Restoration principles emerging from one of the world's largest tidal marsh restoration projects

One of the world's largest tidal wetland restorationprojects was conceived to offset the loss of nekton toonce-through cooling at a power plant on Delaware Bay,USA. An aggregated food chain model was employed toestimate the area of tidal salt marsh required toreplace these losses. The 5040 ha was comprised of twodegraded marsh types – Phragmites- dominatedmarshes and diked salt hay farms – at elevenlocations in oligo-mesohaline and polyhaline reachesof the estuary. At a series of summits convened withnoted experts in the field, it was decided to apply anecological engineering approach (i.e., self design,and minimal intrusion) in a landscape ecologyframework to the restoration designs while at the sametime monitoring long-term success of the project inthe context of a bound of expectation. The latterencompassed a range of reference marsh planforms andacceptable end-points established interactively withtwo advisory committees, numerous resource agencies,the permitting agency and multiple-stakeholder groups.In addition to the technical recommendations providedby the project's advisors, public health and safety,property protection and public access to the restoredsites were a constant part of the dialogue between theutility, its consulting scientists and theresource/permitting agencies. Adaptive management wasused to maintain the restoration trajectories, ensurethat success criteria were met in a timely fashion,and to protect the public against potential effects ofsalt intrusion into wells and septic systems, andagainst upland flooding. Herbicide spray, followed byprescribed burns and altered microtopography were usedat Phragmites-dominated sites, and excavation ofhigher order channels and dike breaching were themethods used to initiate the restorations at the dikedsalt hay farms. Monitoring consisted of evaluating therate of re-vegetation and redevelopment of naturaldrainage networks, nekton response to therestorations, and focused research on nutrient flux,nekton movements, condition factors, trophic linkages,and other specific topics. Because of its size anduniqueness, the Estuary Enhancement Program as thisproject is known, has become an important case studyfor scientists engaged in restoration ecology and theapplication of ecological engineering principles. Thehistory of this project, and ultimately theRestoration Principles that emerged from it, are thesubjects of this paper. By documenting the pathways tosuccess, it is hoped that other restoration ecologistsand practitioners will benefit from the experiences wehave gained.     

A major lung cancer susceptibility locus maps to chromosome 6q23-25

Lung cancer is a major cause of death in the United States and other countries. The risk of lung cancer is greatly increased by cigarette smoking and by certain occupational exposures, but familial factors also clearly play a major role. To identify susceptibility genes for familial lung cancer, we conducted a genomewide linkage analysis of 52 extended pedigrees ascertained through probands with lung cancer who had several first-degree relatives with the same disease. Multipoint linkage analysis, under a simple autosomal dominant model, of all 52 families with three or more individuals affected by lung, throat, or laryngeal cancer, yielded a maximum heterogeneity LOD score (HLOD) of 2.79 at 155 cM on chromosome 6q (marker D6S2436). A subset of 38 pedigrees with four or more affected individuals yielded a multipoint HLOD of 3.47 at 155 cM. Analysis of a further subset of 23 multigenerational pedigrees with five or more affected individuals yielded a multipoint HLOD score of 4.26 at the same position. The 14 families with only three affected relatives yielded negative LOD scores in this region. A predivided samples test for heterogeneity comparing the LOD scores from the 23 multigenerational families with those from the remaining families was significant (P=.007). The 1-HLOD multipoint support interval from the multigenerational families extends from C6S1848 at 146 cM to 164 cM near D6S1035, overlapping a genomic region that is deleted in sporadic lung cancers as well as numerous other cancer types. Parametric linkage and variance-components analysis that incorporated effects of age and personal smoking also supported linkage in this region, but with somewhat diminished support. These results localize a major susceptibility locus influencing lung cancer risk to 6q23-25.     

