Assessing the effects of cognitive experiments on the welfare of captive chimpanzees (Pan troglodytes) by direct comparison of activity budget between wild and captive chimpanzees

We investigated the effects of cognitive experiments by direct comparison of activity budgets between wild and captive chimpanzees. One goal of captive management is to ensure that the activity budgets of captive animals are as similar as possible to those of their wild counterparts. However, such similarity has rarely been achieved. We compared the activity budget among three groups of chimpanzees: wild chimpanzees in Bossou (Guinea, n = 10), and captive chimpanzees who participated in cognitive experiments (experimental chimpanzees, n = 6) or did not participate in the experiments (nonexperimental chimpanzees, n = 6) at the Primate Research Institute (Japan). The experimental chimpanzees voluntarily participated in computer‐controlled cognitive tasks and small pieces of fruits were provided as rewards. The data from captivity were obtained on the experimental days (weekdays) and nonexperimental days (weekends). In both study sites, we followed each chimpanzee from about 7 a.m. until the time when chimpanzees started to rest in the evening. The behaviors were recorded every 1 min. The results showed that on weekdays, feeding time and resting time of the experimental chimpanzees were almost the same as those of wild chimpanzees. However, for the nonexperimental chimpanzees, feeding time was significantly shorter and resting time was longer than those of the wild chimpanzees. In contrast, no difference was found in feeding time or resting time of the two groups of captive chimpanzees on weekends. The results suggested that the cognitive experiments worked as an efficient method for food‐based enrichment. Am. J. Primatol. 73:1231–1238, 2011. © 2011 Wiley Periodicals, Inc.     

Phyletic relationships of protein structures based on spatial preference of residues

Summary A structure-based scoring matrix MDPRE was derived from amino acid spatial preferences in protein structures. Sequence alignment and evolutionary studies by using MDPRE matrix gave similar results as those from ordinary sequence and structure alignments. It is interesting that a matrix derived from structure data solely could give comparable alignment results, strongly indicating the intimate connection between protein sequences and structures. The branch order and length from this approach were close to those obtained by a structure comparison method. Thus, by applying this structure-based matrix, the trees obtained should reflect evolutionary characteristics of protein structure. This approach takes advantage over a direct structure comparison in that (1) only a sequence and MDPRE matrix are needed, making it simple and widely applicable (especially in the absence of 3-dimensional protein structure data); (2) an established algorithm for sequence alignment and tree building could be employed, providing opportunities for direct comparison between matrices from different methodologies. One of the most striking features of this method is its capability to detect protein structure homologies when the sequence identities are low. This was well reflected in the given examples of the alignment of dinucleotidebinding domains.     

Inter- and Intralocus Recombination Drive MHC Class IIB Gene Diversification in a Teleost, the Three-Spined Stickleback Gasterosteus aculeatus

The mutational mechanism underlying the striking diversity in MHC (major histocompatibility complex) genes in vertebrates is still controversial. In order to evaluate the role of inter- and intragenic recombination in MHC gene diversification, we examined patterns of nucleotide polymorphism across an exon/intron boundary in a sample of 31 MHC class IIB sequences of three-spined stickleback (Gasterosteus aculeatus). MHC class IIB genes of G. aculeatus were previously shown to be under diversifying (positive) selection in mate choice and pathogen selection experiments. Based on recoding of alignment gaps, complete intron 2 sequences were grouped into three clusters using maximum-parsimony analysis. Two of these groups had >90% bootstrap support and were tentatively assigned single locus status. Intron nucleotide diversity within and among loci was low (p-distance within and among groups = 0.016 and 0.019, respectively) and fourfold lower than the rate of silent mutations in exon 2, suggesting that noncoding regions are homogenized by frequent interlocus recombination. A substitution analysis using GENECONV revealed as many intergenic conversion events as intragenic ones. Recombination between loci may explain the occurrence of sequence variants that are particularly divergent, as is the case in three-spined stickleback, with nucleotide diversity attaining d_N = 0.39 (peptide-binding residues only). For both MHC class II loci we also estimated the amount of intragenic recombination as population rate (4N_er) under the coalescent and found it to be approximately three times higher compared to point mutations (Watterson estimate per gene, 4N_eμ). Nonindependence of molecular evolution across loci and frequent recombination suggest that MHC class II genes of bony fish may follow different evolutionary dynamics than those of mammals. Our finding of widespread recombination suggests that phylogenies of MHC genes should not be based on coding segments but rather on noncoding introns. [Reviewing Editor: Dr. Richard Kliman]     

