Repeatability and contingency in the evolution of a key innovation in phage lambda

The processes responsible for the evolution of key innovations, whereby lineages acquire qualitatively new functions that expand their ecological opportunities, remain poorly understood. We examined how a virus, bacteriophage λ, evolved to infect its host, Escherichia coli, through a novel pathway. Natural selection promoted the fixation of mutations in the virus's host-recognition protein, J, that improved fitness on the original receptor, LamB, and set the stage for other mutations that allowed infection through a new receptor, OmpF. These viral mutations arose after the host evolved reduced expression of LamB, whereas certain other host mutations prevented the phage from evolving the new function. This study shows the complex interplay between genomic processes and ecological conditions that favor the emergence of evolutionary innovations.     

Catchment-Scale Variation in the Nitrate Concentrations of Groundwater Seeps in the Catskill Mountains,New York,U.S.A.

Forested headwater streams in the Catskill Mountains of New York show significant among-catchment variability in mean annual nitrate (NO₃ ^-) concentrations. Large contributions from deep groundwater with high NO₃ ^-concentrations have been invoked to explain high NO₃ ^-concentrations in stream water during the growing season. To determine whether variable contributions of groundwater couldexplain among-catchment differences in streamwater, we measuredNO₃ ^- concentrations in 58 groundwater seeps distributed across six catchments known to have different annual average streamwater concentrations. Seeps were identified based on release from bedrock fractures and beddingplanes and had consistently lower temperatures than adjacentstreamwaters. Nitrate concentrations in seeps ranged from neardetection limits (0.005 mg NO₃ ^--N/L) to 0.75 mg NO₃ ^--N/L. Within individual catchments, groundwaterresidence time does not seem to strongly affect NO₃ ^-concentrations because in three out of four catchments therewere non-significant correlations between seep silica (SiO₂) concentrations, a proxy for residence time, andseep NO₃ ^- concentrations. Across catchments, therewas a significant but weak negative relationship betweenNO₃ ^- and SiO₂ concentrations. The large rangein NO₃ ^- concentrations of seeps across catchmentssuggests: 1) the principal process generating among-catchmentdifferences in streamwater NO₃ ^- concentrations mustinfluence water before it enters the groundwater flow system and 2) this process must act at large spatial scales becauseamong-catchment variability is much greater than intra-catchmentvariability. Differences in the quantity of groundwater contribution to stream baseflow are not sufficient to account for differences in streamwater NO₃ ^- concentrationsamong catchments in the Catskill Mountains.     

Studies of selenium-containing volatiles in roasted coffee

Coffee has been an important and heavily used beverage in many cultures over a long period of time. Although sulfur species have been found to be abundant constituents, no work to date has explored the presence of selenium analogues. Investigation of volatile selenium species from green coffee beans, roasted beans, and brewed coffee drink was performed using solid phase microextraction (SPME) sample preconcentration in conjunction with GC/ICP-MS. Several volatile selenium species at trace levels were detected from roasted coffee beans as well as in the steam from brewed coffee drinks. No detectable selenium (and sulfur) species, however, were found in the headspace of green beans, indicating that selenium-containing volatiles are formed during roasting, as is the case for the sulfur volatiles. Matching standards were prepared and used to identify the compounds found in coffee. Artificial supplementation of the green coffee beans with selenium before roasting was performed to further characterize the selenium-containing volatiles formed during the coffee-roasting process.     

Chromatographic fingerprinting of <Emphasis Type="Italic">Lupinus luteus</Emphasis> L. (Leguminosae) main secondary metabolites: a case of domestication affecting crop variability

