Impact of simian immunodeficiency virus infection on chimpanzee population dynamics.

Like human immunodeficiency virus type 1 (HIV-1), simian immunodeficiency virus of chimpanzees (SIVcpz) can cause CD4+ T cell loss and premature death. Here, we used molecular surveillance tools and mathematical modeling to estimate the impact of SIVcpz infection on chimpanzee population dynamics. Habituated (Mitumba and Kasekela) and non-habituated (Kalande) chimpanzees were studied in Gombe National Park, Tanzania. Ape population sizes were determined from demographic records (Mitumba and Kasekela) or individual sightings and genotyping (Kalande), while SIVcpz prevalence rates were monitored using non-invasive methods. Between 2002-2009, the Mitumba and Kasekela communities experienced mean annual growth rates of 1.9% and 2.4%, respectively, while Kalande chimpanzees suffered a significant decline, with a mean growth rate of -6.5% to -7.4%, depending on population estimates. A rapid decline in Kalande was first noted in the 1990s and originally attributed to poaching and reduced food sources. However, between 2002-2009, we found a mean SIVcpz prevalence in Kalande of 46.1%, which was almost four times higher than the prevalence in Mitumba (12.7%) and Kasekela (12.1%). To explore whether SIVcpz contributed to the Kalande decline, we used empirically determined SIVcpz transmission probabilities as well as chimpanzee mortality, mating and migration data to model the effect of viral pathogenicity on chimpanzee population growth. Deterministic calculations indicated that a prevalence of greater than 3.4% would result in negative growth and eventual population extinction, even using conservative mortality estimates. However, stochastic models revealed that in representative populations, SIVcpz, and not its host species, frequently went extinct. High SIVcpz transmission probability and excess mortality reduced population persistence, while intercommunity migration often rescued infected communities, even when immigrating females had a chance of being SIVcpz infected. Together, these results suggest that the decline of the Kalande community was caused, at least in part, by high levels of SIVcpz infection. However, population extinction is not an inevitable consequence of SIVcpz infection, but depends on additional variables, such as migration, that promote survival. These findings are consistent with the uneven distribution of SIVcpz throughout central Africa and explain how chimpanzees in Gombe and elsewhere can be at equipoise with this pathogen.

Structure analysis of CCR5 from human and primates

It is well known that the chemokine receptor CCR5 plays very important roles in HIV-1 virus infection. A three-dimensional molecular model of human CCR5 was generated by SYBYL, a distance geometry-based homologous modeling package, using the corresponding transmembrane domain of bacteriorhodopsin as the template. On the basis of human CCR5 model, we also built 18 3D molecular models of CCR5 in primates from Pongo pygmaeus, Pygathrix nemaeus, Macaca assameniss, Trachy-pithecus phayrei, T. francoisi, M. arotoides, Rhinopithecus roxellance, R, bieti, R. avunculus, Hylobates leucogenys, Pan troglodytes, Gorilla gorilla, Cercopithecus aethiops 1, C. aethiops 2, Papio hamadryas M. mulatta, M. fascicularis and M. nemestrina. Structural analyses and statistics results suggested that the main-chains of the primate CCR5 were similar to that of the human CCR5 and that the fit-RMS deviation values of these primate CCR5 were less than 0.1 Angstrom. Moreover, the structures of these CCR5 proteins, except those of the African green monkey 1 (C.aet1), do not have a remarkable difference. It is proved that the 14th residue is possibly very important in the inhibition infections by M-tropic HIV-1, and it is also demonstrated that the 13th residue of human CCR5 was changed from asparagine into aspartic acid in all these primates. It means that the primate CCR5 no longer depend on CD4 for efficient entry, but human CCR5 may have evolved subsequently due to the use of CD4 as a receptor, allowing the high-affinity chemokine receptor-binding site of HIV to be sequestered from host immune surveillance. (C) 2000 Elsevier Science B.V. All rights reserved.

