A critical review and a new proposal of karyotype asymmetry indices

In literature seven different methods of evaluating karyotype asymmetry – the TF%, the As K%, Stebbins' classification, the Rec and the Syi, the A₁ and the A₂, the DI, and the A – are used for the elucidation of phylogenetic relationships and taxonomic treatments within a particular group or taxon. The investigation of these seven methods reveals that the intervals used by Stebbins to separate the different types of karyotype asymmetry are very broad and only one quantitative parameter, the A₂ index, correctly describes the variation in chromosome length in a complement. A new asymmetry index (AI) is proposed to measure karyotype asymmetry and a new parameter, the CV_CI, is offered, that precisely assesses the relative variation in centromere position in a complement. The AI index, the CV_CI and the CV_CL (=A₂ × 100) have the potential to display even minor karyotypic variations. Thus, these three indices together increase the precision of results in comparison with other existing methods. All this has important consequences as regards the interpretation of the results of karyological studies.     

国产7种乌头属植物的核型研究

本文报道了国产7种乌头属植物（两色乌头（Aconitum alboviolaceum Kom.,牛扁 A.barbartum var.puberulum Ledeb.,蔓乌头A.volubile Pall.,展毛蔓乌头 A.ciliare DC.,北乌头 A.kusnezoffii Reichb.,蒿叶乌头 A.artemisiaefolium Bar.et Skv.,细叶乌头 A.macrorhgnchum Turcz.）的核型。其中展毛蔓乌头、蒿叶乌头和细叶乌头的核型为首次报道。本文还首次指出乌头属中具多年生根状茎的牛扁亚属植物的核型没有明显的二型性,而具二年生块根的乌头正属植物的核型的二型性十分明显。此外还讨论了细叶乌头及展毛蔓乌头的系统位置,认为它们与蔓乌头有较近的亲缘关系。     

Reconstruction of gross avian genome structure,organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor

Background

The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed.

Results

Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species’ genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n = 80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes.

Conclusions

Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1060) contains supplementary material, which is available to authorized users.     

Interstitial telomeric repeats as markers of evolutionary changes in the mammalian karyotype: Human chromosome 2

The presence of conserved telomeric repeats represented by the hexamer (TTAGGG)_n at the chromosomal termini is necessary for the correct functioning and stability of chromosomes. A number of the genomes of mammals, including human, are known to contain interstitial telomeric sequences located far from the chromosomal termini. It is assumed that these repeats mark the regions of fusions or other rear-rangements of ancestral chromosomes. Exact localization of all interstitial telomeric sequences in the genome could significantly advance the understanding of the mechanisms of karyotype evolution and speciation. In this context, software was developed to search for degenerate interstitial telomeric repeats in complete sequences of mammalian chromosomes. The evolutionary significance of such repeats was demonstrated by the example of human chromosome 2. The results are available at http://www.bionet.nsc.ru/labs/theorylabmain/orlov/telomere/.     

城市空间形态离散度指数NDIS构建与应用

中国土地资源有限,需要可持续的、紧凑的城市空间形态与布局,因此,全面度量城市空间形态的紧凑性具有重要意义。通过6个情境分析了离散度指数DIS的优缺点,识别出DIS值在反映城市形态紧凑程度方面的不足,进而提出了一种新的城市空间形态紧凑度指数,即标准化离散度指数NDIS。NDIS不受城市面积规模的影响,且具有唯一性,利于城市紧凑度的横向和纵向比较,能更好地指示城市空间形态。NDIS值越大,城市越离散。进一步将NDIS与成熟使用的标准化紧凑度指数NCI结合,用于分析中国35座城市的空间形态紧凑性,研究结果表明:(1) NDIS最大值是兰州市的1.64,最小值是石家庄市的1.14,均值1.29±0.12(SE); NCI最大值是郑州市0.39,最小值是宁波市的0.1,均值0.24±0.07(SE);(2) NDIS与NCI虽然具有中等程度的相关性(r=-0.44,P0.01),但是NDIS把城市斑块间的距离关系表达得更为准确;(3)将NDIS与NCI结合,能够更加全面地指示城市空间形态的紧凑程度。准确、全面的衡量中国城市的空间形态,则需要与更多的景观格局指数结合使用。     

