Mutations in a human ROBO gene disrupt hindbrain axon pathway crossing and morphogenesis

The mechanisms controlling axon guidance are of fundamental importance in understanding brain development. Growing corticospinal and somatosensory axons cross the midline in the medulla to reach their targets and thus form the basis of contralateral motor control and sensory input. The motor and sensory projections appeared uncrossed in patients with horizontal gaze palsy with progressive scoliosis (HGPPS). In patients affected with HGPPS, we identified mutations in the ROBO3 gene, which shares homology with roundabout genes important in axon guidance in developing Drosophila, zebrafish, and mouse. Like its murine homolog Rig1/Robo3, but unlike other Robo proteins, ROBO3 is required for hindbrain axon midline crossing.     

Biogeochemistry. Sulfate reducers--dominant players in a low-oxygen world?

Sulfate reducing bacteria can adapt to extreme physical and chemical conditions and play an important role in global geochemical cycles, but their role in the formation of ore deposits has remained controversial. Strong support for such a role is provided by Labrenz et al., who have discovered sulfate-reducing bacteria that can tolerate low levels of oxygen and can precipitate zinc sulfide minerals. The results may have implications for bioremediation and may provide clues to processes that may have been more widespread in the geologic past.     

Ultrafast electron crystallography of interfacial water

We report direct determination of the structures and dynamics of interfacial water on a hydrophilic surface with atomic-scale resolution using ultrafast electron crystallography. On the nanometer scale, we observed the coexistence of ordered surface water and crystallite-like ice structures, evident in the superposition of Bragg spots and Debye-Scherrer rings. The structures were determined to be dominantly cubic, but each undergoes different dynamics after the ultrafast substrate temperature jump. From changes in local bond distances (OH.O and O.O) with time, we elucidated the structural changes in the far-from-equilibrium regime at short times and near-equilibration at long times.     

High-throughput mapping of a dynamic signaling network in mammalian cells

Signaling pathways transmit information through protein interaction networks that are dynamically regulated by complex extracellular cues. We developed LUMIER (for luminescence-based mammalian interactome mapping), an automated high-throughput technology, to map protein-protein interaction networks systematically in mammalian cells and applied it to the transforming growth factor-beta (TGFbeta) pathway. Analysis using self-organizing maps and k-means clustering identified links of the TGFbeta pathway to the p21-activated kinase (PAK) network, to the polarity complex, and to Occludin, a structural component of tight junctions. We show that Occludin regulates TGFbeta type I receptor localization for efficient TGFbeta-dependent dissolution of tight junctions during epithelial-to-mesenchymal transitions.     

Graduate students' teaching experiences improve their methodological research skills

Science, technology, engineering, and mathematics (STEM) graduate students are often encouraged to maximize their engagement with supervised research and minimize teaching obligations. However, the process of teaching students engaged in inquiry provides practice in the application of important research skills. Using a performance rubric, we compared the quality of methodological skills demonstrated in written research proposals for two groups of early career graduate students (those with both teaching and research responsibilities and those with only research responsibilities) at the beginning and end of an academic year. After statistically controlling for preexisting differences between groups, students who both taught and conducted research demonstrate significantly greater improvement in their abilities to generate testable hypotheses and design valid experiments. These results indicate that teaching experience can contribute substantially to the improvement of essential research skills.     

Effects of diluted and undiluted treated wastewater on the growth,physiological aspects and visual quality of potted lantana and polygala plants

In many nurseries in the Mediterranean area irrigation water supply is a major problem due to climatic conditions, and it is important to evaluate alternative water resources, such as treated wastewater, for ornamental plant production. For this reason, a nursery study was conducted in order to determine: (1) the effect of irrigation with a saline reclaimed wastewater (reused water) on the growth and visual quality of Lantana camara and Polygala myrtifolia, and (2) the effectiveness of the mixing the same water with canal water to reduce any negative effects observed with the reused water. Potted plants were irrigated with reused water, canal water and reused water diluted 50% with canal water. The results suggest that polygala can be irrigated with reused water since visual damage is minimal and growth reduction very slight, which seems to be related with the plant's low accumulation of saline ions. In lantana, reused water led to an excessive uptake of chloride, sodium and boron in the leaves, which was associated with defoliation, leaf burn, leaf chlorosis and damage to the photosynthetic apparatus, diminishing both growth and its aesthetic value. The dilution of reused water alleviated some negative effects in lantana, but not sufficiently to avoid a significant loss of plant quality.     