猕猴白化病分子机制和灵长类的分子进化研究

酪氨酸酶是黑色素合成当中的关键酶。人酪氨酸酶基因包括5个外显子，在染色体11q14-q21位置上占据了约50kb长的区域。对人类眼皮肤型白化病（Oculocutaneous albinism, OCA)的许多研究表明，该病主要是由于酪氨酸酶基因的突变引起的。昆明动物研究所白化猴研究小组数十年来一直从事白化猕猴的培育和研究工作，目前饲养着2只白化猕猴和它们的后代，这提供了我们研究猕猴白化分子机制目的条件。为了弄清猕猴白化病的分子机制，我们根据人酪氨酸酶基因序列设计了5对PCR引物扩增相应的5个外显子，序列分析表明，白化猕猴珍珍酪氨酸酶基因第184个密码子第2位置（外显子1的核苷酸位置551）处发生一个C→A的无义突变，使编码丝氨酸（Ser)的密码子变成了一个终止密码，这样后面1038bp的核苷酸片段（346个氨基酸残基）被截断，导致酪氨酸酶翻译不完全，迄今为止，并没有发现合成黑色素的第二条生化途径，因此由于该酶不能行使正常功能而将导致黑色素不能正常表达。这可能是导致该例猕猴白化病的原因。为了解酪氨酸酶基因序列变异的规律及其与功能的关系，探讨该基因作为系统发育研究中遗传标记的有效性，我们测定了黑猩猩（Pan troglodytes)、倭黑猩猩（Pan paniscus)、大猩猩（Gorilla gorilla)、猩猩(Pongo pygmaeus)、长臂猿（Hylobates lar)、食蟹猴（Macaca fascicularis)、狒狒（Simia cynocephalus)、猕猴（Macaca mulatta)、熊猴（Macaca assamensis)、菲氏叶猴（Presbytis p. crepusculus)、白臀叶猴（Pygathrix nemaeus)、滇金丝猴（Rhinopithecus r. bieti）和蛛猴（Ateles paniscus)13个灵长类中代表种的酪氨酸酶基因全部5个外显子的DNA序列。基于这些序列，用简约法构建了分子系统树。结果表明，人猿超科与旧大陆猴各自形成一单系群。人猿超科各物种和旧大陆猴有明显分化，人与大猩猩的关系比人与黑猩猩的关系近。酪氨酸酶基因在解决灵长类系统发育关系上是一个较有用的基因。为了进一步了解中国猕猴（Macaca mulatta)的亚种分化和不同地理群体间的基因流状况，我们测定了来自中云南、广西、福建、海南、浙江、河南、湖南、湖北、安徽、四川、贵州和越南猕猴共96只个体和一只外群食蟹猴的线粒体DNA控制区576bp的DNA序列，基于这些序列，运用距离法对中国恒河猴的分子进行和遗传多样性进行了分析，我们的研究结果显示，云南、四川和湖南猕猴群体与其它群体存在显著分析，海南群体内遗传多样性最低、四川、广西、浙江、福建和越南群体内遗传多样性较丰富。中国猕猴的分化可能存在三条路线。中国猕猴的遗传多样性较丰富。

Functional evolution of mammalian odorant receptors.

The mammalian odorant receptor (OR) repertoire is an attractive model to study evolution, because ORs have been subjected to rapid evolution between species, presumably caused by changes of the olfactory system to adapt to the environment. However, functional assessment of ORs in related species remains largely untested. Here we investigated the functional properties of primate and rodent ORs to determine how well evolutionary distance predicts functional characteristics. Using human and mouse ORs with previously identified ligands, we cloned 18 OR orthologs from chimpanzee and rhesus macaque and 17 mouse-rat orthologous pairs that are broadly representative of the OR repertoire. We functionally characterized the in vitro responses of ORs to a wide panel of odors and found similar ligand selectivity but dramatic differences in response magnitude. 87% of human-primate orthologs and 94% of mouse-rat orthologs showed differences in receptor potency (EC50) and/or efficacy (dynamic range) to an individual ligand. Notably dN/dS ratio, an indication of selective pressure during evolution, does not predict functional similarities between orthologs. Additionally, we found that orthologs responded to a common ligand 82% of the time, while human OR paralogs of the same subfamily responded to the common ligand only 33% of the time. Our results suggest that, while OR orthologs tend to show conserved ligand selectivity, their potency and/or efficacy dynamically change during evolution, even in closely related species. These functional changes in orthologs provide a platform for examining how the evolution of ORs can meet species-specific demands.

Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex.

The human neocortex differs from that of other great apes in several notable regards, including altered cell cycle, prolonged corticogenesis, and increased size [1-5]. Although these evolutionary changes most likely contributed to the origin of distinctively human cognitive faculties, their genetic basis remains almost entirely unknown. Highly conserved non-coding regions showing rapid sequence changes along the human lineage are candidate loci for the development and evolution of uniquely human traits. Several studies have identified human-accelerated enhancers [6-14], but none have linked an expression difference to a specific organismal trait. Here we report the discovery of a human-accelerated regulatory enhancer (HARE5) of FZD8, a receptor of the Wnt pathway implicated in brain development and size [15, 16]. Using transgenic mice, we demonstrate dramatic differences in human and chimpanzee HARE5 activity, with human HARE5 driving early and robust expression at the onset of corticogenesis. Similar to HARE5 activity, FZD8 is expressed in neural progenitors of the developing neocortex [17-19]. Chromosome conformation capture assays reveal that HARE5 physically and specifically contacts the core Fzd8 promoter in the mouse embryonic neocortex. To assess the phenotypic consequences of HARE5 activity, we generated transgenic mice in which Fzd8 expression is under control of orthologous enhancers (Pt-HARE5::Fzd8 and Hs-HARE5::Fzd8). In comparison to Pt-HARE5::Fzd8, Hs-HARE5::Fzd8 mice showed marked acceleration of neural progenitor cell cycle and increased brain size. Changes in HARE5 function unique to humans thus alter the cell-cycle dynamics of a critical population of stem cells during corticogenesis and may underlie some distinctive anatomical features of the human brain.

