Proteomics methods for probing molecular mechanisms in signal transduction1

The ovarian follicle of ruminants: the path from conceptus to adult

This review resulted from an international workshop and presents a consensus view of critical advances over the past decade in our understanding of follicle function in ruminants. The major concepts covered include: (1) the value of major genes; (2) the dynamics of fetal ovarian development and its sensitivity to nutritional and environmental influences; (3) the concept of an ovarian follicle reserve, aligned with the rise of anti-Müllerian hormone as a controller of ovarian processes; (4) renewed recognition of the diverse and important roles of theca cells; (5) the importance of follicular fluid as a microenvironment that determines oocyte quality; (6) the 'adipokinome' as a key concept linking metabolic inputs with follicle development; and (7) the contribution of follicle development to the success of conception. These concepts are important because, in sheep and cattle, ovulation rate is tightly regulated and, as the primary determinant of litter size, it is a major component of reproductive efficiency and therefore productivity. Nowadays, reproductive efficiency is also a target for improving the 'methane efficiency' of livestock enterprises, increasing the need to understand the processes of ovarian development and folliculogenesis, while avoiding detrimental trade-offs as greater performance is sought.

Variations in the Temperature-Humidity Index and Dorsal Fat Thickness during the Last Trimester of Gestation and Early Postpartum Period Affect Fertility of Bos indicus Cows in the Tropics

In order to measure the influence of the temperature-humidity index (THI) and the variation of fat thickness on reproductive performance, ninety-two Bos indicus cows kept under grazing conditions were used in two farms in Veracruz (Mexico) and Puntarenas (Costa Rica). THI was calculated with the average environmental temperature and relative humidity. Measurements of fat thickness (FAT) were taken two weeks apart from the last trimester of gestation to approximately 80 days postpartum (dpp). Natural breeding was used in both farms. Time to conception was calculated based on the interval from days at risk to conception (DRC), which had to be at least 28 dpp. THI was between 65.4 ± 2.9 and 73.2 ± 1.5 in Veracruz and 75.4 ± 0.26 and 76.5 ± 0.55 in Puntarenas. Variations in THI were observed in Puntarenas whereas in Veracruz THI variations were more prominent. In Veracruz, loss of fat during the last trimester of gestation was on average 8.5%, whereas in the postpartum period it was 18.4% (P = 0.042). In Puntarenas, the variation in the last trimester of gestation was on average 18.7% and in the postpartum period was 10.5% (P = 0.012). The relative change in FAT in Veracruz was 36.7%, and in Puntarenas it was 29.3%. Overall, 60% of the cows became pregnant. FAT decreased the interval of DRC (R²=0.06; P=0.033) with a high relationship (R²=0.76; P< 0.0001) between THI and time to conception, in both farms. In conclusion, THI levels influence the reproductive performance in early postpartum period affecting DRC.

Multipronged quantitative proteomic analyses indicate modulation of various signal transduction pathways in human meningiomas

Meningiomas (MGs) are frequent tumors of the CNS originating from the meningeal layers of the spinal cord and the brain. In this study, comparative tissue proteomic analysis of low and high grades of MGs was performed by using iTRAQ-based quantitative proteomics in combination with ESI-quadrupole-TOF and Q-Exactive MS, and results were validated by employing ELISA. Combining the results obtained from two MS platforms, we were able to identify overall 4308 proteins (1% false discover rate), among which 2367 exhibited differential expression (more than and equal to 2 peptide and ≥ 1.5-fold in at least one grade) in MGs. Several differentially expressed proteins were found to be associated with diverse signaling pathways, including integrin, Wnt, Ras, epidermal growth factor receptor, and FGR signaling. Proteins, such as vinculin or histones, which act as the signaling activators to initiate multiple signaling pathways, were found to be upregulated in MGs. Quite a few candidates, such as protein S-100A6, aldehyde dehydrogenase mitochondrial, AHNAK, cytoskeleton-associated protein 4, and caveolin, showed sequential increase in low- and high-grade MGs, whereas differential expressions of collagen alpha-1 (VI), protein S100-A9, 14 kDa phosphohistidine phosphatase, or transgelin-2 were found to be grade specific. Our findings provide new insights regarding the association of various signal transduction pathways in MG pathogenesis and may introduce new opportunities for the early detection and prognosis of MGs.

