DOES LINKAGE DISEQUILIBRIUM GENERATE HETEROZYGOSITY‐FITNESS CORRELATIONS IN GREAT REED WARBLERS?

Heterozygosity-fitness correlations (HFCs) at noncoding genetic markers are commonly assumed to reflect fitness effects of heterozygosity at genomewide distributed genes in partially inbred populations. However, in populations with much linkage disequilibrium (LD), HFCs may arise also as a consequence of selection on fitness loci in the local chromosomal vicinity of the markers. Recent data suggest that relatively high levels of LD may prevail in many ecological situations. Consequently, LD may be an important factor, together with partial inbreeding, in causing HFCs in natural populations. In the present study, we evaluate whether LD can generate HFCs in a small and newly founded population of great reed warblers (Acrocephalus arundinaceus). For this purpose dyads of full siblings of which only one individual survived to adult age (i.e., returned to breed at the study area) were scored at 19 microsatellite loci, and at a gene region of hypothesized importance for survival, the major histocompatibility complex (MHC). By examining siblings, we controlled for variation in the inbreeding coefficient and thus excluded genome-wide fitness effects in our analyses. We found that recruited individuals had significantly higher multilocus heterozygosity (MLH), and mean d2 (a microsatellite-specific variable), than their nonrecruited siblings. There was a tendency for the survivors to have a more diverse MHC than the nonsurvivors. Single-locus analyses showed that the strength of the genotype-survival association was especially pronounced at four microsatellite loci. By using genotype data from the entire breeding population, we detected significant LD between five of 162 pairs of microsatellite loci after accounting for multiple tests. Our present finding of a significant within-family multilocus heterozygosity-survival association in a nonequilibrium population supports the view that LD generates HFCs in natural populations.     

Fecundity and MHC affects ejaculation tactics and paternity bias in sand lizards

We demonstrate that extending copulation enhances probability of paternity in sand lizards and that determinants of copulation duration depend on a males' mating order (first or second). First males, with no information on presence of rivals, extend copulation when mating with a more fecund female. Second males, however, adjust copula duration in relation to a first male's relatedness with his female, which there is reason to believe can be deduced from the MHC-related odor of the copulatory plug. Male-female relatedness negatively influences a male's probability of paternity, and when second males are in a favored role (i.e., the first male is the one more closely related to the female), second males transfer larger ejaculates, resulting in higher probability of paternity. This result corroborates predictions from recent theoretical models on sperm expenditure theory incorporating cryptic female choice and sexual conflict. More specifically, the results conform to a "random roles" model, which depicts males as being favored by some females and disfavored by others, but not to a "constant-type" model, in which a male is either favored or disfavored uniformly by all females in a population.     

鸡MD基因5'侧翼区多态性与鸡生长和体组成性状的相关研究

苹果酸脱氢酶(Malate Dehydrogenase,MD)是一种氧化还原性酶,参与体内多种能量代谢反应.它可以催化苹果酸氧化脱羧生成丙酮酸和CO2,并使NADP+还原成NADPH,NADPH是脂肪酸合成所必需的载体,棕榈酸可以利用生成的NADPH来合成长链脂肪酸,MD的活性与脂肪酸合成效率之间存在密切的相关,MD也参与体内骨骼肌、心肌的能量代谢,并对肌纤维的生长有一定的调节作用.根据鸡MD基因的5侧翼区序列设计一对引物,用直接测序的方法在侧翼区检测多态性位点,在235bp(GenBank登录号U49693)处发现一个SNP位点,此位点是一个限制性内切酶(SphⅠ酶)发生变化的位点.以东北农业大学高低脂双向选择系的第8世代肉鸡和东农F2资源群体为实验材料,用PCR-RFLP的方法进行基因型分析,建立适合的统计模型,进行基因型与生长和体组成性状的相关分析.结果表明在高低脂系第8世代肉鸡中AA基因型个体的腹脂重和腹脂率显著高于BB基因型个体(P＜0.05);BB基因型个体的大胸肌重和大胸肌率显著高于AA基因型个体(P＜0.05).在东农F2资源家系中BB基因型个体的大胸肌重和大胸肌率显著高于AA和AB基因型个体(P＜0.05);AA基因型个体的肝脏重和肝脏率显著高于BB基因型个体(P＜0.05).综上所述,MD基因可能是影响鸡生长和体组成性状的主效基因或与控制生长和体组成性状的主效基因相连锁.     

Segregation Analysis on Genetic System of Quantitative Traits in Plants

Based on the traditional polygene inheritance model of quantitative traits,the author suggests the major gene and polygene mixed inheritance model.The model was considered as a general one,while the pure major gene and pure polygene inheritance model was a specific case of the general model.Based on the proposed theory,the author established the segregation analysis procedure to study the genetic system of quantitative traits of plants.At present,this procedure can be used to evaluate the genetic effect of individual major genes (up to two to three major genes),the collective genetic effect of polygene,and their heritability value.This paper introduces how to establish the procedure,its main achievements,and its applications.An example is given to illustrate the steps,methods,and effectiveness of the procedure.     

