Shell differentiation and engrailed expression in the Ilyanassa embryo

 We have used in situ hybridization and immunocytochemistry to study the expression of the engrailed-related gene, Ily-en in embryos of the marine mud snail Ilyanassa obsoleta. We find that Ily-en is only expressed in shell gland cells. Only mRNAs localized in the shell gland hybridize to an antisense probe of the Ily-en homeobox. Similarly, only shell gland cells or shell-forming cells are stained by the monoclonal antibody 4D9, which was raised to the engrailed-class protein from Drosophila. Ilyanassa embryos made deficient in vegetal cytoplasm by removing the third polar lobe fail to differentiate an organized external shell. They do however make some randomly oriented internal shell fragments in which Ily-en is expressed. Because Ily-en is expressed in shell gland cells of both normal and lobeless embryos, we conclude that the determinant(s) required for Ily-en expression are not exclusively localized in the polar lobe. Received: 16 October 1997 / Accepted: 9 January 1998     

A new fourier transform approach for protein coding measure based on the format of the Z curve

MOTIVATION: At the core of most protein gene-finding algorithms are the coding measures used to make a decision on coding/non-coding. Of the protein coding measures, the Fourier measure is one of the most important. However, due to the limited length of the windows usually used, the accuracy of the measure is not satisfactory. This paper is devoted to improving the accuracy by lengthening the sequence to amplify the periodicity of 3 in the coding regions. RESULTS: A new algorithm is presented called the lengthen-shuffle Fourier transform algorithm. For the same window length, the percentage accuracy of the new algorithm is 6-7% higher than that of the ordinary Fourier transform algorithm. The resulting percentage accuracy (average of specificity and sensitivity) of the new measure is 84.9% for the window length 162 bp. AVAILABILITY: The program is available on request fromC.- T. Zhang. Contact: ctzhang@tju.edu.cn      

Do Leptin Levels Predict Weight Gain?—A 5-Year Follow-Up Study in Mauritius

Objective : To investigate whether relative baseline leptin levels predict long-term changes in adiposity and/or its distribution. Research Methods and Procedures : In a longitudinal study of 2888 nondiabetic Mauritians aged 25 years to 74 years who participated in population-based surveys in 1987 and 1992, changes in body mass index (BMI), waist/hip ratio (WHR), and waist circumference were compared between “hyperleptinemic,” “normoleptinemic,” and “hypoleptinemic” groups. “Relative leptin levels” were calculated as standardized residuals from the regression of log₁₀ leptin on baseline BMI to provide a leptin measure independent of BMI. Analyses were performed within each sex. A linear regression model was used to assess the effect of standardized residuals on changes in BMI, WHR, and waist circumference, independent of baseline BMI, age, fasting insulin, and ethnicity. Results : After adjusting for age and baseline BMI by analysis of covariance, there was no difference in changes in BMI, WHR, or waist circumference between men with low, normal, or high relative leptin levels. Among women, there was a significant difference in ΔWHR across leptin groups, such that the largest increase occurred in the “normal” leptin group. For both men and women, the linear regression models explained ?10% of variation in dependent variables, and the only significant independent variables were age, BMI, and being of Chinese origin, compared with Indian origin. Discussion : These findings do not support a role for leptin concentration in predicting weight gain or changes in fat distribution in adults over a 5-year period.     

Sonic Hedgehog Controls the Phenotypic Fate and Therapeutic Efficacy of Grafted Neural Precursor Cells in a Model of Nigrostriatal Neurodegeneration

The expression of soluble growth and survival promoting factors by neural precursor cells (NPCs) is suggested to be a prominent mechanism underlying the protective and regenerative effects of these cells after transplantation. Nevertheless, how and to what extent specific NPC-expressed factors contribute to therapeutic effects is not well understood. Using RNA silencing, the current study investigated the roles of two donor NPC molecules, namely glial cell-line derived neurotrophic factor (GDNF) and sonic hedgehog (SHH), in the protection of substantia nigra dopamine neurons in rats treated with 6-hydroxydopamine (6-OHDA). Analyses indicate that as opposed to the knock-down of GDNF, SHH inhibition caused a profound decline in nigrostriatal neuroprotection. Further, SHH silencing also curbed endogenous neurogenesis and the migration of host brdU⁺/dcx⁺ neural precursors into the striatum, which was present in the animals receiving control or GDNF silenced NPCs. A change in graft phenotype, mainly reflected by a reduced proportion of undifferentiated nestin⁺ cells, as well as a significantly greater host microglial activity, suggested an important role for these processes in the attenuation of neuroprotection and neurogenesis upon SHH silencing. Overall these studies reveal core mechanisms fundamental to grafted NPC-based therapeutic effects, and delineate the particular contributions of two graft-expressed molecules, SHH and GDNF, in mediating midbrain dopamine neuron protection, and host plasticity after NPC transplantation.     

