锅柄式PCR及其在混合谱系白血病基因断裂区中的应用

染色体11q23的混合谱系白血病(MLL)基因的断裂点簇集群区(BCR)的转位,可引起婴儿急性白血病及与DNA拓扑异构酶Ⅱ抑制剂的生化治疗法相关的白血病。由于MLL基因包括大约30个不同的转位伴侣基因,几个断裂点所在的伴侣基因的序列还不清楚,因而对MLL基因断裂点的PCR克隆是很困难的。锅柄式PCR,即用已知5'端序列和未知的3'端伴侣基因序列以形似一个锅和一个柄的模板扩增断裂点基因DNA,是一种克隆MLL基因断裂区的新方法,可以扩增未知3'端序列的断裂点簇集群区。     

Optimization and application of real-time PCR method for detecting the expression levels of nitrogen assimilation-related genes in rice

By optimizing the Mg²⁺ concentration, Taq enzyme dosage, SYBR Green I (SGI) concentration, and plate reading temperature in PCR system, we established the method for detecting the expression levels of nitrogen assimilation-related genes in rice by using RT-PCR technique. Based on this qualified method, we investigated the variations of OsAMT1.1 (one of nitrogen uptake genes) and OsGlt1 (one of nitrogen metabolism genes) expression levels in rice seedlings under conditions of varying nitrogen supply. The results show that by optimizing the parameters in the PCR system to fit the characters of target genes best, we can successfully quantify the low-abundant nitrogen transport and metabolism genes in rice quickly and exactly using fluorescence RT-PCR technique. Published in Russian in Fiziologiya Rastenii, 2006, Vol. 53, No. 4, pp. 625–636. The text was submitted by the authors in English.     

Contrasting genetic structures across two hybrid zones of a tropical reef fish, Acanthochromis polyacanthus (Bleeker 1855)

Hybrid zones are natural laboratories offering insights into speciation processes. Narrow hybrid zones are less common in the sea than on land consistent with higher dispersal among marine populations. Acanthochromis polyacanthus is an unusual bony marine fish with philopatric dispersal that exists as allopatric stocks of white, bicoloured and black fish on the Great Barrier Reef (GBR). At two latitudes, different morphs coexist and hybridize at narrow contact zones. Sequence data from mitochondrial Hypervariable Region 1 revealed contrasting patterns of introgression across these zones. At the northern hybrid zone, a single clade of mitochondrial haplotypes was found in all white fish, hybrids and tens of kilometres into pure bicoloured stock. At the southern hybrid zone, there was no introgression of mitochondrial genes into black fish and hybrids shared the bicoloured haplotypes. Based on this asymmetry, we postulate that black fish from the southern GBR have experienced a selective sweep of their mitochondrial genome, which has resulted in almost total reproductive isolation.     

No evidence for survival selection on carotenoid-based nestling coloration in great tits (Parus major)

In several vertebrate species evidence supports the hypothesis that carotenoid-based coloration of adults has evolved due to sexual selection. However, in some birds already the nestlings display carotenoid-based coloration. Because the nestling's body plumage is typically moulted before the first reproductive event, sexual selection cannot explain the evolution of these carotenoid-based traits. This suggests that natural selection might be the reason for its evolution. Here we test whether the carotenoid-based nestling coloration of great tits (Parus major) predicts survival after fledging. Contrary to our expectation, the carotenoid-based plumage coloration was not related to short- nor to long-term survival in the studied population. Additionally, no prefledging selection was detectable in an earlier study. This indicates that the carotenoid-based coloration of nestling great tits is currently not under natural selection and it suggests that past selection pressures or selection acting on correlated traits may have led to its evolution.     

FGF ligand family mRNA expression profile for mouse preimplantation embryos, early gestation human placenta, and mouse trophoblast stem cells

Signaling by fibroblast growth factor (FGF) is essential is for trophoblast stem (TS) cells and preimplantation embryos. FGF4 provides essential signaling, but the expression of the complete set of 23 FGF family members has not been analyzed. Here, semi-quantitative RT-PCR and microarray analyses were used to define expression of all FGF ligand mRNA. RT-PCR was done for developmentally important FGF subfamilies, FGF10/FGF22 and FGF8/FGF17/FGF18 as well as FGF11. FGF4 and FGF18 are detected at highest levels by RT-PCR and microarrays. FGF10 was detected at low levels in both assays. FGF11 was detected at moderate levels by microarray, but not by RT-PCR. FGF17 was detected at low levels by array and moderate levels by RT-PCR. FGF8 and FGF22 were detected by RT-PCR, but not by microarrays during late cleavage divisions. FGF8, FGF5, and FGF9 were detected in the oocyte by microarray. FGF2, FGF3, and FGF7 were not detected by RT-PCR or microarrays and FGF13, FGF14, and FGF23 were not detected by microarray. Since a major role of FGF is to maintain TS cells, we tested human and mouse placental cell lines and early gestation human placenta for expression of FGF ligands. Expression in mouse TS cells was compared with preimplantation embryos, and human placental cell line expression was compared with human placenta, to infer which ligands are expressed in placental lineage vs. other cell lineages. The data suggest that human and mouse placenta share FGF18 and its high expression suggests preimplantation and early placental function.     

Development of single-cell PCR methods for the Raphidophyceae

Many Raphidophytes are important algal bloom-forming species. Morphology-based identification of these species is often ambiguous, however, as many species are very similar in shape and size. To accurately detect the presence of these species in pre-bloom conditions, single-cell PCR is probably the most rapid and convenient method. However, direct single-cell PCRs with conserved primers are apparently not effective, probably due to the impermeability of the cell wall. We report here an effective detergent-based pre-PCR cell lysis method, which turned out to be a critical step for effective single-cell PCR of the Raphidophytes. Two PCR-based methods, nested SC-PCR and SC-RAPD, were evaluated. The nested SC-PCR involves two consecutive PCRs, the first of which is performed with the D1 and D2 primers (external primers) resulting in an amplification of a partial LSU rRNA gene. The second amplification is performed with primers targeting the LSU domain and specifically annealing to Chattonella ovata and Chattonella marina only. The SC-RAPD performed with the established random primers, RP1–RP4, produced unique haplotypes that could be exploited to differentiate the two Chattonella species. The assay was demonstrated to be sensitive, with the lowest detection limit of a single Raphidophyceae cell. The method developed is a valuable tool for the study of intra-specific variations of the Raphidophytes and represents a platform for further development of species-specific SC-RAPD for all members of the Raphidophyceae.     

Thirty‐two single nucleotide polymorphism markers for high‐throughput genotyping of sockeye salmon

We characterize 32 single nucleotide polymorphism genotyping assays for resolving genotypic variation in sockeye salmon Oncorhynchus nerka in the Pacific Rim. These assays are based on the 5′‐nuclease reaction and thus facilitate high‐throughput genotyping with minimal optimization time. Minor allele frequency differences (Δq) among collections were between 4.7% and 97.9%, resulting in per locus F_ST estimates of 0.02–0.71 with an average of 0.22.