Rapid evolution of cancer/testis genes on the X chromosome.

BACKGROUND: Cancer/testis (CT) genes are normally expressed only in germ cells, but can be activated in the cancer state. This unusual property, together with the finding that many CT proteins elicit an antigenic response in cancer patients, has established a role for this class of genes as targets in immunotherapy regimes. Many families of CT genes have been identified in the human genome, but their biological function for the most part remains unclear. While it has been shown that some CT genes are under diversifying selection, this question has not been addressed before for the class as a whole. RESULTS: To shed more light on this interesting group of genes, we exploited the generation of a draft chimpanzee (Pan troglodytes) genomic sequence to examine CT genes in an organism that is closely related to human, and generated a high-quality, manually curated set of human:chimpanzee CT gene alignments. We find that the chimpanzee genome contains homologues to most of the human CT families, and that the genes are located on the same chromosome and at a similar copy number to those in human. Comparison of putative human:chimpanzee orthologues indicates that CT genes located on chromosome X are diverging faster and are undergoing stronger diversifying selection than those on the autosomes or than a set of control genes on either chromosome X or autosomes. CONCLUSION: Given their high level of diversifying selection, we suggest that CT genes are primarily responsible for the observed rapid evolution of protein-coding genes on the X chromosome.

Report of a chimeric origin of transposable elements in a bovine-coding gene

Despite the wide distribution of transposable elements (TEs) in mammalian genomes, part of their evolutionary significance remains to be discovered. Today there is a substantial amount of evidence showing that TEs are involved in the generation of new exons in different species. In the present study, we searched 22,805 genes and reported the occurrence of TE-cassettes in coding sequences of 542 cow genes using the RepeatMasker program. Despite the significant number (542) of genes with TE insertions in exons only 14 (2.6%) of them were translated into protein, which we characterized as chimeric genes. From these chimeric genes, only the FAST kinase domains 3 (FASTKD3) gene, present on chromosome BTA 20, is a functional gene and showed evidence of the exaptation event. The genome sequence analysis showed that the last exon coding sequence of bovine FASTKD3 is ∼85% similar to the ART2A retrotransposon sequence. In addition, comparison among FASTKD3 proteins shows that the last exon is very divergent from those of Homo sapiens, Pan troglodytes and Canis familiares. We suggest that the gene structure of bovine FASTKD3 gene could have originated by several ectopic recombinations between TE copies. Additionally, the absence of TE sequences in all other species analyzed suggests that the TE insertion is clade-specific, mainly in the ruminant lineage. ©FUNPEC-RP.

A dog at the keyboard: using arbitrary signs to communicate requests

As a consequence of domestication, dogs have a special readiness for communication with humans. We here investigate whether a dog might be able to acquire and consistently produce a set of arbitrary signs in her communication with humans, as was demonstrated in ""linguistic"" individuals of several species. A female mongrel dog was submitted to a training schedule in which, after basic command training and after acquiring the verbal labels of rewarding objects or activities, she learned to ask for such objects or activities by selecting lexigrams and pressing keys on a keyboard. Systematic records taken during spontaneous interaction with one of the experimenters showed that lexigrams were used in an appropriate, intentional way, in accordance with the immediate motivational context. The dog only utilized the keyboard in the experimenter`s presence and gazed to him more frequently after key pressing than before, an indication that lexigram use did have communicative content. Results suggest that dogs may be able to learn a conventional system of signs associated to specific objects and activities, functionally analogous to spontaneous soliciting behaviors and point to the potential fruitfulness of the keyboard/lexigram procedure for studying dog communication and cognition. This is the first report to systematically analyze the learning of arbitrary sign production in dogs.

