Two complementary perspectives on inter-individual genetic distance

This paper examines population structure through the prism of pairwise genetic distances. Two complementary perspectives, framed as two simple questions, are explored: Q1: What is the probability that a random pair of individuals from the same local population is more genetically dissimilar than a random pair from two distinct populations? Q2: On average, how genetically different are two individuals from the same local population, in comparison with two individuals chosen from any two distinct populations? Models are developed to provide quantitative answers for the two questions, given allele frequencies across any number of markers from two diploid populations. The probability from Q1 is shown to drop to zero with increasing number of genetic markers even for very closely-related populations and rare alleles. The average genetic dissimilarity of two individuals from distinct populations diverges from the average dissimilarity of two individuals from the same population by a percentage dependent on estimates of population differentiation. This perspective also suggests a measure of population distance based on the intuitive notion of pairwise genetic distance, along with a simple method of estimation. Results from recent empirical research on inter-individual genetic distance in human populations are analyzed in the context of the theoretical framework.     

Molecular evolution of the zinc-containing long-chain alcohol dehydrogenase genes

Phylogenetic relationships and rates of nucleotide substitution were studied for alcohol dehydrogenase (ADH) genes by using DNA sequences from mammals and plants. Mammalian ADH sequences include the three class I genes and a class II gene from humans and one gene each from baboon, rat, and mouse. Plant sequences include two ADH genes each from maize and rice, three genes from barley, and one gene each from wheat and two dicots, Arabidopsis and pea. Phylogenetic trees show that relationships among ADH genes are generally consistent with taxonomic relationships: mammalian and plant ADH genes are classified into two distinct groups; primate class I genes are clustered; and two dicot sequences are clustered separately from monocot sequences. Accelerated evolution has been detected among the duplicated ADH genes in plants, in which synonymous substitutions occurred more often within the coenzyme-binding domain than within the catalytic domains.     

Genetic heterogeneity of Pneumocystis carinii from rats of several regions and strains

Pneumocystis carinii is a major opportunistic pathogen which has been found in the lungs of a wide variety of mammalian host species, and the fact suggests the possibility of intraspecific variation. Until now, P. carinii from different mammalian species are differentiated as subspecies, and the rats are known to be infected by two subspecies. The present study investigated genetic heterogeneity of P. carinii isolates from two strains of rats in Korea and China by molecular karyotyping, RFLP and sequencing analysis. Karyotypes of P. carinii were grouped into three, two from two strains of rats in Korea and one from rats in China. However RFLP of PCR product of ribosomal and MSG gene of the P. carinii isolates showed same pattern. The sequence homology rates of alpha-tubulin DNA of the P. carinii isolates were 96% in Seoul Wistar rats, 93% in Seoul Sprague-Dawley rats, and 85% in Chinese Sprague-Dawley rats. The present finding confirmed that P. carinii from rats in Korea are grouped into two karyotype strains which are different from that of P. carinii from rats in China. The Chinese isolate shows a little different sequences of alpha-tubulin DNA.     

A revision of the tribe Plectrothripini of fungus-feeding Thysanoptera (Phlaeothripidae: Phlaeothripinae)

Abstract The tribe Plectrothripini is redefined with examination of its systematic relationships. Keys are provided to the ten genera and forty-seven species in this tribe; one genus and eighteen species are newly described; one genus and two species are newly synonymized; two genera, Chiridothrips and Eurytrichothrips , are here removed from this tribe. The species of the tribe occur throughout the tropical and subtropical regions of the world; seventeen species are recorded from the Oriental Region, seventeen species from the Neotropical Region, ten species from the Afrotropical Region, two from Australia and one from the Pacific. They seem to be fungus-feeders, being found mainly under the bark of trees or on dead branches.     

