were resolved for each anion. At the lower substrate concentrations, less than 10 micromolar, the apparent low K_ms of NO₃⁻ and NO₂⁻ uptake were 7 and 9 micromolar, respectively, and were similar to those of the low K_m system in uninduced roots. At substrate concentrations between 10 and 200 micromolar, the apparent high K_m values of NO₃⁻ uptake ranged from 34 to 36 micromolar and of NO₂⁻ uptake ranged from 41 to 49 micromolar. A linear system was also found in induced seedlings at concentrations above 500 micromolar. Double reciprocal plots indicated that NO₃⁻ and NO₂⁻ inhibited the uptake of each other competitively in both uninduced and induced seedlings; however, K_i values showed that NO₃⁻ was a more effective inhibitor than NO₂⁻. Nitrate and NO₂⁻ transport by both the low and high K_m systems were greatly inhibited by p-hydroxymercuribenzoate, whereas the linear system was only slightly inhibited.     

Genotypic variation for drought tolerance in cotton (Gossypium hirsutum L.): Leaf gas exchange and productivity

Although water-limited environments are detrimental to cotton growth and productivity worldwide, identification of cotton (Gossypium hirsutum L.) genotypes that are less sensitive to drought may improve productivity in drought prone areas. The objective of the study was to assess genotypic variation for drought tolerance in cotton varieties using physiological attributes as selection criteria, and to determine the relationship of physiological attributes with productivity traits. The association of target physiological traits for drought tolerance (photosynthetic rate (P_n), stomatal conductance (g_s), and transpiration rate (E)) with productivity traits under well-watered (W₁) and water-limited (W₂) regimes was analyzed using 32 public cotton cultivars/bred lines in two field experiments conducted during the normal cotton growing seasons 2003 and 2004. Seed cotton yield (SCY) and biological yield (BY) were markedly affected under W₂ regime in all cultivars except the outstanding performance of CIM-1100 and RH-510 proving their superiority to other cultivars in drought tolerance. Conversely, FH-901, FH-634, and FH-2000 were high yielding under W₁ regime; however, exhibited a sharp decline in yield under W₂ regime. A positive correlation between SCY and BY under water stress (r=0.44 in 2003; r=0.69 in 2004) indicates that BY is also a primary determinant of SCY under water stress and genetic improvement of BY under water-limited environment may also improve SCY. P_n, g_s, and E were significantly reduced by water stress. Substantial genotypic variation for gas exchange attributes existed among the cotton cultivars. A positive association (P<0.01) was observed between g_s and E under both regimes in both years indicating the prevalence of stomatal control of transpiration. The positive association (P<0.01) between P_n and g_s in both years in W₂ regime indicates also a major role of stomatal effects in regulating leaf photosynthesis under water-limited conditions. P_n was significantly correlated with SCY (P<0.01) and BY (P<0.05 in 2003; P<0.01 in 2004) in W₂ regime; however, the level of these associations was not significant in W₁ regime. These findings demonstrate that association of P_n with productivity is effective under water-limited environment and may be useful as a selection criterion in breeding programs with the objective of improving drought tolerance and SCY under water-limited environments. Moreover, association between SCY and BY under water stress suggests that genetic improvement of BY under water stress may also improve SCY.     

Prediction of Structure of Human WNT-CRD (FZD) Complex for Computational Drug Repurposing

The observed genetic alterations of various extracellular and intracellular WNT (Wingless, Int-1 proto-oncogene) signaling components can result in an increase or decrease in gene expression, and hence can be obstructed proficiently. These genetics target sites may include the prevention of WNT-FZD (Frizzled) binding, destruction of β-catenin and formation of Axin, APC and GSK-3β complex. Hence, the localized targeting of these interacting partners can help in devising novel inhibitors against WNT signaling. Our present study is an extension of our previous work, in which we proposed the co-regulated expression pattern of the WNT gene cluster (WNT-1, WNT-6, WNT-10A and WNT-10B) in human breast carcinoma. We present here the computationally modeled three dimensional structure of human WNT-1 in complex with the FZD-1 CRD (Cysteine Rich Domain) receptor. The dimeric cysteine-rich domain was found to fit into the evolutionarily conserved U-shaped groove of WNT protein. The two ends of the U- shaped cleft contain N-terminal and C-terminal hydrophobic residues, thus providing a strong hydrophobic moiety for the frizzled receptor and serving as the largest binding pocket for WNT-FZD interaction. Detailed structural analysis of this cleft revealed a maximum atomic distance of ∼28 Å at the surface, narrowing down to ∼17 Å and again increasing up to ∼27 Å at the bottom. Altogether, structural prediction analysis of WNT proteins was performed to reveal newer details about post-translational modification sites and to map the novel pharmacophore models for potent WNT inhibitors.     