Major histocompatibility complex polymorphism: dynamics and consequences of parasite-mediated local adaptation in fishes

Parasitism is a common form of life and represents a strong selective pressure for host organisms. In response to this evolutionary pressure, vertebrates have developed genetically coded defences such as the major histocompatibility complex (MHC). Mechanisms of parasite-mediated selection not only maintain outstanding polymorphism in these genes but have also been proposed to further promote host population divergence and ultimately speciation because it can drive evolution of local adaptation in which MHC genes play a crucial role. This review first highlights the dynamics and complexity of parasite-mediated selection in natural systems, which not only depends on dominating parasite strategies and on the taxonomic diversity of the parasite community but also includes the differences in parasite communities between habitats and niches, creating divergent selection on locally adapted populations. Then the different ways in which MHC genes potentially allow vertebrates to respond to these dynamics and to adapt locally are outlined. Finally, it is proposed that varying selection strength in time and space may lead to variation in the strength of precopulatory reproductive isolation which has evolved to maintain local adaptation.     

Optimal Packaging of FIV Genomic RNA Depends upon a Conserved Long-range Interaction and a Palindromic Sequence within gag

The feline immunodeficiency virus (FIV) is a lentivirus that is related to human immunodeficiency virus (HIV), causing a similar pathology in cats. It is a potential small animal model for AIDS and the FIV-based vectors are also being pursued for human gene therapy. Previous studies have mapped the FIV packaging signal (ψ) to two or more discontinuous regions within the 5′ 511 nt of the genomic RNA and structural analyses have determined its secondary structure. The 5′ and 3′ sequences within ψ region interact through extensive long-range interactions (LRIs), including a conserved heptanucleotide interaction between R/U5 and gag. Other secondary structural elements identified include a conserved 150 nt stem-loop (SL2) and a small palindromic stem-loop within gag open reading frame that might act as a viral dimerization initiation site. We have performed extensive mutational analysis of these sequences and structures and ascertained their importance in FIV packaging using a trans-complementation assay. Disrupting the conserved heptanucleotide LRI to prevent base pairing between R/U5 and gag reduced packaging by 2.8-5.5 fold. Restoration of pairing using an alternative, non-wild type (wt) LRI sequence restored RNA packaging and propagation to wt levels, suggesting that it is the structure of the LRI, rather than its sequence, that is important for FIV packaging. Disrupting the palindrome within gag reduced packaging by 1.5-3-fold, but substitution with a different palindromic sequence did not restore packaging completely, suggesting that the sequence of this region as well as its palindromic nature is important. Mutation of individual regions of SL2 did not have a pronounced effect on FIV packaging, suggesting that either it is the structure of SL2 as a whole that is necessary for optimal packaging, or that there is redundancy within this structure. The mutational analysis presented here has further validated the previously predicted RNA secondary structure of FIV ψ.     

Crystal structure of Leishmania major oligopeptidase B gives insight into the enzymatic properties of a trypanosomatid virulence factor

Oligopeptidase B (OPB) is a serine peptidase with dibasic substrate specificity. It is found in bacteria, plants, and trypanosomatid pathogens, where it has been identified as a virulence factor and potential drug target. In this study we expressed active recombinant Leishmania major OPB and provide the first structure of an oligopeptidase B at high resolution. The crystallographic study reveals that OPB comprises two domains, a catalytic and a propeller domain, linked together by a hinge region. The structure has been determined in complex with the oligopeptide, protease-inhibitor antipain, giving detailed information on the enzyme active site and extended substrate binding pockets. It shows that Glu-621 plays a critical role in the S1 binding pocket and, along with Phe-603, is largely responsible for the enzyme substrate specificity in P1. In the S2 binding pocket, Tyr-499 was shown to be important for substrate stability. The structure also allowed an investigation into the function of residues highlighted in other studies including Glu-623, which was predicted to be involved in the S1 binding pocket but is found forming an inter-domain hydrogen bond. Additional important salt bridges/hydrogen bonds between the two domains were observed, highlighting the significance of the domain interface in OPB. This work provides a foundation for the study of the role of OPBs as virulence factors in trypanosomatids. It could facilitate the development of specific OPB inhibitors with therapeutic potential by exploiting its unique substrate recognition properties as well as providing a model for OPBs in general.     

Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes

Since determining the crystallographic structure of all peptide-MHC complexes is infeasible, an accurate prediction of the conformation is a critical computational problem. These models can be useful for determining binding energetics, predicting the structures of specific ternary complexes with T-cell receptors, and designing new molecules interacting with these complexes. The main difficulties are (1) adequate sampling of the large number of conformational degrees of freedom for the flexible peptide, (2) predicting subtle changes in the MHC interface geometry upon binding, and (3) building models for numerous MHC allotypes without known structures. Whereas previous studies have approached the sampling problem by dividing the conformational variables into different sets and predicting them separately, we have refined the Biased-Probability Monte Carlo docking protocol in internal coordinates to optimize a physical energy function for all peptide variables simultaneously. We also imitated the induced fit by docking into a more permissive smooth grid representation of the MHC followed by refinement and reranking using an all-atom MHC model. Our method was tested by a comparison of the results of cross-docking 14 peptides into HLA-A*0201 and 9 peptides into H-2K(b) as well as docking peptides into homology models for five different HLA allotypes with a comprehensive set of experimental structures. The surprisingly accurate prediction (0.75 A backbone RMSD) for cross-docking of a highly flexible decapeptide, dissimilar to the original bound peptide, as well as docking predictions using homology models for two allotypes with low average backbone RMSDs of less than 1.0 A illustrate the method's effectiveness. Finally, energy terms calculated using the predicted structures were combined with supervised learning on a large data set to classify peptides as either HLA-A*0201 binders or nonbinders. In contrast with sequence-based prediction methods, this model was also able to predict the binding affinity for peptides to a different MHC allotype (H-2K(b)), not used for training, with comparable prediction accuracy.     

Major histocompatibility complex class IIB allele polymorphism and its association with resistance/susceptibility to Vibrio anguillarum in Japanese flounder (Paralichthys olivaceus)

The full length of major histocompatibility complex (MHC) class IIB cDNA was cloned from a Chinese population of Paralichthys olivaceus by homology cloning and rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR). The MHC IIB genomic sequence is 1,864 bp long and consists of 34-bp 5′UTR, 741-bp open reading frame, 407-bp 3′UTR, 96-bp intron1, 392-bp intron2, 85-bp intron3, and 109-bp intron4. Phylogenetic analysis showed that the putative MHC class IIB amino acid of the Chinese P. olivaceus shared 28.3% to 85.4% identity with that of the reported MHC class IIB in other species. A significant association between MHC IIB polymorphism and disease resistance/susceptibility was found in Chinese P. olivaceus. Thirteen different MHC IIB alleles were identified among 411 clones from 84 individuals. Among the 280 (268) nucleotides, 32 (11.4%) nucleotide positions were variable. Most alleles such as alleles a, b, c, d, e, f, j, k, i, m were commonly found in both resistant and susceptible stock. Via χ² test, allele d was significantly more prevalent in individuals from susceptible stock than from resistant stock, and their percentages were 23.80% and 7.14%, respectively. In addition, allele g occurred in 9 and allele h in 4 of 42 resistant individuals that were not present in the susceptible stock; their percentages were 21.4% and 9.52%, respectively. Although allele l was found only in 8 individuals from the susceptible stock, its percentage is 19.05%.     

Contours of the hominoid lateral tibial condyle with implications for Australopithecus

Tibial condyle shape is alleged to vary among fossil tibiae attributed to Australopithecus, and has been argued to reflect functional differences of the knee. Convex anteroposterior curvature of the lateral tibial condyle in A. africanus has been interpreted to indicate a more chimpanzee-like locomotor repertoire than the flatter lateral tibial condyles of A. afarensis (Berger and Tobias, 1996, J. Hum. Evol. 30, 343). Alternatively, Latimer, Ohman, and Lovejoy (1987, Am. J. Phys. Anthropol. 74, 155) have suggested that in response to increased transarticular loads accompanied by larger body mass, joints should become flatter as size increases, both within and among species, so that the variation observed among hominin fossils reflects size alone rather than functional differences. In this study, three-dimensional surface areas of the lateral tibial condyle of humans, chimpanzees, and gorillas were computed using a Digibot II (Digibotics) laser scanner and the DataSculpt v.4.6 engineering software package to evaluate joint surface contours, and compared to two-dimensional surface area and arc and chord length measurements of the anteroposterior and mediolateral axes. Extant species measurements were then compared to those of A. afarensis (A.L. 129-1b, A.L. 288-1aq, A.L. 333x-26, A.L. 333-42) and A. africanus (Stw 514a). Results do not support the hypothesis that A. afarensis and A. africanus differ in condylar topology. They also do not support the hypothesis that joint surfaces become flatter with increased transarticular load accompanying increased body size, as curvature of the lateral tibial condyle in anteroposterior and mediolateral planes is not negatively allometric. However, femoral condylar shape is not included in this study, which may better reflect joint surface responses to increased body size. Finally, there is no basis from this study to reconstruct differences in locomotor behavior among fossil hominin taxa based on lateral tibial condyle morphology.