The IH-NMR-study of the copper surrounding in plantacyanin

The 300-MHz proton NMR spectra of oxidized, reduced and apo-forms of plantacyanin were studied. The data obtained show that one of two histidines is far from copper whereas the other is a ligand of the metal. Ligands of copper are also two methionines and, possibly, tryptophan. Although the surrounding of copper in plastocyanin consists of two sulfur and two nitrogen atoms, only histidine and methionine are invariant ligand amino acids of the metal in these two copper proteins from plants.     

Mutual synergistic protein folding in split intein

Inteins are intervening protein sequences that undergo self-excision from a precursor protein with the concomitant ligation of the flanking polypeptides. Split inteins are expressed in two separated halves, and the recognition and association of two halves are the first crucial step for initiating trans-splicing. In the present study, we carried out the structural and thermodynamic analysis on the interaction of two halves of DnaE split intein from Synechocystis sp. PCC6803. Both isolated halves (IN and IC) are disordered and undergo conformational transition from disorder to order upon association. ITC (isothermal titration calorimetry) reveals that the highly favourable enthalpy change drives the association of the two halves, overcoming the unfavourable entropy change. The high flexibility of two fragments and the marked thermodynamic preference provide a robust association for the formation of the well-folded IN/IC complex, which is the basis for reconstituting the trans-splicing activity of DnaE split intein.     

Presence and stoichiometry of two forms of subunit 6 of the mitochondrial ATPase complex of yeast

One of the mitochondrically coded components of the yeast mitochondrial ATPase complex (subunit 6) can be resolved into two components on certain polyacrylamide gels in the presence of sodium dodecyl sulfate. Purification of the ATPase complex from commercially processed yeast as well as immunoprecipitation of the holo-enzyme from cells labeled in vivo with 14C-labeled amino acids demonstrate that both forms of subunit 6 are physically associated with the assembled enzyme and present in two copies each per complex. One-dimensional papain-generated peptide maps of the two components are identical except for the mobility of a single fragment. It is concluded that the two components of subunit 6 are different forms of a single protein and are present on an average of two copies each per complex.     

Evolutionary implications of a complex pattern of DNA sequence homology extending far upstream of the hsp70 genes at loci 87A7 and 87C1 in Drosophila melanogaster

Genes coding for the major 70,000 M_r heat shock protein (hsp70) are found at two loci, 87A7 and 87C1, in Drosophila melanogaster. At 87A7 they are present as two genes in diverging orientation, whilst at 87C1 two tandemly repeated distal copies are separated from a single copy in divergent orientation by about 40,000 bases of DNA. Within this 40,000 bases are found the αβ heat-induced genes, interspersed with γ elements. In this paper we report the isolation and characterization of the proximal hsp70 gene from locus 87C1. The DNA sequence upstream from this gene shows greater than 98% homology with that of αγ, suggesting that the γ element interspersed with αβ sequences originated from this position. In addition, we present the DNA sequence between the two genes in a cloned DNA segment from 87A7, and compare the sequence with those from 87C1. We find a complex pattern of nucleotide sequence homology extending far upstream of the hsp70 genes at the two loci. The evolution of the present arrangement at these two loci is discussed.     

Relationships among recent models for insect population dynamics with variable rates of development

A classification scheme for those population models which allow variation in development rates is proposed, based on two ways of modifying standard age-structured models. The resulting classes of models are termed development index models and sojourn time models. General formulations for the two classes of models are developed from two basic balance equations, and numerous specific models from the literature are shown to fit into the scheme. Concepts from competing risks theory are shown to be important in understanding the interplay between mortality and maturation. Relationships among the classes are investigated both for the most general forms of the models and for the simpler forms often used. The scheme can provide guidance in developing appropriate insect population models for specific modelling situations.Contribution 3878871     