Array-based proteomic approaches to study signal transduction pathways: prospects, merits and challenges

Very often dysfunctional aspects of various signalling networks are found to be associated with human diseases and disorders. The major characteristics of signal transduction pathways are specificity, amplification of the signal, desensitisation and integration, which is accomplished not solely, but majorly by proteins. Array-based profiling of protein-protein and other biomolecular interactions is a versatile approach, which holds immense potential for multiplex interactome mapping and provides an inclusive representation of the signal transduction pathways and networks. Protein microarrays such as analytical protein microarrays (antigen-antibody interactions, autoantibody screening), RP microarrays (interaction of a particular ligand with all the possible targets in cell), functional protein microarrays (protein-protein or protein-ligand interactions) are implemented for various applications, including analysis of protein interactions and their significance in signalling cascades. Additionally, successful amalgamation of the array-based approaches with different label-free detection techniques allows real-time analysis of interaction kinetics of multiple interaction events simultaneously. This review discusses the prospects, merits and limitations of different variants of array-based techniques and their promising applications for studying the modifications and interactions of biomolecules, and highlights the studies associated with signal transduction pathways and their impact on disease pathobiology.

Reproductive and productive response to suckling restriction and dietary flushing in primiparous grazing beef cows

The objectives of the present experiment were to analyse the reproductive and productive responses to suckling-restriction treatments and flushing in primiparous grazing beef cows. During 3 years, 153 primiparous anoestrus cows were assigned randomly to one of four treatments in a 2 by 2 factorial arrangement of suckling-management treatments and flushing. Suckling-restriction treatments started at 61 ± 10 days postpartum and consisted of applying nose plates to calves for 12 days (i.e. TS treatment) or 5 days of isolation of the calf from the cow followed by applying nose plates to calves for 7 days as calves were reunited with their mothers (i.e. IS treatment). Nutritional treatments (flushing v. control) started at the beginning of the breeding season, immediately after the suckling-restriction treatments were finished (73 ± 10 days postpartum), with cows receiving or not receiving 2 kg/day of whole-rice middling for 22 days. Cow body condition score (BCS) was recorded every 20 days from calving until 120 days postpartum. Duration of postpartum anoestrus (PPA) and probability of cyclicity were estimated by plasma progesterone concentrations analysed in weekly samples. Pregnant cows were determined by ultrasound 42 days after bull introduction (early pregnancy; EP) and 30 days after the end of the breeding season (total pregnancy; TP). BCS at calving and changes in BCS from calving to the day of BCS nadir (ΔBCS) varied among years depending on forage availability and weather conditions. Increased cow BCS at calving decreased PPA (b = –41 days, P < 0.0001) and, in interaction with ΔBCS, increased EP (P < 0.008) and TP (P < 0.003). Calf weights at weaning and average daily gain were not affected by suckling-restriction or flushing treatments. Isolated temporary suckling control reduced PPA by 11 days when compared with temporary suckling control (P < 0.004). Flushing increased EP by 40%, which was also affected by BCS at calving and was greater in cows that gained, than in those that maintained or lost BCS. We conclude that flushing was useful in improving early pregnancy rates of primiparous beef cows with ‘suboptimal’ body condition (lower than 4.5) at calving and grazing native pasture.

