Molecular dynamics and combined docking studies for the identification of Zaire ebola virus inhibitors

Ebola virus (EBOV) is a lethal human pathogen with a risk of global spread of its zoonotic infections, and Ebolavirus Zaire specifically has the highest fatality rate amongst other species. There is a need for continuous effort towards having therapies, as a single licensed treatment to neutralize the EBOV is yet to come into reality. This present study virtually screened the MCULE database containing almost 36 million compounds against the structure of a Zaire Ebola viral protein (VP) 35 and a consensus scoring of both MCULE and CLCDDW docking programs remarked five compounds as potential hits. These compounds, with binding energies ranging from –7.9 to –8.9?kcal/mol, were assessed for predictions of their physicochemical and bioactivity properties, as well as absorption, distribution, metabolism, excretion, and toxicity (ADMET) criteria. The results of the 50?ns molecular dynamics simulations showed the presence of dynamic stability between ligand and protein complexes, and the structures remained significantly unchanged at the ligand-binding site throughout the simulation period. Both docking analysis and molecular dynamics simulation studies suggested strong binding affinity towards the receptor cavity and these selected compounds as potential inhibitors against the Zaire Ebola VP 35. With respect to inhibition constant values, bioavailability radar and other physicochemical properties, compound A (MCULE-1018045960-0-1) appeared to be the most promising hit compound. However, the ligand efficiency and ligand efficiency scale need improvement during optimization, and also validation via in vitro and in vivo studies are necessary to finally make a lead compound in treating Ebola virus diseases.

Communicated by Ramaswamy H. Sarma     

Presence of Cuckoo reliably indicates high bird diversity: A case study in a farmland area

Here we studied the occurrence of Cuckoo Cuculus canorus and top predators as indicators of biodiversity in agro ecosystems of Western Poland, to identify local hotspots. Bird species richness and land-use diversity were used as measures of biodiversity. The relationship between the presence of Cuckoos and four avian top predators with biodiversity measures were examined using Generalized Linear Mixed Models.Cuckoos were mainly distributed on sites with greater species richness, but were absent from the low species richness sites, while the top predators were distributed uniformly. The performance of the best models using the presence of Cuckoo was 27% higher than the best models using top predators. Our results highlight the predictive capacity of Cuckoos as an indicator of bird species richness than top predators and the usefulness of this species in biodiversity studies. The cookoo is charismatic, widespread across the main types of landscapes, and is easy to detect from its song. Importantly, our findings propose that cookoo can be used as effective and cheap tool to monitor the high bird diversity in different European countries.     

Identification and functional analysis of outer kinetochore genes in the holocentric insect Bombyx mori

The kinetochore creates chromosomal attachment sites for microtubules. The kinetochore-microtubule interface plays an important role in ensuring accurate transmission of genetic information to daughter cells. Bombyx mori is known to possess holocentric chromosomes, where spindle microtubules attach along the entire length of the chromosome. Recent evidence suggests that CENP-A and CENP-C, which are essential for centromere structure and function in other species, have lost in holocentric insects, implying that B. mori is able to build its kinetochore regardless of the lack of CENP-A and CENP-C. Here we report the identification of three outer kinetochore genes in the silkworm B. mori by using bioinformatics and RNA interference-based screening. While the homologs of Ndc80 and Mis12 have strong similarity with those of other organisms, the five encoded proteins (BmNuf2, BmSpc24, BmSpc25, BmDsn1 and BmNnf1) are highly diverged from their counterparts in other species. Microscopic studies show that the outer kinetochore protein is distributed along the entire length of the chromosomes, which is a key feature of holocentric chromosomes. We also demonstrate that BmDsn1 forms a heterotrimeric complex with BmMis12 and BmNnf1, which acts as a receptor of the Ndc80 complex. In addition, our study suggests that a small-scale RNAi-based candidate screening is a useful approach to identify genes which may be highly divergent among different species.     

Significant decrease in local butterfly community during the last 15 years in a calcareous hill of the middle Korea

Recently the significant decreases of species richness and abundance among terrestrial animals including butterflies are reported due to habitat change, overexploitation, and global warming. We compared the butterfly species composition and abundance from 1999 and 2014–2015 in a calcareous hill site of the middle part of Korea using a line transect method. There was a significant decrease in the number of individuals (abundance) and the number of species (richness) from 1999 to 2014–2015. This decrease was more prevalent among northern species than southern species, and the local extinct species were more prevalent among northern species, showing the influence of global warming on butterfly assemblages. However, no impact of habitat change was observed because of maintenance of the grasslands, which is caused by the dry soils of the calcareous region.     

