Use of Radiation Hybrid panels to map genetic loci

The mapping of genetic loci within organisms has been accelerated by the advent of Radiation Hybrid (RH) panels. These panels are available for humans and non-humans including mice, baboon, rat, and canine. This article contains a general protocol for the use of the Genebridge 4 whole genome RH panel to map a human locus. This protocol may also be adjusted to suit the other RH panels currently available.     

SolVES模型价值转移方法对不同空间尺度的响应评估

随着人类对生态系统服务压力的不断增加,生态系统服务社会价值的评估变得至关重要。利用SolVES模型将太白山国家森林公园的社会价值转移到牛背梁国家森林公园和秦岭山地,评估两者的社会价值并探讨不同尺度下转移结果的差异。结果表明:1)牛背梁国家森林公园游憩价值指数与高程负相关,美学价值指数与高程正相关,羚牛谷山水观光游憩区的游憩价值较高,高山风光区的美学价值较高;2)秦岭山地的游憩价值与高程正相关,美学价值与高程负相关,森林公园的游憩价值较高,山地整体美学价值指数偏低;3)秦岭山地的社会价值集中于高程1000—2000m、坡度25°—35°处,而牛背梁国家森林公园的社会价值分布规律不明显;4)不同尺度下相同的转移模型输出的转移结果与环境变量的关系存在差异。SolVES模型的价值转移子模型是一个可以进行生态系统服务社会价值评估的快速有效的工具,但应根据需求精度选择合适的统计模型。     

生物信息学软件研究的可视化分析

以Web of Science数据库为数据来源,利用Cite Space和UCINET软件对发表在Nucleic Acids Research期刊上有关生物信息学软件研究的文献做了可视化分析,揭示了该领域的研究力量、作者团队与高被引作者、知识基础、期刊分布、研究热点与前沿,为生物信息学软件的研究和发展提供必要的参考依据。     

Comparative analysis of conditional reporter alleles in the developing embryo and embryonic nervous system

A long-standing problem in development is understanding how progenitor cells transiently expressing genes contribute to complex anatomical and functional structures. In the developing nervous system an additional level of complexity arises when considering how cells of distinct lineages relate to newly established neural circuits. To address these problems, we used both cumulative marking with Cre/loxP and Genetic Inducible Fate Mapping (GIFM), which permanently and heritably marks small populations of progenitors and their descendants with fine temporal control using CreER/loxP. A key component used in both approaches is a conditional phenotyping allele that has the potential to be expressed in all cell types, but is quiescent because of a loxP flanked Stop sequence, which precedes a reporter allele. Upon recombination, the resulting phenotyping allele is ‘turned on’ and then constitutively expressed. Thus, the reporter functions as a high fidelity genetic lineage tracer in vivo. Currently there is an array of reporter alleles that can be used in marking strategies, but their recombination efficiency and applicability to a wide array of tissues has not been thoroughly described. To assess the recombination/marking potential of the reporters, we utilized CreER^T under the control of a Wnt1 transgene (Wnt1-CreER^T) as well as a cumulative, non-inducible En1^Cre knock-in line in combination with three different reporters: R26R (LacZ reporter), Z/EG (EGFP reporter), and Tau-Lox-STOP-Lox-mGFP-IRES-NLS-LacZ (membrane-targeted GFP/nuclear LacZ reporter). We marked the Wnt1 lineage using each of the three reporters at embryonic day (E) 8.5 followed by analysis at E10.0, E12.5, and in the adult. We also compared cumulative marking of cells with a history of En1 expression at the same stages. We evaluated the reporters by whole-mount and section analysis and ascertained the strengths and weaknesses of each of the reporters. Comparative analysis with the reporters elucidated complexities of how the Wnt1 and En1 lineages contribute to developing embryos and to axonal projection patterns of neurons derived from these lineages.     

Revised karyotyping and gene mapping of the Biomphalaria glabrata embryonic (Bge) cell line

