Rex1/Zfp42 is dispensable for pluripotency in mouse ES cells

Background  

Rex1/Zfp42 has been extensively used as a marker for the undifferentiated state of pluripotent stem cells. However, its function in pluripotent stem cells including embryonic stem (ES) cells remained unclear although its involvement in visceral endoderm differentiation in F9 embryonal carcinoma (EC) cells was reported.     

Molecular dynamics study of the KcsA potassium channel

The structural, dynamical, and thermodynamic properties of a model potassium channel are studied using molecular dynamics simulations. We use the recently unveiled protein structure for the KcsA potassium channel from Streptomyces lividans. Total and free energy profiles of potassium and sodium ions reveal a considerable preference for the larger potassium ions. The selectivity of the channel arises from its ability to completely solvate the potassium ions, but not the smaller sodium ions. Self-diffusion of water within the narrow selectivity filter is found to be reduced by an order of magnitude from bulk levels, whereas the wider hydrophobic section of the pore maintains near-bulk self-diffusion. Simulations examining multiple ion configurations suggest a two-ion channel. Ion diffusion is found to be reduced to approximately (1)/(3) of bulk diffusion within the selectivity filter. The reduced ion mobility does not hinder the passage of ions, as permeation appears to be driven by Coulomb repulsion within this multiple ion channel.     

Controls on Shumard Oak (Quercus shumardii) Establishment into the Cross Timbers Ecotone of Oklahoma: Implications for Restoration

To better understand how the Cross Timbers ecotone between U.S. eastern deciduous forest and tallgrass prairie is organized and maintained, I set out seedlings of Shumard oak (Quercus shumardii) for 1 year with treatments of water addition, trenching in pots to reduce belowground competition, burning, and patch type. I found that (1) seedlings in pots survived twice as much as those without pots and seedlings in unburned areas survived up to four times as much as those in burned areas; (2) seedlings in pots grew twice as fast as those planted directly in the soil without a pot; and (3) whereas adding water, planting in a pot, and planting under shrubs all increased leaf chlorophyll absorption, it was when the seedling was watered, under a shrub, or in a pot that chlorophyll increases were 2‐fold. Results suggest these management and restoration strategies to increase Cross Timbers oak establishment: first reduce belowground competition by the resident grasses; second, do not burn; and third, use shrubs as a facilitating tool. Adding water to tree seedlings should be used as a management tool only after others have been tried and failed. Finally, an ecotone conceptual vegetation model is presented both to incorporate the results and to explain how ecotones may be managed, restored, and maintained.     

Topological analysis of a haloacid permease of a Burkholderia sp. bacterium with a PhoA-LacZ reporter

Background  

2-Haloacids can be found in the natural environment as degradative products of natural and synthetic halogenated compounds. They can also be generated by disinfection of water and have been shown to be mutagenic and to inhibit glyceraldehyde-3-phosphate dehydrogenase activity. We have recently identified a novel haloacid permease Deh4p from a bromoacetate-degrading bacterium Burkholderia sp. MBA4. Comparative analyses suggested that Deh4p is a member of the Major Facilitator Superfamily (MFS), which includes thousands of membrane transporter proteins. Members of the MFS usually possess twelve putative transmembrane segments (TMS). Deh4p was predicted to have twelve TMS. In this study we characterized the topology of Deh4p with a PhoA-LacZ dual reporters system.     

Algorithms and software for support of gene identification experiments

MOTIVATION: Gene annotation is the final goal of gene prediction algorithms. However, these algorithms frequently make mistakes and therefore the use of gene predictions for sequence annotation is hardly possible. As a result, biologists are forced to conduct time-consuming gene identification experiments by designing appropriate PCR primers to test cDNA libraries or applying RT-PCR, exon trapping/amplification, or other techniques. This process frequently amounts to 'guessing' PCR primers on top of unreliable gene predictions and frequently leads to wasting of experimental efforts. RESULTS: The present paper proposes a simple and reliable algorithm for experimental gene identification which bypasses the unreliable gene prediction step. Studies of the performance of the algorithm on a sample of human genes indicate that an experimental protocol based on the algorithm's predictions achieves an accurate gene identification with relatively few PCR primers. Predictions of PCR primers may be used for exon amplification in preliminary mutation analysis during an attempt to identify a gene responsible for a disease. We propose a simple approach to find a short region from a genomic sequence that with high probability overlaps with some exon of the gene. The algorithm is enhanced to find one or more segments that are probably contained in the translated region of the gene and can be used as PCR primers to select appropriate clones in cDNA libraries by selective amplification. The algorithm is further extended to locate a set of PCR primers that uniformly cover all translated regions and can be used for RT-PCR and further sequencing of (unknown) mRNA.      

