Low-coverage massively parallel pyrosequencing of cDNAs enables proteomics in non-model species: comparison of a species-specific database generated by pyrosequencing with databases from related species for proteome analysis of pea chloroplast envelopes

Proteomics is a valuable tool for establishing and comparing the protein content of defined tissues, cell types, or subcellular structures. Its use in non-model species is currently limited because the identification of peptides critically depends on sequence databases. In this study, we explored the potential of a preliminary cDNA database for the non-model species Pisum sativum created by a small number of massively parallel pyrosequencing (MPSS) runs for its use in proteomics and compared it to comprehensive cDNA databases from Medicago truncatula and Arabidopsis thaliana created by Sanger sequencing. Each database was used to identify proteins from a pea leaf chloroplast envelope preparation. It is shown that the pea database identified more proteins with higher accuracy, although the sequence quality was low and the sequence contigs were short compared to databases from model species. Although the number of identified proteins in non-species-specific databases could potentially be increased by lowering the threshold for successful protein identifications, this strategy markedly increases the number of wrongly identified proteins. The identification rate with non-species-specific databases correlated with spectral abundance but not with the predicted membrane helix content, and strong conservation is necessary but not sufficient for protein identification with a non-species-specific database. It is concluded that massively parallel sequencing of cDNAs substantially increases the power of proteomics in non-model species.     

Association of increased basement membrane invasiveness with absence of estrogen receptor and expression of vimentin in human breast cancer cell lines.

Lack of estrogen receptor (ER) and presence of vimentin (VIM) associate with poor prognosis in human breast cancer. We have explored the relationships between ER, VIM, and invasiveness in human breast cancer cell lines. In the matrigel outgrowth assay, ER+/VIM- (MCF-7, T47D, ZR-75-1), and ER-/VIM- (MDA-MB-468, SK-Br-3) cell lines were uninvasive, while ER-/VIM+ (BT549, MDA-MB-231, MDA-MB-435, MDA-MB-436, Hs578T) lines formed invasive, penetrating colonies. Similarly, ER-/VIM+ cell lines were significantly more invasive than either the ER+/VIM- or ER-/VIM- cell lines in the Boyden chamber chemoinvasion assay. Invasive activity in nude mice was only seen with ER-/VIM+ cell lines MDA-MB-231, MDA-MB-435 and MDA-MB-436. Hs578T cells (ER-/VIM+) showed hematogenous dissemination to the lungs in one of five mice, but lacked local invasion. The ER-/VIM+ MCF-7ADR subline was significantly more active than the MCF-7 cells in vitro, but resembled the wild-type MCF-7 parent in in vivo activity. Data from these cell lines suggest that human breast cancer progression results first in the loss of ER, and subsequently in VIM acquisition, the latter being associated with increased metastatic potential through enhanced invasiveness. The MCF-7ADR data provide evidence that this transition can occur in human breast cancer cells. Vimentin expression may provide useful insights into mechanisms of invasion and/or breast cancer cell progression.     

Ecological Consequences of Animal Migration: Prey Partial Migration Affects Predator Ecology and Prey Communities

Ecosystems - Patterns of animal migration and the ecological forces that shape them have been studied for centuries. Yet ecological impacts caused by the migration, such as altered...     

Alteration of gonadotrophin and steroid hormone release, and of ovarian function by a GnRH antagonist in gilts

This study examined the impact of the gonadotrophin-releasing hormone (GnRH) antagonist Antarelix on LH, FSH, ovarian steroid hormone secretion, follicular development and pituitary response to LHRH in cycling gilts. Oestrous cycle of 24 Landrace gilts was synchronised with Regumate (for 15 days) followed by 800 IU PMSG 24h later. In experiment 1, Antarelix (n=6 gilts) was injected i.v. (0.5mg per injection) twice daily on four consecutive days from day 3 to 6 (day 0=last day of Regumate feeding). Control gilts (n=6) received saline. Blood was sampled daily, and every 20 min for 6h on days 2, 4, 6, 8 and 10. In experiment 2, gilts (n=12) were assigned to the following treatments: Antarelix; Antarelix + 50 microg LHRH on day 4; Antarelix + 150 microg LHRH on day 4 or control, 50 microg LHRH only on day 4. Blood samples were collected daily and every 20 min for 6h on days 2, 4 and 6 to assess LH pulsatility. Ovarian follicular development was evaluated at slaughter.Antarelix suppressed (P<0.05) serum LH concentrations. The amount of LH released on days 4-9 (experiment 1) was 8.80 versus 36.54 ngml(-1) (S.E.M.=6.54). The pattern of FSH, and the preovulatory oestradiol rise was not affected by GnRH antagonist. Suppression of LH resulted in a failure (P<0.05) of postovulatory progesterone secretion. Exogenous LHRH (experiment 2) induced a preovulatory-like LH peak, however in Antarelix treated gilts the LH surge started earlier and its duration was less compared to controls (P<0.01). Furthermore, the amount of LH released from day 4 to 5 was lower (P<0.01) in Antarelix, Antarelix + 50 and Antarelix + 150 treated animals compared to controls. No differences were estimated in the number of LH pulses between days and treatment. Pulsatile FSH was not affected by treatment. Mean basal LH levels were lower (P<0.05) after antagonist treatment compared to controls. Antarelix blocked the preovulatory LH surge and ovulation, but the effects of Antarelix were reduced by exogenous LHRH treatment. The development of follicles larger than 4mm was suppressed (P<0.05) by antagonist treatment.In conclusion, Antarelix treatment during the follicular phase blocked preovulatory LH surge, while FSH and oestradiol secretion were not affected. Antarelix failed to alter pulsatile LH and FSH secretor or pituitary responsiveness to LHRH during the preovulatory period.     