A new locus for late-onset, progressive, hereditary hearing loss DFNA20 maps to 17q25

We report the localization of DFNA20, a gene causing dominant, nonsyndromic, progressive hearing loss in a three-generation Midwestern family, to chromosome 17q25. Affected family members show a bilateral, sloping, progressive, sensorineural hearing loss, first evident at 6000 and 8000 Hz, that can be identified in some family members in the early teens and is clearly evident by the early twenties. As age increases, the degree of hearing loss increases with threshold shifts seen at all frequencies. Linkage to known hereditary hearing loss loci was excluded. A genome-wide screen detected positive linkage to D17S784 (LOD(Z) = 6.62; θ = 0). Haplotype analysis refines the DFNA20 critical region to 12 cM between D17S1806 and D17S668. Radiation hybrid mapping with Stanford G3 and TNG panels was used to evaluate the genes ACTG1, GRIN2C, FKHL13, P4HB, SPARC, and ARHGDIA as candidates for DFNA20.     

Smoking related cancers and loci at chromosomes 15q25, 5p15, 6p22.1 and 6p21.33 in the Polish population

Genetic factors associated with the risk of smoking related cancers have until recently remained elusive. Since the publication of a genome-wide association study (GWAS) on lung cancer new genetic loci have been identified that appear to be associated with disease risk. In this replication study we genotyped 14 single nucleotide polymorphisms (SNPs) located at the 5p12.3-p15.33, 6p21.3-p22.1, 6q23-q27 and 15q25.1 loci in 874 lung, 450 bladder, 418 laryngeal cancer cases and cancer-free controls, matched by year of birth and sex to the cases. Our results revealed that loci in the chromosome region 15q25.1 (rs16969968[A], rs8034191[G]) and 5p15 (rs402710[T]) are associated with lung cancer risk in the Polish population (smoking status adjusted OR = 1.45, 1.35, 0.77; p ≤ 0.0001, 0.0005, 0.002; 95%CI 1.23-1.72, 1.14-1.59, 0.66-0.91 respectively). None of the other regions analyzed herein were implicated in the risk of lung, bladder or laryngeal cancer. This study supports previous findings on lung cancer but fails to show association of SNPs located in 15q25.1 and 5p15 region with other smoking related cancers like bladder and laryngeal cancer.     

Sixty years of environmental change in the world's largest freshwater lake – Lake Baikal, Siberia

High-resolution data collected over the past 60 years by a single family of Siberian scientists on Lake Baikal reveal significant warming of surface waters and long-term changes in the basal food web of the world's largest, most ancient lake. Attaining depths over 1.6 km, Lake Baikal is the deepest and most voluminous of the world's great lakes. Increases in average water temperature (1.21 °C since 1946), chlorophyll a (300% since 1979), and an influential group of zooplankton grazers (335% increase in cladocerans since 1946) may have important implications for nutrient cycling and food web dynamics. Results from multivariate autoregressive (MAR) modeling suggest that cladocerans increased strongly in response to temperature but not to algal biomass, and cladocerans depressed some algal resources without observable fertilization effects. Changes in Lake Baikal are particularly significant as an integrated signal of long-term regional warming, because this lake is expected to be among those most resistant to climate change due to its tremendous volume. These findings highlight the importance of accessible, long-term monitoring data for understanding ecosystem response to large-scale stressors such as climate change.     

Inferring population trends for the world's largest fish from mark-recapture estimates of survival

