Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning

<p>Abstract</p> <p>Background</p> <p>Viruses have a profound influence on both the ecology and evolution of marine plankton, but the genetic diversity of viral assemblages, particularly those in deeper ocean waters, remains poorly described. Here we report on the construction and analysis of a viral metagenome prepared from below the euphotic zone in a temperate, eutrophic bay of coastal California.</p> <p>Methods</p> <p>We purified viruses from approximately one cubic meter of seawater collected from 200m depth in Monterey Bay, CA. DNA was extracted from the virus fraction, sheared, and cloned with no prior amplification into a plasmid vector and propagated in <it>E. coli </it>to produce the MBv200m library. Random clones were sequenced by the Sanger method. Sequences were assembled then compared to sequences in GenBank and to other viral metagenomic libraries using BLAST analyses.</p> <p>Results</p> <p>Only 26% of the 881 sequences remaining after assembly had significant (E ≤ 0.001) BLAST hits to sequences in the GenBank nr database, with most being matches to bacteria (15%) and viruses (8%). When BLAST analysis included environmental sequences, 74% of sequences in the MBv200m library had a significant match. Most of these hits (70%) were to microbial metagenome sequences and only 0.7% were to sequences from viral metagenomes. Of the 121 sequences with a significant hit to a known virus, 94% matched bacteriophages (Families <it>Podo</it>-, <it>Sipho</it>-, and <it>Myoviridae</it>) and 6% matched viruses of eukaryotes in the Family <it>Phycodnaviridae </it>(5 sequences) or the Mimivirus (2 sequences). The largest percentages of hits to viral genes of known function were to those involved in DNA modification (25%) or structural genes (17%). Based on reciprocal BLAST analyses, the MBv200m library appeared to be most similar to viral metagenomes from two other bays and least similar to a viral metagenome from the Arctic Ocean.</p> <p>Conclusions</p> <p>Direct cloning of DNA from diverse marine viruses was feasible and resulted in a distribution of virus types and functional genes at depth that differed in detail, but were broadly similar to those found in surface marine waters. Targeted viral analyses are useful for identifying those components of the greater marine metagenome that circulate in the subcellular size fraction.</p

Abnormal Intracellular Accumulation and Extracellular Aβ Deposition in Idiopathic and Dup15q11.2-q13 Autism Spectrum Disorders

<div><h3>Background</h3><p>It has been shown that amyloid ß (Aβ), a product of proteolytic cleavage of the amyloid β precursor protein (APP), accumulates in neuronal cytoplasm in non-affected individuals in a cell type–specific amount.</p> <h3>Methodology/Principal Findings</h3><p>In the present study, we found that the percentage of amyloid-positive neurons increases in subjects diagnosed with idiopathic autism and subjects diagnosed with duplication 15q11.2-q13 (dup15) and autism spectrum disorder (ASD). In spite of interindividual differences within each examined group, levels of intraneuronal Aβ load were significantly greater in the dup(15) autism group than in either the control or the idiopathic autism group in 11 of 12 examined regions (p<0.0001 for all comparisons; Kruskall-Wallis test). In eight regions, intraneuronal Aβ load differed significantly between idiopathic autism and control groups (p<0.0001). The intraneuronal Aβ was mainly N-terminally truncated. Increased intraneuronal accumulation of Aβ_17–40/42 in children and adults suggests a life-long enhancement of APP processing with α-secretase in autistic subjects. Aβ accumulation in neuronal endosomes, autophagic vacuoles, Lamp1-positive lysosomes and lipofuscin, as revealed by confocal microscopy, indicates that products of enhanced α-secretase processing accumulate in organelles involved in proteolysis and storage of metabolic remnants. Diffuse plaques containing Aβ_1–40/42 detected in three subjects with ASD, 39 to 52 years of age, suggest that there is an age-associated risk of alterations of APP processing with an intraneuronal accumulation of a short form of Aβ and an extracellular deposition of full-length Aβ in nonfibrillar plaques.</p> <h3>Conclusions/Significance</h3><p>The higher prevalence of excessive Aβ accumulation in neurons in individuals with early onset of intractable seizures, and with a high risk of sudden unexpected death in epilepsy in autistic subjects with dup(15) compared to subjects with idiopathic ASD, supports the concept of mechanistic and functional links between autism, epilepsy and alterations of APP processing leading to neuronal and astrocytic Aβ accumulation and diffuse plaque formation.</p> </div

Growth and water relations of field-grown Valencia orange trees under long-term partial rootzone drying

Climate, soil water potential (SWP), leaf relative water content (RWC), stem water potential (WPstem), stomatal conductance (gs), trunk, shoot and fruit growth of 'Valencia' orange trees were monitored during five consecutive seasons (2007â2012) to study water status and growth responses to irrigation placement or volume. 48 adult trees were exposed to conventional irrigation (CI, 100% of crop evapotranspiration on both sides of the rootzone), partial rootzone drying (PRD, 50% of CI water only on one alternated side of the rootzone) and continuous deficit irrigation (DI, 50% of CI water on both sides of the rootzone). Reducing irrigation volumes by 55% (DI) over CI increased leaf water deficit by 27% and reduced 'Valencia' fruit growth by 15% but not shoot or trunk growth. Similar water savings by PRD did not induce significant growth reductions. Differences in fruit growth rates determined 17% yield reduction in DI but not PRD trees. If we consider integrals of data across each season, PRD induced milder soil and leaf water deficit than DI but similar stomatal conductance. Tree daily water consumption (Etree) estimated from daily leaf transpiration was significantly lower in PRD and DI than in CI. Fruit growth efficiency (growth rate per unit Etree) was similar in all irrigation treatments, while shoot growth efficiency was higher in PRD than in CI. In PRD, an increased shoot growth efficiency rather than fruit growth efficiency is most likely due to water and assimilates being diverted from fruit to shoot growth under high VPD conditions. Although these results show good evidence of an irrigation placement effect inducing an advantage of the PRD strategy in 'Valencia' orange in terms of milder soil and leaf water deficit and more sustainable fruit growth compared to DI, PRD did not induce any significant advantage in terms of final yield over a simple reduction of irrigation volumes

Stomatal control by chemical signalling and the exploitation of of this mechanism to increase water use efficiency in agriculture.

Stomatal behaviour of plants in drying soil can be regulated by (long distance) chemical signals that provide the shoot with some measure of water availability. Although much emphasis has been placed on the plant hormone abscisic acid (ABA) as a central component of the signalling process, soil drying will modify the delivery to the shoot of a range of potential chemical signals. Here we consider the role that changes in the xylem sap pH might play in determining the access that ABA has to sites of action on the guard cells. We also show how redistribution of inorganic ions between different compartments in the leaf (localized chemical signalling) can provide sensitive control of stomata and water loss in response to potentially damaging changes in leaf temperature. Partial root zone drying is an irrigation technique that has been developed to allow exploitation of the plant’s long distance signalling system. When the system is optimized, stomatal behaviour, shoot water status and leaf growth can be regulated such that water use efficiency (fruit yield/water used) can be significantly increased. We show how an understanding of the drought stress physiology of the whole plant can lead to substantial saving of irrigation water in agriculture