Diverse Roles of ERECTA Family Genes n Plant Development

Multiple receptor-like kinases （RLKs） enable intercellular communication that coordinates growth and development of plant tissues. ERECTA family receptors （ERfs） are an ancient family of leucine-rich repeat RLKs that in Arabidopsis consists of three genes： ERECTA, ERL1, and ERL2. ERfs sense secreted cysteine-rich peptides from the EPF/EPFL family and transmit the signal through a MAP kinase cascade. This review discusses the functions of ERfs in stomata development, in regulation of longitudinal growth of aboveground organs, during reproductive development, and in the shoot apical meristem. In addition the role of ERECTA in plant responses to biotic and abiotic factors is examined.     

Plant pleiotropic drug resistance transporters： Transport mechanism,gene expression,and function

Pleiotropic drug resistance （PDR） transporters belonging to the ABCG subfamily of ATP-binding cassette （ABC） transporters are identified only in fungi and plants. Members of this family are expressed in plants in response to various biotic and abiotic stresses and transport a diverse array of moleculesacross membranes, Although their detailed transport mechanism is largely unknown, they play important roles in detoxification processes, preventing water loss, transport of phytohormones, and secondary metabolites. This review provides insights into transport mechanisms of plant PDR transporters, their expression profiles, and multitude functions in plants.     

Roles of small RNAs in plant disease resistance

The interaction between plants and pathogens represents a dynamic competition between a robust immune system and efficient infectious strategies. Plant innate immunity is composed of complex and highly regulated molecular networks, which can be triggered by the perception of either conserved or race‐specific pathogenic molecular signatures. Small RNAs are emerging as versatile regulators of plant development, growth and response to biotic and abiotic stresses. They act in different tiers of plant immunity, including the pathogen‐associated molecular pattern‐triggered and the effector‐triggered immunity. On the other hand, pathogens have evolved effector molecules to suppress or hijack the host small RNA pathways. This leads to an arms race between plants and pathogens at the level of small RNA‐mediated defense.Here, we review recent advances in small RNA‐mediated defense responses and discuss the challenging questions in this area.     

Intravital multiphoton photoconversion with a cell membrane dye

Photoconversion, an irreversible shift in a fluorophore emission spectrum after light exposure, is a powerful tool for marking cellular and subcellular compartments and tracking their dynamics in vivo. This paper reports on the photoconversion properties of Di‐8‐ANEPPS, a commercially available membrane dye. When illuminated with near‐infrared femtosecond laser pulses, Di‐8‐ANEPPS undergoes multiphoton photoconversion as indicated by the supralinear dependence of the conversion rate ρ_pc on the incident power (), and by the ability to photoconvert a thin optical section in a three‐dimensional matrix. The characteristic emission spectrum changed from red to blue, and ratiometric analysis on single cells in vitro revealed a 65‐fold increase in the blue to red wavelength ratio after photoconversion. The spectral shift is preserved in vivo for hours, making Di‐8‐ANEPPS a useful dye for intravital cell marking and tracking applications.

     

speed‐ne: Software to simulate and estimate genetic effective population size (Ne) from linkage disequilibrium observed in single samples

The genetic effective population size, N_e, can be estimated from the average gametic disequilibrium () between pairs of loci, but such estimates require evaluation of assumptions and currently have few methods to estimate confidence intervals. speed‐ne is a suite of matlab computer code functions to estimate from with a graphical user interface and a rich set of outputs that aid in understanding data patterns and comparing multiple estimators. speed‐ne includes functions to either generate or input simulated genotype data to facilitate comparative studies of estimators under various population genetic scenarios. speed‐ne was validated with data simulated under both time‐forward and time‐backward coalescent models of genetic drift. Three classes of estimators were compared with simulated data to examine several general questions: what are the impacts of microsatellite null alleles on , how should missing data be treated, and does disequilibrium contributed by reduced recombination among some loci in a sample impact . Estimators differed greatly in precision in the scenarios examined, and a widely employed estimator exhibited the largest variances among replicate data sets. speed‐ne implements several jackknife approaches to estimate confidence intervals, and simulated data showed that jackknifing over loci and jackknifing over individuals provided ~95% confidence interval coverage for some estimators and should be useful for empirical studies. speed‐ne provides an open‐source extensible tool for estimation of from empirical genotype data and to conduct simulations of both microsatellite and single nucleotide polymorphism (SNP) data types to develop expectations and to compare estimators.     

