Quantifying community assembly processes and identifying features that impose them

Spatial turnover in the composition of biological communities is governed by (ecological) Drift, Selection and Dispersal. Commonly applied statistical tools cannot quantitatively estimate these processes, nor identify abiotic features that impose these processes. For interrogation of subsurface microbial communities distributed across two geologically distinct formations of the unconfined aquifer underlying the Hanford Site in southeastern Washington State, we developed an analytical framework that advances ecological understanding in two primary ways. First, we quantitatively estimate influences of Drift, Selection and Dispersal. Second, ecological patterns are used to characterize measured and unmeasured abiotic variables that impose Selection or that result in low levels of Dispersal. We find that (i) Drift alone consistently governs ∼25% of spatial turnover in community composition; (ii) in deeper, finer-grained sediments, Selection is strong (governing ∼60% of turnover), being imposed by an unmeasured but spatially structured environmental variable; (iii) in shallower, coarser-grained sediments, Selection is weaker (governing ∼30% of turnover), being imposed by vertically and horizontally structured hydrological factors;(iv) low levels of Dispersal can govern nearly 30% of turnover and be caused primarily by spatial isolation resulting from limited exchange between finer and coarser-grain sediments; and (v) highly permeable sediments are associated with high levels of Dispersal that homogenize community composition and govern over 20% of turnover. We further show that our framework provides inferences that cannot be achieved using preexisting approaches, and suggest that their broad application will facilitate a unified understanding of microbial communities.     

Site frequency spectra from genomic SNP surveys

Genomic survey data now permit an unprecedented level of sensitivity in the detection of departures from canonical evolutionary models, including expansions in population size and selective sweeps. Here, we examine the effects of seemingly subtle differences among sampling distributions on goodness of fit analyses of site frequency spectra constructed from single nucleotide polymorphisms. Conditioning on the observation of exactly two alleles in a random sample results in a site frequency spectrum that is independent of the scaled rate of neutral substitution (θ). Other sampling distributions, including conditioning on a single mutational event in the sample genealogy or randomly selecting a single mutation from a genealogy with multiple mutations, have distinct site frequency spectra that show highly significant departures from the predictions of the biallelic model. Some aspects of data filtering may contribute to significant departures of site frequency spectra from expectation, apart from any violation of the standard neutral model.     

Late Pleistocene,Upper Palaeolithic Sleds from eastern North America

Here are described two sleds, presumed to date to the time of the Clovis (Llano) archaeological culture or approximately 13,500-12,500 years ago, that were discovered at saline springs in New York state and Kentucky state. For what purpose these sleds may have been intended and why they were abandoned are addressed by referring to eastern Eurasian ethnography. The proboscidean components used in their construction may have restricted use of these sleds to ritual activities.     

Expression ofMbR4, a TIR-NBS type of appleR Gene, confers resistance to bacterial spot disease inArabidopsis

A single disease resistance gene candidate,MbR4, was isolated from the wild-type apple speciesMalus baccta. This gene was predicted to encode motifs characteristic of the Toll Interleukin 1 Receptor (TIR) — Nucleotide Binding Site (NBS) of theR gene. Starting with an isolated cDNA clone, genomic clones were obtained via inverse polymerase chain reaction (IPCR). TheMbR4 gene has a single open reading frame (ORF) of 2178 nucleotides, a 41-b untranslated 5’ region, a 21-b untranslated 3’ region, and a predicted protein of 726 amino acids (82 kDa). Its deduced amino acid sequence resembles the N protein of tobacco and the NL25 protein of potato. Ectopic expression ofMbR4 induced enhanced resistance in transgenicArabidopsis plants against the virulent pathogen,Pseudomonas syringae pv.tomato DC3000. Microarray analysis confirmed the induction of defense-related gene expression in pathogen-free 35S::MbR4 heterologousArabidopsis plants, thereby indicating that theMbR4 gene likely activates a pathogen-independent resistance pathway, rather than a gene-for-gene pathway. Our results suggest thatMbR4 plays a role in theR gene, and may be a source of resistance for cultivated apple species.     

Micromammals and the formation of the Name Chamber at Sterkfontein, South Africa

The depositional history of the Name Chamber at the Sterkfontein early hominid site is complex, as is the case with most such cavities. Unravelling this history may therefore benefit from the input of less usual lines of evidence to complement baseline geological investigations. In this case, micromammalian remains from the Western Talus of the Name Chamber provide tentative evidence for the depositional history of these deposits. Correlation of samples based on minimum numbers of individuals referred to genera occurring in one third or more of the samples suggests that a large proportion of the Western Talus material, particularly that from the area infiltrated by the Eastern Talus deposit, originated in the vicinity of squares P54, Q54 and Q55 in the main excavation, from a depth spanning the boundary between Acheulean and Oldowan levels in Member 5. Differences in general diversity between the samples from the main excavation and some from the Name Chamber support the proposal that surface sediments of the homogeneous deposits have been contaminated by material entering the cavern during the 1994 opening of the feeder shaft. Initial taphonomic analysis indicates that all samples, both the original and those from the Name Chamber, were accumulated by the same avian predator, that is, one or more of three owl species (barn owl Tyto alba, grass owl Tyto capensis and marsh owl Asio capensis).     