A simple interferon assay as an adjunct for determining the genus of origin of cell cultures

Summary A short, simple test involving interferon-mediated protection of cells in vitro from cytopathogenic effects produced by vesicular stomatitis virus or Sindbis virus has been developed to help in determining the genus of origin of cells. By using the observed pattern of protection of five cell types by five interferons, cells could be grouped as of primate, rabbit, rat, and mouse origins. The primate grouping resulted from bilateral cross-reactions between the human and monkey systems. An unexpected observation was that African green monkey interferon preparations protect both monkey and rat cells, but not the converse. Chromosomal analysis of the cell cultures confirmed the genus determined by the interferon test.     

Multiple Ty-mediated chromosomal translocations lead to karyotype changes in a wine strain of Saccharomyces cerevisiae.

Enological strains of Saccharomyces cerevisiae display a high level of chromosome length polymorphism, but the molecular basis of this phenomenon has not yet been clearly defined. In order to gain further insight into the molecular mechanisms responsible for the karyotypic variability, we examined the chromosomal constitution of a strain known to possess aberrant chromosomes. Our data revealed that the strain carries four rearranged chromosomes resulting from two reciprocal translocations between chromosomes III and I, and chromosomes III and VII. The sizes of the chromosomal fragments exchanged through translocation range from 40 to 150 kb. Characterization of the breakpoints indicated that the translocations involved the RAHS of chromosome III, a transposition hot-spot on the right arm of chromosome I and a region on the left arm of chromosome VII. An analysis of the junctions showed that in all cases Ty elements were present and suggested that the translocations result from recombination between transposable Ty elements. The evidence for multiple translocations mediated by Ty elements in a single strain suggests that spontaneous Ty-driven rearrangement could be quite common and may play a major role in the alteration of karyotypes in natural and industrial yeasts. Received: 18 December 1998 / Accepted: 26 March 1999     

A simple stepwise procedure of deriving selection index with restrictions

Summary A simplified alternative procedure was derived for computing selection indices with various restrictions. The procedure involved construction of a sub-index for the unrestricted traits by the conventional methods (Smith-Hazel index approach) and construction of a sub-index for the restricted traits based on the restrospective index approach. The two subindices were then combined to obtain the desired index which met the prespecified restriction. The formulation is straightforward and easy to compute and does not involve the complicated formula as does the derivation of restricted index by the use of the Lagrange multiplier method. As a consequence of simplification, the proposed procedure is approximate in terms of optimal gain in net merit. The procedure presented can also be extended to derive an index with simultaneous imposition of multiple restrictions. Numerical examples were given to illustrate the use of this alternative approach.Animal Research Centre Contribution No. 1251     

Mammalian nonsynonymous sites are not overdispersed: comparative genomic analysis of index of dispersion of mammalian proteins

It is often stated that patterns of nonsynonymous rate variation among mammalian lineages are more irregular than expected or overdispersed under the neutral model, whereas synonymous sites conform to the neutral model. Here we reexamined genome-wide patterns of the variance to mean ratio, or index of dispersion (R), of substitutions in proteins from human, mouse, and dog. Contrary to the prevailing notion, we found that the mean index of dispersion for nonsynonymous sites of mammalian proteins is not significantly different from 1. We propose that earlier analyses were biased because the data included disproportionately more protein hormones, which tend to be more dispersed than genes in other functional categories. Synonymous sites exhibit greater degree of dispersion than nonsynonymous sites, although similar to earlier estimates and potentially due to errors associated with correction for multiple hits. Overall, our analysis identifies strong genome-wide generation-time effect and natural selection as important determinants of among-lineage variation of protein evolutionary rates. Furthermore, patterns of lineage-specific selective constraint are consistent with the nearly neutral model of molecular evolution.     

A simple and inexpensive high pressure liquid chromatographic system as an adjunct to gas chromatography in identification of amino acid phenylthiohydantoins.

