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31.
Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis 总被引：6，自引：0，他引：6
Using sequence data from the 28S ribosomal RNA (rRNA) genes of selected
vertebrates, we investigated the effects that constraints imposed by
secondary structure have on the phylogenetic analysis of rRNA sequence
data. Our analysis indicates that characters from both base-pairing regions
(stems) and non-base-pairing regions (loops) contain phylogenetic
information, as judged by the level of support of the phylogenetic results
compared with a well-established tree based on both morphological and
molecular data. The best results (the greatest level of support of
well-accepted nodes) were obtained when the complete data set was used.
However, some previously supported nodes were resolved using either the
stem or loop bases alone. Stem bases sustain a greater number of
compensatory mutations than would be expected at random, but the number is
< 40% of that expected under a hypothesis of perfect compensation to
maintain secondary structure. Therefore, we suggest that in phylogenetic
analyses, the weighting of stem characters be reduced by no more than 20%,
relative to that of loop characters. In contrast to previous suggestions,
we do not recommend weighting of stem positions by one-half, compared with
that of loop positions, because this overcompensates for the constraints
that selection imposes on the secondary structure of rRNA.
相似文献
32.
TT Chowdhury S Arghandawi J Brand OO Akanji DL Bader DM Salter DA Lee 《Arthritis research & therapy》2008,10(2):R35
Background
Nitric oxide and prostaglandin E2 (PGE2play pivotal roles in both the pathogenesis of osteoarthritis and catabolic processes in articular cartilage. These mediators are influenced by both IL-1β and mechanical loading, and involve alterations in the inducible nitric oxide synthase (iNOS) and cyclo-oxygenase (COX)-2 enzymes. To identify the specific interactions that are activated by both types of stimuli, we examined the effects of dynamic compression on levels of expression of iNOS and COX-2 and involvement of the p38 mitogen-activated protein kinase (MAPK) pathway. 相似文献33.
The complexity of genetic pathways for hearing is beginning to be amenable to unraveling by systematic functional genomic analysis. Genome-wide mutagenesis studies in the mouse are beginning to shed further light on the structure and regulation of the machinery of hearing. 相似文献
34.
Dor Mohammad Kordi-Tamandani Roya Sahranavard Adam Torkamanzehi 《Molecular biology reports》2012,39(12):10889-10893
Methylation and expression profile of CpG islands were examined in the promoters of the brain-derived neurotrophic factor (BDNF) and dopamine transporter (DAT1) genes. These are well known to be involved in the pathophysiology of psychiatric disorders such as schizophrenia. Genomic DNA was extracted from peripheral blood of 80 patients with schizophrenia and 71 healthy controls. Methylation pattern was studied by Methylation-Specific PCR. RNA expression analysis was done on extracted RNA from blood samples from patients suffering from schizophrenia (n?=?17) and healthy controls (n?=?17). Frequency of the BDNF gene methylation was highlighted as a statistically significant relationship between cases and controls regarding decreased risk of disease in comparison to unmethylated patterns (OR?=?0.24; 95?% CI?=?1.11–0.50; P?=?0.00007). For the DAT1 gene, this relationship was insignificant in 61 cases (76.25?%) and 52 controls (73.23?%) (OR?=?1.17; 95?% CI?=?0.53–2.61). Estimates of relative gene expression revealed a statistically significant association of the BDNF gene between schizophrenic patients and healthy controls (Mean?±?SD: 13.3920?±?15.19 and 0.437?±?0.328, P?=?0.0001) respectively; however, it was not significant for the DAT1 gene. This first hand evidence, regarding BDNF and DAT1 gene methylation and their expression profile with risk of schizophrenia, indicated a significant function for the BDNF gene in the development of schizophrenia. However, further populations with large sample sizes need to be studied to verify the exact role of BDNF in mental disorders such as schizophrenia. 相似文献
35.
Emerging evidence suggests a role of dysfunction of glutamatergic neurotransmission and its receptors in the pathophysiology of schizophrenia (SCZ). This study evaluated whether the promoter hypermethylation and RNA expression pattern of GMR2 (glutamate metabotropic receptor), GMR5, GMR8, and GRIA3 (glutamate receptor, ionotropic alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) are associated with the risk of schizophrenia between schizophrenia patients and healthy controls. 相似文献
36.
Null mutants of the neural‐specific γ‐isotype of protein kinase C (γ‐PKC) have demonstrated differential responses to acute administration of ethanol in comparison with wild‐type animals. Previous studies have shown that the mutants are less sensitive to ethanol‐induced loss of righting response. Null mutants also consume more ethanol and exhibit less behavioral inhibition. In order to determine if these sensitivity differences extend to ethanol activation of locomotor activity in an open‐field arena, baseline activity and the effect of two low doses of ethanol were assessed in γ‐PKC null mutants and wild‐type littermates. Null mutants demonstrated higher levels of baseline activity than did their wild‐type counterparts. Further analysis revealed that a 1.0 g/kg dose of ethanol increased locomotor activity in males and females of both genotypes, whereas only null mutant males were activated by a 1.25 g/kg ethanol dose. The current study demonstrates that male γ‐PKC null mutants exhibit increased sensitivity to activating doses of ethanol in contrast to previous findings of decreased sensitivity to higher, depressive doses. This reflects the pleiotropic effects of the γ‐PKC null mutation on the behavioral effects of ethanol. 相似文献
37.
Roderic DM Page 《BMC bioinformatics》2007,8(1):158
Background
TreeBASE is currently the only available large-scale database of published organismal phylogenies. Its utility is hampered by a lack of taxonomic consistency, both within the database, and with names of organisms in external genomic, specimen, and taxonomic databases. The extent to which the phylogenetic knowledge in TreeBASE becomes integrated with these other sources is limited by this lack of consistency. 相似文献38.
Background
Life Science Identifiers (LSIDs) are persistent, globally unique identifiers for biological objects. The decentralised nature of LSIDs makes them attractive for identifying distributed resources. Data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA sequences) are distributed over many different providers, and this community has adopted LSIDs as the identifier of choice. 相似文献39.
Background
The NCBI taxonomy provides one of the most powerful ways to navigate sequence data bases but currently users are forced to formulate queries according to a single taxonomic classification. Given that there is not universal agreement on the classification of organisms, providing a single classification places constraints on the questions biologists can ask. However, maintaining multiple classifications is burdensome in the face of a constantly growing NCBI classification. 相似文献40.
Jeroen Lakerveld Sandra DM Bot Marijke J Chinapaw Maurits W van Tulder Patricia van Oppen Jacqueline M Dekker Giel Nijpels 《BMC endocrine disorders》2008,8(1):1-11