A Simple Allele-Specific PCR Assay for Detecting <Emphasis Type="Italic">FAD2</Emphasis> Alleles in Both A and B Genomes of the Cultivated Peanut for High-Oleate Trait Selection

In cultivated tetraploid peanut (2n = 4x = 40, AABB), the conversion of oleic acid to linoleic acid is mainly catalyzed by the Δ¹² fatty acid desaturase (FAD). Two homoeologous genes (FAD2A and FAD2B) encoding for the desaturase are located on the A and B genomes, respectively. Abolishing or reducing the desaturase activity by gene mutation can significantly increase the oleic acid/linoleic acid ratio. F435-derived high-oleate peanut cultivars contain two key mutations within the Δ¹² fatty acid desaturase gene which include a 1-bp substitution of G:C→A:T in the A genome and a 1-bp insertion of A:T in the B genome. Both of these mutations contribute to abolishing or reducing the desaturase activity, leading to accumulation of oleate versus linoleate. Currently, detection of FAD2 alleles can be achieved by a cleaved amplified polymorphic sequence marker for the A genome and a real-time polymerase chain reaction (PCR) marker for the B genome; however, detection of these key mutations has to use different assay platforms. Therefore, a simple PCR assay for detection of FAD2 alleles on both genomes was developed by designing allele-specific primers and altering PCR annealing temperatures. This assay was successfully used for detecting FAD2 alleles in peanut. Gas chromatography (GC) was used to determine fatty acid composition of PCR-assayed genotypes. The results from the PCR assay and GC analysis were consistent. This PCR assay is quick, reliable, economical, and easy to use. Implementation of this PCR assay will greatly enhance the efficiency of germplasm characterization and marker-assisted selection of high oleate in peanut.     

Novel Partial Reductive Pathway for 4-Chloronitrobenzene and Nitrobenzene Degradation in Comamonas sp. Strain CNB-1

Comamonas sp. strain CNB-1 grows on 4-chloronitrobenzene (4-CNB) and nitrobenzene as sole carbon and nitrogen sources. In this study, two genetic segments, cnbB-orf2-cnbA and cnbR-orf1-cnbCaCbDEFGHI, located on a newly isolated plasmid, pCNB1 (ca. 89 kb), and involved in 4-CNB/nitrobenzene degradation, were characterized. Seven genes (cnbA, cnbB, cnbCa, cnbCb, cnbD, cnbG, and cnbH) were cloned and functionally expressed in recombinant Escherichia coli, and they were identified as encoding 4-CNB nitroreductase (CnbA), 1-hydroxylaminobenzene mutase (CnbB), 2-aminophenol 1,6-dioxygenase (CnbCab), 2-amino-5-chloromuconic semialdehyde dehydrogenase (CnbD), 2-hydroxy-5-chloromuconic acid (2H5CM) tautomerase, and 2-amino-5-chloromuconic acid (2A5CM) deaminase (CnbH). In particular, the 2A5CM deaminase showed significant identities (31 to 38%) to subunit A of Asp-tRNA^Asn/Glu-tRNA^Gln amidotransferase and not to the previously identified deaminases for nitroaromatic compound degradation. Genetic cloning and expression of cnbH in Escherichia coli revealed that CnbH catalyzed the conversion of 2A5CM into 2H5CM and ammonium. Four other genes (cnbR, cnbE, cnbF, and cnbI) were tentatively identified according to their high sequence identities to other functionally identified genes. It was proposed that CnbH might represent a novel type of deaminase and be involved in a novel partial reductive pathway for chloronitrobenzene or nitrobenzene degradation.     

A revision of the <Emphasis Type="Italic">Heterospathe elegans</Emphasis> (<Emphasis Type="Italic">Arecaceae</Emphasis>) complex in New Guinea

Summary  Three closely affiliated species of Heterospathe Scheff. (H. elegans (Becc.) Becc., H. humilis Becc. and H. versteegiana Becc.) from New Guinea are revised. They are reduced to a single species which is divided into two subspecies, and the new combination H. elegans subsp. humilis (Becc.) M. S. Trudgen & W. J. Baker is made. The subspecies can be readily distinguished by their growth habit. Epitypes are designated for the three previously published names, as informative material on the habit is not included in the existing type specimens. A new, potentially related species is described as H. pullenii M. S. Trudgen & W. J. Baker.     

Targeting cleavage and polyadenylation specific factor 1 via shRNA inhibits cell proliferation in human ovarian cancer

Cleavage and polyadenylation specificity factor 1 (CPSF1), a member of CPSF complex, has been reported to play a key role in pre-mRNA 3′-end formation, but its possible role in ovarian cancer remains unclear. In the present study, we found the mRNA level of CPSF1 was overexpressed in ovarian cancer tissues using Oncomine Cancer Microarray database. Then the loss-of-function assays, including CCK-8, colony formation and flow cytometry assays, were performed to determine the effects of CPSF1 on cell viability, proliferation, cell cycle and apoptosis of human ovarian cancer cell lines (SKOV-3 and OVCAR-3). The results indicated that depletion of CPSF1 suppressed cell viability, impaired colony formation ability, induced cell cycle arrest at G0/G1 phase and promoted cell apoptosis in ovarian cancer cells. Furthermore, knockdown of CPSF1 upregulated the expression of cleaved caspase-3 and PARP and downregulated CDK4/cyclin D1 expression. These data suggested that CPSF1 could promote ovarian cancer cell growth and proliferation in vitro and its depletion might serve as a potential therapeutic target for human ovarian cancer.     