Effects of flow on lateral interactions of fish and shrimps with off-channel habitats in a large river-floodplain system

Off-channel habitats play a crucial role in the life-cycles of many riverine fish species, but lateral movements of fish into these habitats are poorly understood. We tested how flow dynamics affects the movement of fish and shrimps between the main river channel and different types of off-channel habitats: a riverine lake and a wetland. Our study site was the lower Waikato River, North Island, New Zealand, where there are numerous off-channel habitats. Fish were sampled using directional fyke nets. Shortfin eel (Anguilla australis) migrated mostly into the wetland at night, particularly during high river flows. Common bullies (Gobiomorphus cotidianus) were most abundant during the day and in low-discharge conditions, moving mostly into the riverine lake, whereas freshwater shrimp (Paratya curvirostris) moved mostly into the wetland. High numbers of non-native larval common carp (Cyprinus carpio) moved out of the wetland with retreating flood water. This study emphasises the importance of lateral connectivity and flooding in functioning of this river system where numerous native fish, but also exotic fish, used off-channel habitats. Floodplain management strategies should promote ‘controlled connectivity’ measures that provide access for native species at key times while limiting opportunities for introduced species to utilise their favoured off-channel habitats.     

A new factor stimulating peptidoglycan hydrolysis to separate daughter cells in Caulobacter crescentus

Cell division in Gram‐negative bacteria involves the co‐ordinated invagination of the three cell envelope layers to form two new daughter cell poles. This complex process starts with the polymerization of the tubulin‐like protein FtsZ into a Z‐ring at mid‐cell, which drives cytokinesis and recruits numerous other proteins to the division site. These proteins are involved in Z‐ring constriction, inner‐ and outer‐membrane invagination, peptidoglycan remodelling and daughter cell separation. Three papers in this issue of Molecular Microbiology, from the teams of Lucy Shapiro, Martin Thanbichler and Christine Jacobs‐Wagner, describe a novel protein, called DipM for Division Involved Protein with LysM domains, that is required for cell division in Caulobacter crescentus. DipM localizes to the mid‐cell during cell division, where it is necessary for the hydrolysis of the septal peptidoglycan to remodel the cell wall. Loss of DipM results in severe defects in cell envelope constriction, which is deleterious under fast‐growth conditions. State‐of‐the‐art microscopy experiments reveal that the peptidoglycan is thicker and that the cell wall is incorrectly organized in DipM‐depleted cells compared with wild‐type cells, demonstrating that DipM is essential for reorganizing the cell wall at the division site, for envelope invagination and cell separation in Caulobacter.     

Productivity differences between dandelion (Taraxacum officinale; Asteraceae) clones from pollution impacted versus non-impacted soils

Common dandelions (Taraxacum officinale Weber, sensu lato; Asteraceae) introduced to North America form an assemblage of asexual (agamospermous), clonal lineages derived from Eurasian mixed sexual and asexual populations. We investigated whether selection for more pollution tolerant clonal lineages occurs at polluted sites and selection for more pollution intolerant lineages occurs at unpolluted sites. We tested the above hypothesis by performing reciprocal greenhouse productivity experiments in which unique dandelion clones (12 clones, identified by DNA fingerprinting, from each site type) sampled from two unpolluted and two polluted (moderately enhanced Cu, Pb and Zn soil concentrations) sites were grown pairwise in both unpolluted (nutrient solution only) and polluted (nutrient solution + Cu, Pb and Zn) media (n?=?48 paired tests for each media type). Dandelion clones from polluted sites produced fewer and smaller leaves, shorter roots and smaller root diameters, reduced shoot and root dry weights, and reduced total biomass compared to clones from unpolluted sites when clones were grown in unpolluted-media (P?≤?0.05). In contrast, clones taken from unpolluted sites were shown to produce significantly fewer and shorter leaves, shorter roots and smaller root diameters, reduced shoot and root dry weights, reduced total biomass, a reduced shoot : root biomass ratio, and have much lower survival compared to clones from polluted sites when both were grown in polluted-media (P?≤?0.05). These results reveal that there was increased selection against unpolluted-site clonal lineages in polluted-media and against polluted-site clonal lineages in unpolluted-media. Across all treatments, clones from unpolluted sites growing in unpolluted-media had the highest proximate measures of fitness. Overall, these findings provide insight into the relationships among anthropogenic environmental contamination and the consequent effects of selective forces acting on dandelion clones and their population genetic architecture.     

