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- Bradnam, K. R., et al.
(författare)
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Assemblathon 2 : Evaluating de novo methods of genome assembly in three vertebrate species
- 2013
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Ingår i: GigaScience. - : BioMed Central (BMC). - 2047-217X. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results: In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions: Many current genome assemblers produced useful assemblies, containing a significant representation of their genes and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.
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| 2. |
- Dunham, I, et al.
(författare)
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The DNA sequence of human chromosome 22
- 1999
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 402:6761, s. 489-495
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Tidskriftsartikel (refereegranskat)
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| 3. |
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| 4. |
- Scherer, SW, et al.
(författare)
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Human chromosome 7: DNA sequence and biology
- 2003
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Ingår i: Science (New York, N.Y.). - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 300:5620, s. 767-772
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Tidskriftsartikel (refereegranskat)abstract
- DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. This approach enabled the discovery of candidate genes for developmental diseases including autism.
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| 5. |
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| 6. |
- Stavridis, Stavros I., et al.
(författare)
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Cocultures of rat sensorimotor cortex and spinal cord slices to investigate corticospinal tract sprouting
- 2009
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Ingår i: Spine. - 0362-2436 .- 1528-1159. ; 34:23, s. 2494-2499
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Tidskriftsartikel (refereegranskat)abstract
- STUDY DESIGN: Experimental study of corticospinal axonal sprouting in an organotypic slice culture model. OBJECTIVE: To develop an in vitro model that simplifies the study of various factors regulating neuronal regeneration. SUMMARY OF BACKGROUND DATA: Spinal cord injury leads to permanent neurologic damage, mainly due to the inability of the adult central nervous system to regenerate. Much attention has been focused on promoting axonal regeneration and sprouting, either by exogenous administration of various neurotrophic factors or by the antagonization of factors inhibiting regeneration. METHODS: An in vitro system that allows coculture of slices from rat sensorimotor cortex and spinal cord (p4) was established. Two groups of cultures were investigated: In the first group, intact spinal cord slices were cultured adjacent to sensorimotor cortex slices, while in the second group the spinal cord slices were sagittally cut into halves, with the sectioned interface placed directly adjacent to the sensorimotor cortex, to prevent the spinal white matter from interference. Each group was further divided into 2 subgroups: The neurotrophin-3 (NT-3) group, where the culture medium contained 50 ng/mL NT-3 and the control group treated with normal culture medium. Sensorimotor cortex pyramidal neurons were anterogradely labeled with Mini-Ruby, a 10 kD biotinylated dextran amine. RESULTS: Cocultures of cortical and spinal cord tissue were propagated in vitro, and axonal sprouting occurred. The group of cocultures treated with NT-3 showed an improved cortical cytoarchitecture, and sprouting axons were more frequently observed. In NT-3-treated cocultures where spinal cord gray matter was directly opposed to cortical slices sprouting axons entered the adjacent spinal cord tissue. This phenomenon was not observed if spinal cord pia mater and white matter were opposed to the cortical slices, or if NT-3 was absent. CONCLUSION: Our data suggest that the absence of repellent factors such as white matter and the presence of neurotrophic factors promote axonal sprouting. Cocultures of sensorimotor cortex and spinal cord slices combined with anterograde axonal labeling could provide a valuable in vitro model for the simplified screening of factors influencing corticospinal tract regeneration.
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