Issue Information

Cover Image Left: Close‐up photograph of a hairy plant of Arabidopsis halleri subsp. gemmifera. Right: Larva of Phaedon brassicae feeding on a glabrous plant. Photographs by Yasuhiro Sato. Locality: Taka‐cho, Hyogo, Japan

     

Receptor-Like Kinases in Plant Innate Immunity

Plants employ a highly effective surveillance system to detect potential pathogens, which is critical for the success of land plants in an environment surrounded by numerous microbes. Recent efforts have led to the identification of a number of immune receptors and components of immune receptor complexes. It is now clear that receptor-like kinases （RLKs） and receptor-like proteins （RLPs） are key pattern-recognition receptors （PRRs） for microbe- and plant-derived molecular patterns that are associated with pathogen invasion. RLKs and RLPs involved in immune signaling belong to large gene families in plants and have undergone lineage specific expansion. Molecular evolution and population studies on phytopathogenic molecular signatures and their receptors have provided crucial insight into the co-evolution between plants and pathogens.     

High‐throughput identification of protein mutant stability computed from a double mutant fitness landscape

The effect of a mutation on protein stability is traditionally measured by genetic construction, expression, purification, and physical analysis using low‐throughput methods. This process is tedious and limits the number of mutants able to be examined in a single study. In contrast, functional fitness effects can be measured in a high‐throughput manner by various deep mutational scanning tools. Using protein GB 1, we have recently demonstrated the feasibility of estimating the mutational stability effect ( G) of single‐substitution based on the functional fitness profile of all double‐substitutions. The principle is to identify genetic backgrounds that have an exhausted stability margin. The functional effect of an additional substitution on these genetic backgrounds can then be used to compute the mutational G based on the biophysical relationship between functional fitness and thermodynamic stability. However, to identify such genetic backgrounds, the approach described in our previous study required a benchmark dataset, which is a set of known mutational G. In this study, a benchmark‐independent approach is developed. The genetic backgrounds of interest are identified using k‐means clustering with the integration of structural information. We further demonstrated that a reasonable approximation of G can also be obtained without taking structural information into account. In summary, this study describes a novel method for computing G from double‐substitution functional fitness profiles alone, without relying on any known mutational G as a benchmark.     

Split‐root systems applied to the study of the legume‐rhizobial symbiosis: What have we learned?

Split‐root system (SRS) approaches allow the differential treatment of separate and independent root systems, while sharing a common aerial part. As such, SRS is a useful tool for the discrimination of systemic (shoot origin) versus local (root/nodule origin) regulation mechanisms. This type of approach is particularly useful when studying the complex regulatory mechanisms governing the symbiosis established between legumes and Rhizobium bacteria. The current work provides an overview of the main insights gained from the application of SRS approaches to understand how nodule number (nodulation autoregulation) and nitrogen fixation are controlled both under non‐stressful conditions and in response to a variety of stresses. Nodule number appears to be mainly controlled at the systemic level through a signal which is produced by nodule/root tissue, translocated to the shoot, and transmitted back to the root system, involving shoot Leu‐rich repeat receptor‐like kinases. In contrast, both local and systemic mechanisms have been shown to operate for the regulation of nitrogenase activity in nodules. Under drought and heavy metal stress, the regulation is mostly local, whereas the application of exogenous nitrogen seems to exert a regulation of nitrogen fixation both at the local and systemic levels.     

Issue Information

Cover Image Flowering individuals of Solidago virgaurea. Photographed by Koichi Takahashi. Mt. Norikura, Honshu, Japan

     

Monochromatic subdiffusive spatial frequency domain imaging provides in‐situ sensitivity to intratumoral morphological heterogeneity in a murine model

For the first time, spatially resolved quantitative metrics of light scattering recovered with sub‐diffusive spatial frequency domain imaging (sd‐SFDI) are shown to be sensitive to changes in intratumoral morphology and viability by direct comparison to histopathological analysis. Two freshly excised subcutaneous murine tumor cross‐sections were measured with sd‐SFDI, and recovered optical scatter parameter maps were co‐registered to whole mount histology. Unique clustering of the optical scatter parameters vs. γ (i.e. diffuse scattering vs. relative backscattering) evaluated at a single wavelength showed complete separation between regions of viable tumor, aggresive tumor with stromal growth, varying levels of necrotic tumor, and also peritumor muscle. The results suggest that with further technical development, sd‐SFDI may represent a non‐destructive screening tool for analysis of excised tissue or a non‐invasive approach to investigate suspicious lesions without the need for exogenous labels or spectrally resolved imaging.