Stretching-induced orientation to improve mechanical properties of electrospun pan nanocomposites

Partially aligned and oriented polyacrylonitrile(PAN)-based nanofibers were electrospun from PAN and SWNTs/PAN in the solution of dimethylformamide(DMF) to make the carbon nanofibers. The as-spun nanofibers were hot-stretched in an oven to enhance its orientation and crystallinity. Then it were stabilized at 250 square under a stretched stress, and carbonized at 1000 square in N-2 atmosphere by fixing the length of the stabilized nanofiber to convert them into carbon nanofibers. With this hot-stretched process and with the introduction of SWNTs, the mechanical properties will be enhanced correspondingly. The crystallinity of the stretched fibers confirmed by X-ray diffraction has also increased. For PAN nanofibers, the improved fiber alignment and crystallinity resulted in the increased mechanical properties, such as the modulus and tensile strength of the nanofibers. It was concluded that the hot-stretched nanofiber and the SWNTs/PAN nanofibers can be used as a potential precursor to produce high-performance carbon composites.

Management of a high grade pan stage schedule to reduce the steam consumption

MOST PAN stages in Australian factories use only five or six batch pans for the high grade massecuite production and operate these in a fairly rigid repeating production schedule. It is common that some of the pans are of large dropping capacity e.g. 150 to 240 t. Because of the relatively small number and large sizes of the pans, steam consumption varies widely through the schedule, often by ±30% about the mean value. Large fluctuations in steam consumption have implications for the steam generation/condensate management of the factory and the evaporators when bleed vapour is used. One of the objectives of a project to develop a supervisory control system for a pan stage is to (a) reduce the average steam consumption and (b) reduce the variation in the steam consumption. The operation of each of the high grade pans within the schedule at Macknade Mill was analysed to determine the idle (or buffer) time, time allocations for essential but unproductive operations (e.g. pan turn round, charging, slow ramping up of steam rates on pan start etc.), and productive time i.e. the time during boil-on of liquor and molasses feed. Empirical models were developed for each high grade pan on the stage to define the interdependence of the production rate and the evaporation rate for the different phases of each pan’s cycle. The data were analysed in a spreadsheet model to try to reduce and smooth the total steam consumption. This paper reports on the methodology developed in the model and the results of the investigations for the pan stage at Macknade Mill. It was found that the operation of the schedule severely restricted the ability to reduce the average steam consumption and smooth the steam flows. While longer cycle times provide increased flexibility the steam consumption profile was changed only slightly. The ability to cut massecuite on the run among pans, or the use of a high grade seed vessel, would assist in reducing the average steam consumption and the magnitude of the variations in steam flow.

Out of the frying pan and into the fire – forging a career in a temporary workplace : a new perspective for HR?

Recent literature acknowledges the need for new career development models to support the way that careers evolve in the 21st century workplace (Bloch 2005). This is particularly so within temporary organisation forms, and for those pursuing a career in project management (Hölzle 2010). Our research, explores how project managers working on projects and within temporary organisation forms and those working on project-linked contracts access the development opportunities they require to remain employable in an era of project-by-project employment. Set in Australia where a project-based economy (Crawford, French and Lloyd-Walker 2013) and contract work have led to casualisation of the workforce (Connell & Burgess, 2006; McKeown & Hanley (2009) the results suggest new approaches to career development may be required.

Pan-Plasmodium band sensitivity for Plasmodium falciparum detection in combination malaria rapid diagnostic tests and implications for clinical management

Background: Malaria rapid diagnostic tests (RDTs) are appropriate for case management, but persistent antigenaemia is a concern for HRP2-detecting RDTs in endemic areas. It has been suggested that pan-pLDH test bands on combination RDTs could be used to distinguish persistent antigenaemia from active Plasmodium falciparum infection, however this assumes all active infections produce positive results on both bands of RDTs, an assertion that has not been demonstrated. Methods: In this study, data generated during the WHO-FIND product testing programme for malaria RDTs was reviewed to investigate the reactivity of individual test bands against P. falciparum in 18 combination RDTs. Each product was tested against multiple wild-type P. falciparum only samples. Antigen levels were measured by quantitative ELISA for HRP2, pLDH and aldolase. Results: When tested against P. falciparum samples at 200 parasites/μL, 92% of RDTs were positive; 57% of these on both the P. falciparum and pan bands, while 43% were positive on the P. falciparum band only. There was a relationship between antigen concentration and band positivity; ≥4 ng/mL of HRP2 produced positive results in more than 95% of P. falciparum bands, while ≥45 ng/mL of pLDH was required for at least 90% of pan bands to be positive. Conclusions: In active P. falciparum infections it is common for combination RDTs to return a positive HRP2 band combined with a negative pan-pLDH band, and when both bands are positive, often the pan band is faint. Thus active infections could be missed if the presence of a HRP2 band in the absence of a pan band is interpreted as being caused solely by persistent antigenaemia.