Genetic relationship among several pig populations in East Asia analysed by blood groups and serum protein polymorphisms

The gene frequencies were calculated to investigate genetic variation apparent in blood group and serum protein systems in Asian native pigs. The results revealed that gene frequencies were generally similar in the nine pig populations, except in some systems. Differences of gene frequencies were recognized in HpY and Cpc detected on Taoyuan pigs of Taiwan and Ohmini pigs of Japan, respectively. TfC and AmC alleles were found in eight pig populations except Ohmini pigs. The overall genetic distances were calculated by gene frequencies of 13 loci and it was observed that Taoyuan pigs are closer to Ohmini pigs than to Short-ear pigs of Taiwan and other East Asian native pigs. However, the genetic distances between Asian native pigs and European or American breeds were larger than those among East Asian native pig populations.     

Genetic relationship among several pig populations in East Asia analysed by blood groups and serum protein polymorphisrns

The gene frequencies were calculated to investigate genetic variation apparent in blood group and serum protein systems in Asian native pigs. The results revealed that gene frequencies were generally similar in the nine pig populations, except in some systems. Differences of gene frequencies were recognized in Hp^Y and Cp^c detected on Taoyuan pigs of Taiwan and Ohmini pigs of Japan, respectively. Tf^C and Am^C alleles were found in eight pig populations except Ohmini pigs.
The overall genetic distances were calculated by gene frequencies of 13 loci and it was observed that Taoyuan pigs are closer to Ohmini pigs than to Short-ear pigs of Taiwan and other East Asian native pigs. However, the genetic distances between Asian native pigs and European or American breeds were larger than those among East Asian native pig populations.     

Polyploidy, alien species and invasiveness in Polish angiosperms

Chromosome numbers, mainly for Polish flora, were examined in order to investigate whether such features as chromosome numbers and polyploid frequencies are correlated with a plant’s origin (native vs. alien) and invasiveness. Polyploid frequencies were estimated using three methods: the 11 and 14 thresholds and the 3.5 x value. Comparisons of the 2n values were done on different levels: in all angiosperms and in dicots and monocots separately. Invasive and non-invasive plants were compared in the entire dataset and in alien species only. Significant differences in both chromosome numbers and polyploid frequencies between alien and native species were observed. In most cases, native plants had more chromosomes and were more abundant in polyploids than in alien species. Also, monocots had higher polyploid frequencies than dicots. Comparisons of invasive and non-invasive plants done for all of the data and only for alien species showed that invasive species generally had more chromosomes and polyploids were more frequent in them than in the latter group; however, these differences were not always statistically significant. Possible explanations for these observations are discussed.     

How well can we predict native contacts in proteins based on decoy structures and their energies?

One strategy for ab initio protein structure prediction is to generate a large number of possible structures (decoys) and select the most fitting ones based on a scoring or free energy function. The conformational space of a protein is huge, and chances are rare that any heuristically generated structure will directly fall in the neighborhood of the native structure. It is desirable that, instead of being thrown away, the unfitting decoy structures can provide insights into native structures so prediction can be made progressively. First, we demonstrate that a recently parameterized physics-based effective free energy function based on the GROMOS96 force field and a generalized Born/surface area solvent model is, as several other physics-based and knowledge-based models, capable of distinguishing native structures from decoy structures for a number of widely used decoy databases. Second, we observe a substantial increase in correlations of the effective free energies with the degree of similarity between the decoys and the native structure, if the similarity is measured by the content of native inter-residue contacts in a decoy structure rather than its root-mean-square deviation from the native structure. Finally, we investigate the possibility of predicting native contacts based on the frequency of occurrence of contacts in decoy structures. For most proteins contained in the decoy databases, a meaningful amount of native contacts can be predicted based on plain frequencies of occurrence at a relatively high level of accuracy. Relative to using plain frequencies, overwhelming improvements in sensitivity of the predictions are observed for the 4_state_reduced decoy sets by applying energy-dependent weighting of decoy structures in determining the frequency. There, approximately 80% native contacts can be predicted at an accuracy of approximately 80% using energy-weighted frequencies. The sensitivity of the plain frequency approach is much lower (20% to 40%). Such improvements are, however, not observed for the other decoy databases. The rationalization and implications of the results are discussed.     

Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host

Synonymous codon replacement can change protein structure and function, indicating that protein structure depends on DNA sequence. During heterologous protein expression, low expression or formation of insoluble aggregates may be attributable to differences in synonymous codon usage between expression and natural hosts. This discordance may be particularly important during translation of the domain boundaries (link/end segments) that separate elements of higher ordered structure. Within such regions, ribosomal progression slows as the ribosome encounters clusters of infrequently used codons that preferentially encode a subset of amino acids. To replicate the modulation of such localized translation rates during heterologous expression, we used known relationships between codon usage frequencies and secondary protein structure to develop an algorithm ("codon harmonization") for identifying regions of slowly translated mRNA that are putatively associated with link/end segments. It then recommends synonymous replacement codons having usage frequencies in the heterologous expression host that are less than or equal to the usage frequencies of native codons in the native expression host. For protein regions other than these putative link/end segments, it recommends synonymous substitutions with codons having usage frequencies matched as nearly as possible to the native expression system. Previous application of this algorithm facilitated E. coli expression, manufacture and testing of two Plasmodium falciparum vaccine candidates. Here we describe the algorithm in detail and apply it to E. coli expression of three additional P. falciparum proteins. Expression of the "recoded" genes exceeded that of the native genes by 4- to 1,000-fold, representing levels suitable for vaccine manufacture. The proteins were soluble and reacted with a variety of functional conformation-specific mAbs suggesting that they were folded properly and had assumed native conformation. Codon harmonization may further provide a general strategy for improving the expression of soluble functional proteins during heterologous expression in hosts other than E. coli.     

Biological invasions and the acoustic niche: the effect of bullfrog calls on the acoustic signals of white-banded tree frogs

Invasive species are known to affect native species in a variety of ways, but the effect of acoustic invaders has not been examined previously. We simulated an invasion of the acoustic niche by exposing calling native male white-banded tree frogs (Hypsiboas albomarginatus) to recorded invasive American bullfrog (Lithobates catesbeianus) calls. In response, tree frogs immediately shifted calls to significantly higher frequencies. In the post-stimulus period, they continued to use higher frequencies while also decreasing signal duration. Acoustic signals are the primary basis of mate selection in many anurans, suggesting that such changes could negatively affect the reproductive success of native species. The effects of bullfrog vocalizations on acoustic communities are expected to be especially severe due to their broad frequency band, which masks the calls of multiple species simultaneously.     

Dietary characterization of the endangered salt marsh harvest mouse and sympatric rodents using DNA metabarcoding

The salt marsh harvest mouse (Reithrodontomys raviventris; RERA) is an endangered species endemic to the coastal wetlands of the San Francisco Estuary, California. RERA are specialized to saline coastal wetlands, and their historical range has been severely impacted by landscape conversion and the introduction of non‐native plant and rodent species. A better understanding of their diet is needed to assess habitat quality, particularly in relation to potential competitors. We investigated three questions using DNA metabarcoding with ITS2 and trnL markers: (1) Do RERA specialize on the native plant, pickleweed (Salicornia pacifica), (2) Do RERA consume non‐native plants, and (3) What is the dietary niche breadth and overlap with three sympatric native and non‐native rodents? RERA diet was dominated by two plants, native Salicornia and non‐native salt bush (Atriplex spp.), but included 48 plant genera. RERA diet breadth was narrowest in fall, when they consumed the highest frequencies of Salicornia and Atriplex, and broadest in spring, when the frequencies of these two plants were lowest. Diet breadth was slightly lower for RERA than for co‐occurring species in pairwise comparisons. All four species consumed similarly high frequencies of wetland plants, but RERA consumed fewer grasses and upland plants, suggesting that it may be less suited to fragmented habitat than sympatric rodents. Diet overlap was lowest between RERA and the native California vole (Microtis californicus). In contrast, RERA diet overlapped substantially with the native western harvest mouse (R. megalotis) and non‐native house mouse (Mus musculus), suggesting potential for competition if these species become sufficiently abundant.     

