Germination ecology of invasive alien Anthemis cotula helps it synchronise its successful recruitment with favourable habitat conditions

Anthemis cotula is a widespread invasive alien species in Kashmir Himalaya. Being a winter annual, the species reproduces entirely by achenes and synchrony between germination requirements of the species and the habitat conditions must be of critical importance in its invasiveness. To examine how the achenes of different ages respond to different environmental cues, two laboratory experiments were performed wherein effects of different nitrogen applications and growth hormones under continuous light and dark conditions were explored. Results show that the achenes are positively photoblastic and have requirement for after‐ripening. Nitrogen applied either as potassium nitrate or as thiourea significantly improved achene germination both under continuous light and dark conditions. Although kinetin (6‐furfurylaminopurine) did not influence achene germination, gibberellic acid (GA₃) applied at 1.0 mM concentration had the most significant effect on the final percentage germination under both light and dark conditions. These results suggest that the achenes have an elaborate mechanism of sensing the habitat conditions that helps them to synchronise their germination with favourable environmental conditions – a strategy that aids the species in ensuring recruitment, survival and its spread in Kashmir Himalaya.     

Protective effect of L-carnitine on testicular ischaemia-reperfusion injury in rats

Testicular torsion is a urological emergency referred to as 'acute scrotum', because inappropriate treatment can lead to male subfertility and infertility. A possible cause of testicular damage is the ischaemia-reperfusion (I/R) injury attributed to oxygen free radicals. L-carnitine, a vitamin-like antioxidant, plays a pivotal role in the maturation of spermatozoa within the reproductive tract. The aim of the present paper was to determine the protective effect of L-carnitine on testicular I/R-induced injury. Thirty-two male rats were divided into 4 groups (n = 8). Testicular torsion was created by rotating the right testis 720 degrees in a clockwise direction. Group 1: sham-operated control; group 2: ischaemia; group 3: I/R; group 4: ischaemia-L-carnitine treatment-reperfusion group. L-carnitine (500 mg kg(-1), intraperitoneally) was administered before 30 min of detorsion in Group 4. After torsion (5 h) and detorsion (5 h), bilateral orchidectomy was performed. The malondialdehyde (MDA) level was evaluated in testes. Histopathologically, Johnsen's spermatogenesis criteria and mean seminiferous tubule diameter (MSTD) measurements were used. Testicular MDA levels were higher in the torsion group compared to the sham-control group (p < 0.05). Detorsion (reperfusion) caused a further increase in MDA levels (p < 0.05). Pretreatment with L-carnitine prevented a further increase in MDA levels (p < 0.05). Histologically, torsion caused some separation among germinal cells in the seminiferous tubules, which became much more prominent in the I/R group but was attenuated with L-carnitine pretreatment. In conclusion, L-carnitine pretreatment may have a protective effect in experimental testicular torsion-detorsion model in rats by its well-known antioxidant potential.     

Microresonator mass sensors for detection of Bacillus anthracis Sterne spores in air and water

Towards the goal of developing a real-time monitoring device for microorganisms, we demonstrate the use of microcantilevers as resonant mass sensors for detection of Bacillus anthracis Sterne spores in air and liquid. The detection scheme was based on measuring resonant frequency decrease driven by thermally induced oscillations, as a result of the added mass of the spores with the use of a laser Doppler vibrometer (LDV). Viscous effects were investigated by comparing measurements in air and deionized (DI) water along with theoretical values. Moreover, biological experiments were performed which involved suspending spores onto the cantilevers and performing mass detection in air and water. For detection of spores in water, the cantilevers were functionalized with antibodies in order to fix the spores onto the surface. We demonstrate that as few as 50 spores on the cantilever can be detected in water using the thermal noise as excitation source. Measurement sensitivity of 9.23 Hz/fg for air and 0.1 Hz/fg for water were obtained. These measurements were compared with theoretical values and sources of improvement in cantilever sensitivity in a viscous medium were also discussed. It is expected that by driving the cantilevers and using higher order modes, detection of a single spore in liquids should be achievable.     

