Apparent competition drives community-wide parasitism rates and changes in host abundance across ecosystem boundaries

Species have strong indirect effects on others, and predicting these effects is a central challenge in ecology. Prey species sharing an enemy (predator or parasitoid) can be linked by apparent competition, but it is unknown whether this process is strong enough to be a community-wide structuring mechanism that could be used to predict future states of diverse food webs. Whether species abundances are spatially coupled by enemy movement across different habitats is also untested. Here, using a field experiment, we show that predicted apparent competitive effects between species, mediated via shared parasitoids, can significantly explain future parasitism rates and herbivore abundances. These predictions are successful even across edges between natural and managed forests, following experimental reduction of herbivore densities by aerial spraying over 20ha. This result shows that trophic indirect effects propagate across networks and habitats in important, predictable ways, with implications for landscape planning, invasion biology and biological control

Genome sequence of cauliflower mosaic virus identified in earwigs (Doru luteipes) through a metagenomic approach.

Here we report the first complete genome sequence of a cauliflower mosaic virus from Brazil, obtained from the gut content of the predator earwig (Doru luteipes). This virus has a genome of 8,030 nucleotides (nt) and shares 97% genome-wide identity with an isolate from Argentina

Assessing the time dependence of reconnection with Poynting's theorem: MMS observations

We investigate the time dependence of electromagnetic-field-to-plasma energy conversion in the electron diffusion region of asymmetric magnetic reconnection. To do so, we consider the terms in Poynting's theorem. In a steady state there is a perfect balance between the divergence of the electromagnetic energy flux $\nabla \cdot \vec{S}$ and the conversion between electromagnetic field and particle energy $\vec{J} \cdot \vec{E}$. This energy balance is demonstrated with a particle-in-cell simulation of reconnection. We also evaluate each of the terms in Poynting's theorem during an observation of a magnetopause reconnection region by Magnetospheric Multiscale (MMS). We take the equivalence of both sides of Poynting's theorem as an indication that the errors associated with the approximation of each term with MMS data are small. We find that, for this event, balance between $\vec{J}\cdot\vec{E}=-\nabla\cdot\vec{S}$ is only achieved for a small fraction of the energy conversion region at/near the X-point. Magnetic energy was rapidly accumulating on either side of the current sheet at roughly three times the predicted energy conversion rate. Furthermore, we find that while $\vec{J}\cdot\vec{E}>0$ and $\nabla\cdot\vec{S}<0$ are observed, as is expected for reconnection, the energy accumulation is driven by the overcompensation for $\vec{J}\cdot\vec{E}$ by $-\nabla\cdot\vec{S}>\vec{J}\cdot\vec{E}$. We note that due to the assumptions necessary to do this calculation, the accurate evaluation of $\nabla\cdot\vec{S}$ may not be possible for every MMS-observed reconnection event; but if possible, this is a simple approach to determine if reconnection is or is not in a steady-state.Comment: Resubmitted to GRL after minor rev. on 1 February 201

Knemidokoptinid (Epidermoptidae: Knemidokoptinae) mite infestation in wild red-crowned parakeets (cyanoramphus novaezelandiae): Correlations between macroscopic and microscopic findings

During a study on health and disease in Red-crowned Parakeets (Cyanoramphus novaezelandiae) on Tiritiri Matangi Island and Little Barrier Island (Hauturu-o-Toi) in New Zealand between 2011 and 2013, an outbreak of feather loss prompted the collection of skin biopsies (n5135) under anesthesia from the head of captured birds. A subset of samples (n57) was frozen to obtain whole specimens for identification of ectoparasites. Mites (range 1–11) were observed in 79/135 (58.5%) skin biopsies, whereas feather loss was only found in 47/142 (33.1%) birds captured during the sampling period. Compact orthokeratotic hyperkeratosis and acanthosis were found in association with mites. Procnemidocoptes janssensi (Acari: Epidermoptidae, Knemidokoptinae) was identified from whole mites obtained from skin biopsies. We describe the presence, pathology, and stages of infestation for knemidokoptinid mange in a wild parrot population in New Zealand. Given the clinical and pathologic changes observed and poor knowledge of the parasite’s New Zealand host and geographic distribution, further work is recommended for this and sympatric parrots, to understand relationships between the host, parasite, environment, and expression of disease. Results from this study reinforce the value of including biopsy samples for the investigation of skin disease in wild birds, particularly to link etiologic agents with pathologic changes

Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East

Viruses of the genus Mastrevirus (family Geminiviridae) are transmitted by leafhoppers and infect either mono- or dicotyledonous plants. Here we have determined the full length sequences of 49 dicot-infecting mastrevirus isolates sampled in Australia, Eritrea, India, Iran, Pakistan, Syria, Turkey and Yemen. Comprehensive analysis of all available dicot-infecting mastrevirus sequences showed the diversity of these viruses in Australia to be greater than in the rest of their known range, consistent with earlier studies, and that, in contrast with the situation in monocot-infecting mastreviruses, detected inter-species recombination events outnumbered intra-species recombination events. Consistent with Australia having the greatest diversity of known dicot-infecting mastreviruses phylogeographic analyses indicating the most plausible scheme for the spread of these viruses to their present locations, suggest that most recent common ancestor of these viruses is likely nearer Australia than it is to the other regions investigated.Department of HE and Training approved lis