Information EHF-interactions in a system of live objects (human platelets)

The molecular informational interaction has been first detected in a system that involves human platelets, exposed to electromagnetic EHF-fluctuations at frequencies of molecular spectra of radiation and absorption of nitric oxide (150.176-150.644 HHz), and native platelets. It has been established that the incubation of a native platelet rich plasma with a similar plasma, exposed to a 5-minute effect of electromagnetic EHF-fluctuations at frequencies of molecular spectra of radiation and absorption of nitric oxide at a mode of peak and frequent modulation of a signal under in vitro conditions, causes a significant (P < 0.05) inhibition of platelet functional activity in the native plasma, in comparison with control. This was displayed by a decreased platelet activation and falling platelet aggregation ability. Some possible mechanisms of interaction are suggested to explain the described effect.     

Nanosecond transient resonance Raman spectra of the FeII-CO and FeIII-NO photolysis products of horseradish peroxidase

Resonance Raman spectra, obtained with 7 ns pulsed laser excitation, are reported for the photoproducts of the FeII-CO and FeIII-NO adducts of horseradish peroxidase. The porphyrin skeletal frequencies are the same as those observed for unligated FeII and FeIII (native) horseradish peroxidase, respectively. The absence of unrelaxed spectra is discussed in relation to the photoproduct frequency shifts and relaxations observed previously for hemoglobin. It is proposed that protein conformational changes which are likely to be associated with the hydrogen-bonding interactions in the horseradish peroxidase heme pocket may not produce detectable changes in the porphyrin skeletal mode frequencies.     

Characterization of the glyceraldehyde-3-phosphate dehydrogenase gene [correction of glyceraldehyde-3-phosphate gene] and the use of its promoter for heterologous expression in Cryptococcus neoformans, a human pathogen.

The GPD gene encoding glyceraldehyde-3-phosphate dehydrogenase was isolated from Cryptococcus neoformans, a heterobasidiomycetous yeast that is pathogenic to humans. The gene contains 11 introns, differing from the conserved intron positions found in the GPD genes of Basidiomycetes. The predicted amino-acid sequence of this gene is extremely similar to that reported from GPD proteins of other basidiomycetes. The promoter region of the C. neoformans GPD gene was similar to those of other basidiomycetes. Plasmid constructs containing up to 1600 base pairs upstream of the native GPD open reading frame were used to express either the native URA5 gene in a ura5 mutant or the heterologous hphI gene (a bacterial gene that confers resistance to the aminoglycoside hygromycin) in a wild-type strain of C. neoformans. Transformation frequencies resulting from the plasmid-borne Gpdp::URA5 gene were at levels similar to those of the native URA5, which suggested that all the sequences necessary for proper expression were present. Transformation frequencies using the Gpdp::hphI gene constructs were poor. However, addition of DNA sequences flanking the 3'-end of an native C. neoformans gene significantly improved the transformation frequencies resulting from the expression of the heterologous hphI gene.     

Site‐specific responses of native and exotic species to disturbances in a mesic grassland community

Abstract. Grassland communities are increasingly recognized as disturbance‐dependent ecosystems, yet there are few replicated, multi‐site studies documenting vegetation responses to varying frequencies and types of grassland disturbance. Even so, land managers frequently manipulate disturbance regimes in an attempt to favour native grassland plants over exotic species. We conducted a factorial experiment testing three frequencies of clipping combined with litter accumulation, litter removal, and soil disturbance within the highly threatened California coastal prairie plant community. We monitored the response of native/exotic, grass/forb plant guilds once a year for four years. More frequent clipping reduced cover of exotic grasses and favoured exotic forbs, whereas native species were largely unaffected by clipping frequency. Litter accumulation, litter removal, and soil disturbance did not affect vegetation composition. Effects of litter accumulation may take longer than our experiment allowed, and soil disturbance due to our treatments was not sufficiently strong to show consistent effects relative to mammalian soil disturbance. Treatment response of some plant guilds differed among sites, highlighting the importance of replicating experiments at several sites before recommending conservation management practices.     