The primary structure of initiation factor IF3 from Bacillus stearothermophilus

The complete amino acid sequence of the initiation factor IF3 from Bacillus stearothermophilus has been elucidated. This was achieved by splitting the protein with trypsin, Staphylococcus protease or cyanogen bromide. The amino acid sequence was determined by manual Edman degradation, using the DABITC/PITC double-coupling method. The IF3 molecule contains 171 amino acids and has an M_r of 19 677. The sequence was compared to the homologous molecule from Escherichia coli; about 50% of the amino acid residues were found to be identical.     

狂犬病病毒SRV9疫苗株糖蛋白核酸序列及抗原特性研究

狂犬病病毒SRV9株是经克隆获得的中等蚀斑口服弱毒疫苗候选株,具有安全和免疫原性较好等。本试验根据狂犬病病毒糖蛋白核苷酸5'末端和3'末端序列设计了一对引物,通过反转录－聚合酶链式反应（RT－PCR）分别扩增了SRV9及其母源株SAD B19糖蛋白的全长cDNA,测序结果表明,SRV9和SAD B19糖蛋白cDNA读框长1575bp,编码524氨基酸残基的多肽。通过和其母源株SAD B19核苷酸序列比较发现,SRV9析158,575,931位碱基分别出现了G→A,A→G和A→G的转换,相应地导致第53位,192位,311位氨基酸出现了Gly→Glu,His→Arg,Thr→Ala突变。和我国现行的和疫苗株ERA的核苷酸和氨基酸比较,有10个碱其不同,7个氨基酸发生改变。经Jameson-Wolf抗原表位优势图分析发现。SRV9在192位氨基酸的改变,导致该部位产生了一个新的潜在抗原位点。由于狂犬病病毒糖蛋白是诱导机体产生中和抗体唯一抗原,因此,上述氨基酸的改变可能与其特殊的蚀斑特性和其安全性提高有关。保持对毒株的氨基酸序列分析也是监测其特性的重要手段之一。     

景观生态学中的尺度分析方法

多尺度空间分析法是发现和识别景观特征尺度的主要方法.当前这类方法很多,缺乏归类和对比分析评价.基于空间类型变量和数值变量,对多尺度空间分析方法进行了重新梳理.同时对当前常用的尺度分析方法:半方差分析、尺度方差分析、小波分析和孔隙度指数分析,以中国三北防护林为例,对比了各种尺度分析方法的特点和优劣.结果表明,在特征尺度的识别上:小波方差方法清晰明了;半方差分析法灵活简捷,结果明显;尺度方差分析法和孔隙度指数法在本研究中的判识结果不甚明显.在计算速度上:半方差分析法计算量最大、耗时最长,尺度方差次之,小波方差速度最快,孔隙度指数法计算速度快于前两种,慢于小波方差分析方法.半方差分析方法简单灵活,而且相关理论方法成熟,但缺乏对大尺度格局的整体把握,而小波分析恰恰能很好的弥补这一不足.最后提出,半方差分析和小波变换相结合将会是最优的尺度分析方法.     

Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences: II. Four taxa without a molecular clock

Summary The statistical properties of sample estimation and bootstrap estimation of phylogenetic variability from a sample of nucleotide sequences were studied by considering model trees of three taxa with an outgroup. The cases of constant and varying rates of nucleotide substitution were compared. From sequences obtained by simulation, phylogenetic trees were constructed by using the maximum parsimony (MP) and neighbor joining (NJ) methods. The effectiveness and consistency of the MP method were studied in terms of proportions of informative sites. The results of simulation showed that bootstrap estimation of the confidence level for an inferred phylogeny can be used even under unequal rates of evolution if the rate differences are not large so that the MP method is not misleading. The condition under which the MP method becomes misleading (inconsistent) is more stringent for slowly evolving sequences than for rapidly evolving ones, and it also depends on the length of the internal branch. If the rate differences are large so that the MP method becomes consistently misleading, then bootstrap estimation will reinforce an erroneous conclusion on topology. Similar conclusions apply to the NJ method with uncorrected distances. The NJ method with corrected distances performs poorly when the sequence length is short but can avoid the inconsistency problem if the sequence length is long and if the distances can be estimated accurately.Offprint requests to: W.-H. Li     