     

Summary goodness‐of‐fit statistics for binary generalized linear models with noncanonical link functions

Generalized linear models (GLM) with a canonical logit link function are the primary modeling technique used to relate a binary outcome to predictor variables. However, noncanonical links can offer more flexibility, producing convenient analytical quantities (e.g., probit GLMs in toxicology) and desired measures of effect (e.g., relative risk from log GLMs). Many summary goodness‐of‐fit (GOF) statistics exist for logistic GLM. Their properties make the development of GOF statistics relatively straightforward, but it can be more difficult under noncanonical links. Although GOF tests for logistic GLM with continuous covariates (GLMCC) have been applied to GLMCCs with log links, we know of no GOF tests in the literature specifically developed for GLMCCs that can be applied regardless of link function chosen. We generalize the Tsiatis GOF statistic originally developed for logistic GLMCCs, (), so that it can be applied under any link function. Further, we show that the algebraically related Hosmer–Lemeshow () and Pigeon–Heyse (J²) statistics can be applied directly. In a simulation study, , , and J² were used to evaluate the fit of probit, log–log, complementary log–log, and log models, all calculated with a common grouping method. The statistic consistently maintained Type I error rates, while those of and J² were often lower than expected if terms with little influence were included. Generally, the statistics had similar power to detect an incorrect model. An exception occurred when a log GLMCC was incorrectly fit to data generated from a logistic GLMCC. In this case, had more power than or J².     

Effective size of density‐dependent populations in fluctuating environments

Reliable estimates of effective population size are of central importance in population genetics and evolutionary biology. For populations that fluctuate in size, harmonic mean population size is commonly used as a proxy for (multi‐) generational effective size. This assumes no effects of density dependence on the ratio between effective and actual population size, which limits its potential application. Here, we introduce density dependence on vital rates in a demographic model of variance effective size. We derive an expression for the ratio in a density‐regulated population in a fluctuating environment. We show by simulations that yearly genetic drift is accurately predicted by our model, and not proportional to as assumed by the harmonic mean model, where N is the total population size of mature individuals. We find a negative relationship between and N. For a given N, the ratio depends on variance in reproductive success and the degree of resource limitation acting on the population growth rate. Finally, our model indicate that environmental stochasticity may affect not only through fluctuations in N, but also for a given N at a given time. Our results show that estimates of effective population size must include effects of density dependence and environmental stochasticity.     

Back Cover: Autofluorescence and white light imaging‐guided endoscopic Raman and diffuse reflectance spectroscopy for in vivo nasopharyngeal cancer detection (J. Biophotonics 4/2018)

An integrated 4‐modality endoscopy system combining white light imaging, autofluorescence imaging, diffuse reflectance spectroscopy and Raman spectroscopy technologies was developed for in vivo endoscopic nasopharyngeal cancer detection. Both high diagnostic sensitivity (98.6%) and high specificity (95.1%) for differentiating cancer from normal tissue sites were achieved using this system combined with multivariate diagnostic algorithm, demonstrating great potential for improving real‐time, in vivo diagnosis of cancer at endoscopy. Further details can be found in the article by Duo Lin et al. ( e201700251 )

     

Issue Information

Main flower‐visitng insects of Bidens fronds. Photographed by Bing Zhou in Jían City, Jiangxi Province, China. Cover picture from: Reproductive biological characteristics potentially contributed to invasiveness in an alien invasive plant Bidens frondosa, Yan XH et al. See pages 107–116. Article link here .

     

Issue Information

Cover Image Left: Flowering individuals of Gastrodia elata. Right: Individual flowers of Gastroidia elate. Photographed by Naoto Sugiura. Rebun Island, Hokkaido, Japan

     

Raman spectroscopic identification of Mycobacterium tuberculosis

In this study, Raman microspectroscopy has been utilized to identify mycobacteria to the species level. Because of the slow growth of mycobacteria, the per se cultivation‐independent Raman microspectroscopy emerges as a perfect tool for a rapid on‐the‐spot mycobacterial diagnostic test. Special focus was laid upon the identification of Mycobacterium tuberculosis complex (MTC) strains, as the main causative agent of pulmonary tuberculosis worldwide, and the differentiation between pathogenic and commensal nontuberculous mycobacteria (NTM). Overall the proposed model considers 26 different mycobacteria species as well as antibiotic susceptible and resistant strains. More than 8800 Raman spectra of single bacterial cells constituted a spectral library, which was the foundation for a two‐level classification system including three support vector machines. Our model allowed the discrimination of MTC samples in an independent validation dataset with an accuracy of 94% and could serve as a basis to further improve Raman microscopy as a first‐line diagnostic point‐of‐care tool for the confirmation of tuberculosis disease.

     

Issue Information

Cover Image Left: Papaver fauriei growing only on the gravelly alpine slopes of Mt. Rishiri. Right: Cultivated poppies (Papaver sp.) found in seaside towns on Rishiri Island. Photographed by Kazuki Kosugi and Tetsuya Kondo. Rishiri Island, Hokkaido, Japan