Suppression of population growth of the Japanese mealybug, <Emphasis Type="Italic">Planococcus kraunhiae</Emphasis> (Hemiptera: Pseudococcidae), by using an attractant for indigenous parasitoids in persimmon orchards

We previously reported that two parasitic wasps, Anagyrus sawadai Ishii and Leptomastix dactylopii Howard, are strongly attracted to (2,4,4-trimethyl-2-cyclohexenyl)methyl butyrate (cyclolavandulyl butyrate, CLB), a cyclization product of the sex pheromone of the Japanese mealybug, Planococcus kraunhiae (Kuwana). These wasps attacked more P. kraunhiae in the presence of CLB in our field experiments. In the present study, we showed that these CLB-attracted wasps parasitized and suppressed the mealybug population increase in field persimmon orchards, which would lead to reducing mealybug damage on commercial products. Although many attractants for natural enemies are reported, compounds such as CLB that suppress pest population growth in fields are scarce. Moreover, to the best of our knowledge, this is currently the only example to demonstrate that the “non-natural” enemy that does not typically attack the pest under natural conditions can be enrolled in biological control by using its attractant.     

Effects of diet type,developmental stage,and gut compartment in the gut bacterial communities of two <Emphasis Type="Italic">Cerambycidae species</Emphasis> (Coleoptera)

The gut bacterial community of wood-feeding beetles has been examined for its role on plant digestion and biocontrol method development. Monochamus alternatus and Psacothea hilaris, both belonging to the subfamily Lamiinae, are woodfeeding beetles found in eastern Asia and Europe and generally considered as destructive pests for pine and mulberry trees, respectively. However, limited reports exist on the gut bacterial communities in these species. Here, we characterized gut bacterial community compositions in larva and imago of each insect species reared with host tree logs and artificial diets as food sources. High-throughput 454 pyrosequencing of bacterial 16S rRNA gene revealed 225 operational taxonomic units (OTUs) based on a 97% sequences similarity cutoff from 138,279 sequence reads, the majority of which were derived from Proteobacteria (48.2%), Firmicutes (45.5%), and Actinobacteria (5.2%). The OTU network analysis revealed 7 modules with densely connected OTUs in specific gut samples, in which the distributions of Lactococcus-, Kluyvera-, Serratia-, and Enterococcus-related OTUs were distinct between diet types or developmental stages of the host insects. The gut bacterial communities were separated on a detrended correspondence analysis (DCA) plot and by c-means fuzzy clustering analysis, according to diet type. The results from this study suggest that diet was the main determinant for gut bacterial community composition in the two beetles.     

European honeybee defense against Japanese yellow hornet using heat generation by bee‐balling behavior

The Japanese honeybee, Apis cerana japonica Radoszkowski, uses unique generation of heat by bee‐balling to defend against, overheat and kill predacious Japanese hornets. We have now observed the European honeybee, Apis mellifera Linnaeus, using similar bee‐balling behavior and heat generation against the Japanese yellow hornet, Vespa simillima xanthoptera Cameron. We monitored temperatures in the center of the bee‐ball and inside thoracic muscles of the captured hornet and found that the thoracic internal temperature (45.8 ± 2.32°C) was higher than that of the bee‐ball (44.0 ± 0.96°C). Although the thoracic temperature of captured hornets rose to the upper lethal level, defending European bees also showed some stinging attempts against the hornet, unlike the sympatric Japanese honeybee, which never stings during bee‐balling. The European honeybee bee‐balling behavior consists of three phases: (i) heating; (ii) heat‐retaining; and (iii) break up. Our results suggest that European honeybees kill hornets by raising the body temperature of hornets rapidly without stinging. The tactics of bee‐balling against hornets are complex and may be performed by extended division of labor.     

Distribution of the Argentine ant, Linepithema humile, along the Seto Inland Sea, western Japan: Result of surveys in 2003–2005

The distribution of the Argentine ant, Linepithema humile, was investigated in 65 cities or towns along the Seto Inland Sea, western Japan in 2003–2005. Our results include all available information of their distribution in Japan until 2005. Argentine ants have invaded Aichi Prefecture (Tahara‐shi), Hyogo Prefecture (Kobe‐shi), Hiroshima Prefecture (Hiroshima‐shi, Fuchu‐cho, Hatsukaichi‐shi, Ono‐cho and Otake‐shi), and Yamaguchi Prefecture (Iwakuni‐shi and Yanai‐shi). The most widespread distribution was found around Hatsukaichi‐shi including the westernmost part of Hiroshima‐shi and the easternmost of Ono‐cho.