Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach

High throughput sequencing methods are widely used in analyses of microbial diversity, but are generally applied to small numbers of samples, which precludes characterization of patterns of microbial diversity across space and time. We have designed a primer-tagging approach that allows pooling and subsequent sorting of numerous samples, which is directed to amplification of a region spanning the nuclear ribosomal internal transcribed spacers and partial large subunit from fungi in environmental samples. To test the method for phylogenetic biases, we constructed a controlled mixture of four taxa representing the Chytridiomycota, Zygomycota, Ascomycota and Basidiomycota. Following cloning and colony restriction fragment length polymorphism analysis, we found no significant difference in representation in 19 of the 23 tested primers. We also generated a clone library from two soil DNA extracts using two primers for each extract and compared 456 clone sequences. Community diversity statistics and contingency table tests applied to counts of operational taxonomic units revealed that the two DNA extracts differed significantly, while the pairs of tagged primers from each extract were indistinguishable. Similar results were obtained using UniFrac phylogenetic comparisons. Together, these results suggest that the pig-tagged primers can be used to increase ecological inference in high throughput sequencing projects on fungi.     

Uses and Conservation of Plant Species in a National Park—A Case Study of Ben En, Vietnam

Uses and Conservation of Plant Species in a National Park—A Case Study of Ben En, Vietnam. This paper surveys the use of wild and cultivated plants by local people in Ben En National Park, Vietnam, and analyzes its impact on the conservation status of some of the utilized species. A total of 208 species used for a range of nonmedicinal purposes are listed. See Hoang et al. (2008a) for 230 medicinal plants used in the park. Most species are used for food. The use of plants contributes very significantly to the livelihood of local people in the park, but the current use patterns are not sustainable and would lead to local extinction of rare and endangered species if no additional conservation measures are introduced. Men collect nonmedicinal plants more often than women. A total of 38 useful plant species are commercialized, and contribute 12% of the average income of individual households. Bamboo shoots of Schizostachyum funghomii (Poaceae) are the most important for income generation. The monetary equivalent of noncommercialized useful plants probably far exceeds the value of the traded plant products. Plant use is independent of the ethnicity of the different populations living in the park. Larger households make use of a greater variety of useful plant species than small families. Abundant species in the forest have a higher use index (UI) than less common species. Out of the 208 useful species, as many as 27 were found to be endangered locally, many more than the 11 or 8 endangered species included in national or global red lists. Currently, useful plants, especially important timber trees, are more abundant in the less disturbed parts of the park, far away from the villages, indicating the pressures of illegal logging and harvesting near villages on the ecosystems.     

Continuities in stone flaking technology at Liang Bua, Flores, Indonesia

This study examines trends in stone tool reduction technology at Liang Bua, Flores, Indonesia, where excavations have revealed a stratified artifact sequence spanning 95 k.yr. The reduction sequence practiced throughout the Pleistocene was straightforward and unchanging. Large flakes were produced off-site and carried into the cave where they were reduced centripetally and bifacially by four techniques: freehand, burination, truncation, and bipolar. The locus of technological complexity at Liang Bua was not in knapping products, but in the way techniques were integrated. This reduction sequence persisted across the Pleistocene/Holocene boundary with a minor shift favoring unifacial flaking after 11 ka. Other stone-related changes occurred at the same time, including the first appearance of edge-glossed flakes, a change in raw material selection, and more frequent fire-induced damage to stone artifacts. Later in the Holocene, technological complexity was generated by “adding-on” rectangular-sectioned stone adzes to the reduction sequence. The Pleistocene pattern is directly associated with Homo floresiensis skeletal remains and the Holocene changes correlate with the appearance of Homo sapiens. The one reduction sequence continues across this hominin replacement.     

A link between maze learning and hippocampal expression of neuroleukin and its receptor gp78

Neuroleukin (NLK) is a multifunctional protein involved in neuronal growth and survival, cell motility and differentiation, and glucose metabolism. We report herein that hippocampal expression of NLK and its receptor gp78 is associated with maze learning in rats. First, mRNA levels of NLK and gp78 were significantly increased in hippocampi of male Fischer-344 rats following training in the Stone T-maze and the Morris water maze. Second, a parallel increase was found in hippocampal NLK and gp78 proteins after maze learning. Third, NLK and gp78 mRNA and protein expression in hippocampus was reduced in a group of aged rats that showed more errors during the acquisition of the Stone maze task as compared with young rats. Finally, application of recombinant NLK to hippocampal neurons significantly enhanced glutamate-induced ion currents, functional molecular changes that have been correlated with learning in vivo. Taken together, our results identify a novel association of hippocampal expression of NLK and its receptor gp78 with rat maze learning. Interaction of NLK with gp78 and subsequent signaling may strengthen synaptic mechanisms underlying learning and memory formation.     

