In‐depth and 3‐dimensional exploration of the budding yeast phosphoproteome

Phosphorylation is one of the most dynamic and widespread post‐translational modifications regulating virtually every aspect of eukaryotic cell biology. Here, we assemble a dataset from 75 independent phosphoproteomic experiments performed in our laboratory using Saccharomyces cerevisiae. We report 30,902 phosphosites identified from cells cultured in a range of DNA damage conditions and/or arrested in distinct cell cycle stages. To generate a comprehensive resource for the budding yeast community, we aggregate our dataset with the Saccharomyces Genome Database and another recently published study, resulting in over 46,000 budding yeast phosphosites. With the goal of enhancing the identification of functional phosphorylation events, we perform computational positioning of phosphorylation sites on available 3D protein structures and systematically identify events predicted to regulate protein complex architecture. Results reveal hundreds of phosphorylation sites mapping to or near protein interaction interfaces, many of which result in steric or electrostatic “clashes” predicted to disrupt the interaction. With the advancement of Cryo‐EM and the increasing number of available structures, our approach should help drive the functional and spatial exploration of the phosphoproteome.     

Estrus synchronization and ovarian hyper‐stimulation treatments have negligible effects on cumulus oocyte complex gene expression whereas induction of ovulation causes major expression changes

The effects of exogenous hormones, used for estrus synchronization and ovarian hyper stimulation, on cumulus oocyte complexes (COCs) gene expression in sexually mature rats were determined using microarrays. Gene expression in COCs collected from GnRH (G_trt), GnRH + eCG (G + E_trt), and GnRH + eCG + hCG (G + E + H_trt) treatments were compared to COCs from naturally cycling (NC) rats before the preovulatory luteninizing hormone surge. There was no significant difference in gene expression among NC, G_trt, and G + E_trt; however, over 2,600 genes were significantly different between NC and G + E + H_trt (P < 0.05). Genes upregulated in G + E + H_trt encode for: proteins that are involved in prostaglandin synthesis (Ptgs2, Pla2g4a, and Runx1) and cholesterol biosynthesis (Hmgcr, Sc4mol, and Dhcr24); receptors that allow cholesterol uptake (Ldlr and Scarb1), regulate progesterone synthesis (Star), and inactivate estrogen (Sult1e1); and downstream effectors of LH signal (Pgr, Cebpb, Creb3l1, Areg, Ereg, and Adamts1). Conversely, G + E + H_trt downregulated genes encoding proteins involved in: DNA replication and cell cycle progression (Ccne2, Orc5l, Rad50, and Mcm6); reproductive developmental process; and granulosa cell expansion (Gdf9, Bmp15, Amh, Amhr2, Bmpr1b, Tgfb2, Foxl2, Pde3a, Esr2, Fshr, Ybx2, Ccnd2, Ccnb1ip1, and Zp3); maternal effect genes required for embryo development (Zar1, Npm2, Nlrp5, Dnmt1, H1foo, and Zfp57); amino acid degradation; and ketogenesis (Hmgcs2, and Cpt1b). These results from the rat show that hormones used for estrus synchronization (G_trt) and ovarian hyper stimulation (G + E_trt) had minimal effects on gene expression, whereas induction of ovulation (G + E + H_trt) caused major changes in gene expression of rat COCs. This study provides comprehensive information about regulated genes during late follicle development and ovulation induction. Mol. Reprod. Dev. © 2013 Wiley Periodicals, Inc.     

Distinguishing metastatic triple‐negative breast cancer from nonmetastatic breast cancer using second harmonic generation imaging and resonance Raman spectroscopy

Triple‐negative breast cancer (TNBC) is an aggressive subset of breast cancer that is more common in African‐American and Hispanic women. Early detection followed by intensive treatment is critical to improving poor survival rates. The current standard to diagnose TNBC from histopathology of biopsy samples is invasive and time‐consuming. Imaging methods such as mammography and magnetic resonance (MR) imaging, while covering the entire breast, lack the spatial resolution and specificity to capture the molecular features that identify TNBC. Two nonlinear optical modalities of second harmonic generation (SHG) imaging of collagen, and resonance Raman spectroscopy (RRS) potentially offer novel rapid, label‐free detection of molecular and morphological features that characterize cancerous breast tissue at subcellular resolution. In this study, we first applied MR methods to measure the whole‐tumor characteristics of metastatic TNBC (4T1) and nonmetastatic estrogen receptor positive breast cancer (67NR) models, including tumor lactate concentration and vascularity. Subsequently, we employed for the first time in vivo SHG imaging of collagen and ex vivo RRS of biomolecules to detect different microenvironmental features of these two tumor models. We achieved high sensitivity and accuracy for discrimination between these two cancer types by quantitative morphometric analysis and nonnegative matrix factorization along with support vector machine. Our study proposes a new method to combine SHG and RRS together as a promising novel photonic and optical method for early detection of TNBC.     

