Biomedical subjects

Shaolin Liu

Publications and source records attributed to Shaolin Liu.

4 recordsLinked to original sources

PubMed2006

CMD: a Cotton Microsatellite Database resource for Gossypium genomics.

BACKGROUND: The Cotton Microsatellite Database (CMD) http://www.cottonssr.org is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding. DESCRIPTION: At present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays data for three of the microsatellite projects that have been screened against a panel of core germplasm. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage. A suite of online microsatellite data mining tools are accessible at CMD. These include an SSR server which identifies microsatellites, primers, open reading frames, and GC-content of uploaded sequences; BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs, and CMap, a viewer for comparing cotton SSR maps. CONCLUSION: The collection of publicly available cotton SSR markers in a centralized, readily accessible and curated web-enabled database provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp.

Chromosome Mapping↗

PubMed2006

Exact word matches in rice pseudomolecules.

Using pseudomolecules of assembled genomic sequence, we computed the frequencies of 6 to 24 bp oligonucleotide (oligo) "words" across the genome of rice (Oryza sativa L. subsp. japonica). All oligos of 10 or fewer basepairs were repeated at least 12 times in the genome. The percentage of unique (non-repeated) oligos ranged from 0.1% for 12 bp oligos to 76.0% for 24 bp oligos. For three 200 kb regions, we annotated each nucleotide position with the genome-wide frequency of the 18 bp oligo starting at that position. These frequencies formed landscapes consisting of high- and low-frequency zones. Low-frequency zones contained occasional high-frequency spikes; these may represent footprints of RIM2 transposon activity. BLASTn searches of high-frequency non-SSR (simple sequence repeat) 18 bp oligos returned few sequences from species other than rice. These results demonstrate that, in rice, words are not randomly used between different regions within the same genome, and indicate that words that are frequently repeated within the rice genome tend to be unique to rice.

Base Sequence↗

PubMed2004

EC_oligos: automated and whole-genome primer design for exons within one or between two genomes.

SUMMARY: EC_oligos designs oligonucleotides (oligos) from exons of annotated genomic sequence information. It can automatically and rapidly select oligos that are conserved between two sets of sequence data, and can pair up oligos for use as PCR primers. It can do this on a whole-genome scale and according to user-defined criteria. AVAILABILITY: The source code, executable program and user manual are available at ftp://ftp.ebi.ac.uk/pub/software/dos/EC_oligos/.

Algorithms↗

PubMed2003

Roles of protein kinase A and protein kinase G in synaptic plasticity in the visual cortex.

Monocular deprivation leads to clear physiological and anatomical changes in the visual cortex known as ocular dominance plasticity. Protein kinase A (PKA) is necessary for ocular dominance plasticity, while protein kinase G (PKG) is not. We have now tested the role of PKA and PKG in long-term potentiation (LTP) and long-term depression (LTD). We have shown that PKA inhibitors have a major effect on both LTP and LTD in the visual cortical slices, whereas a PKG inhibitor affects LTP but not LTD. The PKA activator, 8-chloroadenosine-3',5'-monophosphorothioate, Sp-isomer (Sp-8-Cl-cAMPS), by itself induces a slowly rising form of LTP, which is occluded by theta-burst stimulation (TBS)-induced LTP. These results support the point that the PKA signaling pathway is crucial for neuronal plasticity in visual cortex, and the dissociation of the role of PKA and PKG in long-term synaptic plasticity in the visual cortex suggests that LTP alone is not sufficient to support ocular dominance plasticity, or LTD plays a more fundamental role than LTP in ocular dominance plasticity.

Animals↗