Secondary metabolites (SMs), such as alkaloids and raffinose oligosaccharides (RFOs), play important roles in plant physiology. Although alkaloid and RFO phenotypic variation has been reported for yellow lupin (Lupinus luteus L.), most evaluations have used a reduced number of accessions; thus, limiting the understanding of accumulation patterns and variation ranges. The main goal of this research was to assess alkaloid and RFO content in a diverse L. luteus sample to understand possible SM accumulation patterns across this legume species. Eighteen yellow lupin accessions were analyzed using high performance thin layer chromatography to provide insights on seed and leaf RFO and alkaloid phenotypic variation. Co-dominant markers (170) were used to examine genetic relationships among L. luteus accessions and possible accumulation patterns across closely related genotypes. Significant differences were observed for seed and leaf RFOs. Total seed RFO accumulation ranged from 79.738 to 131.079 mg g^?1. Raffinose, stachyose, and verbascose were observed in all genotypes’ seeds, but at different RFO concentrations. Raffinose was the only RFO detected in leaves (2.793–0.4224 mg g^?1). Total alkaloid accumulation ranged from 0.22 to 15.12 and 0.00 to 8.007 mg g^?1 for seeds and leaves, respectively. Lupinine, sparteine, and gramine were observed in seeds and leaves, and showed a wide range of variation. Neighbor-Joining (NJ) analysis showed an apparent pattern of seed alkaloid accumulation, most likely due to domestication events. However, high RFO accumulating accessions were scattered across the NJ tree. Alkaloid and RFO significant phenotypic variation will not only help to understand the roles of these SMs in L. luteus, but also to uncover the genetic basis behind their accumulation.     

Detection of antibodies to West Nile virus in equine sera using microsphere immunoassay.

One hundred and ninety-one sera from horses that recently were exposed to West Nile virus (WNV) by either vaccination or natural infection or that were not vaccinated and remained free of infection were used to evaluate fluorescent microsphere immunoassays (MIAs) incorporating recombinant WNV envelope protein (rE) and recombinant nonstructural proteins (rNS1, rNS3, and rNS5) for detection of equine antibodies to WNV. The rE MIA had a diagnostic sensitivity and specificity, respectively, of 99.3% and 97.4% for detection of WNV antibodies in the serum of horses that were recently vaccinated or naturally infected with WNV, as compared to the plaque reduction neutralization test (PRNT). The positive rE MIA results were assumed to be WNV-specific because of the close agreement between this assay and the PRNT and the fact that unvaccinated control horses included in this study were confirmed to be free of exposure to the related St Louis encephalitis virus. The NS protein-based MIA were all less sensitive than either the rE MIA or PRNT (sensitivity 0-48.0), although the rNSI MIA distinguished horses vaccinated with the recombinant WNV vaccine from those that were immunized with the inactivated WNV vaccine (P < 0.0001) or naturally infected with WNV (P < 0.0001). The rE MIA would appear to provide a rapid, convenient, inexpensive, and accurate test for the screening of equine sera for the presence of antibodies to WNV.     

Predicting Recovery from Acidic Deposition: Applying a Modified TAF (Tracking and Analysis Framework) Model to Maine (USA) High Elevation Lakes

We adapted a reduced-form model, built to predict the aquatic effects of alternative nitrogen and sulfur emissions scenarios on Adirondack lakes, New York, for use on high elevation lakes of Maine (HELM), USA. The Tracking and Analysis Framework (TAF) model was originally designed to evaluate the biotic, economic, and health effects of acid deposition. The TAF model developed in our study was used to assess the biotic effects of different levels of sulfate deposition resulting from alternative emissions scenarios. The aquatic portion of the model is based on a lumped-parameter watershed chemistry model, MAGIC (Model of Acidification of Groundwater in Catchments). The original TAF model was built by calibrating MAGIC to 33 lakes in the Adirondack Mountains. We calibrated MAGIC to 78 HELM lakes, and built reduced-form models from these MAGIC predictions. We evaluated TAF predictions of acid neutralizing capacity (ANC), a fish acid stress index (ASI), and the probability of fish presence in 2030 for four different SO₂ emissions-reduction scenarios. The most dramatic emissions reduction scenario produced only modest increases in mean ANC (16.8 μeq/L ± 7.9 μeq/L) and slight increases in mean predicted probability of presence of acid-sensitive fish (0.07± 0.09) across all lakes. However, a small number of lakes were predicted to have more substantial increases in ANC and improvements in other conditions for acid-sensitive fish. Our results reflect the reality that many of the high elevation lakes of Maine historically had low ANC and that some were even acidic in pre-industrial times. Thus, ’recovery’ for most of the high elevation lakes of Maine will be modest under any scenario of reduced acidic deposition.     

