Accounting for the power of Nature: using flume and field studies to compare the capacities of bio-energy and fluvial energy to move surficial gravels

River channel, riparian and floodplain forms and dynamics are all influenced strongly by biological processes. However, the influence of macroinvertebrates on entrainment and transport of river sediments remains poorly understood. We use an energy-based approach to explore the capacity of benthic animals to move surficial, gravel-bed particles in field and laboratory settings, and use the results to assess the relative significance of biological and physical benthic processes. Our results showed that in 11 British gravel-bed rivers, the maximum energy content (i.e., calorific content) of macroinvertebrate communities generally matched the flow energy associated with median discharges and, at multiple sites, exceeded that of the 10-year return interval flood. A series of laboratory experiments used to estimate the minimum energy expended by signal crayfish (Pacifastacus leniusculus) when performing geomorphic work established that crayfish move gravel particles at energy levels below that expected of the flow, complicating direct comparisons of the capacity for macroinvertebrates and fluvial flows to influence bed mobility. Our findings suggest that the influence of macroinvertebrate communities in either promoting, or suppressing, mobilisation of the bed may be large compared to equivalent values of fluvial energy. Based on these findings, we conclude that in the gravel-bed rivers studied, the macroinvertebrate community’s potential to perform geomorphic work matches or exceeds the stream power during most of the year. Although our study examined biological and fluvial energy systems separaetely, it is important to recognise that in Nature these systems are highly interactive. It follows that utilising the energy framework presented in this paper could lead to rapid advances in both fluvial biogeomorphology and river management and restoration

Vibrational microscopy and imaging of skin: from single cells to intact tissue

Vibrational microscopy and imaging offer several advantages for a variety of dermatological applications, ranging from studies of isolated single cells (corneocytes) to characterization of endogenous components in intact tissue. Two applications are described to illustrate the power of these techniques for skin research. First, the feasibility of tracking structural alterations in the components of individual corneocytes is demonstrated. Two solvents, DMSO and chloroform/methanol, commonly used in dermatological research, are shown to induce large reversible alterations (α-helix to β-sheet) in the secondary structure of keratin in isolated corneocytes. Second, factor analysis of image planes acquired with confocal Raman microscopy to a depth of 70 μm in intact pigskin, demonstrates the delineation of specific skin regions. Two particular components that are difficult to identify by other means were observed in the epidermis. One small region was formed from a conformationally ordered lipid phase containing cholesterol. In addition, the presence of nucleated cells in the tissue (most likely keratinocytes) was revealed by the spectral signatures of the phosphodiester and cytosine moieties of cellular DNA

Accounting for the power of nature: Using flume and field studies to compare the capacities of bio-energy and fluvial energy to move surficial gravels

River channels, riparian and floodplain forms and dynamics are all influenced strongly by biological processes. However, the influence of macroinvertebrates on entrainment and transport of river sediments remains poorly understood. We use an energy-based approach to explore the capacity of benthic animals to move surficial, gravel-bed particles in field and laboratory settings and use the results to assess the relative significance of biological and physical benthic processes. Our results showed that in 11 British gravel-bed rivers, the maximum energy content (i.e., calorific content) of macroinvertebrate communities generally matched the flow energy associated with median discharges and, at multiple sites, exceeded that of the 10-year return interval flood. A series of laboratory experiments used to estimate the minimum energy expended by signal crayfish (Pacifastacus leniusculus) when performing geomorphic work established that crayfish move gravel particles at energy levels below that expected of the flow, complicating direct comparisons of the capacity for macroinvertebrates and fluvial flows to influence bed mobility. Our findings suggest that the influence of macroinvertebrate communities in either promoting or suppressing, the mobilisation of the bed may be large compared to equivalent values of fluvial energy. Based on these findings, we conclude that in the gravel-bed rivers studied, the macroinvertebrate community's potential to perform geomorphic work matches or exceeds the stream power during most of the year. Although our study examined biological and fluvial energy systems separately, it is important to recognise that in nature, these systems are highly interactive. It follows that utilising the energy framework presented in this paper could lead to rapid advances in both fluvial biogeomorphology and river management and restoration