Cryptic genetic variation and paraphyly in ravens

Widespread species that are morphologically uniform may be likely to harbour cryptic genetic variation. Common ravens (Corvus corax) have an extensive range covering nearly the entire Northern Hemisphere, but show little discrete phenotypic variation. We obtained tissue samples from throughout much of this range and collected mitochondrial sequence and nuclear microsatellite data. Our study revealed a deep genetic break between ravens from the western United States and ravens from throughout the rest of the world. These two groups, the 'California clade' and the 'Holarctic clade' are well supported and over 4% divergent in mitochondrial coding sequence. Microsatellites also reveal significant differentiation between these two groups. Ravens from Minnesota, Maine and Alaska are more similar to ravens from Asia and Europe than they are to ravens from California. The two clades come in contact over a huge area of the western United States, with mixtures of the two mitochondrial groups present in Washington, Idaho and California. In addition, the restricted range Chihuahuan raven (Corvus cryptoleucus) of the south-west United States and Mexico is genetically nested within the paraphyletic common raven. Our findings suggest that the common raven may have formerly consisted of two allopatric groups that may be in the process of remerging.     

Anatomy of acetylcholinesterase catalysis: reaction dynamics analogy for human erythrocyte and electric eel enzymes

The anatomy of catalysis (i.e., reaction dynamics, thermodynamics and transition state structures) is compared herein for acetylcholinesterases from human erythrocytes and Electrophorus electricus. The two enzymes have similar relative activities for the substrate o-nitrochloroacetanilide and o-nitrophenyl acetate. In addition, with each substrate K values and solvent deuterium kinetic isotope effects for kES and kE are similar for the two enzymes. Solvent isotope effects in mixed isotopic buffers indicate that the acylation stages of o-nitrochloroacetanilide turnover by the two enzymes are rate-limited by virtual transition states that are weighted averages of contributions from transition states of serial chemical and physical steps. Similar experiments show that the transition states for Vmax of o-nitrophenyl acetate turnover by the two enzymes are stabilized by simple general acid-base (i.e., one-proton) catalysis. These comparisons demonstrate that acetylcholinesterases from diverse sources display functional analogy in that reaction dynamics and transition state structures are closely similar.     

Homology between two EBV early genes and HSV ribonucleotide reductase and 38K genes.

Computer-matching of amino acid sequences predicted from the complete EBV DNA sequence against the known HSV gene sequences has revealed significant homology between two EBV reading frames and the HSV1 and HSV2 140K and 38K proteins which are associated with ribonucleotide reductase activity. The two genes are arranged tandemly as in HSV though it appears that, unlike HSV, the two mRNAs are not 3' co-terminal. We have mapped two promoters predicted from the DNA sequence for these genes and shown them to be transcribed at a similar stage in the virus life cycle to that of the HSV genes.     

台闽苣苔（苦苣苔科）花部器官的形态发生

在扫描电镜下对台闽苣苔 (T .oldhamii (Hemsl.)Solereder)进行了花部器官形态发生的观察 ,为探索该类群的个体发育、类群间的系统发育关系和进化趋势提供依据。研究发现该属植物萼片、花冠和雄蕊发生式样均为五数花类型 ,它们各自来源于花原基上分化出来的萼片原基、花冠原基和雄蕊原基 ;花冠与雄蕊的两侧对称性与花冠上唇生长稍快和退化雄蕊原基发育迟滞相关 ;萼片原基的发生和发育的顺序是不一致的 :萼片原基发生的式样为近轴中原基—远轴 2原基— 2侧原基 ,发育式样则为近轴中萼片— 2侧萼片—远轴 2萼片 ,花蕾时为镊合状排列。花冠裂片原基的发生和发育式样是一致的 ,即远轴中裂原基 (下唇中裂片 )—远轴 2侧裂原基 (下唇 2侧裂片 )—近轴 2裂原基 (上唇 2裂片 )。花蕾期卷迭式为覆瓦状排列 ,从外向内 :下唇中裂片—下唇 2侧裂片—上唇 2裂片或下唇 2侧裂片—上唇 2裂片—下唇中裂片。雄蕊原基与花冠裂片原基互生 ,前方雄蕊原基在发生上稍迟于后方雄蕊原基 ,后者与退化雄蕊原基几乎同时发生 ,但较小 ,并与近轴心皮 (或柱头上唇 )对生。将该属与玄参科 (Scrophulari aceae)的地黄属 (Rehmannia)、苦苣苔科 (Gesneriaceae)的异叶苣苔属 (Whytockia)和尖舌苣苔属 (Rhynchoglossum)的花部器官比较发现     

Evidence for interactions between batrachotoxin-modified channels in hybrid neuroblastoma cells.