Structure-function relationships of anthocyanins from various anthocyanin-rich extracts on the inhibition of colon cancer cell growth

Anthocyanins are potent antioxidants and may be chemoprotective. However, the structure-function relationships are not well understood. The objectives of this study were to compare the chemoprotective properties of anthocyanin-rich extracts (AREs) with variable anthocyanin profiles to understand the relationship between anthocyanin chemical structure and chemoprotective activity, measured as inhibition of colon cancer cell proliferation. Additionally, the chemoprotective interaction of anthocyanins and other phenolics was investigated. AREs with different anthocyanin profiles from purple corn, chokeberry, bilberry, purple carrot, grape, radish, and elderberry were tested for growth inhibition (GI 50) using a human colorectal adenocarcinoma (HT29) cell line. All AREs suppressed HT29 cell growth to various degrees as follows: purple corn (GI 50 approximately 14 microg of cy-3-glu equiv/mL) > chokeberry and bilberry > purple carrot and grape > radish and elderberry (GI 50 > 100 microg of cy-3-glu equiv/mL). Anthocyanins played a major role in AREs' chemoprotection and exerted an additive interaction with the other phenolics present. Statistical analyses suggested that anthocyanin chemical structure affected chemoprotection, with nonacylated monoglycosylated anthocyanins having greater inhibitory effect on HT-29 cell proliferation, whereas anthocyanins with pelargonidin, triglycoside, and/or acylation with cinnamic acid exerted the least effect. These findings should be considered for crop selection and the development of anthocyanin-rich functional foods.     

Comparing the Effects of Aquatic Stressors on Model Temperate Freshwater Aquatic Communities

Nuisance odors generation from waste and wastewater treatment plants are a cause of public discomfort and complaints. This situation impairs the air quality and represents a growing social and public health problem, especially in developing countries. Several modeling approaches have been developed and successfully implemented in the frame of a wastewater treatment plant for both the biological treatment and physicochemical processes. The mathematical modeling of the odor generation process is still considered a quite complex issue, mainly due to the fact that olfactory nuisance can be caused by many different chemical compounds and the perception of odors is influenced by subjective thresholds. Moreover, the impact of odor sources on air quality is highly conditioned by complex atmospheric dispersion processes. This review presents a critical state-of-art and assessment where information related to odor emissions impact studies as well as modeling applications are compiled and discussed.     

The Buttermilk Creek complex and the origins of Clovis at the Debra L. Friedkin site, Texas

Compelling archaeological evidence of an occupation older than Clovis (~12.8 to 13.1 thousand years ago) in North America is present at only a few sites, and the stone tool assemblages from these sites are small and varied. The Debra L. Friedkin site, Texas, contains an assemblage of 15,528 artifacts that define the Buttermilk Creek Complex, which stratigraphically underlies a Clovis assemblage and dates between ~13.2 and 15.5 thousand years ago. The Buttermilk Creek Complex confirms the emerging view that people occupied the Americas before Clovis and provides a large artifact assemblage to explore Clovis origins.     

The shaping of modern human immune systems by multiregional admixture with archaic humans

Whole genome comparisons identified introgression from archaic to modern humans. Our analysis of highly polymorphic human leukocyte antigen (HLA) class I, vital immune system components subject to strong balancing selection, shows how modern humans acquired the HLA-B*73 allele in west Asia through admixture with archaic humans called Denisovans, a likely sister group to the Neandertals. Virtual genotyping of Denisovan and Neandertal genomes identified archaic HLA haplotypes carrying functionally distinctive alleles that have introgressed into modern Eurasian and Oceanian populations. These alleles, of which several encode unique or strong ligands for natural killer cell receptors, now represent more than half the HLA alleles of modern Eurasians and also appear to have been later introduced into Africans. Thus, adaptive introgression of archaic alleles has significantly shaped modern human immune systems.