Invasion of the acoustic niche: variable responses by native species to invasive American bullfrog calls

Biological invasions are a major threat to biodiversity. Invasive species that use acoustic communication can affect native species through interference in the acoustic niche. The American Bullfrog Lithobates catesbeianus is a highly invasive anuran that is widely distributed in the Brazilian Atlantic Rainforest. Adult male bullfrogs emit loud advertisement calls at frequencies that overlap with the calls of several native species of frogs. Given that spectral overlap is a major factor in acoustic masking, the purpose of this study was to test the effects of the acoustic invasion of L. catesbeianus on native frogs that have calls with and without spectral overlap with the invader. In field experiments, we exposed calling males of two overlapping species and two non-overlapping species to recorded bullfrog vocalizations, white noise, and the vocalization of another native frog species. To identify effects, we compared calls recorded before, during, and after exposure. Our results showed that native species altered their calls in response to the bullfrog calls. However, we also observed similar responses to white noise and heterospecific native calls. Both the invasive and heterospecific calls were emitted at low frequencies, which suggests that the observed responses might be specific to low-frequency calls. Our results provide evidence that the introduction of new sounds can cause native species to modify their calls, and that responses to exogenous sounds are species- and stimulus-specific.     

Immunoglobulin (GM and KM) allotypes and relation to population history in native peoples of British Columbia: Haida and Bella Coola

Differences in the frequencies of GM haplotypes among native peoples of the Americas support the hypothesis that there were three distinct waves of migration from northeast Asia into the Americas: Paleo-Indian, Na-Dene, and Inuit (Eskimo)-Aleut (Salzano and Steinberg: Am. J. Hum. Genet. 17:273-279, 1965; Sukernik and Osipova: Hum. Genet. 61:148-153, 1982; Williams et al.:Am. J. Phys. Anthropol. 66:1-19, 1985; Szathmary: In R Kirk and E Szathmary (eds): Out of Asia: Peopling of the Americas and the Pacific. Canberra: The Journal of Pacific History, Canberra Australian National University, pp. 79-104, 1985). We studied GM allotypes in two linguistically unique populations of Canadian west coast native peoples, the Haida and the Bella Coola, and compared them to GM frequencies in populations that are supposed descendants of the three migrations, in order to investigate the possible genetic relationships of these British Columbia (BC) groups to other native populations. We also estimated the amount of European admixture from the frequency of the Caucasian haplotype, Gm3;5. Results showed that the frequencies in both BC populations of the three common native haplotypes (Gm1,17;21, Gm1,2,17;21, and Gm1,17;15,16), were intermediate between the frequencies in supposed descendants of Paleo-Indian and Na-Dene. These genetic findings are consistent with the controversial hypothesis of archeologist C. Borden (Science 203:963-971, 1979) that, following deglaciation about 13,000 years ago, British Columbia was repopulated by peoples from the north (?Na-Dene) and by culturally distinct peoples from the south (?Paleo-Indian). Caucasian admixture estimates suggested that the Haida and Bella Coola have also experienced moderate amounts (12-20%) of genetic input from European-originating peoples.(ABSTRACT TRUNCATED AT 250 WORDS)     

鸡的血型研究 Ⅹ.我国11个地方鸡种的血型和血浆蛋白质多态分析

对我国11个地方鸡种1087羽鸡群进行了血型和血浆蛋白质多态7个位点22个等位基因的群体遗传学分析。结果表明,血型A、C位点,基因频率各鸡种存在显著差异,B位点则没有显著差异,血型和血浆蛋白质多态位点基因纯合系数普遍较低,血型因子分布在群体中较为分散,表明这些地方品种存在较大的选择潜力。血浆蛋白质多态位点,中国与外国的某些鸡种比较,存在着较大的相同或相异,可能意味着我国和外国鸡种起源上的同缘或品种起源、进化上的多样性。聚类分析表明,这11个地方鸡种可系统聚类成4个类群,其结果与目前人们对这些鸡种的表征分类不尽一致。     

Positive frequency dependence undermines the success of restoration using historical disturbance regimes

