Expression status of let-7a and miR-335 among breast tumors in patients with and without germ-line BRCA mutations

The genetic factors of cancer predisposition remain elusive in the majority of familial and/or early-onset cases of breast cancer (BC). This type of BC is promoted by germ-line mutations that inactivate BRCA1 or BRCA2. On the other hand, recent studies have indicated that alterations in the levels of miRNA expression are linked to this disease. Although BRCA1 and BRCA2 gene mutations have been reported to commonly lead to alterations in genes that encode cancer-related proteins, little is known regarding the putative impact of these mutations on noncoding miRNAs. In the present study, we aimed to determine whether miRNA dysregulation is involved in the pathogenesis of BRCA-mutated BC. An expression analysis of 14 human miRNAs previously shown to be related to BC diagnosis, prognosis, and drug resistance was conducted using tissues from 60 familial and/or early-onset patients whose peripheral blood samples had been screened for BRCA1 and BRCA2 mutations through sequence analysis. Let-7a and miR-335 expression levels were significantly downregulated in the tumors of patients with a BRCA mutation compared with those of patients without a BRCA mutation (P = 0.04 and P = 0.02, respectively). Our results defined the associations between the expression status of let-7a and miR-335 and BRCA mutations. The expression analysis of these miRNAs might be used as biomarkers of the BRCA mutation status of early-onset and/or familial BC.     

Graphiolales: Basidiomycetes parasitic on palms

Graphiola phoenicis was restudied by light microscopy and investigated in detail with the scanning and the transmission electron microscopes. Hyphae of the fruitbody are mainly dikaryotic. Karyogamy occurs in cells which are interpreted as meiosporangia (basidia), and which develop in chains. Shortly after karyogamy, meiosis takes place in these basidia. Primary, sessile meiospores are then formed which later divide and produce thick-walled diaspores. The latter germinate either by hyphae or by yeast-like budding. The nutritional requirements of pure cultures of the yeast stage were also investigated. Life cycle, karyological criteria, ultrastructural details, and chemical tests clearly show thatGraphiola belongs in theBasidiomycetes. The taxonomic position within theHeterobasidiomycetes is discussed and the orderGraphiolales is validated.     

Double Transgenesis of Humanized fat1 and fat2 Genes Promotes Omega-3 Polyunsaturated Fatty Acids Synthesis in a Zebrafish Model

Omega-3 long-chain polyunsaturated fatty acid (n-3 LC-PUFA), especially eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), are essential nutrients for human health. However, vertebrates, including humans, have lost the abilities to synthesize EPA and DHA de novo, majorly due to the genetic absence of delta-12 desaturase and omega-3 desaturase genes. Fishes, especially those naturally growing marine fish, are major dietary source of EPA and DHA. Because of the severe decline of marine fishery and the decrease in n-3 LC-PUFA content of farmed fishes, it is highly necessary to develop alternative sources of n-3 LC-PUFA. In the present study, we utilized transgenic technology to generate n-3 LC-PUFA-rich fish by using zebrafish as an animal model. Firstly, fat1 was proved to function efficiently in fish culture cells, which showed an effective conversion of n-6 PUFA to n-3 PUFA with the n-6/n-3 ratio that decreased from 7.7 to 1.1. Secondly, expression of fat1 in transgenic zebrafish increased the 20:5n-3 and 22:6n-3 contents to 1.8- and 2.4-fold, respectively. Third, co-expression of fat2, a fish codon-optimized delta-12 desaturase gene, and fat1 in fish culture cell significantly promoted n-3 PUFA synthesis with the decreased n-6/n-3 ratio from 7.7 to 0.7. Finally, co-expression of fat1 and fat2 in double transgenic zebrafish increased the 20:5n-3 and 22:6n-3 contents to 1.7- and 2.8-fold, respectively. Overall, we generated two types of transgenic zebrafish rich in endogenous n-3 LC-PUFA, fat1 transgenic zebrafish and fat1/fat2 double transgenic zebrafish. Our results demonstrate that application of transgenic technology of humanized fat1 and fat2 in farmed fishes can largely improve the n-3 LC-PUFA production.     

A high-throughput SNP array in the amphidiploid species Brassica napus shows diversity in resistance genes

Single-nucleotide polymorphisms (SNPs)are molecular markers based on nucleotide variation and can be used for genotyping assays across populations and to track genomic inheritance. SNPs offer a comprehensive genotyping alternative to whole-genome sequencing for both agricultural and research purposes including molecular breeding and diagnostics, genome evolution and genetic diversity analyses, genetic mapping, and trait association studies. Here genomic SNPs were discovered between four cultivars of the important amphidiploid oilseed species Brassica napus and used to develop a B. napus Infinium? array containing 5,306 SNPs randomly dispersed across the genome. Assay success was high, with >94 % of these producing a reproducible, polymorphic genotype in the 1,070 samples screened. Although the assay was designed to B. napus, successful SNP amplification was achieved in the B. napus progenitor species, Brassica rapa and Brassica oleracea, and to a lesser extent in the related species Brassica nigra. Phylogenetic analysis was consistent with the expected relationships between B. napus individuals. This study presents an efficient custom SNP assay development pipeline in the complex polyploid Brassica genome and demonstrates the utility of the array for high-throughput genotyping in a number of related Brassica species. It also demonstrates the utility of this assay in genotyping resistance genes on chromosome A7, which segregate amongst the 1,070 samples.     

