Positive selection and sequence rearrangements generate extensive polymorphism in the gamete recognition protein bindin

Bindin is a gamete recognition protein of sea urchins that mediates species-specific attachment of sperm to an egg-surface receptor during fertilization. Sequences of bindin from closely related urchins show fixed species-specific differences. Within species, highly polymorphic bindin alleles result from point substitution, insertion/deletion, and recombination. Since speciation, positive selection favoring allelic variants has generated diversity in bindin polypeptides. Intraspecific bindin variation can be tolerated by the egg receptor, which suggests functional parallels between this system and other flexible recognition systems, including immune recognition. These results show that polymorphism in mate recognition loci required for rapid evolution of sexual isolation can arise within natural populations.      

Photosynthesis and root growth in Spartina alterniflora in relation to root zone aeration

Spartina alterniflora Lois. is a dominant species growing in intermediate and saline marshes of the US Gulf coast and Atlantic coastal marshes. S. alterniflora plants were subjected to a range of soil redox potential (Eh) conditions representing a well aerated to reduced conditions in a rhizotron system under controlled environmental conditions. The low soil Eh resulted in inhibition of root elongation shortly after treatment initiation. Root elongation was reduced as soil Eh approached values below ca. +350 mV. Substantial decrease in root elongation was noted when soil Eh fell below +200 mV. Generally, net photosynthetic rate (PN) decreased as soil Eh was reduced, with substantial reductions in PN found when Eh approached negative values. Average PN was reduced to 87, 64, and 44% of control under +340, +245, and -180 mV treatments, respectively. The reductions in root elongation and PN in response to low soil Eh indicated the adverse effects of low soil Eh on plant functioning and the need for periods of soil aeration that allow plants to resume normal functioning. Thus periods of drainage allowing soil aeration during the growing season appear to be critical to S. alterniflora by providing favorable conditions for root growth and gas exchange with important implications for plant carbon fixation.     

Efficacy of the hydrogeomorphic model (HGM): A case study from western Tennessee

Hydrogeomorphic models (HGM) for wetland classification and functional assessment have been developed for several regions in the United States. However, validation of models is lacking, even though models are already in use and the general idea is that each is a working model, developing over time with new ideas and information. We examined the HGM developed for western Tennessee using novel data collected from six stream systems, two channelized, two channelized and leveed, and two unchannelized. The western Tennessee HGM has the ability to differentiate altered and unaltered rivers based mainly on changes to hydrologic floodplain functions, although functional capacity index values were validated from independent measures. Effects of channelization were confounded in western Tennessee by other disturbances, channel recovery processes, and variability due to levee construction. Levees render the greatest change to floodplains as they disconnect the channel and floodplain system, decreasing water tables and possible exchanges. One of the main factors controlling productivity along channels without levees was sedimentation. We recommend that estimated rates of sedimentation be incorporated into an updated version of the HGM. Variability of human alterations and natural floodplain heterogeneity suggest landscape factors (e.g., beta diversity, degree of ponding) and use of gradient indices may result in greater resolution for determining functional capacity of low gradient, riverine systems.     

Cytogenetic studies in Eigenmannia virescens (Sternopygidae, Gymnotiformes) and new inferences on the origin of sex chromosomes in the Eigenmannia genus

Background

Previous studies suggested that multiple domestication events in South and South-East Asia (Yunnan and surrounding areas) and India have led to the genesis of modern domestic chickens. Ha Giang province is a northern Vietnamese region, where local chickens, such as the H'mong breed, and wild junglefowl coexist. The assumption was made that hybridisation between wild junglefowl and Ha Giang chickens may have occurred and led to the high genetic diversity previously observed. The objectives of this study were i) to clarify the genetic structure of the chicken population within the Ha Giang province and ii) to give evidence of admixture with G. gallus. A large survey of the molecular polymorphism for 18 microsatellite markers was conducted on 1082 chickens from 30 communes of the Ha Giang province (HG chickens). This dataset was combined with a previous dataset of Asian breeds, commercial lines and samples of Red junglefowl from Thailand and Vietnam (Ha Noï). Measurements of genetic diversity were estimated both within-population and between populations, and a step-by-step Bayesian approach was performed on the global data set.

Results

The highest value for expected heterozygosity (> 0.60) was found in HG chickens and in the wild junglefowl populations from Thailand. HG chickens exhibited the highest allelic richness (mean A = 2.9). No significant genetic subdivisions of the chicken population within the Ha Giang province were found. As compared to other breeds, HG chickens clustered with wild populations. Furthermore, the neighbornet tree and the Bayesian clustering analysis showed that chickens from 4 communes were closely related to the wild ones and showed an admixture pattern.

Conclusion

In the absence of any population structuring within the province, the H'mong chicken, identified from its black phenotype, shared a common gene pool with other chickens from the Ha Giang population. The large number of alleles shared exclusively between Ha Giang chickens and junglefowl, as well as the results of a Bayesian clustering analysis, suggest that gene flow has been taking place from junglefowl to Ha Giang chickens.     