CyberKnife versus multicatheter interstitial brachytherapy for accelerated partial breast irradiation: a dosimetrical assessment with focus on organs at risk

BackgroundThe purpose of the study was to dosimetrically compare multicatheter interstitial brachytherapy (MIBT) and stereotactic radiotherapy with CyberKnife (CK) for accelerated partial breast irradiation with special focus on dose to organs at risk (OARs).Materials and methodsTreatment plans of thirty-one patients treated with MIBT were selected and additional CK plans were created on the same CT images. The OARs included ipsilateral non-target and contralateral breast, ipsilateral and contralateral lung, skin, ribs, and heart for left sided cases. The fractionation was identical (4 × 6.25 Gy). Dose-volume parameters were calculated for both techniques and compared.ResultsThe D90 of the PTV for MIBT and CK were similar (102.4% vs. 103.6%, p = 0.0654), but in COIN the MIBT achieved lower value (0.75 vs. 0.91, p < 0.001). Regarding the V100 parameter of non-target breast CK performed slightly better than MIBT (V100: 1.1% vs. 1.6%), but for V90, V50 and V25 MIBT resulted in less dose. Every examined parameter of ipsilateral lung, skin, ribs and contralateral lung was significantly smaller for MIBT than for CK. Protection of the heart was slightly better with MIBT, but only the difference of D2cm³ was statistically significant (17.3% vs. 20.4%, p = 0.0311). There were no significant differences among the dose-volume parameters of the contralateral breast.ConclusionThe target volume can be properly irradiated by both techniques with high conformity and similar dose to the OARs. MIBT provides more advantageous plans than CK, except for dose conformity and the dosimetry of the heart and contralateral breast. More studies are needed to analyze whether these dosimetrical findings have clinical significance.     

A cDNA clone encoding the ADP/ATP translocase of Drosophila melanogaster shows a high degree of similarity with the mammalian ADP/ATP translocases

Summary A complementary DNA clone encoding the ADP/ATP translocase in Drosophila melanogaster has been identified. It has been shown by sequence analysis to contain a single open reading frame that encodes a polypeptide 297 amino acids long. This polypeptide shows extensive similarities to the known eukaryotic translocase polypeptides, the similarity being greatest (up to 80% identity) to the mammalian ADP/ATP translocases. In situ hybridization to polytene chromosomes of D. melanogaster with the sequence characterized in this study showed localization at a single site on the X chromosome at 9E. DNA transfer hybridization experiments suggest that more than one gene coding for the ADP/ATP translocase is present in the D. melanogaster genome.Offprint requests to: S.G. Tsitilou     

Structural characteristics of a novel antifreeze protein from the longhorn beetle Rhagium inquisitor

Antifreeze proteins (AFPs) are characterized by their capacity to inhibit the growth of ice and are produced by a variety of polar fish, terrestrial arthropods and other organisms inhabiting cold environments. This capacity reflects their role as stabilizers of supercooled body fluids. The longhorn beetle Rhagium inquisitor is known to express AFPs in its body fluids. In this work we report on the primary structure and structural characteristics of a 12.8 kDa AFP from this beetle (RiAFP). It has a high capacity to evoke antifreeze activity as compared to other known insect AFPs and it is structurally unique in several aspects. In contrast to the high content of disulfide bond-formation observed in other coleopteran AFPs, RiAFP contains only a single such bond. Six internal repeat segments of a thirteen residue repeat pattern is irregularly spaced apart throughout its sequence. The central part of these repeat segments is preserved as TxTxTxT, which is effectively an expansion of the TxT ice-binding motif found in the AFPs of several known insect AFPs.