Genetic species delineation among branching Caribbean Porites corals

Coral species are difficult to discern because of their morphological plasticity, long generation times, and slow rates of mitochondrial DNA evolution. Among Caribbean representatives of the genus Porites are three named species (P. divaricata, P. furcata, and P. porites) with branching colony morphologies whose validity as genetically isolated species has been debated. We present sequence data from the mitochondrial control region, nuclear ITS, and nine single-copy nuclear loci for the Caribbean Porites and a related eastern Pacific species. mtDNA sequences were nearly invariant among the three branching species and their crustose sister P. branneri, and ITS sequences from these four were intermingled. An information theoretic analysis provided no support for upholding the three named Caribbean branching species. Both a clustering analysis and an analysis of molecular variance showed that sequence variation from the three branching forms is partitioned more by geography than by taxonomy. Multi-locus coalescent phylogenetic analysis provided a calibrated estimate for the nuclear DNA substitution rate (0.14 % Ma^?1) close to that for other corals. Because no generalities have emerged from genetic investigations of the validity of morphologically defined coral species, the use of single-copy nuclear data is likely to be important in testing problematic species designations.     

Molecular evidence to reconcile taxonomic instability in mahseer species (Pisces: Cyprinidae) of India

The mahseers are an important group of fishes endemic to Asia with most species considered threatened. Conservation plans to save declining wild populations are hindered by unstable taxonomy, and detailed systematic review could form a solid platform for future management and conservation. D-loop and cytochrome c oxidase I (COI) mtDNA sequences were examined in nine mahseer species of Tor, Neolissochilus, and Naziritor. Pseudogenes amplified in a portion of the species limited the utility of the D-loop region. ABGD analysis, NJ, ML, and MP methods and genetic distance (TrN?+?I?+?G) using COI data revealed concordant species delimiting patterns. The three genera were monophyletic, separated as distinct clades (TrN?+?I?+?G 0.064 to 0.106), and Naziritor was flagged as a separate genus, distinct from Puntius (TrN?+?I?+?G 0.196). Out of seven nominal species known for Tor cogeners from India, only five were recovered with mtDNA data (TrN?+?I?+?G 0.000 to 0.037) and two species could not be distinguished with the molecular data set employed. Tor mosal, synonymized as Tor putitora, was rediscovered as a distinct species (TrN?+?I?+?G 0.031) based on its type locality. Tor mussulah was confirmed as a separate species (TrN?+?I?+?G 0.019 to 0.026). Two valid species, Tor macrolepis and T. mosal mahanadicus, were not distinct from T. putitora (TrN?+?I?+?G 0.00). The high divergence with mtDNA data failed to validate T. mosal mahanadicus as a subspecies of T. mosal (TrN?+?I?+?G 0.031). Morphological outliers discovered within the distribution range of Tor tor (TrN?+?I?+?G 0.022 to 0.025) shared the same lineage with T. putitora (TrN?+?I?+?G 0.002 to 0.005), indicating a new extended distribution of the Himalayan mahseer T. putitora in the rivers of the Indian central plateau. The findings indicate the need for integrating molecular and morphological tools for taxonomic revision of the Tor and Naziritor genera, so that taxa are precisely defined for accurate in situ and ex situ conservation decisions.     

On the carrying behaviour of basic South American primates

InCallithrix, Saguinus, Aotus, andCallicebus other group members than the mother participate in infant care. Differences among these species are obvious in respect to the time of being off any caregiver, and in respect to the carrying position (Aotus andCallicebus). Alloparental care, a basic behaviour pattern in these species, has evolved from the parking behaviour of the prosimians. The infants are «parked» at other group members.     

