Leaf gall polymorphism and molecular phylogeny of a new Bruggmanniella species (Diptera: Cecidomyiidae: Asphondyliini) associated with Litsea acuminata (Lauraceae) in Taiwan,with ecological comparisons and a species description

Two types of cecidomyiid leaf galls, cup‐shaped and umbrella‐shaped, occur on Litsea acuminata (Lauraceae) in Taiwan. Based on the concept of gall shapes as “extended phenotypes” of gall inducers, these two types could be induced by different gall midge species. However, galls with intermediate shapes between the two types were recently discovered, which implies that possible genetic exchanges occur between the gall inducers of both types. To clarify the taxonomic status of gall midges responsible for the two types of galls on L. acuminata, we undertook taxonomic, molecular phylogenetic and ecological studies. Our findings show that the two gall types are induced by the same Bruggmanniella species and the species is new to science. We describe the species forming this range of galls as Bruggmanniella litseae sp. n. , and compare their geographical distribution, galling position and morphometry. Based on our results, a possible evolutionary scenario of B. litseae sp. n. is discussed.     

When to start and when to stop: Effects of climate on breeding in a multi‐brooded songbird

Climate warming has been shown to affect the timing of the onset of breeding of many bird species across the world. However, for multi‐brooded species, climate may also affect the timing of the end of the breeding season, and hence also its duration, and these effects may have consequences for fitness. We used 28 years of field data to investigate the links between climate, timing of breeding, and breeding success in a cooperatively breeding passerine, the superb fairy‐wren (Malurus cyaneus). This multi‐brooded species from southeastern Australia has a long breeding season and high variation in phenology between individuals. By applying a “sliding window” approach, we found that higher minimum temperatures in early spring resulted in an earlier start and a longer duration of breeding, whereas less rainfall and more heatwaves (days > 29°C) in late summer resulted in an earlier end and a shorter duration of breeding. Using a hurdle model analysis, we found that earlier start dates did not predict whether or not females produced any young in a season. However, for successful females who produced at least one young, earlier start dates were associated with higher numbers of young produced in a season. Earlier end dates were associated with a higher probability of producing at least one young, presumably because unsuccessful females kept trying when others had ceased. Despite larger scale trends in climate, climate variables in the windows relevant to this species’ phenology did not change across years, and there were no temporal trends in phenology during our study period. Our results illustrate a scenario in which higher temperatures advanced both start and end dates of individuals’ breeding seasons, but did not generate an overall temporal shift in breeding times. They also suggest that the complexity of selection pressures on breeding phenology in multi‐brooded species may have been underestimated.     

Fire affects the taxonomic and functional composition of soil microbial communities,with cascading effects on grassland ecosystem functioning

Fire is a crucial event regulating the structure and functioning of many ecosystems. Yet few studies have focused on how fire affects taxonomic and functional diversities of soil microbial communities, along with changes in plant communities and soil carbon (C) and nitrogen (N) dynamics. Here, we analyze these effects in a grassland ecosystem 9 months after an experimental fire at the Jasper Ridge Global Change Experiment site in California, USA. Fire altered soil microbial communities considerably, with community assembly process analysis showing that environmental selection pressure was higher in burned sites. However, a small subset of highly connected taxa was able to withstand the disturbance. In addition, fire decreased the relative abundances of most functional genes associated with C degradation and N cycling, implicating a slowdown of microbial processes linked to soil C and N dynamics. In contrast, fire stimulated above‐ and belowground plant growth, likely enhancing plant–microbe competition for soil inorganic N, which was reduced by a factor of about 2. To synthesize those findings, we performed structural equation modeling, which showed that plants but not microbial communities were responsible for significantly higher soil respiration rates in burned sites. Together, our results demonstrate that fire ‘reboots’ the grassland ecosystem by differentially regulating plant and soil microbial communities, leading to significant changes in soil C and N dynamics.     

Deceptive pollination of Calanthe by skippers that commonly act as nectar thieves

Flowers have developed different strategies to attract pollinators through visual or olfactory signals. Most flowers offer pollinators a reward (e.g. nectar and pollen) for the pollination service. However, one‐third of Orchidaceae have been shown not to provide a reward. Calanthe are terrestrial orchids distributed throughout China, Nepal, Japan and tropical Asia. Despite its high diversity, the pollination biology of Calanthe remains largely unknown, even though it is an important aspect of plant conservation. In the study, through field surveying, there were three Hesperiidae butterflies pollinating two species of Calanthe and the pollination behavior differed between the two species of Calanthe, which might lead to different fruit setting rates. There was no nectar in the flowers of the two species, indicating deceptive pollination. Using a glass cylinder experiment, it was deduced that the two species of Calanthe were most likely to attract pollinators by generalized food deception. Interestingly, Hesperiidae butterflies were traditionally thought to be nectar thieves and generally do not transmit pollinia. However, our findings showed that, in this case, the thieves were deceived by the plants and pollinated them for free.     

