Random forests, a novel approach for discrimination of fish populations using parasites as biological tags

Due to the complexity of host-parasite relationships, discrimination between fish populations using parasites as biological tags is difficult. This study introduces, to our knowledge for the first time, random forests (RF) as a new modelling technique in the application of parasite community data as biological markers for population assignment of fish. This novel approach is applied to a dataset with a complex structure comprising 763 parasite infracommunities in population samples of Atlantic cod, Gadus morhua, from the spawning/feeding areas in five regions in the North East Atlantic (Baltic, Celtic, Irish and North seas and Icelandic waters). The learning behaviour of RF is evaluated in comparison with two other algorithms applied to class assignment problems, the linear discriminant function analysis (LDA) and artificial neural networks (ANN). The three algorithms are used to develop predictive models applying three cross-validation procedures in a series of experiments (252 models in total). The comparative approach to RF, LDA and ANN algorithms applied to the same datasets demonstrates the competitive potential of RF for developing predictive models since RF exhibited better accuracy of prediction and outperformed LDA and ANN in the assignment of fish to their regions of sampling using parasite community data. The comparative analyses and the validation experiment with a 'blind' sample confirmed that RF models performed more effectively with a large and diverse training set and a large number of variables. The discrimination results obtained for a migratory fish species with largely overlapping parasite communities reflects the high potential of RF for developing predictive models using data that are both complex and noisy, and indicates that it is a promising tool for parasite tag studies. Our results suggest that parasite community data can be used successfully to discriminate individual cod from the five different regions of the North East Atlantic studied using RF.     

大鼠心肌缺血再灌注损伤模型的实验研究

目的 制备一种新型的心肌急性缺血再灌注损伤模型,以探讨一种更符合临床实际需求的实验方法.方法 将20只雌性SD(Sprague-Dawley)大鼠随机分成2组(对照组、实验组),采用结扎主动脉根部引起心肌缺血5min再灌注30 min建立心肌急性缺血再灌注模型;通过应用透射电镜观察心肌细胞超微结构的改变,同时检测心肌组织匀浆丙二醛(Maleic Dialdehyde,MDA)含量、超氧化物歧化酶(Superoxide Dismutase,SOD)活力.结果 透射电镜下超微结构显示实验组较对照组明显加重了心肌组织结构和线粒体的损害;实验组心肌组织MDA明显高于对照组(P<0.01),而SOD明显低于对照组(P<0.01).结论 本实验成功建立了方法简便、易于操作、取材范围广泛的心肌缺血再灌注损伤模型,为心肌缺血再灌注损伤研究提供了一种更为可行的模型.     

Genetic polymorphims of estrogen receptor alpha −397 PvuII (T>C) and −351 XbaI (A>G) in a portuguese population: prevalence and relation with breast cancer susceptibility

Estrogen receptor alpha (ERα), that mediates the biologic effects of estrogen in estrogen-sensitive tissues like breast, is genetically polymorphic. To evaluate the association between ?397 PvuII (T>C) and ?351 XbaI (A>G) restriction fragment length polymorphisms (RFLPs) in intron 1 of ERα gene and susceptibility of breast cancer, we undertook a case–control study in BRCA1 185delAG and 5382insC/BRCA2 6174delT negative Portuguese women. The study population consisted of 107 patients with histological diagnosis of breast cancer and 121 women with no history of breast cancer. Genomic DNA was extracted from blood samples and genotyping analyses were performed by PCR–RFLP. XbaI polymorphism was associated with a significant reduced risk of breast cancer for carriers of the x allele in homozygozity (OR 0.178; 95 % CI 0.070–0.456; P < 0.001) or heterozigozity (OR 0.223; 95 % CI 0.089–0.561; P = 0.001). The PvuII polymorphism was associated with a non-significantly reduced risk. The combined analysis of PvuII and XbaI polymorphisms revealed none synergistic effect of the two genotypes, except for simultaneous carriers of pp and xx genotypes, that have a reduced risk of breast cancer (OR 0.226; 95 % CI 0.049–1.035; P = 0.044). The combination of PvuII and XbaI genotypes into haplotypes showed that carriers of two copies of the px (ppxx) haplotype had a reduced risk of breast cancer (OR 0.405; 95 % CI 0.194–0.843; P = 0.014), compared with PX (PPXX + PPXx + PpXX + PpXx) haplotypes. PvuII and XbaI polymorphisms were in linkage disequilibrium both in cases (D = 0.044, r² = 0.049, X² = 5.216, P = 0.022) and controls (D = 0.090, r² = 0.139, X² = 16.819, P < 0.001), but not in the entire sample population analyzed as a whole (D = 0.087, r² = 0.0076, X² = 1.733, P = 0.188). In conclusion, in this case–control study we found that ERα gene XbaI polymorphism may modify individual susceptibility for breast cancer in this population.     

Global Analysis of Transcriptional Regulation by Poly(ADP-ribose) Polymerase-1 and Poly(ADP-ribose) Glycohydrolase in MCF-7 Human Breast Cancer Cells

Poly(ADP-ribose) polymerase-1 (PARP-1) and poly(ADP-ribose) glycohydrolase (PARG) are enzymes that modify target proteins by the addition and removal, respectively, of ADP-ribose polymers. Although a role for PARP-1 in gene regulation has been well established, the role of PARG is less clear. To investigate how PARP-1 and PARG coordinately regulate global patterns of gene expression, we used short hairpin RNAs to stably knock down PARP-1 or PARG in MCF-7 cells followed by expression microarray analyses. Correlation analyses showed that the majority of genes affected by the knockdown of one factor were similarly affected by the knockdown of the other factor. The most robustly regulated common genes were enriched for stress-response and metabolic functions. In chromatin immunoprecipitation assays, PARP-1 and PARG localized to the promoters of positively and negatively regulated target genes. The levels of chromatin-bound PARG at a given promoter generally correlated with the levels of PARP-1 across the subset of promoters tested. For about half of the genes tested, the binding of PARP-1 at the promoter was dependent on the binding of PARG. Experiments using stable re-expression of short hairpin RNA-resistant catalytic mutants showed that PARP-1 and PARG enzymatic activities are required for some, but not all, target genes. Collectively, our results indicate that PARP-1 and PARG, nuclear enzymes with opposing enzymatic activities, localize to target promoters and act in a similar, rather than antagonistic, manner to regulate gene expression.     