A simple and inexpensive system has been developed in our laboratory for the identification and quantitation of amino acid phenylthiohydantoins by high pressure liquid chromatography. Isocratic methodology has been employed, so that expensive complex gradient makers can be avoided. The method is rapid, and retention times of 10 min or less are obtained in all but one case. This paper presents the rationale and details of the method, and demonstrates a comparison between gas-liquid chromatograms and high pressure liquid chromatograms of selected residues from actual automated sequence analyses of both sperm whale myoglobin and egg white lysozyme. The method is intended to complement rather than replace gas-liquid chromatography, as it cannot completely resolve all 20 phenylthiohydantoins, but rather identifies easily those residues which are difficult or impossible by gas chromatography.     

A clinical guide to surface-EMG-assisted stretching as an adjunct to chronic musculoskeletal pain rehabilitation

Therapeutic stretching is a vital component of chronic musculoskeletal pain rehabilitation for increasing range of motion and counteracting the effects of physical deconditioning. Surface EMG biofeedback is currently being used to facilitate movement and to maximize effective stretching with patients in an interdisciplinary chronic pain rehabilitation program for disabled workers. A clinical protocol with case examples is presented.     

QTc dispersion as a novel marker in identifying patients requiring an epicardial approach for ablation of scar mediated ventricular tachycardia

IntroductionEpicardial exit sites of ventricular tachycardia (VT) are frequently encountered during VT ablation requiring an epicardial ablation approach for successful elimination of VT. We sought to assess the utility of repolarization markers in identifying individuals requiring an epicardial ablation approach in addition to an endocardial approach.Methods32 patients who underwent successful ablation for scar mediated VT were included in the study. Fourteen patients who required a combined endocardial and epicardial VT ablation were defined as epicardial VT group (Epi) whereas 18 patients who were successfully ablated from the endocardium alone constituted the endocardial VT group (Endo). Repolarization markers during sinus rhythm were compared between the two groups.ResultsA higher QTc max and QTc dispersion were seen in the Epi group compared to Endo group (479 ± 34 vs 449 ± 20, p = 0.008 and 63 ± 13 vs 38 ± 8, p = 0.001, respectively). Ts-p and Ts-p/Tp-e were higher in the Epi group (166 ± 23 vs 143 ± 23, p = 0.008 and 1.55 ± 0.26 vs 1.3 ± 0.21, p < 0.005). On multivariate regression, QTc dispersion was an independent predictor of the need for an epicardial approach to ablation. A QTc dispersion more than 51.5 msec identified individuals requiring a combined epicardial and endocardial approach to ablation with a sensitivity of 92.9% and a specificity of 100%.ConclusionsPatients requiring an epicardial ablation have a higher QTc dispersion. A value greater than 51.5 msec reliably differentiates between the two groups with high sensitivity and specificity.     

Karyology of the Atlantic forest rodent Juliomys (Cricetidae): A new karyotype from southern Brazil

Juliomys is a small rodent from the family Cricetidae which inhabits the Atlantic forest and forests from Argentina to eastern Brazil. The three species recognized so far have different karyotypes. In this paper, we describe a new karyotype with 2n = 32, FN = 48 found in Juliomys specimens from a high-altitude area in the Atlantic forest of southern Brazil. The karyotype was analyzed after G- and C-banding and silver staining of the nucleolus organizer regions (Ag-NOR) and its G-banding patterns were compared with those of the newly described species Juliomys ossitenuis (2n = 20, FN = 36). The 2n = 32 karyomorph presented peculiar features and was very different from those of the other species of the genus: J. pictipes (2n = 36, FN = 34), J. rimofrons (2n = 20, FN = 34) and J. ossitenuis (2n = 20, FN = 36). Differences were mostly due to centric and tandem fusions, pericentric inversion and loss of heterochromatin. The karyotype represents a powerful tool to differentiate Juliomys species and our data suggest that the karyotype described herein belongs to a new species.     