1. Precise estimates of demographic rates are key components of population models used to predict the effects of stochastic environmental processes, harvest scenarios and extinction probability. 2. We used a 12-year photographic identification library of whale sharks from Ningaloo Reef, Western Australia to construct Cormack-Jolly-Seber (CJS) model estimates of survival within a capture-mark-recapture (CMR) framework. Estimated survival rates, population structure and assumptions regarding age at maturity, longevity and reproduction frequency were combined in a series of age-classified Leslie matrices to infer the potential trajectory of the population. 3. Using data from 111 individuals, there was evidence for time variation in apparent survival (phi) and recapture probability (p). The null model gave a phi of 0.825 (95% CI: 0.727-0.893) and p = 0.184 (95% CI: 0.121-0.271). The model-averaged annual phi ranged from 0.737 to 0.890. There was little evidence for a sex effect on survival. 4. Using standardized total length as a covariate in the CMR models indicated a size bias in phi. Ignoring the effects of time, a 5-m shark has a phi = 0.59 and a 9 m shark has phi = 0.81. 5. Of the 16 model combinations considered, 10 (63%) indicated a decreasing population (lambda < 1). For models based on age at first reproduction (alpha) of 13 years, the mean age of reproducing females at the stable age distribution (A) ranged from 15 to 23 years, which increased to 29-37 years when alpha was assumed to be 25. 6. All model scenarios had higher total elasticities for non-reproductive female survival [E(s(nr))] compared to those for reproductive female survival [E(s(r))]. 7. Assuming relatively slow, but biologically realistic, vital rates (alpha = 25 and biennial reproduction) and size-biased survival probabilities, our results suggest that the Ningaloo Reef population of whale sharks is declining, although more reproductive data are clearly needed to confirm this conclusion. Combining relatively precise survival estimates from CMR studies with realistic assumptions of other vital rates provides a useful heuristic framework for determining the vulnerability of large oceanic predators for which few direct data exist.     

Distal monosomy of the long arm of chromosome 6 (6q25----6qter) inherited by maternal translocation t(6q;17q)

Two half-sisters with distal monosomy of the long arm of chromosome 6 (q25----qter) inherited by maternal translocation t(6q;17q) were investigated. The clinical manifestations of these patients are compared with eight cases reported in the literature for further characterization of the 6q-syndrome. The cytogenetic diagnosis of alterations involving small chromosome fragments and the different origins of this type of deletion are also discussed.     

A region of primer binding variation at the D6S265 locus associated with HLA-A25 and HLA-A26 antigens

D6S265 is a polymorphic dinucleotide repeat, mapped within 70 kb centromeric of HLA-A, on chromosome 6p21.3. While genotyping families for genetic linkage analysis, allele non-amplification resulting in apparent non-Mendelian inheritance was observed at the D6S265 locus in 15 individuals, on chromosomes carrying the HLA-A25 and HLA-A26 antigens. The D6S265 locus was sequenced in a variant individual homozygous for allele non-amplification, and in a non-HLA-A25/-A26 individual, homozygous for D6S265 allele 1. Five base changes were identified in the reverse primer binding region of the variant individual, effectively preventing annealing of the 3 primer to the template.     

Bacterial diversity in the cecum of the world's largest living rodent (Hydrochoerus hydrochaeris)

The capybara (Hydrochoerus hydrochaeris) is the world's largest living rodent. Native to South America, this hindgut fermenter is herbivorous and coprophagous and uses its enlarged cecum to digest dietary plant material. The microbiota of specialized hindgut fermenters has remained largely unexplored. The aim of this work was to describe the composition of the bacterial community in the fermenting cecum of wild capybaras. The analysis of bacterial communities in the capybara cecum is a first step towards the functional characterization of microbial fermentation in this model of hindgut fermentation. We sampled cecal contents from five wild adult capybaras (three males and two females) in the Venezuelan plains. DNA from cecal contents was extracted, the 16S rDNA was amplified, and the amplicons were hybridized onto a DNA microarray (G2 PhyloChip). We found 933 bacterial operational taxonomic units (OTUs) from 182 families in 21 bacterial phyla in the capybara cecum. The core bacterial microbiota (present in at least four animals) was represented by 575 OTUs. About 86% of the cecal bacterial OTUs belong to only five phyla, namely, Firmicutes (322 OTUs), Proteobacteria (301 OTUs), Bacteroidetes (76 OTUs), Actinobacteria (69 OTUs), and Sphirochaetes (37 OTUs). The capybara harbors a diverse bacterial community that includes lineages involved in fiber degradation and nitrogen fixation in other herbivorous animals.