High through-put sequencing of the Parhyale hawaiensis mRNAs and microRNAs to aid comparative developmental studies

Understanding the genetic and evolutionary basis of animal morphological diversity will require comparative developmental studies that use new model organisms. This necessitates development of tools for the study of genetics and also the generation of sequence information of the organism to be studied. The development of next generation sequencing technology has enabled quick and cost effective generation of sequence information. Parhyale hawaiensis has emerged as a model organism of choice due to the development of advanced molecular tools, thus P. hawaiensis genetic information will help drive functional studies in this organism. Here we present a transcriptome and miRNA collection generated using next generation sequencing platforms. We generated approximately 1.7 million reads from a P. hawaiensis cDNA library constructed from embryos up to the germ band stage. These reads were assembled into a dataset comprising 163,501 transcripts. Using the combined annotation of Annot8r and pfam2go, Gene Ontology classifications was assigned to 20,597 transcripts. Annot8r was used to provide KEGG orthology to our transcript dataset. A total of 25,292 KEGG pathway assignments were defined and further confirmed with reciprocal blast against the NCBI nr protein database. This has identified many P. hawaiensis gene orthologs of key conserved signalling pathways involved in development. We also generated small RNA sequences from P. hawaiensis, identifying 55 conserved miRNAs. Sequenced small RNAs that were not annotated by stringent comparison to mirBase were used to search the Daphnia pulex for possible novel miRNAs. Using a conservative approach, we have identified 51 possible miRNA candidates conserved in the Daphnia pulex genome, which could be potential crustacean/arthropod specific miRNAs. Our study presents gene and miRNA discovery in a new model organism that does not have a sequenced genome. The data provided by our work will be valuable for the P. hawaiensis community as well as the wider evolutionary developmental biology community

DHA Supplemented in Peptamen Diet Offers No Advantage in Pathways to Amyloidosis: Is It Time to Evaluate Composite Lipid Diet?

Numerous reports have documented the beneficial effects of dietary docosahexaenoic acid (DHA) on beta-amyloid production and Alzheimer's disease (AD). However, none of these studies have examined and compared DHA, in combination with other dietary nutrients, for its effects on plaque pathogenesis. Potential interactions of DHA with other dietary nutrients and fatty acids are conventionally ignored. Here we investigated DHA with two dietary regimes; peptamen (pep+DHA) and low fat diet (low fat+DHA). Peptamen base liquid diet is a standard sole-source nutrition for patients with gastrointestinal dysfunction. Here we demonstrate that a robust AD transgenic mouse model shows an increased tendency to produce beta-amyloid peptides and amyloid plaques when fed a pep+DHA diet. The increase in beta-amyloid peptides was due to an elevated trend in the levels of beta-secretase amyloid precursor protein (APP) cleaving enzyme (BACE), the proteolytic C-terminal fragment beta of APP and reduced levels of insulin degrading enzyme that endoproteolyse beta-amyloid. On the contrary, TgCRND8 mice on low fat+DHA diet (based on an approximately 18% reduction of fat intake) ameliorate the production of abeta peptides and consequently amyloid plaques. Our work not only demonstrates that DHA when taken with peptamen may have a tendency to confer a detrimental affect on the amyloid plaque build up but also reinforces the importance of studying composite lipids or nutrients rather than single lipids or nutrients for their effects on pathways important to plaque development

Significant Effects of Antiretroviral Therapy on Global Gene Expression in Brain Tissues of Patients with HIV-1-Associated Neurocognitive Disorders