A simple chlorophyll fluorescence parameter that correlates with the rate coefficient of photoinactivation of Photosystem II

A method of partitioning the energy in a mixed population of active and photoinactivated Photosystem II (PS II) complexes based on chlorophyll fluorescence measurements is presented. There are four energy fluxes, each with its quantum efficiency: a flux associated with photochemical electron flow in active PS II reaction centres (J_{PS II}), thermal dissipation in photoinactivated, non-functional PS IIs (J_NF), light-regulated thermal dissipation in active PS IIs (J_NPQ) and a combined flux of fluorescence and constitutive, light-independent thermal dissipation (J_f,D). The four quantum efficiencies add up to 1.0, without the need to introduce an ‘excess’ term E, which in other studies has been claimed to be linearly correlated with the rate coefficient of photoinactivation of PS II (k_pi). We examined the correlation of k_pi with various fluxes, and found that the combined flux (J_NPQ + J_f,D= J_pi) is as well correlated with k_pi as is E. This combined flux arises from F_s/F_m^′, the ratio of steady-state to maximum fluorescence during illumination, which represents the quantum efficiency of combined non-photochemical dissipation pathways in active PS IIs. Since F_s/F_m^′ or its equivalent, J_pi, is a likely source of events leading to photoinactivation of PS II, we conclude that F_s/F_m^′ is a simple predictor of k_pi.     

The use of an oligonucleotide that hybridizes to DNA sequences interspersed in the genome of members of the genusPhytophthora as an adjunct to morphological criteria in species identification

An oligonucleotide (primer), designed from a conserved region of the multi-allelicb locus of the basidiomycete fungusUstilago maydis, generated reproducible PCR fingerprints inPhytophthora species. The primer hybridized in a species-specific manner to nucleotide sequences interspersed in the genome of the closely related members ofPhytophthora taxonomic group IV. We recommend the use of this PCR procedure as an alternative method for resolving the close taxonomic affinity of some members of the genusPhytophthora.     

Ovarian weight as an index of fecundity, maturity, and spawning periodicity

Ovarian weight and related indices such as gonadosomatic index were used to index fecundity, egg maturity, and spawning season in gizzard shad Dorosoma cepedianum . Individually, in simple regression, fecundity and mean egg volume each accounted for only about 50% of the variability in ovarian weight. Together, in multiple regression, fecundity and mean egg volume accounted for 86% of the variation in ovarian weight. The percentage of the variability in ovarian weight explained by each independent variable, while holding constant the value of the other independent variable (partial coefficient of determination), was 72% for fecundity and 78% for mean egg volume. Thus, ovarian weight of gizzard shad confounded information about fecundity and egg maturity and separately could not index them adequately. Attempts to remove the effect of fecundity, so that ovarian weight could serve as an index of maturity, and to remove the effect of egg size so that ovarian weight could serve as an index of fecundity, were unsuccessful. Nevertheless, seasonal oscillations of ovarian weight served as a crude indicator of population Spawning Season.     

T-wave width as an index for quantification of ventricular repolarization dispersion: Evaluation in an isolated rabbit heart model

This study examined the significance of ECG-derived indexes in quantifying ventricular repolarization dispersion (VRD) given its value as a risk marker for severe myocardial arrhythmia. Multilead ECG recordings from an isolated rabbit heart model, including control and globally increased VRD (IVRD) beats, were studied. The IVRD was induced by supplying d-Sotalol (DS) or premature ventricular stimulation (PVS). ECG indexes came from (a) the absolute ECG summation signal, from which we obtained the amplitude and area of the T-wave, and the T-wave width (T_W), which we consider as IVRD indexes, and (b) the Singular Value Decomposition (SVD) of the ECG, from which the θ_PT (angle between the first SVD principal axis and the repolarization axis), T-wave residuum (T_WR), T-wave morphology dispersion (T_MD), unnormalized T_MD (UT_MD), and θ_RT (the angle between the depolarization and the repolarization vectors) were estimated as IVRD indexes. Results were compared with the classical QT-based VRD indexes (σ_QTe, standard deviation of QT end). The main results are T_W: 78.0±10.3 vs. 133.6±29.6 ms, for control vs. IVRD generated using DS, p<0.005 and 95.2±7.9 vs. 118.5±15.7 ms when PVS was used, p<0.007; σ_QTe: gives 6.5±1.4 vs. 11.6±1.9 ms, for DS p<0.007 and 7.6±2.2 vs. 13.0±3.4 ms for PVS, p<0.007; respectively. θ_PT: 35±51° vs. 117±49°, p<0.009 in DS. We concluded that globally induced IVRD is well reflected by the T_W parameter, being the most sensitive of the studied ones. The IVRD can also be quantified by using the θ_PT index.