The hybrid bacterial foraging algorithm based on many-objective optimizer

A new multi-objective optimized bacterial foraging algorithm - Hybrid Multi-Objective Optimized Bacterial Foraging Algorithm (HMOBFA) is presented in this article. The proposed algorithm combines the crossover-archives strategy and the life-cycle optimization strategy, look for the best method through research area. The crossover-archive strategy with an external archive and internal archive is assigned to different selection principles to focus on diversity and convergence separately. Additionally, according to the local landscape to satisfy population diversity and variability as well as avoiding redundant local searches, individuals can switch their states periodically throughout the colony lifecycle with the life-cycle optimization strategy. all of which may perform significantly well. The performance of the algorithm was examined with several standard criterion functions and compared with other classical multi-objective majorization methods. The examiner results show that the HMOBFA algorithm can achieve a significant enhancement in performance compare with other method and handles many-objective issues with solid complexity, convergence as well as diversity. The HMOBFA algorithm has been proven to be an excellent alternative to past methods for solving the improvement of many-objective problems.     

MMS2plot: An R Package for Visualizing Multiple MS/MS Spectra for Groups of Modified and Non‐Modified Peptides

A large number of post‐translational modifications (PTMs) in proteins are buried in the unassigned mass spectrometric (MS) spectra in shot‐gun proteomics datasets. Because the modified peptide fragments are low in abundance relative to the corresponding non‐modified versions, it is critical to develop tools that allow facile evaluation of assignment of PTMs based on the MS/MS spectra. Such tools will preferably have the ability to allow comparison of fragment ion spectra and retention time between the modified and unmodified peptide pairs or group. Herein, MMS2plot, an R package for visualizing peptide‐spectrum matches (PSMs) for multiple peptides, is described. MMS2plot features a batch mode and generates the output images in vector graphics file format that facilitate evaluation and publication of the PSM assignment. MMS2plot is expected to play an important role in PTM discovery from large‐scale proteomics datasets generated by liquid chromatography‐MS/MS. The MMS2plot package is freely available at https://github.com/lileir/MMS2plot under the GPL‐3 license.     

Over‐Expression of RNA Processing,Heat Shock,and DNA Repair Proteins in Breast Tumor Compared to Normal Tissue

This study identifies the main changes in protein expression in human breast tumors compared to normal breast tissue. Malignant tumors (32) and normal breast tissue samples (23), from formaldehyde‐fixed, paraffin‐embedded specimens are subjected to discovery proteomics using liquid chromatography/tandem mass spectrometry, with spectral counts for quantitation. The dataset contains 1406 proteins. Differential expression is measured using a method that takes advantage of estimates of the percentage of tumor on a slide. This analysis shows that the major classes of proteins over‐expressed by tumors are RNA‐binding, heat shock and DNA repair proteins. RNA‐binding proteins, including heterogeneous nuclear ribonucleoproteins (HNRNPs), SR splice factors (SRSF) and elongation factors form the largest group. Comparison with results from another study demonstrates that the RNA‐binding proteins are associated specifically with malignant transformation, rather than with cell proliferation. HNRNP and SRSF proteins help define splice sites in normal cells. Their over‐expression may dysregulate splicing, which in turn has the potential to promote malignant transformation.     

A chromosome‐scale genome assembly of Antheraea pernyi (Saturniidae,Lepidoptera)

Antheraea pernyi is a semi‐domesticated lepidopteran insect species valuable to the silk industry, human health, and ecological tourism. Owing to its economic influence and developmental properties, it serves as an ideal model for investigating divergence of the Bombycoidea super family. However, studies on the karyotype evolution and functional genomics of A. pernyi are limited by scarce genomic resource. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first high‐quality A. pernyi genome from a single male individual. The genome is 720.67 Mb long with 49 chromosomes and a 13.77‐Mb scaffold N50. Approximately 441.75 Mb, accounting for 60.74% of the genome, was identified as repeats. The genome comprises 21,431 protein‐coding genes, 85.22% of which were functionally annotated. Comparative genomics analysis suggested that A. pernyi diverged from its common ancestor with A. yamamai ~30.3 million years ago, and that chromosome fission contributed to the increased chromosome number. The genome assembled in this work will not only facilitate future research on A. pernyi and related species but also help to progress comparative genomics analyses in Lepidoptera.     

A ROCK inhibitor promotes keratinocyte survival and paracrine secretion,enhancing establishment of primary human melanocytes and melanocyte–keratinocyte co‐cultures

Primary melanocytes isolated from skin and expanded in culture have been widely used for laboratory research and clinical applications. The conventional method to isolate primary melanocytes from skin usually requires about 3–4 weeks of culture for melanocytes to grow sufficiently to passage. Considering that melanocytes comprise only 3%–7% of epidermal cells in normal human skin, it would be extremely helpful to increase the isolation efficiency and shorten the initial culture time to quickly meet various application needs. Here, we report that adding Y‐27632, a Rho kinase inhibitor, into the initial culture medium for 2 days can dramatically increase the yield of melanocytes. We found that Y‐27632 can promote keratinocyte attachment and survival in the melanocyte culture system, resulting in not only better recovery, but also increased proliferation of melanocytes by a paracrine signaling pathway. More specifically, Y‐27632 significantly induced keratinocyte expression of stem cell factor, which played an important role in enhancing the growth of melanocytes. In summary, Y‐27632 could profoundly enhance the yield of primary melanocytes in the initial culture through paracrine effects on keratinocytes.