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101.
102.
Amino acid sequence versus morphological data and the interordinal relationships of mammals 总被引:2,自引:0,他引:2
To a large extent, the mutual affinities of the mammalian orders continue
to puzzle systematists, even though comparative anatomy and amino acid
sequencing offer a massive data base from which these relationships could
potentially be adduced. In the present paper the consistency index--the
number of character states less the number of characters in a data set,
divided by the total number of changes in the character states on a
cladogram--was used to examine the relative resolving powers of recently
published morphological and molecular- sequence data. Consistency indices
were calculated for previously published alpha crystallin A chain and
myoglobin amino acid-sequence cladograms and for four original amino
acid-sequence cladograms (alpha crystallin A, myoglobin, and alpha and beta
hemoglobin); these were found to be comparable to the consistency indices
of morphologically based cladograms. Qualitative comparisons between the
morphologically based and molecularly based trees were also made; only
moderate congruence between the two was observed. Moreover, there was a
general lack of congruence between the cladograms specified by each of the
four proteins. Amino acid-sequence and morphological data agreed on the
placement of edentates as an early eutherian offshoot and on the grouping
of hyracoids, proboscideans, and sirenians. Otherwise there was only
limited congruence: morphology strongly supported the grouping of
lagomorphs and rodents and the alliance of pholidotes and edentates, but
sequence analyses did not. The placement of tubulidentates differed widely
among proteins. Morphology indicated the close association of sirenians
with proboscideans; proteins suggested a pairing of sirenians with
hyracoids. Sequence data did not identify many (morphologically
well-diagnosed) orders as monophyletic (e.g., Lagomorpha).(ABSTRACT
TRUNCATED AT 250 WORDS)
相似文献
103.
Leonardo Restivo Bjrn Gerlach Michael Tsoory Lior Bikovski Sylvia Badurek Claudia Pitzer Isabelle C KosBraun AnneLaure MJ MaussetBonnefont Jonathan Ward Michael Schunn Lucas PJJ Noldus Anton Bespalov Vootele Voikar 《EMBO reports》2021,22(12)
Academic Core Facilities are optimally situated to improve the quality of preclinical research by implementing quality control measures and offering these to their users. Subject Categories: Methods & Resources, Science Policy & PublishingDuring the past decade, the scientific community and outside observers have noted a concerning lack of rigor and transparency in preclinical research that led to talk of a “reproducibility crisis” in the life sciences (Baker, 2016; Bespalov & Steckler, 2018; Heddleston et al, 2021). Various measures have been proposed to address the problem: from better training of scientists to more oversight to expanded publishing practices such as preregistration of studies. The recently published EQIPD (Enhancing Quality in Preclinical Data) System is, to date, the largest initiative that aims to establish a systematic approach for increasing the robustness and reliability of biomedical research (Bespalov et al, 2021). However, promoting a cultural change in research practices warrants a broad adoption of the Quality System and its underlying philosophy. It is here that academic Core Facilities (CF), research service providers at universities and research institutions, can make a difference.It is fair to assume that a significant fraction of published data originated from experiments that were designed, run, or analyzed in CFs. These academic services play an important role in the research ecosystem by offering access to cutting‐edge equipment and by developing and testing novel techniques and methods that impact research in the academic and private sectors alike (Bikovski et al, 2020). Equipment and infrastructure are not the only value: CFs employ competent personnel with profound knowledge and practical experience of the specific field of interest: animal behavior, imaging, crystallography, genomics, and so on. Thus, CFs are optimally positioned to address concerns about the quality and robustness of preclinical research. 相似文献
104.
WS Watkins R Thara BJ Mowry Y Zhang DJ Witherspoon W Tolpinrud MJ Bamshad S Tirupati R Padmavati H Smith D Nancarrow C Filippich LB Jorde 《BMC genetics》2008,9(1):1-17
Background
Major population movements, social structure, and caste endogamy have influenced the genetic structure of Indian populations. An understanding of these influences is increasingly important as gene mapping and case-control studies are initiated in South Indian populations.Results
We report new data on 155 individuals from four Tamil caste populations of South India and perform comparative analyses with caste populations from the neighboring state of Andhra Pradesh. Genetic differentiation among Tamil castes is low (RST = 0.96% for 45 autosomal short tandem repeat (STR) markers), reflecting a largely common origin. Nonetheless, caste- and continent-specific patterns are evident. For 32 lineage-defining Y-chromosome SNPs, Tamil castes show higher affinity to Europeans than to eastern Asians, and genetic distance estimates to the Europeans are ordered by caste rank. For 32 lineage-defining mitochondrial SNPs and hypervariable sequence (HVS) 1, Tamil castes have higher affinity to eastern Asians than to Europeans. For 45 autosomal STRs, upper and middle rank castes show higher affinity to Europeans than do lower rank castes from either Tamil Nadu or Andhra Pradesh. Local between-caste variation (Tamil Nadu RST = 0.96%, Andhra Pradesh RST = 0.77%) exceeds the estimate of variation between these geographically separated groups (RST = 0.12%). Low, but statistically significant, correlations between caste rank distance and genetic distance are demonstrated for Tamil castes using Y-chromosome, mtDNA, and autosomal data.Conclusion
Genetic data from Y-chromosome, mtDNA, and autosomal STRs are in accord with historical accounts of northwest to southeast population movements in India. The influence of ancient and historical population movements and caste social structure can be detected and replicated in South Indian caste populations from two different geographic regions. 相似文献105.