Explaining and Predicting Allostery with Allosteric Database and Modern Analytical Techniques

Allostery is a phenomenon that the protein activity is regulated when a non-functional site on it is bounded. This phenomenon is important in life process and disease therapy. However, it is difficult to study allostery due to the lack of knowledge. Facing this demand, we have created Allosteric Database (ASD) 10 years before to collect numerous kinds of allosteric data. In this review, we will introduce the 4 categories of data in ASD. For each category, we further reviewed how researchers applied ASD data to conduct studies. We focused on their research topics, analytical methods and conclusions. Several discoveries of new drug targets and allosteric modulators driven by ASD are also summarized. We hope this review could inspire researchers with new utilities of ASD data.     

High resolution optical spectra in vivo: Photoactive protochlorophyllide in etiolated leaves at 5 K

We describe here high-resolution spectra of etiolated leaves studied by means of selective monochromatic excitation of fluorescence as well as by hole-burning technique at liquid helium temperature. Up to now site selection spectroscopy has not been successfully applied to biologically active chromophores in vivo. Our results demonstrate that even in the presence of specific pigment-protein and pigment-pigment interactions very narrow purely electronic lines can be obtained in the optical spectra of biological systems.     

Can Coyotes Affect Deer Populations in Southeastern North America?

ABSTRACT The coyote (Canis latrans) is a recent addition to the fauna of eastern North America, and in many areas coyote populations have been established for only a decade or two. Although coyotes are known predators of white-tailed deer (Odocoileus virginianus) in their historic range, effects this new predator may have on eastern deer populations have received little attention. We speculated that in the southeastern United States, coyotes may be affecting deer recruitment, and we present 5 lines of evidence that suggest this possibility. First, the statewide deer population in South Carolina has declined coincident with the establishment and increase in the coyote population. Second, data sets from the Savannah River Site (SRS) in South Carolina indicate a new mortality source affecting the deer population concurrent with the increase in coyotes. Third, an index of deer recruitment at SRS declined during the period of increase in coyotes. Fourth, food habits data from SRS indicate that fawns are an important food item for coyotes during summer. Finally, recent research from Alabama documented significant coyote predation on fawns there. Although this evidence does not establish cause and effect between coyotes and observed declines in deer recruitment, we argue that additional research should proactively address this topic in the region. We identified several important questions on the nature of the deer—coyote relationship in the East.     

The EVect of Release Size on the Probability of Establishment of Biological Control Agents: Gorse Thrips ( Sericothrips staphylinus ) Released Against Gorse ( Ulex europaeus ) in New Zealand

Many biocontrol agents released against alien weeds and pests fail to establish in the field. Here, we ask whether better release strategies could improve the likelihood of successful establishment. A manipulative field experiment was used to investigate the relationship between the probability of establishment and the number of individuals released for a weed biocontrol agent. In this experiment, replicated releases of 10, 30, 90, 270 and 810 gorse thrips, Sericothrips staphylinus Haliday, were made on to isolated gorse bushes in New Zealand. The sampling eY ciency was determined using a further experiment in which known numbers of thrips were released on to bushes. The data obtained showed that in approximately nine out of 10 releases of 10 thrips, at least one thrips would be found. The thrips in the size of release experiment were sampled 1 year after their release. A higher proportion of the small releases became extinct during this time period: thrips were recovered from 100% of the releases of 270 and 810 thrips, but only from 33% of releases of 10, 30 and 90 thrips. Using gorse thrips as an example, a protocol was developed to determine the optimal release size for biocontrol agents. It is suggested that for a fixed number of insects available for release, smaller releases may increase the overall establishment rate. W hile a single large release can easily become extinct by chance, it is extremely unlikely that a large number of small releases will do so over the same time period. The optimal release size (i.e. that which maximizes the average number of successful establishments) for gorse thrips in New Zealand might be fewer than 100 thrips/ release site. This contrasts with the current strategy in New Zealand of 1000 thrips/release and the suggestion in the biocontrol literature that large releases optimize establishment. Over 1 year of observation the thrips had no eVect on gorse growth rate. The EVect of Release Size on the Probability of Establishment of Biological Control Agents: Gorse Thrips ( Sericothrips staphylinus ) Released Against Gorse ( Ulex europaeus ) in New Zealand     

Potassium- and Carbachol-Evoked Release of [3H]Noradrenaline from Human Neuroblastoma Cells, SH-SY5Y

The human neuroblastoma clone SH-SY5Y expresses potassium-, carbachol-, and calcium ionophore A23187-evoked, calcium-dependent release of [3H]noradrenaline. Release in response to carbachol and potassium was greater than additive. Atropine (Ki = 0.33 nM), hexahydrosiladifenidol (Ki = 18 nM), and pirenzepine (Ki = 1,183 nM) completely inhibited the carbachol-evoked noradrenaline release, an order of potency suggesting that an M3 receptor was linked to release. In contrast, noradrenaline release was only partially inhibited by the M2-selective antagonists methoctramine (10(-4) M) and AFDX-116 (10(-4) M), by approximately 14 and 46%, respectively. The nicotinic antagonist d-tubocurarine (10(-4) M) resulted in a partial inhibition of release, a finding suggesting that a nicotinic receptor may also be involved. SH-SY5Y provides a suitable cell line in which to study the biochemical mechanisms underlying the cholinergic receptor regulation of noradrenaline release.