Elucidating protein inter- and intramolecular interacting domains using chemical cross-linking and matrix-assisted laser desorption ionization-time of flight/time of flight mass spectrometry

Among many methods used to investigate protein/protein interactions, chemical cross-linking combined with mass spectrometry remains a vital experimental approach. Mapping peptides modified by cross-linker provides clues about proteins' interacting domains. One complication is that such modification may result from intra- but not intermolecular interactions. Therefore, for overall data interpretation, a combination of results from various platforms is necessary. It is postulated that the secretory isoform of gelsolin regulates several biological processes through interactions with proteins such as actin, fibronectin, vitamin D-binding protein, and unidentified receptors on the surface of eukaryotes; it also has been shown to self-assemble eventually leading to the formation of homo-multimers. As such, it is an excellent model for this study. We used four cross-linkers with arm length ranging from 7.7 to 21.7Å and MALDI-TOF/TOF mass spectrometry as the analytical platform. Results of this study show that MALDI-based mass spectrometry generates high quality data to show lysine residues modified by cross-linkers and combined with existing data based on crystallography (Protein Data Bank, PDB) can be used to discriminate between inter- and intramolecular linking.

Effects of nutritional cues on the duration of the winter anovulatory phase and on associated hormone levels in adult female Welsh pony horses (Equus caballus)

BACKGROUND

Mares have an annual reproductive rhythm, with a phase of inactivity in midwinter. The aim of this study was to determine the impact of food restriction on physiological and metabolic hallmarks of this rhythm.

METHODS

Over three successive years, 3 groups of 10 mares were kept under natural photoperiod. A 'well-fed' group was fed to maintain the mares in good body condition; a 'restricted' group received a diet calculated to keep the mares thin and a 'variable' group was fed during some periods like the 'restricted' group and during some other periods like the 'well-fed' group, with the aim of mimicking the natural seasonal variation of pasture availability, but a few months in advance of this natural rhythm.

RESULTS

Winter ovarian inactivity always occurred and was long in the restricted group. In contrast, in the 'well-fed' group, 40% of mares showed this inactivity, which was shorter than in the other groups. Re-feeding the 'variable' group in autumn and winter did not advance the first ovulation in spring, compared with the 'restricted' group. Measurements of glucose and insulin concentrations in mares from the 'restricted' group during two 24 h periods of blood sampling, revealed no post-prandial peaks. For GH (Growth hormone), IGF-1 and leptin levels, large differences were found between the 'well-fed' group and the other groups. The glucose, insulin, GH and leptin levels but not melatonin level are highly correlated with the duration of ovulatory activity.

CONCLUSIONS

The annual rhythm driven by melatonin secretion is only responsible for the timing of the breeding season. The occurrence and length of winter ovarian inactivity is defined by metabolic hormones.

Postpartum follicular development in Brahman cows under two stocking rates

The aim was to study postpartum follicular population dynamics in Brahman cows in the Mexican humid tropics and under different stocking rates. Lactating adult cows (n = 104) grazed native grammas (Paspalum spp., Axonopus spp.) under two stocking rates: 2.8 (high) or 1.7 (low) cows/ha. Follicle numbers and their size (millimetres) were measured by ovarian ultrasound scanning. Animals detected in oestrus and inseminated were taken out of the study. Both stocking rates produced similar (P < 0.05) body condition scores (BCS) and follicular dynamics. The percent of follicles, averaged over stocking rates, of <4 mm diminished and those of 5-8 mm increased with time, whilst those of >9 mm remained constant; respective values for the previously mentioned sizes were 60 days postpartum (n = 101), 49%, 56% and 5%; 120 days (n = 70), 28%, 66% and 6%; and 180 days (n = 15), 9%, 79% and 12%. There was a positive correlation between BCS and follicle number for size <4 mm (r = 0.73, P < 0.01), whilst for size 5-8 mm, this was negative (r = -0.51, P < 0.05), for follicles >9 mm, no difference was found (r = -0.08, P > 0.05). It was concluded that stocking rate did not affect follicular population dynamics of Brahman cows, but BCS dictated the number and categories of follicles present regardless of the stocking rate utilised.