Anthropogenic alterations of historical disturbance regimes (e.g. suppressing floods and wildfires) is a primary mechanism by which exotic species can come to dominate native communities. Unfortunately, reinstating historical disturbance regimes to restore native communities has achieved mixed success. The presence of positive frequency dependence (PFD) is commonly invoked to explain why exotic plant invasions are so difficult to eradicate. However, models examining PFD have not considered the effect of reintroducing disturbances. Using a spatially explicit individual‐based model, we consider how magnitude and direction of frequency dependence of native and exotic species affects the success of reintroducing disturbances that favour fitness of natives over exotics. Our model illustrates why restoration is difficult; there is a narrow range of parameters that allows for native species to eliminate or coexist with exotics once they have established. Dominance by exotic invaders occurs with moderate initial frequencies of exotic individuals, aggregation of these individuals, or an exotic propagule production advantage. Reintroducing disturbances allows native dominance only when PFD of the exotic is weaker than that of the native species, disturbance intervals are short, and/or exotics are not initially frequent. Our framework provides guidelines for conditions in which the reintroduction of disturbances will effectively restore invaded habitats.     

Population genetics of taiga hunters-deer breeders. Characteristics of the prevalence of HLA system markers among the native population of Central Siberia

The postulated peculiarities of distribution of the HLA antigens in the Evenk population of the Central Siberia indicate this population to be, on the whole, Mongoloid. Prolonged isolated existence of small inbred populations of the Evenks resulted in the number of specific HLA-complex features, such as poor antigen diversity, low level of heterozygosity. Non-homogeneity of gene frequencies was noted, the prevailing genes being A9, B40 with frequencies reaching 50%. Of the remaining alleles found in the Evenks A2, Aw19 in A locus, B5, B15, B17, B27, Bw35 in B locus and Cw2, Cw3, Cw4-in C locus are only widely spread. Similar heterozygosis levels and the HLA-system profiles draw the Evenks and the populations of American Indians and Eskimos closer to one another. On the basis of the fact that significant positive correlation exists between genetic and geographic distances determined for the Evenks and the native populations of America, genetic resemblance of these populations may be considered as evidence for their original relationship. Postulated closeness of native Central-Siberian populations to Americanoids, as regards HLA-system, makes it possible to consider formation of specific complex of HLA-system peculiarities in native American population in the light of their Siberian origin, for the first time.     

A study of interactions of carbonic anhydrase B with water and urea. I. Spin-diffusion parameters that determine individual and cooperative properties of molecules

The rigidity parameter (G), which is characteristic of protein compactness, was studied in native globular carbonic anhydrase B. The dependence of parameter G on power and excitation time of spin-diffusion was expressed analytically. We found out that native carbonic anhydrase B is able to form water-protein units that are probabilistically distributed with respect to their sizes. Large water-protein units can be detected by analyzing the spin-diffusion spectra. The excitation frequencies of spin-diffusion spectra were shifted far away from typical 1H NMR spectra of carbonic anhydrase B.     

Primers for 12 polymorphic microsatellite DNA loci from the guppy (Poecilia reticulata)

Twelve polymorphic microsatellite DNA loci were isolated from genomic guppy DNA. We assessed the level of genetic diversity for these loci using individuals from five native Trinidadian populations. All the loci were polymorphic although there were considerable differences among loci and populations in allele frequencies. Within populations, the number of alleles ranged from 1 to 22 and observed heterozygosities ranged from 0.000 to 0.990. Allele frequencies differed substantially between populations suggesting divergence.     

Association of neuropeptide Y and gonadotrophin-releasing hormone receptor gene SNPs with breeding value for growth and egg production traits in Mazandaran native chickens

Neuropeptide Y (NPY) and gonadotrophin-releasing hormone receptor (GnRHR) are two candidate genes with a wide variety of physiological functions in growth and especially in reproduction processes. We examined the association of one SNP from each of these genes with growth- and egg production-related traits in Mazandaran native chickens. Two hundred and six individuals were genotyped by PCR-RFLP. Marker-trait association analyses were performed using both breeding value and phenotypic information. The data came from 18 successive generations of selection at a Mazandaran native chicken breeding station in Iran. Data were analyzed with a univariate animal model in an ASREML procedure to estimate breeding values of the birds for these traits. Two alleles were found for both genes, A and a alleles for GnRHR, with frequencies of 0.614 and 0.386, B and b alleles for NPY, with frequencies of 0.780 and 0.221, respectively. The additive genetic effects of the GnRHR gene on egg number and egg mass were significant. Also, body weight at sexual maturity was significantly influenced by the NPY gene. We conclude that GnRHR and NPY genes are associated with egg production and growth traits, respectively.