Forced expression of HLA-DM at the surface of dendritic cells increases loading of synthetic peptides on MHC class II molecules and modulates T cell responses

Adoptive transfer of autologous dendritic cells (DCs) loaded with tumor-associated CD4 and CD8 T cell epitopes represents a promising avenue for the immunotherapy of cancer. In an effort to increase the loading of therapeutic synthetic peptides on MHC II molecules, we used a mutant of HLA-DM (DMY) devoid of its lysosomal sorting motif and that accumulates at the cell surface. Transfection of DMY into HLA-DR(+) cells resulted in increased loading of the exogenously supplied HA(307-318) peptide, as well as increased stimulation of HA-specific T cells. Also, on transduction in mouse and human DCs, DMY increased loading of HEL(48-61) and of the tumor Ag-derived gp100(174-190) peptides, respectively. Interestingly, expression of DMY at the surface of APCs favored Th1 differentiation over Th2. Finally, we found that DMY(-) and DMY(+) mouse APCs differentially stimulated T cell hybridomas sensitive to the fine conformation of peptide-MHC II complexes. Taken together, our results suggest that the overexpression of HLA-DMY at the plasma membrane of DCs may improve quantitatively, but also qualitatively, the presentation of CD4 T cell epitopes in cellular vaccine therapies for cancer.     

Isolation of alpha-lactalbumin,beta-lactoglobulin,and bovine serum albumin from cow's milk using gel filtration and anion-exchange chromatography including evaluation of their antigenicity

The aim of this study was to introduce a simple, reproducible, and less expensive method for isolation of alpha-lactalbumin, beta-lactoglobulin, and bovine serum albumin from cow's milk while retaining their antigenicity. Whey (lactoserum) was obtained by isolating casein from defatted milk using hydrochloric acid. Globulins were then precipitated from whey by half-saturated ammonium sulfate and beta-lactoglobulin was purified further using Sephadex G-50 gel filtration. The proteins in the supernatant were also fractionated using diethylaminoethyl cellulose chromatography in which beta-lactoglobulin was separated from alpha-lactalbumin and bovine serum albumin. The latter two proteins that co-eluted in anion-exchange chromatography were then gently isolated from each other by Sephadex G-50 gel filtration. Pure beta-lactoglobulin was also obtained by anion-exchange chromatography of the ammonium sulfate-precipitated globulins. Using enzyme-linked immunosorbent assay (ELISA), Western blotting, and ELISA inhibition assay, antigenicity of the purified proteins was evaluated. Our results showed high purity and well-preserved antigenicity of alpha-lactalbumin, beta-lactoglobulin, and bovine serum albumin thus purified.     

Threshhold for recovery in the marsh halophyte Spartina alterniflora grown under the combined effects of salinity and soil drying

A study quantifying the physiological threshhold at which Spartina alterniflora plants are able to tolerate the interactive effects of salinity and soil drying was conducted in a climate controlled greenhouse. The experiment consisted of two levels of salinity (3-5 ppt, L and 35-38 ppt, H) as well as four dynamic water levels: flooding (water level maintained 3-5 cm above the soil surface at high tide and 10 cm below the soil surface at low tide for entire study duration, F), 8-day drought (water level maintained at least 20 cm below the soil surface at high tide for 8 days then flooded, 8 days), 16-day drought (water level maintained at least 20 cm below the soil surface at high tide for 16 days then flooded, 16 days), and 24-day drought (water level maintained at least 20 cm below the soil surface at high tide for 24 days then flooded, 24 days). Plant gas exchange and growth responses were measured along with soil conditions of redox potential and water potential. Significant decreases were seen in plant gas exchange and growth in response to increases in salinity and soil drying. Survival was 100% for all flooded treatments while increased salinity combined with soil drying decreased survival to 86% in both low salt/24-day drought plants (LD24) and high salt/16-day drought plants (HD16). The lowest survival rate was seen in the high salt/24-day drought treatment (HD24) at 29%. Therefore, it appears that the critical time for recovery from the combined effects of increased salinity and soil drying may greatly diminish after two weeks from the onset of stress conditions. Consequently, if salinity continues to increase along the MRDP, marshes dominated by S. alterniflora may be more susceptible to short-term drought and likewise large-scale marsh browning.     

Recent developments in QM/MM methods towards open-boundary multi-scale simulations

Combined quantum mechanics/molecular mechanics (QM/MM) methods have been widely used in multi-scale modelling and simulations of physical, chemical and biological processes in complex environments. In this review, we provide an overview of the recently developed QM/MM algorithms, with emphasis on our works, towards the ultimate goal of establishing an open boundary between the QM and MM subsystems. The open boundary is characterised by on-the-fly exchanges of partial charges and atoms between the QM and MM subsystems, allowing us to focus on the small QM subsystem of primary interest in dynamics simulations. An open-boundary scheme has the promise to the utilisations of small QM subsystems, high-levels of QM theory and long simulation times, which can potentially lead to new insights.