Depression,Anxiety and Quality of Life in Long-Term Survivors of Malignant Melanoma: A Register-Based Cohort Study

Aim

The purpose of the study was to determine anxiety and depression, quality of life, and their determinants in long-term survivors of malignant melanoma.

Methods

In a state cancer registry a cohort of survivors of malignant melanoma was contacted via the physician registered. Of 1302 contactable patients, 689 (52.2%) completed a questionnaire including the Patient Health Questionnaire with generalized anxiety (GAD-7) and depression (PHQ-9) and the EORTC Quality of Life Questionnaire (EORTC QLQ 30). Based on multiple regression analysis, predictors of quality of life and distress were identified. Comparison data were assessed in two waves of representative face-to-face household surveys of the adult German population.

Results

An average of 8.4 (5.7 to 12.2) years after diagnosis, distress was higher in women compared to men and in middle adulthood (vs. older patients). Symptoms were higher in women than in men, and there was a decline of functioning and increase of symptoms across the age range of both genders. Compared to the general population, there were slightly increased depression and anxiety (only women), but no impaired global quality of life. Yet, survivors evidenced functional decline and more physical symptoms. Distress and reduced quality of life were consistently predicted by lack of social support, fear of recurrence, pessimism and self-blame. Distress was increased by a family history of melanoma, and additional mental and somatic diseases.

Conclusion

Overall, long-term survivors have adjusted well achieving a global quality of life comparable to the general population. Yet, compromised functional dimensions, physical symptoms and distress indicate the need for integrating psychooncological screening into oncological follow-up, which might be guided by predictors such as family history or social support. Further prospective study is needed to determine the course of adaptation to the disease and corroborate the risk factors identified.     

Growth dynamics and potential for cross-dating and multi-century climate reconstruction of Podocarpus falcatus in Ethiopia

Podocarpus falcatus is an indigenous evergreen conifer species of tropical mountain forests in southeastern Ethiopia, showing potential tree ages of around 500 years. To study the influence of seasonal climate on the growth pattern of P. falcatus, we combined high-resolution electronic dendrometer measurements with wood anatomical investigations of microcores from the outermost stem parts collected in monthly intervals. At any time of the year sufficient rain events are able to cause cambial activity in P. falcatus. This permanent growing readiness leads to irregular wood formation with the formation of intra-annual density fluctuations and missing rings. Wood anatomical studies of microcores collected around the circumference of a mature P. falcatus revealed locally different activity status of the cambium on different lobes of the stem. Tree-ring width measurements of stem disks resulted in tentative tree ages that were confirmed by radiocarbon dating of selected wood samples. Although our efforts to cross-date ring-width series from several stem disks were not successful, further sampling in areas with different rainfall regimes, additional radiocarbon dating and measurements of stable isotopes hopefully would enable the establishment of a multi-century-long tree-ring series for climate reconstruction.     

Fine Root Production across a Primary Successional Ecosystem Chronosequence at Mt. Shasta,California

Estimating changes in belowground biomass and production is essential for understanding fundamental patterns and processes during ecosystem development. We examined patterns of fine root production, aboveground litterfall, and forest floor accumulation during forest primary succession at the Mt. Shasta Mudflows ecosystem chronosequence. Fine root production was measured using the root ingrowth cores method over 1 year, and aboveground litterfall was collected over 2 years. Fine root production increased significantly with ecosystem age, but only the youngest ecosystem was significantly different from all of the older ecosystems. Root production was 44.5 ± 13.3, 168.3 ± 20.6, 190.5 ± 33.8, and 236.3 ± 65.4 g m⁻² y⁻¹ in the 77, 255, 616, and >850-year-old ecosystems, respectively. Generally, aboveground litterfall and forest floor accumulation did not follow the same pattern as root production. The relative contribution of fine root production to total fine detrital production increased significantly with ecosystem age, from 14 to 49%, but only the youngest ecosystem was significantly different from all of the older ecosystems. Fine root production was significantly correlated with some measures of soil fertility but was not correlated with leaf or total litterfall, or forest floor accumulation. It was best predicted by soil N concentration alone, but this relationship may not be causal, as soil N concentration was also correlated with ecosystem age. For the oldest ecosystem, fine root production was also measured using the sequential intact cores/compartment-flow model method, and the difference between the two estimates was not significant. Our study suggests that the relative contribution of fine roots to fine detrital production, and hence to soil organic matter accumulation, may increase during forest primary succession.     

Comparative genomics of Thermus thermophilus: Plasticity of the megaplasmid and its contribution to a thermophilic lifestyle

The bacterium Thermus thermophilus grows at temperatures up to 85 degrees C and is equipped with thermostable enzymes of biotechnological interest. The recently decoded genomes of two strains of T. thermophilus, HB27 and HB8, each composed of a chromosome and a megaplasmid, must certainly encode specific strategies to encounter the thermophile challenge. Here, a genome comparison was undertaken to distinguish common functions from the flexible gene pool, which gave some clues about the biological traits involved in a thermophile lifestyle. The chromosomes were highly conserved, with about 100 strain-specific genes probably reflecting adaptations to the corresponding biological niche, such as metabolic specialities and distinct cell surface determinates including type IV pili. The two megaplasmids showed an elevated plasticity. Upon comparison and re-examination of their gene content, both megaplasmids seem to be implicated in assisting thermophilic growth: a large portion of their genes are apparently involved in DNA repair functions. About 30 plasmid-encoded genes exhibit sequence and domain composition similarity to a predicted DNA repair system specific for thermophilic Archaea and bacteria. Moreover, the plasmid-encoded carotenoid biosynthesis gene cluster is interlocked with genes involved in UV-induced DNA damage repair. This illustrates the importance of DNA protection and repair at elevated growth temperatures.