Banana defence responses to Cosmopolites sordidus feeding and methyl jasmonate application

Each year 25–75% of banana and plantain yields are lost because of rhizome damages caused by banana weevil (Cosmopolites sordidus) in growing regions of sub‐Saharan Africa. However, the specific plant defence response of the rhizome tissue in relation to the C. sordidus attack is unknown. Consequently, in this study, we evaluated whether plant defence substances in the rhizome are correlated with the degree of larval damage and whether applications of methyl jasmonate (MJ) elicit a greater induction of the plant defence potential against C. sordidus. Moreover, we attempted to reveal cellular modifications in response to the root feeding herbivore through histochemical staining. The banana cultivars “Km5” and “Mbwazirume” with tolerance and susceptibility to C. sordidus, respectively, were used in a pot experiment to evaluate percent rhizome damage, leaf chlorophyll content, total phenolic content (TPC), antioxidant capacity and cell morphology in response to C. sordidus attack and/or MJ applications compared to untreated control plants. We found that C. sordidus‐induced rhizome damage was 30% in the susceptible cultivar but less than 5% in the tolerant cultivar. The percent rhizome damage was not related to leaf chlorophyll content but showed a significant negative linear relationship to both TPC and antioxidant capacity. Larvae feeding induced a considerably greater increase of polyphenolic defence compounds in Km5 than in Mbwazirume; however, this response was opposite in the MJ treatment, suggesting that the phytohormone induced the susceptible plant to invest more into the synthesis of defence chemicals that in turn lead to reduced C. sordidus damage. Tissue staining demonstrated a greater deposition of lignin and suberin in C. sordidus challenged rhizome, presumably to seal off healthy tissue with a physical barrier from continued pest attack. It is concluded that MJ induces polyphenolics in susceptible Mbwazirume banana that reduced C. sordidus damage.     

Genetic diversity in oak populations under intensive management for fuelwood in the Sierra de Zongolica,Mexico

Firewood and charcoal are used on a daily basis both in rural areas and in cities. This type of energy is produced by one of the most ancient traditional methods, known as coppice, which harvest tree sprouts. There is controversy about its effects on forests: it preserves populations and tree cover of species used, but reduces density, inhibits sexual reproduction and generates genetic erosion. We inquired if it was possible to identify a loss of genetic diversity in oak populations traditionally used for charcoal by the Zongolica Nahuas in Veracruz state, Mexico. We studied populations of Quercus laurina, Quercus calophylla and Quercus rugosa in three different altitudes. Molecular analysis with eight nuclear codominant microsatellites was performed to determine the diversity, structure and gene flow of these species. Results for Q. laurina were Na = 8.458, I = 1.766, Ho = 0.679, polymorphism = 100%, Fis = 0.079, with intraindividual variation of 81.55%. For Q. calophylla: Na = 7.250, I = 1.563, Ho = 0.646, polymorphism = 91.67%, Fis = 0.083, with intraindividual variation of 83.80%. For Q. rugosa: Na = 6.958, I = 1.510, Ho = 0.574, polymorphism = 91.67%, Fis = 0.204, with intraindividual variation of 81.99%; this species shows signals of an early genetic isolation process. Our findings indicate that Quercus genetic diversity for the three species is high and comparable with oak species in Mexico and worldwide. We conclude that at the present, coppice is preserving a historical diversity in adult trees kept alive through sprouting. Nonetheless, problems with coppice systems elsewhere, unregulated harvesting and expansion of pine plantation in the region suggest that further studies, hand in hand with a landscape management approach that improve charcoal and firewood production, may be valuable for Sierra de Zongolica genetic biodiversity conservation.     

Streptomyces luteolifulvus sp. nov., a novel actinomycete isolated from soil in Nanjing,China

During the investigation of exploring potential sources of novel species and natural bioactives, a novel actinomycete, designated strain HIT-DPA4^T, was isolated from a soil sample, which was collected from Nanjing, Jiangsu Province, PR China and characterized using a polyphasic approach. On the basis of 16S rRNA gene sequence similarities and the result of phylogenetic analysis, strain HIT-DPA4^T was most closely related to Streptomyces cyaneus CGMCC 4.1671 ^T, and shared the highest sequence similarity of 98.76%. In addition, the cell walls of the species HIT-DPA4^T contained LL-diaminopimelic acid as the diagnostic diamino acid and the whole-cell hydrolysates were identified as glucose and ribose, and the principal phospholipids were found to be diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol mannoside and phosphatidylmonomethylethanolamine. MK-9(H₆) and MK-9(H₄) were predominant menaquinones; and C_16:0, anteiso-C_15:0 and C_15:0 as major cellular fatty acids of the organism HIT-DPA4^T. Gene Ontology database analysis and antiSMASH server predicted results displayed that strain HIT-DPA4^T was a promising classification units, which has various types of functions and contains multiple biosynthetic gene clusters with the similarity more than 80%. Multilocus sequence analysis (MLSA) of five housekeeping genes (atpD, gyrB, recA, rpoB and trpB) illustrated that Streptomyces luteolifulvus formed a separate branch in the genus Streptomyces. However, a combination of low level of DNA-DNA relatedness and physiological properties indicated that strain HIT-DPA4^T can be distinguished from its phylogenetically related species Streptomyces cyaneus CGMCC 4.1671 ^T. Moreover, gene synteny research could be further differed organism HIT-DPA4^T from similarity species. Therefore, the strain is concluded to represent a novel species of the genus Streptomyces, for which the name Streptomyces luteolifulvus sp. nov. is proposed. The type strain is HIT-DPA4^T (=?CGMCC 4.7558 ^T?=?TISTR 2751 ^T).