The effect of body condition on ovarian activity of free ranging tropical jennies (Equus asinus)

Serial ultrasonography was performed on seven jennies to study the effect of seasonally fluctuating body condition on ovarian activity during the dry, short rainy and long rainy seasons. Kendall Tau correlations and differences of least square mean values were compared. A distinct seasonal pattern was observed both in body condition and ovarian activity. The mean (+/-SD) Body Condition Score (BCS) was lowest during the dry season 2.6 +/- 0.45 when compared with 3.5 +/- 0.52 and 3.9 +/- 0.58 during the short and long rainy seasons, respectively. The mean (+/-SD) number of total follicles was also proportionally low 7.3 +/- 1.6 during the dry season compared with 9.6 +/- 2.4 and 11.3 +/- 3.3 found during the short and the long rainy seasons, respectively. The BCS was positively correlated to the total number of follicles and the diameter of the largest follicle during all seasons. Periods of increasing BCS and transition between seasons with both increasing and decreasing body conditions were strongly correlated to the number and size of ovarian follicles. Seasonal fluctuation in the body condition was found to be the result of variation in feed resource and ovarian activity was also closely following this seasonal pattern. The improvement in body condition has generally, a positive impact on emergence of small growing follicles there by having influence on the total count of ovarian follicles.

Emerging tools for real-time label-free detection of interactions on functional protein microarrays

The availability of extensive genomic information and content has spawned an era of high-throughput screening that is generating large sets of functional genomic data. In particular, the need to understand the biochemical wiring within a cell has introduced novel approaches to map the intricate networks of biological interactions arising from the interactions of proteins. The current technologies for assaying protein interactions--yeast two-hybrid and immunoprecipitation with mass spectrometric detection--have met with considerable success. However, the parallel use of these approaches has identified only a small fraction of physiologically relevant interactions among proteins, neglecting all nonprotein interactions, such as with metabolites, lipids, DNA and small molecules. This highlights the need for further development of proteome scale technologies that enable the study of protein function. Here we discuss recent advances in high-throughput technologies for displaying proteins on functional protein microarrays and the real-time label-free detection of interactions using probes of the local index of refraction, carbon nanotubes and nanowires, or microelectromechanical systems cantilevers. The combination of these technologies will facilitate the large-scale study of protein interactions with proteins as well as with other biomolecules.

Prefractionation techniques in proteome analysis: the mining tools of the third millennium

The present review deals with prefractionation protocols used in proteomic investigation in preparation for mass spectrometry (MS) or two-dimensional electrophoresis (2-DE) map analysis. Briefly, reported methods focus on cell organelle differential centrifugation and on chromatographic approaches, to continue in extenso with a panoply of electrophoretic methods. In the case of chromatography, procedures useful as a prefractionation step, including affinity, ion-exchange, and reversed-phase resins, revealed several hundreds of new species, previously undetected in unfractionated samples. Novel chromatographic prefractionation methods are also discussed such as a multistaged fractionation column, consisting in a set of immobilized chemistries, serially connected in a stack format (an assembly of seven blocks), each capable of harvesting a given protein population. Such a method significantly simplifies the complexity of treated samples while concentrating species, all resulting in a larger number of visible proteins by MS or 2-DE. Electrophoretic prefractionation protocols include all those electrokinetic methodologies which are performed in free solution, essentially all relying on isoelectric focusing steps (although some approaches based on gels and granulated media are also discussed). Devices associated with electrophoretic separation are multichamber apparatus, such as the multicompartment electrolyzers equipped with either isoelectric membranes or with isoelectric beads. Multicup device electrophoresis and several others, exploiting the conventional technique of carrier ampholyte focusing, are reviewed. This review also reports approaches for sample treatments in order to detect low-abundance species. Among others, a special emphasis is made on the reduction of concentration difference between proteins constituting a sample. This latter consists in a library of combinatorial ligands coupled to small beads. Such a library comprises hexameric ligands composed of 20 amino acids, resulting in millions of different structures. When these beads are impregnated with complex proteomes (e.g., human sera) of widely differing protein compositions, they are able to significantly reduce the concentration differences, thus greatly enhancing the possibility to evidence low-abundance species. It is felt that this panoply of methods could offer a strong step forward in "mining below the tip of the iceberg" for detecting the "unseen proteome".