Current records from voltage-clamped membrane patches containing two batrachotoxin-modified sodium channels were analyzed to determine whether these channels are identical and independent. In most two-channel patches, the experimentally observed probabilities that zero, one, or two channels are open differ from the binomial distribution, demonstrating that the two channels are nonidentical or nonindependent or both. From the same current records, we also determined the rate for the transition from two open channels to one open channel and for the transition from one open channel to zero open channels. These data are consistent with closing rates for the two channels that are equal and independent. Both probability and closing rate data can be fit by a model wherein the channels are identical, the closing rates are independent, and the opening rate is greater when the other channel is closed than when it is open. The implications of this model for analyzing noise spectra and current variance are examined.     

Relatedness of penicillin-binding protein 1a genes from different clones of penicillin-resistant Streptococcus pneumoniae isolated in South Africa and Spain.

Penicillin-resistant strains of Streptococcus pneumoniae have been common in South Africa and Spain for several years. Multilocus enzyme electrophoresis identified one clone of capsular type 6B which was prevalent in Spain and another clone of type 23F that was present in both countries. Genes for penicillin-binding proteins (PBPs) in penicillin-resistant strains are often mosaics where parts of the pneumococcal genes are replaced by homologous genes from other species. We have compared the mosaic structures of the PBP 1a genes from the two clones as well as from genetically distinct South African isolates. Four classes of mosaic PBP 1a genes were found that contained blocks of sequences divergent by 6-22% from those of sensitive genes; two classes contained sequences coming from more than one external source. Data are presented showing that the PBP 1a genes from the 23F and the 6B clone are related, and that the two PBP 1a genes from the South African isolates are also related. We suggest that the type 23F clone originated in Spain prior to distribution into other continents.     

Comparative analysis of the Arabidopsis and rice expressed sequence tag (EST) sets

Large numbers of expressed sequence tags (ESTs) have now been generated from a variety of model organisms. In plants, substantial collections of ESTs are available for Arabidopsis and rice, in each case representing significant proportions of the estimated total numbers of genes. Large-scale comparisons of Arabidopsis and rice sequences are especially interesting due to the fact that these two species are representatives of the two subclasses of the flowering plants (Dicotyledonae and Monocotyledonae, respectively). Here we present the results of systematic analysis of the Arabidopsis and rice EST sets. Non-redundant sets of sequences from Arabidopsis and rice were first separately derived and then combined so that gene families in common between the two species could be identified. Our results show that 58% of non-singleton ESTs are derived from genes in gene families common to the two species. These gene families constitute the basis of a core set of higher plant genes.     

两类木蹄层孔菌在酶蛋白水平上的遗传分化

木蹄层孔菌（Ｆｊｏｍｅｓ　ｆｏｍｅｎｔａｒｉｕｓ）在中国东北和日本存在子实体形态不同、寄主范围明显有别的两个类型：小型和大型。用多位点分析方法研究了两者间的遗传分化状况。从两类４１个菌株的４种酶系统中检测出９个基因位点,其中８个位点上的绝大多数酶谱型都不为两者所共有,显示两个类型间的基因交流已极少发生。根据酶谱型频率得出两者间的遗传距离Ｄ＝０．９６５,属于典型的种间遗传分化。上述酶基因分化证据结合子实体形态的显著差异,提示两类木蹄层孔菌是各自独立的种。两个类型的群体在遗传多样性参数上无显著差异,可能暗示两者在起源演化上的同步性。酯酶系统有２个位点上的酶谱为不同类型所特有且稳定而清晰,可作为分子标记用于两类木蹄层孔菌的无子实体鉴定。