广西百色公篓遗址石制品的初步研究

公篓遗址位于广西百色市田阳县境内, 地处百色盆地右江南岸第四级阶地, 地理坐标为23°45.568'N, 106°42.210'E。该遗址最早发现于上世纪八十年代, 当时采集石制品88件, 是百色盆地较早发现的一处旧石器时代遗址; 2010年我们对遗址进行复查时又采集石制品14件, 本文对两次采集的石制品进行了分析。石制品类型有石核、石片、砍砸器、手镐、刮削器、手斧和断块, 其中砍砸器数量最多; 原料来源于遗址附近第四级阶地的砾石层, 有石英岩、硅质岩、石英、粉砂岩、细砂岩和角砾岩6种, 以石英岩为主; 石制品以大型和中型为主, 也有一定数量的小型石制品; 剥片和修理方法主要为锤击法。根据地貌和地层可以判断该遗址年代为中更新世早期。     

Applications of Population Genetics to Animal Breeding,from Wright,Fisher and Lush to Genomic Prediction

Although animal breeding was practiced long before the science of genetics and the relevant disciplines of population and quantitative genetics were known, breeding programs have mainly relied on simply selecting and mating the best individuals on their own or relatives’ performance. This is based on sound quantitative genetic principles, developed and expounded by Lush, who attributed much of his understanding to Wright, and formalized in Fisher’s infinitesimal model. Analysis at the level of individual loci and gene frequency distributions has had relatively little impact. Now with access to genomic data, a revolution in which molecular information is being used to enhance response with “genomic selection” is occurring. The predictions of breeding value still utilize multiple loci throughout the genome and, indeed, are largely compatible with additive and specifically infinitesimal model assumptions. I discuss some of the history and genetic issues as applied to the science of livestock improvement, which has had and continues to have major spin-offs into ideas and applications in other areas.THE success of breeders in effecting immense changes in domesticated animals and plants greatly influenced Darwin’s insight into the power of selection and implications to evolution by natural selection. Following the Mendelian rediscovery, attempts were soon made to accommodate within the particulate Mendelian framework the continuous nature of many traits and the observation by Galton (1889) of a linear regression of an individual’s height on that of a relative, with the slope dependent on degree of relationship. A polygenic Mendelian model was first proposed by Yule (1902) (see Provine 1971; Hill 1984). After input from Pearson, Yule again, and Weinberg (who developed the theory a long way but whose work was ignored), its first full exposition in modern terms was by Ronald A. Fisher (1918) (biography by Box 1978). His analysis of variance partitioned the genotypic variance into additive, dominance and epistatic components. Sewall Wright (biography by Provine 1986) had by then developed the path coefficient method and subsequently (Wright 1921) showed how to compute inbreeding and relationship coefficients and their consequent effects on genetic variation of additive traits. His approach to relationship in terms of the correlation of uniting gametes may be less intuitive at the individual locus level than Malécot’s (1948) subsequent treatment in terms of identity by descent, but it transfers directly to the correlation of relatives for quantitative traits with additive effects.From these basic findings, the science of animal breeding was largely developed and expounded by Jay L. Lush (1896–1982) (see also commentaries by Chapman 1987 and Ollivier 2008). He was from a farming family and became interested in genetics as an undergraduate at Kansas State. Although his master’s degree was in genetics, his subsequent Ph.D. at the University of Wisconsin was in animal reproductive physiology. Following 8 years working in animal breeding at the University of Texas he went to Iowa State College (now University) in Ames in 1930. Wright was Lush’s hero: ‘I wish to acknowledge especially my indebtedness to Sewall Wright for many published and unpublished ideas upon which I have drawn, and for his friendly counsel” (Lush 1945, in the preface to his book Animal Breeding Plans). Lush commuted in 1931 to the University of Chicago to audit Sewall Wright’s course in statistical genetics and consult him. Speaking at the Poultry Breeders Roundtable in 1969: he said, “Those were by far the most fruitful 10 weeks I ever had.” (Chapman 1987, quoting A. E. Freeman). Lush was also exposed to and assimilated the work and ideas of R. A. Fisher, who lectured at Iowa State through the summers of 1931 and 1936 at the behest of G. W. Snedecor.Here I review Lush’s contributions and then discuss how animal breeding theory and methods have subsequently evolved. They have been based mainly on statistical methodology, supported to some extent by experiment and population genetic theory. Recently, the development of genomic methods and their integration into classical breeding theory has opened up ways to greatly enhance rates of genetic improvement. Lush focused on livestock improvement and spin-off into other areas was coincidental; but he had contact with corn breeders in Ames and beyond and made contributions to evolutionary biology and human genetics mainly through his developments in theory (e.g., Falconer 1965; Robertson 1966; Lande 1976, 1979; see also Hill and Kirkpatrick 2010). I make no attempt to be comprehensive, not least in choice of citations.     

王府井东方广场遗址石制品研究

王府井东方广场遗址出土石制品共计1098件,主要来自下文化层。除石锤、石砧和人工石块外,其他石制品的原料几乎全部为黑色燧石。石制品普遍较小,主要为小型和微型。石核数量很少,但石片占石制品总数的一半还多。碎屑在探方中的几个区域密集分布。石器加工精致,刃缘大部分都比较平齐且其上的修疤排列均匀、整齐,尤其表现在端刮器上。原料、类型与技术特点表明,东方广场遗址石制品组合属于中国旧石器时代晚期的以石片为主要特征的文化系列。这一文化系列与周口店北京猿人遗址、周口店第15地点、许家窑遗址等有较多的相似性,推测东方广场石制品组合是由中国旧石器时代早期和中期石器工业演变而来。