The fresh water snail Biomphalaria glabrata (2n = 36) belongs to the taxonomic class Gastropoda (family Planorbidae) and is integral to the spread of the human parasitic disease schistosomiasis. The importance of this mollusc is such that it has been selected as a model molluscan organism for whole genome sequencing. In order to understand the structure and organisation of the B. glabrata’s genome it is important that gene mapping studies are established. Thus, we have studied the genomes of two B. glabrata embryonic (Bge) cell line isolates 1 and 2 grown in separate laboratories, but both derived from Eder L. Hansen’s original culture from the 1970s. This cell line continues to be an important tool and model system for schistosomiasis and B. glabrata. Using these cell line isolates, we have investigated the genome content and established a revised karyotype based on chromosome size and centromere position for these cells. Unlike the original karyotype (2n = 36) established for the cell line, our investigations now show the existence of extensive aneuploidy in both cell line isolates to the extent that the total complement of chromosomes in both greatly exceeds the original cell line’s diploid number of 36 chromosomes. The isolates, designated Bge 1 and 2, had modal chromosome complements of 64 and 67, respectively (calculated from 50 metaphases). We found that the aneuploidy was most pronounced, for both isolates, amongst chromosomes of medium metacentric morphology. We also report, to our knowledge for the first time using Bge cells, the mapping of single-copy genes peroxiredoxin (BgPrx4) and P-element induced wimpy testis (piwi) onto Bge chromosomes. These B. glabrata genes were mapped onto pairs of homologous chromosomes using fluorescence in situ hybridization (FISH). Thus, we have now established a FISH mapping technique that can eventually be utilized for physical mapping of the snail genome.     

Structure of antimicrobial peptides and lipid membranes probed by interface-sensitive X-ray scattering

The conformation and correlations of amphiphilic and antimicrobial peptides and the associated changes of lipid bilayers can be studied in oriented lipid membranes deposited on solid substrates. Here we review recent work on these systems, as studied by modern interface-sensitive X-ray and neutron scattering methods. Density profile, short range order of acyl chains and molecular conformations of peptides and lipids are probed in the fluid state of the bilayer. With an emphasis on technical aspects, we review recent work illustrating the potential of the methods and discuss its potential in the field.     

SSCP-SNP-based conserved ortholog set (COS) markers for comparative genomics in cassava (Manihot esculenta crantz)

The ever increasing body of information on genomics and functional genomics from model plants, and new tools of comparative genomics, provide an opportunity to accelerate the development of molecular markers for increasing the efficiency of breeding of lesser studied crops, so-called “orphan crops.” Conserved ortholog set (COS) markers represent orthologous genes in widely divergent plant species, and are currently the principal tool of choice for comparative genomics. EST sequences of 3 drought tolerance related genes—chalcone synthase (CHS), dihydroflavonol-4-reductase (DHRF) and drought responsive element binding factor 1 (DREB-1) fromMusa sp—were used to identify cassava EST homologs that were then scanned against the Arabidopsis genome database to identify them as COS markers. The CHS and DHRF ESTs were demonstrated to be COS markers, while the DREB EST was shown to belong to a gene family. The three genes were evaluated as single strand conformation polymorphism—single nucleotide polymorphism (SSCP-SNP) markers in the parents of an F1 mapping population and subsequently in the progenies. The DHRF COS marker mapped to linkage group R of the female-derived map while the DREB-1 EST mapped at an end of the male-derived linkage group K. The CHS COS marker could not be mapped because it was not polymorphic in the parents of the mapping population. These new marker tools should accelerate the development of markers associated with genes controlling traits of agronomic interest via the candidate gene loci (CGL) QTL-mapping approach.     

Postembryonic lineages of the Drosophila brain: I. Development of the lineage-associated fiber tracts

Neurons of the Drosophila central brain fall into approximately 100 paired groups, termed lineages. Each lineage is derived from a single asymmetrically-dividing neuroblast. Embryonic neuroblasts produce 1,500 primary neurons (per hemisphere) that make up the larval CNS followed by a second mitotic period in the larva that generates approximately 10,000 secondary, adult-specific neurons. Clonal analyses based on previous works using lineage-specific Gal4 drivers have established that such lineages form highly invariant morphological units. All neurons of a lineage project as one or a few axon tracts (secondary axon tracts, SATs) with characteristic trajectories, thereby representing unique hallmarks. In the neuropil, SATs assemble into larger fiber bundles (fascicles) which interconnect different neuropil compartments. We have analyzed the SATs and fascicles formed by lineages during larval, pupal, and adult stages using antibodies against membrane molecules (Neurotactin/Neuroglian) and synaptic proteins (Bruchpilot/N-Cadherin). The use of these markers allows one to identify fiber bundles of the adult brain and associate them with SATs and fascicles of the larval brain. This work lays the foundation for assigning the lineage identity of GFP-labeled MARCM clones on the basis of their close association with specific SATs and neuropil fascicles, as described in the accompanying paper (Wong et al., 2013. Postembryonic lineages of the Drosophila brain: II. Identification of lineage projection patterns based on MARCM clones. Submitted.).