Identification of Traumatin, a Wound Hormone, as 12-Oxo-trans-10-dodecenoic Acid

12-Oxo-trans-10-dodecenoic acid (trans-10-ODA) is an oxidation product of polyunsaturated fatty acids in plant tissues. The structural similarity of trans-10-ODA and traumatic acid, a compound considered to be a wound hormone, suggested that trans-10-ODA might be a precursor of traumatic acid. Both trans-10-ODA and traumatic acid were active in the Wehnelt bean assay. The results were more consistent with trans-10-ODA than with traumatic acid. Cucumber (Cucumis sativus L. var. National Pickling) hypocotyls also showed a growth increase following treatment with trans-10-ODA, which suggested that trans-10-ODA has a more general influence on plant development than previously ascribed to traumatic acid.     

Mediated pathogenicity of the baculovirus AcMNPV by the venom from Euplectrus comstockii Howard (Hymenoptera: Eulophidae)

The compatibility of the venom from the parasitic species Euplectrus comstockii Howard (Hymenoptera: Eulophidae) with the pathogenicity of Autographa californica (Speyer) (Lepidoptera: Noctuidae) MNPV baculovirus (AcMNPV) was tested in third and fourth instar larvae of Trichoplusia ni (Hübner) (Lepidoptera: Noctuidae). The presence of AcMNPV did not alter the ability of the venom to arrest ecdysis in T. ni larvae. The presence of the venom delayed the rate of viruses by AcMNPV but increased the total mortality rates from days 9 to 14 in both third and fourth instar T. ni larvae. The delay in viruses was minimized by administering the virus prior to envenomation. In the presence of the venom, the final LD50 values were lower for fourth instar larvae than for third instar larvae. Surface response equations were developed to visualize the effect of the venom on the viruses caused by AcMNPV.     

Acid-sensing ion channel 3 mediates peripheral anti-hyperalgesia effects of acupuncture in mice inflammatory pain

Background  

Peripheral tissue inflammation initiates hyperalgesia accompanied by tissue acidosis, nociceptor activation, and inflammation mediators. Recent studies have suggested a significantly increased expression of acid-sensing ion channel 3 (ASIC3) in both carrageenan- and complete Freund's adjuvant (CFA)-induced inflammation. This study tested the hypothesis that acupuncture is curative for mechanical hyperalgesia induced by peripheral inflammation.     

Unnecessary roughness? Testing the hypothesis that predators destined for molecular gut‐content analysis must be hand‐collected to avoid cross‐contamination

Molecular gut‐content analysis enables detection of arthropod predation with minimal disruption of ecosystem processes. Mass‐collection methods, such as sweep‐netting, vacuum sampling and foliage beating, could lead to regurgitation or rupturing of predators along with uneaten prey, thereby contaminating specimens and compromising resultant gut‐content data. Proponents of this ‘cross‐contamination hypothesis’ advocate hand‐collection as the best way to avoid cross‐contamination. However, hand‐collection is inefficient when large samples are needed, as with most ecological research. We tested the cross‐contamination hypothesis by setting out onto potato plants immature Coleomegilla maculata and Podisus maculiventris that had been fed larvae of either Leptinotarsa decemlineata or Leptinotarsa juncta, or unfed individuals of these predator species along with L. decemlineata larvae. The animals were then immediately re‐collected, either by knocking them vigorously off the plants onto a beat cloth and capturing them en masse with an aspirator (‘rough’ treatment) or by hand‐searching and collection with a brush (‘best practice’). Collected predators were transferred in the field to individual vials of chilled ethanol and subsequently assayed by PCR for fragments of cytochrome oxidase I of L. decemlineata and L. juncta. Ten to 39 per cent of re‐collected fed predators tested positive by PCR for DNA of both Leptinotarsa species, and 14–38% of re‐collected unfed predators contained L. decemlineata DNA. Overall levels of cross‐contamination in the rough (31%) and best‐practice (11%) samples were statistically different and supported the cross‐contamination hypothesis. A pilot study on eliminating external DNA contamination with bleach prior to DNA extraction and amplification gave promising results.     

Host regulation and release of parasitism-specific proteins in the system Toxoneuron nigriceps-Heliothis virescens

The braconid wasp Toxoneuron nigriceps induced qualitative and quantitative changes in the protein composition of the moth Heliothis virescens host hemolymph. Total protein concentration was found to be higher in parasitized host 4 days after parasitism as compared to control hosts, mainly due to changes in a particular group of proteins. Host proteins with a molecular mass of 173 and 72 kDa were found in higher levels in the hemolymph of parasitized larvae as control hosts approached pupation, while an 80 kDa peptide was found in reduced concentration in the hemolymph of parasitized hosts. Levels of these three peptides were maintained throughout parasitoid development, while two of them (173 and 72 kDa) were cleared from the host hemolymph close to pupation. Besides the regulation of host proteins, three parasitism-specific proteins (PSPs) were released into the host hemolymph. Two of them (PSP1-MW=116 kDa, pI=6.3; PSP2-MW=114 kDa, pI=6.2) first appeared in the hemolymph of parasitized hosts soon after pupation of control host and increased in concentration as the parasitoid developed. The third PSP (PSP3-MW=56 kDa, pI=5.8) was produced towards the end of parasitoid larval development, close to parasitoid egression. Database searches based on the amino acid composition and amino terminal sequence of PSP1 and PSP2 did not produce any significant matches, while PSP3 was identified as a putative chitinase. Incubation of host derived tissues, parasitoid larvae and teratocytes in 35S conditioned media suggested PSPs were a product of teratocytes. The role of the regulation of host proteins and release of PSPs by teratocytes for the successful development of T. nigriceps are discussed.     

Protein structure similarity from principle component correlation analysis

Background  

Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD) in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities.     

Conditional random pattern model for copy number aberration detection

Background  

DNA copy number aberration (CNA) is very important in the pathogenesis of tumors and other diseases. For example, CNAs may result in suppression of anti-oncogenes and activation of oncogenes, which would cause certain types of cancers. High density single nucleotide polymorphism (SNP) array data is widely used for the CNA detection. However, it is nontrivial to detect the CNA automatically because the signals obtained from high density SNP arrays often have low signal-to-noise ratio (SNR), which might be caused by whole genome amplification, mixtures of normal and tumor cells, experimental noise or other technical limitations. With the reduction in SNR, many false CNA regions are often detected and the true CNA regions are missed. Thus, more sophisticated statistical models are needed to make the CNAs detection, using the low SNR signals, more robust and reliable.