Descriptions of some unusual digeneans from Boops boops L. (Sparidae) and a complete checklist of its metazoan parasites

Six species of digeneans, including three new host records, are described from the bogue Boops boops off the Spanish NE Atlantic and the Mediterranean coasts. The species involved are: Robphildollfusium martinezgomezi López-Román, Gijón-Botella, Kim & Vilca-Choque, 1992, Magnibursatus caudofilamentosa (Reimer, 1971) Gibson & K?ie, 1991, Lepocreadium album Stossich, 1890, Steringotrema pagelli (van Beneden, 1871) Odhner, 1911, Tetrochetus coryphaenae Yamaguti, 1934 and Stephanostomum euzeti Bartoli & Bray, 2004 (metacercaria). B. boops is a new host for 11 metazoan parasites (six digeneans, three acanthocephalans, one copepod and one isopod) recovered in this study. These are reported and incorporated into a complete checklist of the metazoan parasites of B. boops throughout its distributional range. It comprises summarised information for 67 species in 260 host-parasite records and includes the name of the parasite species, the locality of the host, and the author and date of the published record. The taxonomy is updated and annotations are made on the validity of the records and synonymies.     

Bioko: critically important nesting habitat for sea turtles of West Africa

We evaluate the conservation status and threats faced by sea turtle nesting populations at Bioko Island, Equatorial Guinea (Central Africa). Beaches were monitored to obtain a detailed sea turtle nest census and, where possible, tagging of adult females was undertaken. Four sea turtle species were found nesting in the area: the green turtle (Chelonia mydas), the leatherback (Dermochelys coriacea), the olive ridley (Lepidochelys olivacea) and the hawksbill (Eretmochelys imbricata); with the former two species nesting in regionally important numbers. Nesting activity was concentrated between November and February, with a peak in December–January. Tagging and recapture of green turtles in two consecutive seasons suggested an estimated 560 (interquartile range: 420–1,681) and 414 (interquartile range: 190–1,255) nesting females in the area, respectively. Estimated numbers of nesting leatherbacks ranged from 123 to 215 and 243 to 293 in the first and second season, respectively. The other two species were less abundant (olive ridley: 19–29 and 28–43; hawksbill: 4–10 and 2 turtles). Data were compared with more recent surveys in the area and contextualised with information on human related threats. Despite the size of nesting stocks, ongoing permitted and illegal take of adult turtles at the nesting site constitutes a serious threat for these breeding aggregations. Additionally, tag returns from throughout the Gulf of Guinea suggest that the level of take in regional fisheries may also be a major threat.     

Germ band retraction as a landmark in glucose metabolism during <Emphasis Type="Italic">Aedes aegypti</Emphasis> embryogenesis

Background  

The mosquito A. aegypti is vector of dengue and other viruses. New methods of vector control are needed and can be achieved by a better understanding of the life cycle of this insect. Embryogenesis is a part of A. aegypty life cycle that is poorly understood. In insects in general and in mosquitoes in particular energetic metabolism is well studied during oogenesis, when the oocyte exhibits fast growth, accumulating carbohydrates, lipids and proteins that will meet the regulatory and metabolic needs of the developing embryo. On the other hand, events related with energetic metabolism during A. aegypti embryogenesis are unknown.     

Gastrointestinal helminths of Commerson's dolphins Cephalorhynchus commersonii from central Patagonia and Tierra del Fuego.

The stomachs and intestines of 9 Commerson's dolphins incidentally caught in trawl nets in central Patagonia and 23 stranded on beaches in Tierra del Fuego were surveyed for helminth parasites. A total of 267 individuals belonging to 4 species of parasites (1 nematode, 3 digeneans) were found in the dolphins from the first area: Anisakis sp. (larvae type 1 = A. simplex), Braunina cordiformis, Hadwenius sp. and Pholeter gastrophilus. In the Tierra del Fuego dolphins, 142 specimens belonging to 3 species (2 nematodes, 1 digenean, 1 cestode) were found: A. simplex, Hadwenius sp. and Strobilocephalus triangularis. Only 2 of the helminth species were shared in the 2 study areas, A. simplex and Hadwenius sp., and both were more common in central Patagonia. Among the species, A. simplex was most prevalent and abundant in both study areas. In Tierra del Fuego, adults of A. simplex appeared in only 1 host. Hadwenius sp., P. gastrophilus and S. triangularis are new host records for Commerson's dolphin. Species diversity and species richness were low in both study areas. Helminth communities were more diverse in central Patagonia (t = 1.97, df = 258, p < 0.05) and species richness was higher in central Patagonia (S = 4). No differences in diversity were observed between females and males of central Patagonia (t = 1.97, df = 139, p < 0.05) and between females of central Patagonia and Tierra del Fuego. The results may suggest some differences in habitat use, diet and sex between Commerson's dolphin populations in the 2 study areas.