Divergent and reticulate processes in evolution of Ethiopian Lophuromys flavopunctatus species complex: evidence from mitochondrial and nuclear DNA differentiation patterns

Molecular study of mitochondrial and nuclear genes and cytogenetic analysis were performed to examine possible patterns of speciation in the diverse Lophuromys flavopunctatus species complex of Ethiopia. Phylogenetic analysis of mtDNA data resulted in an unresolved bush of ten deeply diverged haplotype groups corresponding to potential species either well supported by various types of character or 'cryptic'. The cytogenetic analysis showed representatives of five of these mtDNA lineages to share an identical karyotype (2 n  = 70, NFa = 84), that has not been found previously in Ethiopia. One of them, L.  cf.  sikapusi , being a member of the L. flavopunctatus species complex, demonstrates remarkable morphological similarity to representatives of another species complex, L. sikapusi s.l ., which might be considered as a result of convergent evolution in analogous environments. Analysis of RAPD data suggests that at least two mtDNA types might have been subject to interspecific transfer due to hybridization. In the case of two sympatric haplotypes of L. brunneus we may assume that the contemporary pattern of variation between them can be explained by relatively recent hybridization with another distinct species, L. flavopunctatus . The formation of two groups belonging to distinct mitochondrial lineages within northern populations could be associated with more complex processes including ancient hybridization.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 301–316.     

Seed predation,disease and germination on landslides in Neotropical lower montane wet forest

Abstract. Seed mortality (caused by predators and pathogens) and germination were compared between Puerto Rico and Costa Rica on landslides in lower montane wet forest. Seeds of six common species on five Puerto Rican landslides and four common species on two Costa Rican landslides were used with a Cecropia species and a Gonzalagunia species included at both sites. In the Puerto Rican experiments Cecropia schreberiana was the only species to show significant seed predation (which was due to insects), pathogens grew from all species and fewer seeds were lost to predators than pathogens. Also in Puerto Rico mean germination across all species was 57 % before dispersal (filled seeds collected while still on the tree) and 71 % after, with Phytolacca rivinoides seeds germinating most abundantly, followed in descending order by Ocotea leucoxylon, Cecropia spec, Miconia racemosa, Palicourea riparia and Gonzalagunia spicata. In the Costa Rican experiments three species had significant predation: Cecropia polyphlebia and Urera caracasana (both due to insects) and Witheringia coccoloboides (due to mammals); pathogenic disease caused more seed loss than predation, and germination was high (61 % pre-dispersal, 69 % post-dispersal). Similarities between these island and mainland sites included (1) percentage of seeds lost to predation and percentage lost to pathogens (all in the 5–15 % range), (2) generalist pathogens which claimed more seeds than predators and (3) majority germination with a general increase after dispersal. Finally sites were dissimilar only in the number of species with significant predation loss and whether it was by insects or mammals, casting doubt on the traditional island/mainland dichotomy.     

Mechanisms of plant response to gradients and after disturbances

Plant responses to gradients and after disturbances are important because they help define key ecosystem functions, such as productivity and decomposition. In this article I review studies that have tended to examine these influences on plants separately, presenting an incomplete view of vegetation dynamics. I then present a conceptual model of interaction between gradients and disturbance focusing on the mechanisms of plant-plant replacement, which largely determine species composition, abundance, and dispersion and are often mediated by changes in resource availability. The model consists of mechanisms that are either interactive and dependent on the presence of the replacing species or noninteractive and driven by the relationship between changing resource conditions in patches and the life histories / ecotolerances of species. The model explores variation in mechanism strength among different disturbances defined primarily by severity (e.g., amount of biomass lost), among gradients that differ in temperature and precipitation, and among species of fundamentally differing life histories. The main assumption is that plants mainly respond to the most limited resource in a given gradient × disturbance situation, as dictated by the relative severity of the disturbance versus the relative severity of the gradient. Finally, I sketch a general theory of plant responses containing the testable hypotheses from the model and also including axioms, assumptions, and deductions arising from these components.

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Resumen  Las condiciones pos disturbios son importantes porque ayudan a definir las claves del funcionamiento de un ecosistema tales como la productividad y la descomposición. En este artículo repaso estudios anteriores, que han tendido a estudiar la influencia de factures en las planta de manera separada, presentando una visión incompleta de la dinámica de la vegetación. En este estudio presento un modelo conceptual de las interaciones entre los gradientes naturales y los disturbios enfocado en los mecanismos de reemplazo planta-planta, los cuales influyen grandemente la composición, abundacia, y disperción de especies en un bosque y usualmente están mediados por cambios en la disponibilidad de recursos. El modelo consiste de mecanismos que interaccionan y dependen de la presencia de reemplazamiento de especies o no interaccionan y están dirigidos por la interrelatión entre cambios en la disponibilidad de recursos en parches y la historia de vida / ecotolerancia de las especies. El modelo explora variaciones en la fuerza del mecanismo entre diferentes disturbios definidos por la severidad (e.g., perdida de biomas), entre gradientes que se diferencia en temperature y presipitación, y entre especies con distintos historias de vida. El planteamiento principal es que las plantas responden mayormente al recurso más limitado en determinado gradiente multiplicado por la situación de disturbio correspondiente, según lo dicta la severidad relativa del disturbio contra la severidad relativa del gradiente. Finalmente, formulo una teoría general de la respuesta de las plantas que contiene la hipótesis comprobable del modelo e incluye axiomas, asunciones, y deducciones que surjen de los componentes.