The fate of Amazonian forest fragments: A 32-year investigation

We synthesize findings to date from the world’s largest and longest-running experimental study of habitat fragmentation, located in central Amazonia. Over the past 32 years, Amazonian forest fragments ranging from 1 to 100 ha have experienced a wide array of ecological changes. Edge effects have been a dominant driver of fragment dynamics, strongly affecting forest microclimate, tree mortality, carbon storage, fauna, and other aspects of fragment ecology. However, edge-effect intensity varies markedly in space and time, and is influenced by factors such as edge age, the number of nearby edges, and the adjoining matrix of modified vegetation surrounding fragments. In our study area, the matrix has changed markedly over the course of the study (evolving from large cattle pastures to mosaics of abandoned pasture and regrowth forest) and this in turn has strongly influenced fragment dynamics and faunal persistence. Rare weather events, especially windstorms and droughts, have further altered fragment ecology. In general, populations and communities of species in fragments are hyperdynamic relative to nearby intact forest. Some edge and fragment-isolation effects have declined with a partial recovery of secondary forests around fragments, but other changes, such as altered patterns of tree recruitment, are ongoing. Fragments are highly sensitive to external vicissitudes, and even small changes in local land-management practices may drive fragmented ecosystems in markedly different directions. The effects of fragmentation are likely to interact synergistically with other anthropogenic threats such as logging, hunting, and especially fire, creating an even greater peril for the Amazonian biota.     

Species-specific sensitivity of earthworm coelomocytes to dermal metal (Cd,Cu, Ni,Pb, Zn) exposures: Methodological approach

Earthworm immune-competent cells (coelomocytes) can be adversely affected by soil metal contamination. The aim of the present paper was to perform comparative studies on the coelomocytes of four lumbricid species dermally exposed for 2 days to filter paper soaked with Ni, Cu, Zn, Cd, or Pb chlorides (1 mM). Coelomocytes were expelled by electro-stimulation, counted, and assayed ex vivo by flow cytometry and spectrofluorometry. The coelomocytes of Allolobophora chlorotica and Dendrobaena veneta contain both amoebocytes and riboflavin-storing eleocytes; consequently, they were subjected to assays based on flow cytometric quantification of autofluorescent eleocytes and spectrofluorometric measurement of riboflavin content in coelomocyte lysates. In Al. chlorotica, the number of coelomocytes, the percentage of eleocytes, and the amount of riboflavin were significantly lower in Cu-exposed worms although these cytometric parameters were less affected by Ni, Zn, Cd exposure, and entirely unaffected by Pb exposure. In D. veneta, such cellular effects were also only observed in Cu-exposed worms. The coelomic fluids of Aporrectodea caliginosa and Lumbricus rubellus are constitutionally impoverished of eleocytes; therefore, these species could not be subjected to assays measuring the riboflavin content of these granular cells. Rather, the amoebocytes of Ap. caliginosa and L. rubellus were subjected to flow cytometric measurements of in vitro neutral red uptake (NR). However, the NR uptake assay was technically demanding, requiring a strictly normalized incubation period over all samples to yield useful comparative data. In contrast, the riboflavin content in the coelomocyte lysates of eleocyte-rich species appears to be a robust and convenient immune-function biomarker of environmental stress.     

Changes in the genetic structure of Bacteria and microbial activity in an agricultural soil amended with tannery sludge

The application of tannery sludge to soils is a form of recycling; however, few studies have examined the impacts of this practice on soil microbial properties. We studied effects of two applications (2006 and 2007) of tannery sludge (with a low chromium content) on the structure of the bacterial community and on the microbial activity of soils. We fertilized an agricultural area in Rolândia, Paraná state, Brazil with different doses of sludge based on total N content, which ranged from 0 to 1200 kg N ha⁻¹. Sludge remained on the soil surface for three months before being plowed. Soils were sampled seven times during the experiment. Bacterial community structure, assessed by denaturing gradient gel electrophoresis (DGGE), was modified by the application of tannery sludge. Soon after the first application, there was clear separation between the bacterial communities in different treatments, such that each dose of sludge was associated with a specific community. These differences remained until 300 days after application and also after the second sludge application, but 666 days after the beginning of the experiment no differences were found in the bacterial communities of the lowest doses and the control. The principal response curve (PRC) analysis showed that the first sludge application strongly stimulated biological activity even 300 days after application. The second application also stimulated activity, but at a lower magnitude and for a shorter time, given that 260 days after the second application there was no difference in biological activity among treatments. PRC also showed that the properties most influenced by the application of tannery sludge were enzymatic activities related to N cycling (asparaginase and urease). The redundancy analysis (RDA) showed that tannery sludge’s influence on microbial activity is mainly related to increases in inorganic N and soil pH. Results showed that changes in the structure of the bacterial community in the studied soils were directly related to changes of their biological activity.