Predicting Secchi disk depth from average beam attenuation in a deep,ultra-clear lake

We addressed potential sources of error in estimating the water clarity of mountain lakes by investigating the use of beam transmissometer measurements to estimate Secchi disk depth. The optical properties Secchi disk depth (SD) and beam transmissometer attenuation (BA) were measured in Crater Lake (Crater Lake National Park, Oregon, USA) at a designated sampling station near the maximum depth of the lake. A standard 20 cm black and white disk was used to measure SD. The transmissometer light source had a nearly monochromatic wavelength of 660 nm and a path length of 25 cm. We created a SD prediction model by regression of the inverse SD of 13 measurements recorded on days when environmental conditions were acceptable for disk deployment with BA averaged over the same depth range as the measured SD. The relationship between inverse SD and averaged BA was significant and the average 95% confidence interval for predicted SD relative to the measured SD was ±1.6 m (range = −4.6 to 5.5 m) or ±5.0%. Eleven additional sample dates tested the accuracy of the predictive model. The average 95% confidence interval for these sample dates was ±0.7 m (range = −3.5 to 3.8 m) or ±2.2%. The 1996–2000 time-series means for measured and predicted SD varied by 0.1 m, and the medians varied by 0.5 m. The time-series mean annual measured and predicted SD’s also varied little, with intra-annual differences between measured and predicted mean annual SD ranging from −2.1 to 0.1 m. The results demonstrated that this prediction model reliably estimated Secchi disk depths and can be used to significantly expand optical observations in an environment where the conditions for standardized SD deployments are limited.     

The extent and significance of petroleum hydrocarbon contamination in Crater Lake,Oregon

In order to evaluate hydrocarbon inputs to Crater Lake from anthropogenic and natural sources, samples of water, aerosol, surface slick and sediment were collected and analyzed by gas chromatography-mass spectrometry (GC-MS) for determination of their aliphatic and aromatic hydrocarbon concentrations and compositions. Results show that hydrocarbons originate from both natural (terrestrial plant waxes and algae) and anthropogenic (petroleum use) sources and are entering the lake through direct input and atmospheric transport. The concentrations of petroleum hydrocarbons range from low to undetectable. The distributions and abundances of n-alkanes, polycyclic aromatic hydrocarbons (PAH) and unresolved complex mixture (UCM) from petroleum are similar for all surface slick sampling sites. The estimated levels of PAH in surface slicks range from 7–9 ng/m² which are low. Transport of petroleum-derived hydrocarbons from the lake surface has resulted in their presence in some sediments, particularly near the boat operations mooring (total petroleum HC = 1440 μg/kg, dry wt. compared to naturally derived n-alkanes, 240 μg/kg, dry wt.). The presence of biomarkers such as the tricyclic terpanes, hopanes and steranes in shallow sediments further confirms petroleum input from boat traffic. In the deep lake sediments, petroleum hydrocarbon concentrations were very low (16 μg/kg, dry wt.). Very low concentrations of PAH were detected in shallow sediments (17–40 μg/kg at 5 m depth near the boat operations) and deep sediments (3–15 μg/kg at 580 m depth). The individual PAH concentrations in sediments (μg/kg or ppb range) are at least three orders of magnitude less than reported threshold effects levels (mg/kg or ppm range, test amphipod Hyalella azteca). Therefore, no adverse effects are expected to occur in benthic biota exposed to these sediments. Boating activities are leaving a detectable level of petroleum in surface waters and lake sediments but these concentrations are very low.