     

On computation of semiparametric maximum likelihood estimators with shape constraints

Large sample theory of semiparametric models based on maximum likelihood estimation (MLE) with shape constraint on the nonparametric component is well studied. Relatively less attention has been paid to the computational aspect of semiparametric MLE. The computation of semiparametric MLE based on existing approaches such as the expectation‐maximization (EM) algorithm can be computationally prohibitive when the missing rate is high. In this paper, we propose a computational framework for semiparametric MLE based on an inexact block coordinate ascent (BCA) algorithm. We show theoretically that the proposed algorithm converges. This computational framework can be applied to a wide range of data with different structures, such as panel count data, interval‐censored data, and degradation data, among others. Simulation studies demonstrate favorable performance compared with existing algorithms in terms of accuracy and speed. Two data sets are used to illustrate the proposed computational method. We further implement the proposed computational method in R package BCA1SG , available at CRAN.     

Rejoinder to Discussions on “Approval policies for modifications to machine learning‐based software as a medical device: A study of bio‐creep”

We thank the discussants for sharing their unique perspectives on the problem of designing automatic algorithm change protocols (aACPs) for machine learning‐based software as a medical device. Both Pennello et al. and Rose highlighted a number of challenges that arise in real‐world settings, and we whole‐heartedly agree that substantial extensions of our work are needed to understand if and how aACPs can be safely deployed in practice. Our work demonstrated that aACPs that appear to be harmless may allow for biocreep, even when the data distribution is assumed to be representative and stationary over time. While we investigated two solutions that protect against this specific issue, many more statistical and practical challenges remain and we look forward to future research on this topic.     

A penalized structural equation modeling method accounting for secondary phenotypes for variable selection on genetically regulated expression from PrediXcan for Alzheimer's disease

As the global burden of mental illness is estimated to become a severe issue in the near future, it demands the development of more effective treatments. Most psychiatric diseases are moderately to highly heritable and believed to involve many genes. Development of new treatment options demands more knowledge on the molecular basis of psychiatric diseases. Toward this end, we propose to develop new statistical methods with improved sensitivity and accuracy to identify disease‐related genes specialized for psychiatric diseases. The qualitative psychiatric diagnoses such as case control often suffer from high rates of misdiagnosis and oversimplify the disease phenotypes. Our proposed method utilizes endophenotypes, the quantitative traits hypothesized to underlie disease syndromes, to better characterize the heterogeneous phenotypes of psychiatric diseases. We employ the structural equation modeling using the liability‐index model to link multiple genetically regulated expressions from PrediXcan and the manifest variables including endophenotypes and case‐control status. The proposed method can be considered as a general method for multivariate regression, which is particularly helpful for psychiatric diseases. We derive penalized retrospective likelihood estimators to deal with the typical small sample size issue. Simulation results demonstrate the advantages of the proposed method and the real data analysis of Alzheimer's disease illustrates the practical utility of the techniques. Data used in preparation of this article were obtained from the Alzheimer's Disease Neuroimaging Initiative database.     

The interaction between host and host plant influences the oviposition and performance of a generalist ectoparasitoid

The successful development of parasitoids of herbivores depends on the quality of their host, which is often affected by the host plant. Therefore, a parasitoid’s oviposition decisions will directly depend on the host, but also on plant quality. Here, we investigated the direct effects of host species and the indirect effects of the host’s food plant on the oviposition decisions and performance of the gregarious ectoparasitoid Euplectrus platyhypenae Howard (Hymenoptera: Eulophidae). With a series of no‐choice experiments, we determined the oviposition and performance of the parasitoid on: (1) two caterpillar species, fall armyworm, Spodoptera frugiperda JE Smith (Lepidoptera: Noctuidae), and velvet armyworm, Spodoptera latifascia Walker, reared on maize (Zea mays L., Poaceae), (2) the same caterpillars reared on maize, bean (Phaseolus vulgaris L., Fabaceae), or squash (Cucurbita pepo L., Cucurbitaceae) leaves, and (3) S. latifascia caterpillars reared on leaves of wild and cultivated lima bean, Phaseolus lunatus L. All these insects and plants originate from Mesoamerica where they have coexisted for thousands of years in the traditional agricultural system known as Milpa in which maize, beans, and squash are planted together. We found that the preferred and best combination of host and host plant for parasitoid performance was S. frugiperda on maize. Parasitoids laid larger clutches, had higher survival, and more females and larger adults emerged from S. frugiperda reared on maize. However, when both caterpillar species were reared on squash, S. latifascia was the better host. Contrary to the literature, S. frugiperda was not able to develop on bean plants. Results from the lima bean experiment showed that parasitoid performance was best when S. latifascia was reared on leaves of cultivated compared to wild lima bean. These findings are discussed in the context of mixed cropping in which the ability of generalist parasitoids to switch among hosts and host plant species could be advantageous for pest management.