BD Pascal MJ Chalmers SA Busby CC Mader MR Southern NF Tsinoremas PR Griffin 《BMC bioinformatics》2007,8(1):156
Background
The combination of mass spectrometry and solution phase amide hydrogen/deuterium exchange (H/D exchange) experiments is an effective method for characterizing protein dynamics, and protein-protein or protein-ligand interactions. Despite methodological advancements and improvements in instrumentation and automation, data analysis and display remains a tedious process. The factors that contribute to this bottleneck are the large number of data points produced in a typical experiment, each requiring manual curation and validation, and then calculation of the level of backbone amide exchange. Tools have become available that address some of these issues, but lack sufficient integration, functionality, and accessibility required to address the needs of the H/D exchange community. To date there is no software for the analysis of H/D exchange data that comprehensively addresses these issues. 相似文献106.
107.
G Nivaler EA Zimmerman R Defendini AS Liotta DT Kreiger MJ Brownstein 《The Journal of cell biology》1979,81(1):50-58
Adrenocorticotropin and β-lipotropin (β-LPH) have been localized by immunoperoxidase methods in nerve cells and fibers of the hypothalamus and brain stem of the ewe. 6-μm sections were immunostained first for either ACTH or β-LPH. The reaction products and the antibody complexes were then eluted completely from the tissue, and the same section was immunostained for the second peptide. Absorption of the primary antisera with a variety of peptide fragments of ACTH and β-LPH demonstrated, immunocytochemically as well as by radioimmunoassay, that the ACTH and β-LPH antisera were directed to the COOH- and NH(2)-termini of the peptides, respectively. Neither antiserum recognized any portion of the heterologous peptide. In the sequential staining procedure on the same tissue section, preincubation of the antisera with the homologous peptide abolished the staining, whereas preincubation with the heterologous peptide did not affect it, regardless of the order followed. Every nerve cell in the arcuate nucleus that contained ACTH also contained β-LPH, but β-LPH cells appeared, probably falsely, to be twice as numerous as ACTH cells. β-LPH-positive fibers in and beyond the hypothalamus were also more numerous and stained more intensively than ACTH fibers. The salient exception was fibers in the infundibular zona externa, where the opposite was true. Our observations establish that ACTH and β-LPH are contained in the same nerve cells They stongly favor biosynthesis in brain, probably from a common precursor molecule, as has been demonstrated in the pituitary gland. The complexity of the cytologic distribution pattern described suggests that the two peptides are not processed in the same manner by the nerve cell. 相似文献
108.
Anna E van der Windt Esther Haak Ruud HJ Das Nicole Kops Tim JM Welting Marjolein MJ Caron Niek P van Til Jan AN Verhaar Harrie Weinans Holger Jahr 《Arthritis research & therapy》2010,12(3):R100
Introduction
Chondrocytes experience a hypertonic environment compared with plasma (280 mOsm) due to the high fixed negative charge density of cartilage. Standard isolation of chondrocytes removes their hypertonic matrix, exposing them to nonphysiological conditions. During in vitro expansion, chondrocytes quickly lose their specialized phenotype, making them inappropriate for cell-based regenerative strategies. We aimed to elucidate the effects of tonicity during isolation and in vitro expansion on chondrocyte phenotype. 相似文献109.
Herman MJ Sontrop Perry D Moerland René van den Ham Marcel JT Reinders Wim FJ Verhaegh 《BMC bioinformatics》2009,10(1):389-22
Background
Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for the observed discrepancies are the measurement error associated with each feature and the choice of preprocessing method. Microarray data are known to be subject to technical variation and the confidence intervals around individual point estimates of expression levels can be wide. Furthermore, the estimated expression values also vary depending on the selected preprocessing scheme. In microarray breast cancer classification studies, however, these two forms of feature variability are almost always ignored and hence their exact role is unclear. 相似文献110.
Femke AH van der Linden Jolijn J Kragt Margarethe van Bon Martin Klein Alan J Thompson Henk M van der Ploeg Chris H Polman Bernard MJ Uitdehaag 《BMC neurology》2008,8(1):2