The interplay between mitochondria and store-operated Ca2+ entry: Emerging insights into cardiac diseases

Store-operated Ca²⁺ entry (SOCE) machinery, including Orai channels, TRPCs, and STIM1, is key to cellular calcium homeostasis. The following characteristics of mitochondria are involved in the physiological and pathological regulation of cells: mitochondria mediate calcium uptake through calcium uniporters; mitochondria are regulated by mitochondrial dynamic related proteins (OPA1, MFN1/2, and DRP1) and form mitochondrial networks through continuous fission and fusion; mitochondria supply NADH to the electron transport chain through the Krebs cycle to produce ATP; under stress, mitochondria will produce excessive reactive oxygen species to regulate mitochondria-endoplasmic reticulum interactions and the related signalling pathways. Both SOCE and mitochondria play critical roles in mediating cardiac hypertrophy, diabetic cardiomyopathy, and cardiac ischaemia-reperfusion injury. All the mitochondrial characteristics mentioned above are determinants of SOCE activity, and vice versa. Ca²⁺ signalling dictates the reciprocal regulation between mitochondria and SOCE under the specific pathological conditions of cardiomyocytes. The coupling of mitochondria and SOCE is essential for various pathophysiological processes in the heart. Herein, we review the research focussing on the reciprocal regulation between mitochondria and SOCE and provide potential interplay patterns in cardiac diseases.     

Reproductive tissues-specific meta-QTLs and candidate genes for development of heat-tolerant rice cultivars

Plant Molecular Biology - By integrating genetics and genomics data, reproductive tissues-specific and heat stress responsive 35 meta-QTLs and 45 candidate genes were identified, which could be...     

Collision avoidance and a looming sensitive neuron: size matters but biggest is not necessarily best

Locusts possess visual neurons that can be uniquely identified in each locust and that respond selectively to looming stimuli, giving the animal a warning of impending collision. It has been suggested that one such neuron, the lobula giant movement detector (LGMD), issues this warning by generating a peak in its response that occurs ca. 25 ms after a looming object reaches a subtense of 17 degrees on the eye. This peak is proposed to be a trigger for escape behaviour. We use both modelling and electrophysiological techniques to show that this early peak in LGMD response is not the 'essential functional variable' used naturally by the locust to trigger escape, but rather results from the unnaturally large stimulus used in the previous experimental work. The natural predators of Locusta in Africa, where the locust evolved, are small birds such as the fiscal shrike Lanius collaris humeralis and the carmine bee-eater Merops nubicus, with pectoral diameters of 40-45 mm (measurements from museum specimens). Locusta in flight are less than 100 mm wing tip to wing tip. When a locust views small approaching objects, the response of the LGMD continues to increase throughout the object's approach and the locust is able to trigger escape behaviours without the LGMD response peaking prior to collision.     

Lipid rafts mediate association of LFA-1 and CD3 and formation of the immunological synapse of CTL

Lipid rafts accumulate in the immunological synapse formed by an organized assembly of the TCR/CD3, LFA-1, and signaling molecules. However, the precise role of lipid rafts in the formation of the immunological synapse is unclear. In this study, we show that LFA-1 on CTL is constitutively active and mediates Ag-independent binding of CTL to target cells expressing its ligands. LFA-1 and CD3 on CTL, but not resting T cells, colocalize in lipid rafts. Binding of LFA-1 on CTL to targets initiates the formation of the immunological synapse, which is formed by LFA-1, CD3, and ganglioside GM1 distributed in the periphery of the cell contact site and cholesterol is more widely distributed. The formation of this synapse is Ag independent, but the recognition of Ag by the TCR induces accumulation of tyrosine phosphorylated proteins in the synapse as well as redistribution of the microtubule organization center toward the cell contact site. Our results suggest that LFA-1 recruits lipid rafts and the TCR/CD3 to the synapse, and facilitates efficient and rapid activation of CTL.