Seasonality and historic trends in the reef fisheries of Pulau Banggi, Sabah, Malaysia

The reef fisheries of Pulau (meaning “island” in Malay) Banggi, Sabah are not managed, and lack baseline fisheries data despite forming part of a proposed marine park. Thus, a combination of qualitative and quantitative approaches was applied to obtain a baseline picture about the past and present state of the fisheries. Fish landings were monitored, and fisher interviews conducted to investigate seasonal effects and historical changes in Banggi’s reef fisheries. Monsoon winds were a major driver of seasonal differences in catch quantities for the hook and line, but not the gillnet fishery. Spatial distribution of fishing effort and target species also differed by season. Fishers consistently indicated that Banggi’s fisheries were declining, with a suggested three to four times decrease in catch rates over the last 20 years. Interestingly, it appeared that substantial decreases began in the year 2000. The responses of fishers to seasonal changes, and the resultant implications for management are discussed. Importantly, the need for immediate management policies to prevent further declines and to maintain sustainable reef fisheries is stressed. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.

Support Vector Machine-based method for predicting subcellular localization of mycobacterial proteins using evolutionary information and motifs

Background

Annotations that describe the function of sequences are enormously important to researchers during laboratory investigations and when making computational inferences. However, there has been little investigation into the data quality of sequence function annotations. Here we have developed a new method of estimating the error rate of curated sequence annotations, and applied this to the Gene Ontology (GO) sequence database (GOSeqLite). This method involved artificially adding errors to sequence annotations at known rates, and used regression to model the impact on the precision of annotations based on BLAST matched sequences.

Results

We estimated the error rate of curated GO sequence annotations in the GOSeqLite database (March 2006) at between 28% and 30%. Annotations made without use of sequence similarity based methods (non-ISS) had an estimated error rate of between 13% and 18%. Annotations made with the use of sequence similarity methodology (ISS) had an estimated error rate of 49%.

Conclusion

While the overall error rate is reasonably low, it would be prudent to treat all ISS annotations with caution. Electronic annotators that use ISS annotations as the basis of predictions are likely to have higher false prediction rates, and for this reason designers of these systems should consider avoiding ISS annotations where possible. Electronic annotators that use ISS annotations to make predictions should be viewed sceptically. We recommend that curators thoroughly review ISS annotations before accepting them as valid. Overall, users of curated sequence annotations from the GO database should feel assured that they are using a comparatively high quality source of information.     

Intron-containing hairpin RNA interference vector for OBP8 show promising mortality in peach potato aphid

Myzus persicae is a devastating pest affecting potato production. Intron-containing hairpin RNA (ihpRNA) silenced the odorant-binding protein 8 (OBP8) for enhanced protection against Myzus persicae in potatoes. OBP8 was isolated from M. persicae, sequenced, with the allotment of GenBank ID. ERNAi was used to design siRNA targets from OBP8 with no off-targets. Multiple Sequence Alignment show M. persicae OBP8 resemblance with Acyrthosiphon pisum, Rhopalosiphum maidis, Aphis fabae, and Sitobion avenae. dsRNA-OBP8 (7 µg/µL) oral feeding resulted in a 69% mortality, and 58% OBP8 reduced expression 8D post-feeding compared to control. Golden Gate cloning is used for RNA interference taking advantage of type IIs restriction enzyme Eco31I. ihpRNA-OBP8 introduced by agroinfiltration in Solanum tuberosum. Transgenic S. tuberosum fed Myzus show 57.6% mortality and 49% reduction in OBP8 expression 8D post-feeding, compared to control. This work proves OBP8 as promising ihpRNA targets in potato and related crops for whom Myzus is a destructive pest.

     

Receptor dimerization dynamics as a regulatory valve for plasticity of type I interferon signaling

Type I interferons (IFNs) activate differential cellular responses through a shared cell surface receptor composed of the two subunits, IFNAR1 and IFNAR2. We propose here a mechanistic model for how IFN receptor plasticity is regulated on the level of receptor dimerization. Quantitative single-molecule imaging of receptor assembly in the plasma membrane of living cells clearly identified IFN-induced dimerization of IFNAR1 and IFNAR2. The negative feedback regulator ubiquitin-specific protease 18 (USP18) potently interferes with the recruitment of IFNAR1 into the ternary complex, probably by impeding complex stabilization related to the associated Janus kinases. Thus, the responsiveness to IFNα2 is potently down-regulated after the first wave of gene induction, while IFNβ, due to its ∼100-fold higher binding affinity, is still able to efficiently recruit IFNAR1. Consistent with functional data, this novel regulatory mechanism at the level of receptor assembly explains how signaling by IFNβ is maintained over longer times compared with IFNα2 as a temporally encoded cause of functional receptor plasticity.