The determination of molecular weights of biologically active proteins by cetyltrimethylammonium bromide-polyacrylamide gel electrophoresis

A novel cetyltrimethylammonium bromide-polyacrylamide gel electrophoresis system which is useful for the separation of native forms of proteins consistent with their molecular weights is reported here. Many proteins examined in this system demonstrated the same association patterns which have been shown by other techniques to exist under nondenaturing conditions. In addition, biological activity could be assayed directly in the gel after electrophoresis. Based on the peculiar characteristics of cetyltrimethylammonium bromide, a possible explanation which may account for the behavior of proteins in this system is presented.     

West Nile virus cluster analysis and vertical transmission in Culex pipiens complex mosquitoes in Sacramento and Yolo Counties,California, 2011

West Nile virus (WNV) is now endemic in California, with annual transmission documented by the statewide surveillance system. Although much is known about the horizontal avian‐mosquito transmission cycle, less is known about vertical transmission under field conditions, which may supplement virus amplification during summer and provide a mechanism to infect overwintering female mosquitoes during fall. The current study identified clusters of WNV‐infected mosquitoes in Sacramento and Yolo Counties, CA, during late summer 2011 and tested field‐captured ovipositing female mosquitoes and their progeny for WNV RNA to estimate the frequency of vertical transmission. Space‐time clustering of WNV‐positive Culex pipiens complex pools was detected in the northern Elk Grove area of Sacramento County between July 18 and September 18, 2011 (5.22 km radius; p<0.001 and RR=7.80). Vertical transmission by WNV‐infected females to egg rafts was 50% and to larvae was 40%. The estimated minimal filial infection rate from WNV‐positive, ovipositing females was 2.0 infected females/1,000. The potential contribution of vertical transmission to WNV maintenance and amplification are discussed.     

Individual quality and age affect responses to an energetic constraint in a cavity-nesting bird

Individual variation in life-history trade-offs can be causedby differences in quality and age. We tested for individualvariation in parental investment in incubating tree swallows(Tacyhcineta bicolor) subjected to a feather-clipping manipulation.Individual quality influenced how females were affected by featherclipping; lower quality clipped females showed a greater reductionin incubation and a greater loss of body condition than higherquality clipped females compared with controls. Most importantly,responses during incubation influenced nestling traits; lowerquality clipped females, particularly those losing the mostbody mass, raised nestlings in the poorest condition. Therewas no difference in incubation patterns of control females,but older clipped females suffered self-maintenance costs andraised offspring in better condition. In contrast, younger clippedfemales passed costs on to offspring through lower egg temperaturesand reduced nestling condition while maintaining their own condition.Overall, we found a strong individual quality effect: at thepopulation level, there was a trade-off between investing inincubation and maintaining parental condition, but among individuals,there was a positive correlation between change in parentalcondition and offspring quality. Individual differences in parentalstrategy can be important causes of life-history variation,especially through subtle, but important, aspects of reproductionsuch as maintaining egg temperature during incubation.     

Size,shape, and sex‐dependent variation in force production by crayfish chelae

The ability to generate large closing forces is important for many animals. Several studies have demonstrated that bite or pinching force capacity is usually related to the linear dimensions of the closing apparatus. However, relatively few studies have applied geometric morphometrics to examine the effects of size‐independent shape on force production, particularly in studies of crustacean pinching force. In this study, we utilized traditional and geometric morphometric techniques to compare the pinching force of Procambarus clarkii crayfish to their chela morphology. We found that males possessed larger chelae and pinched harder than females, but that their chela shape and size were weak predictors of strength. Female pinching force was significantly affected by both chela size and shape, with shape variation along the short axis of the claw contributing most to pinching force. We discuss our results in the context of reliable signaling of strength by males and females, and the different selective forces acting on chela shape in the two sexes.     

Non-destructive transformation ofArabidopsis

Culture conditions are reported in which roots ofArabidopsis thaliana grow abundantly along the surface of, rather than down into, a solid matrix. Such root segments can be explanted without killing of the plant, which can then complete its life cycle. Non-destructive explanting permits transformation of heterozygous plants without preventing subsequent segregation and of plants that can only be obtained from a population segregating for a marker expressed late in growth. Moreover, the speed and abundance of surface root growth provides a rapid non-destructive phenotypic assay of response to selective conditions.