Antiretroviral therapy (ART) has reduced morbidity and mortality in HIV-1 infection; however HIV-1-associated neurocognitive disorders (HAND) persist despite treatment. The reasons for the limited efficacy of ART in the brain are unknown. Here we used functional genomics to determine ART effectiveness in the brain and to identify molecular signatures of HAND under ART. We performed genome-wide microarray analysis using Affymetrix U133 Plus 2.0 Arrays, real-time PCR, and immunohistochemistry in brain tissues from seven treated and eight untreated HAND patients and six uninfected controls. We also determined brain virus burdens by real-time PCR. Treated and untreated HAND brains had distinct gene expression profiles with ART transcriptomes clustering with HIV-1-negative controls. The molecular disease profile of untreated HAND showed dysregulated expression of 1470 genes at p<0.05, with activation of antiviral and immune responses and suppression of synaptic transmission and neurogenesis. The overall brain transcriptome changes in these patients were independent of histological manifestation of HIV-1 encephalitis and brain virus burdens. Depending on treatment compliance, brain transcriptomes from patients on ART had 83% to 93% fewer dysregulated genes and significantly lower dysregulation of biological pathways compared to untreated patients, with particular improvement indicated for nervous system functions. However a core of about 100 genes remained similarly dysregulated in both treated and untreated patient brain tissues. These genes participate in adaptive immune responses, and in interferon, cell cycle, and myelin pathways. Fluctuations of cellular gene expression in the brain correlated in Pearson's formula analysis with plasma but not brain virus burden. Our results define for the first time an aberrant genome-wide brain transcriptome of untreated HAND and they suggest that antiretroviral treatment can be broadly effective in reducing pathophysiological changes in the brain associated with HAND. Aberrantly expressed transcripts common to untreated and treated HAND may contribute to neurocognitive changes defying ART

HIV-1 Replication in the Central Nervous System Occurs in Two Distinct Cell Types

Human immunodeficiency virus type 1 (HIV-1) infection of the central nervous system (CNS) can lead to the development of HIV-1-associated dementia (HAD). We examined the virological characteristics of HIV-1 in the cerebrospinal fluid (CSF) of HAD subjects to explore the association between independent viral replication in the CNS and the development of overt dementia. We found that genetically compartmentalized CCR5-tropic (R5) T cell-tropic and macrophage-tropic HIV-1 populations were independently detected in the CSF of subjects diagnosed with HIV-1-associated dementia. Macrophage-tropic HIV-1 populations were genetically diverse, representing established CNS infections, while R5 T cell-tropic HIV-1 populations were clonally amplified and associated with pleocytosis. R5 T cell-tropic viruses required high levels of surface CD4 to enter cells, and their presence was correlated with rapid decay of virus in the CSF with therapy initiation (similar to virus in the blood that is replicating in activated T cells). Macrophage-tropic viruses could enter cells with low levels of CD4, and their presence was correlated with slow decay of virus in the CSF, demonstrating a separate long-lived cell as the source of the virus. These studies demonstrate two distinct virological states inferred from the CSF virus in subjects diagnosed with HAD. Finally, macrophage-tropic viruses were largely restricted to the CNS/CSF compartment and not the blood, and in one case we were able to identify the macrophage-tropic lineage as a minor variant nearly two years before its expansion in the CNS. These results suggest that HIV-1 variants in CSF can provide information about viral replication and evolution in the CNS, events that are likely to play an important role in HIV-associated neurocognitive disorders

High energy collision-induced dissociation (CID) product ion spectra of isomeric polyhydroxy sugars

High energy (4 keV) collision-induced dissociation (CID) product ion spectra have been obtained for a series of isomeric sugar molecules of close structural similarity. The reproducibility of the approach has been established and the spectra shown to have significant differences. These differences have been rationalised in terms of conventional mass spectrometric fragmentation rules. The data have also been subjected to analysis using chemometric methods, which require no specialist mass spectrometric input. The resulting classification of the data shows good agreement with the conventional interpretation approach. (C) 2003 Elsevier B.V. All rights reserved