Expression profile of MAGI2 gene as a novel biomarker in combination with major deregulated genes in prostate cancer

Complex molecular changes that occur during prostate cancer (PCa) progression have been described recently. Whole genome sequencing of primary PCa samples has identified recurrent gene deletions and rearrangements in PCa. Specifically, these molecular events disrupt the gene loci of phosphatase and tensin homolog (PTEN) and membrane-associated guanylate kinase inverted-2 (MAGI2). In the present study, we analyzed the expression profile of MAGI2 gene in a cohort of clinical PCa (n = 45) and benign prostatic hyperplasia (BPH) samples (n = 36) as well as three PCa cell lines. We also studied the expression of PCa-related genes, including PTEN, NKX3.1, SPINK1, DD3, AMACR, ERG, and TMPRSS2-ERG fusion in the same samples. The expression of MAGI2 mRNA was significantly down-regulated in PC3, LNCaP and DU-145 PCa cell lines (p = 0.000), and also in clinical tumor samples (Relative expression = 0.307, p = 0.002, [95 % CI 0.002–12.08]). The expression of PTEN, NKX3.1, SPINK1, DD3, and AMACR genes was significantly deregulated in prostate tumor samples (p range 0.000–0.044). A significant correlation was observed between MAGI2 and NKX3.1 expression in tumor samples (p = 0.006). Furthermore, the inclusion of MAGI2 in the gene panel improved the accuracy for discrimination between PCa and BPH samples with the sensitivity and specificity of 0.88 [CI 0.76–0.95] and 0.83 [CI 0.68–0.92], respectively. The data presented here suggest that MAGI2 gene can be considered as a novel component of gene signatures for the detection of PCa.     

Response of the population size and community structure of Paenibacillus spp. to different fertilization regimes in a long-term experiment of red soil

Background and aims

Paenibacillus spp. are widely considered to impact the fertility and health of soil. The aim of this study was to evaluate how different fertilization regimes affect the population size and community structure of Paenibacillus spp. over a long period of time in red soil.

Methods

Soil samples were collected from a long-term experiment and were then analyzed using real-time PCR and PCR-DGGE. The correlation analysis, PCA and RDA were used to explore the relationships among Paenibacillus spp. population, community structure and soil properties in different treatments.

Results

The pH was seriously decreased only by the application of chemical fertilizer. The largest population of Paenibacillus spp. was found in the soil treated with organic fertilizer application, while the richest diversity was observed in the soil treated only with the chemical fertilizer. The Paenibacillus spp., Paenibacillus alkaliterrae, Paenibacillus campinasensis, and Paenibacillus xylanilyticus were found in all treatments. Paenibacillus castaneae was found in the soil treated with NPK, and Paenibacillus pabuli was specifically observed in the lime-amended treatment. Paenibacillus taichungensis and Paenibacillus prosopidis were detected in the soil treated with only chemical fertilizer. Except for the ammonium and pH, all the tested soil fertility parameters (total C, total N, nitrate, available K and available P) could significantly affect both the Paenibacillus spp. population number and diversity. The soil pH was significantly correlated with Paenibacillus spp. diversity only.

Conclusions

Our results indicate that the different long-term fertilization regimes have varied impact on both the Paenibacillus spp. population size and the diversity of the community associated with the soil properties tested. These results can help to enrich the information on the response of beneficial soil microbes to different long-term fertilization regimes.     

Predicted effects of increasing salinity on the crustacean zooplankton community of Pyramid Lake,Nevada

Since 1933 the salinity of Pyramid Lake, Nevada, U.S.A., has increased 32% to nearly 5.5‰. We tested the hypothesis that further increases of 1.5 to 2 times (1.5× to 2×) its present salinity would significantly reduce species richness and alter population structures of the existing crustacean zooplankton community. Three strategies were applied: in addition to monitoring zooplankton in semicontrolled indoor microcosms at 1×, 1.5× and 2× and conducting range-finding, acute, and chronic salinity bioassays, the present zooplankton community of Walker Lake (2×) was compared with that existing in Pyramid Lake (1×). Ceriodaphnia quadrangula and Diaphanosoma leuchtenbergianum, both collected from Pyramid Lake, were lacking in Walker Lake. Populations of Cyclops vernalis were significantly lower and those of Diaptomus sicilis and Moina hutchinsoni were significantly higher in Walker Lake than in Pyramid Lake. Densities of Ceriodaphnia and Cyclops were low in microcosms at salinities > 1×. Diaphanosoma could not be maintained in microcosms, regardless of salinity. Numbers of Diaptomus and Moina in microcosms were proportional to salinity level. Short-term LC50 salinities (‰) were as follows: Diaphanosoma, 6.5; Ceriodaphnia, 7.1; Diaptomus, 13.3; Cyclops, 14.8; and Moina, 17.8. Multiple-generation, chronic bioassays were run only on Cyclops and Diaptomus. Three generations of Cyclops were produced at salinities of 4.0 to 8.5‰, but not at 9.8‰ or higher. Diaptomus was unable to complete three generations at salinities ?9.6‰. We speculate that high salinity in Walker Lake may indirectly benefit Diaptomus by negatively affecting predatory Cyclops, and benefit Moina by causing extinction of competing salinity-intolerant Diaphanosoma and Ceriodaphnia. Except for the response of Diaptomus, results from bioassays were in general agreement with results from microcosms and with field data. Untested predator-prey interactions could be responsible for the apparent discrepancy.