CRlncRNA: a manually curated database of cancer-related long non-coding RNAs with experimental proof of functions on clinicopathological and molecular features

Background

Recent studies demonstrated that long non-coding RNAs (lncRNAs) could be intricately implicated in cancer-related molecular networks, and related to cancer occurrence, development and prognosis. However, clinicopathological and molecular features for these cancer-related lncRNAs, which are very important in bridging lncRNA basic research with clinical research, fail to well settle to integration.

Results

After manually reviewing more than 2500 published literature, we collected the cancer-related lncRNAs with the experimental proof of functions. By integrating from literature and public databases, we constructed CRlncRNA, a database of cancer-related lncRNAs. The current version of CRlncRNA embodied 355 entries of cancer-related lncRNAs, covering 1072 cancer-lncRNA associations regarding to 76 types of cancer, and 1238 interactions with different RNAs and proteins. We further annotated clinicopathological features of these lncRNAs, such as the clinical stages and the cancer hallmarks. We also provided tools for data browsing, searching and download, as well as online BLAST, genome browser and gene network visualization service.

Conclusions

CRlncRNA is a manually curated database for retrieving clinicopathological and molecular features of cancer-related lncRNAs supported by highly reliable evidences. CRlncRNA aims to provide a bridge from lncRNA basic research to clinical research. The lncRNA dataset collected by CRlncRNA can be used as a golden standard dataset for the prospective experimental and in-silico studies of cancer-related lncRNAs. CRlncRNA is freely available for all users at http://crlnc.xtbg.ac.cn.

     

多能干细胞诱导分化为肾脏类器官的研究进展与挑战

用于分化为多种类型细胞的多能干细胞(PSC)体外培养技术已被广泛应用于生物学领域中.由PSC分化而来的肾脏类器官可基本还原生物体内肾脏的组织结构和部分功能,在肾脏疾病模型研究和药物筛选中有重要作用,继续改善肾脏类器官的结构、功能和成熟度将会对肾脏再生治疗提供极大的帮助.研究肾脏类器官的重点在于体外准确模拟体内肾脏的发育...     

A lateral-displacement flume for fish behavior and stranding studies during simulated pulsed flows

In regulated rivers, fluctuating water depths associated with pulsed discharges may strand small fish in side channels and pools. Quantitative assessments of stranded fish are difficult in field studies (e.g., due to unknown effects of avian and terrestrial vertebrate predators). To assess such lateral displacement and stranding on juvenile stream fishes, we designed, constructed, and tested (with three species) a 2 × 1-m, lateral-displacement flume. The flume featured a main channel that never drained and a raised, wide “floodplain” channel that alternately flooded, with a simulated pulse, and became dewatered. The floodplain contained four pools, with different shapes and draining capacities, in which fish could become stranded as the water level subsided. Fish-stranding rates (8%) in this relatively compact laboratory flume, after exposure to simulated pulsed stream flows, were comparable to those observed in past investigations using larger, artificial streams.     

Informing conservation by identifying range shift patterns across breeding habitats and migration strategies

A species distribution combines the resources and climatic tolerances that allow an individual or population to persist. As these conditions change, one mechanism to maintain favorable resources is for an organism to shift its range. Much of the research examining range shifts has focused on dynamic distribution boundaries wheras the role of species breeding habitat or migration strategies on shift tendencies has received less attention. We expand on previous research by using a large suite of avian species (i.e., 277), analyzing observed abundance-weighted average latitudes, and categorizing species by breeding environment and migration strategy. We used the North American Breeding Bird Survey dataset to address two questions: (1) Has the center of observed abundance for individual species shifted latitudinally? (2) Is there a relationship between migration strategy or breeding habitat and range shifts? Results indicate the majority of species have experienced poleward range shifts over the last 43 years, and birds breeding in all habitat showed trends of poleward shift but only those species breeding in scrub-shrub and grassland environments were different from zero. Additionally, species that are short distance migrants are experiencing significant poleward shifts while Neotropical and permanent residents had shifts that were not different from zero. Our findings do support the general trend expected from climate driven changes (i.e., > 52 % shifting poleward), however, the proportion of species exhibiting equatorial shifts (24 %) or no significant shifts (23 %) illustrates the complex interplay between land cover, climate, species interactions, and other forces that can interact to influence breeding ranges over time. Regardless of the mechanisms driving range shifts, our findings emphasize the need for connecting and expanding habitats for those species experiencing range shifts. This research describes the patterns of breeding birds through central North America and we encourage future research to focus on the mechanisms driving these patterns.