The mechanism of the amidases: mutating the glutamate adjacent to the catalytic triad inactivates the enzyme due to substrate mispositioning

All known nitrilase superfamily amidase and carbamoylase structures have an additional glutamate thatis hydrogen bonded to the catalytic lysine in addition to the Glu, Lys, Cys “catalytic triad.” In the amidase from Geobacillus pallidus, mutating this glutamate (Glu-142) to a leucine or aspartate renders the enzyme inactive. X-ray crystal structure determination shows that the structural integrity of the enzymeismaintained despite themutation with the catalytic cysteine (Cys-166), lysine (Lys-134), and glutamate (Glu- 59)in positions similar to those of the wild-type enzyme. In the case of the E142L mutant, a chloride ion is located in the position occupied by Glu-142 O 1 in the wild-type enzyme andinteracts with the active site lysine. In the case of the E142D mutant, this site is occupied by Asp-142 O1.In neither case is an atom located at the position of Glu-142 O 2 in the wild-type enzyme. The active site cysteine of the E142Lmutant was found to form aMichael adduct with acrylamide, which is a substrate of the wild-type enzyme, due to an interaction that places the double bond of the acrylamide rather than the amide carbonyl carbon adjacent to the active site cysteine. Our results demonstrate that in the wild-type active site a crucial role is played by the hydrogen bond between Glu-142 O 2 and the substrate amino groupin positioning the substrate with the correct stereoelectronic alignment to enable the nucleophilic attack on the carbonyl carbon by the catalytic cysteine

Validation of a score tool for measurement of histological severity in juvenile dermatomyositis and association with clinical severity of disease.

OBJECTIVES: To study muscle biopsy tissue from patients with juvenile dermatomyositis (JDM) in order to test the reliability of a score tool designed to quantify the severity of histological abnormalities when applied to biceps humeri in addition to quadriceps femoris. Additionally, to evaluate whether elements of the tool correlate with clinical measures of disease severity. METHODS: 55 patients with JDM with muscle biopsy tissue and clinical data available were included. Biopsy samples (33 quadriceps, 22 biceps) were prepared and stained using standardised protocols. A Latin square design was used by the International Juvenile Dermatomyositis Biopsy Consensus Group to score cases using our previously published score tool. Reliability was assessed by intraclass correlation coefficient (ICC) and scorer agreement (α) by assessing variation in scorers' ratings. Scores from the most reliable tool items correlated with clinical measures of disease activity at the time of biopsy. RESULTS: Inter- and intraobserver agreement was good or high for many tool items, including overall assessment of severity using a Visual Analogue Scale. The tool functioned equally well on biceps and quadriceps samples. A modified tool using the most reliable score items showed good correlation with measures of disease activity. CONCLUSIONS: The JDM biopsy score tool has high inter- and intraobserver agreement and can be used on both biceps and quadriceps muscle tissue. Importantly, the modified tool correlates well with clinical measures of disease activity. We propose that standardised assessment of muscle biopsy tissue should be considered in diagnostic investigation and clinical trials in JDM

Appearances can be deceptive: Revealing a hidden viral infection with deep sequencing in a plant quarantine context

Comprehensive inventories of plant viral diversity are essential for effective quarantine and sanitation efforts. The safety of regulated plant material exchanges presently relies heavily on techniques such as PCR or nucleic acid hybridisation, which are only suited to the detection and characterisation of specific, well characterised pathogens. Here, we demonstrate the utility of sequence-independent next generation sequencing (NGS) of both virus-derived small interfering RNAs (siRNAs) and virion-associated nucleic acids (VANA) for the detailed identification and characterisation of viruses infecting two quarantined sugarcane plants. Both plants originated from Egypt and were known to be infected with Sugarcane streak Egypt Virus (SSEV; Genus Mastrevirus, Family Geminiviridae), but were revealed by the NGS approaches to also be infected by a second highly divergent mastrevirus, here named Sugarcane white streak Virus (SWSV). This novel virus had escaped detection by all routine quarantine detection assays and was found to also be present in sugarcane plants originating from Sudan. Complete SWSV genomes were cloned and sequenced from six plants and all were found to share .91% genomewide identity. With the exception of two SWSV variants, which potentially express unusually large RepA proteins, the SWSV isolates display genome characteristics very typical to those of all other previously described mastreviruses. An analysis of virus-derived siRNAs for SWSV and SSEV showed them to be strongly influenced by secondary structures within both genomic single stranded DNA and mRNA transcripts. In addition, the distribution of siRNA size frequencies indicates that these mastreviruses are likely subject to both transcriptional and post-transcriptional gene silencing. Our study stresses the potential advantages of NGS-based virus metagenomic screening in a plant quarantine setting and indicates that such techniques could dramatically reduce the numbers of non-intercepted virus pathogens passing through plant quarantine stations