Tropicalisation of temperate seagrass meadows in Western Australia: Predicting the impact of tropical herbivorous fishes on temperate seagrass meadows

Rising sea temperatures through climate change produce shifts in the distribution of tropical species to temperate regions, a process termed “tropicalisation”. The poleward expansion of tropical herbivores into temperate seagrass meadows is predicted to increase grazing pressure and alter ecosystem services and processes in these seagrass systems. This study attempted to examine the effects of tropicalisation on temperate seagrass meadows along the western coast of Australia, where the increasing abundance of tropical consumers such as the herbivorous Siganus fuscescens has already been documented. Through the assessment of fish assemblages in seagrass meadows and the grazing levels on seagrass in 2001 and 2016/17, as well as in situ and mesocosm feeding preference experiments, this study attempted to estimate the grazing rates and impact that the growing abundance of S. fuscescens may have in temperate seagrass meadows. Shifts in the grazing rates on seagrass between 2001 and 2016/17 were inconsistent, varying between seagrass species and location. Based on observational data on the bites on seagrass leaves, rates of consumption increased for Posidonia sinuosa while no similar pattern was found for Posidonia australis. This was despite an apparent greater consumption on P. australis compared to P. sinuosa in 2001, and the minimal amount of grazing on tethered seagrass. The higher observed level of P. sinuosa consumption in 2016/17 is likely explained by the changed herbivorous fish species composition, even though no fish were clearly observed feeding on seagrass in the current study. The tropical herbivore S. fuscescens was more abundant in 2016/17 that 2001, although abundances were patchy and no fish was observed feeding on seagrass. The higher level of P. sinuosa consumption in 2016/17, compared to 2001, supports the prediction that with increasing abundances in temperate seagrass ecosystems, tropical herbivores will enhance the consumption of seagrass. However, seagrass consumption is likely to be strongly influenced by the availability of macroalgae which were shown as the preferred food sources. Feeding trials in mesocosms were compromised by the large number of deaths and the limited grazing on natural food sources by S. fuscescens, suggesting that the population in the Perth region is susceptible to adverse handling and husbandry effects. To maximise the survival rate of captured fish, the fishing and handling procedures were altered to adapt to the ongoing observations in the response of fish to handling in the field or in the mesocosm facilities. Lesson learned from the capture, handling and husbandry of S. fuscescens in feeding trials in the current study will hopefully provide greater success for feeding preference experiments in the future. The sampling program initiated in 2001 and repeated in 2016/17 provides base-line data and the opportunity to monitor and track the shift in abundances of tropical herbivores and resultant increases in grazing rates to test the above predictions. The consequences of tropicalisation will depend on the variety of abiotic and biotic factors, including the fish assemblages in the area, the abundance of tropical species, the availability of food, and the feeding preferences that invading species will develop in response to the changed environmental conditions

Modeling of Gap Gene Expression in <i>Drosophila Kruppel</i> Mutants

The segmentation gene network in Drosophila embryo solves the fundamental problem of embryonic patterning: how to establish a periodic pattern of gene expression, which determines both the positions and the identities of body segments. The gap gene network constitutes the first zygotic regulatory tier in this process. Here we have applied the systems-level approach to investigate the regulatory effect of gap gene Kruppel (Kr) on segmentation gene expression. We acquired a large dataset on the expression of gap genes in Kr null mutants and demonstrated that the expression levels of these genes are significantly reduced in the second half of cycle 14A. To explain this novel biological result we applied the gene circuit method which extracts regulatory information from spatial gene expression data. Previous attempts to use this formalism to correctly and quantitatively reproduce gap gene expression in mutants for a trunk gap gene failed, therefore here we constructed a revised model and showed that it correctly reproduces the expression patterns of gap genes in Kr null mutants. We found that the remarkable alteration of gap gene expression patterns in Kr mutants can be explained by the dynamic decrease of activating effect of Cad on a target gene and exclusion of Kr gene from the complex network of gap gene interactions, that makes it possible for other interactions, in particular, between hb and gt, to come into effect. The successful modeling of the quantitative aspects of gap gene expression in mutant for the trunk gap gene Kr is a significant achievement of this work. This result also clearly indicates that the oversimplified representation of transcriptional regulation in the previous models is one of the reasons for unsuccessful attempts of mutant simulations.</p

Pathology of Sarcoidosis and Differential Diagnostics of other Granulomatous Diseases

Granulomatous diseases are the heterogeneous group of the conditions of different etiologies with a variety of clinic syndromes and morphological features and nonuniform sensitivity to therapy, and the existence of granulomas as general dominate histological expression. Granuloma is indicative of chronic inflammation involving cells of the macrophage system and other inflammatory cells. After the antigen exposure, the activation of T-lymphocytes, macrophages, and epithelioid histiocytes leads to granuloma formation. Granuloma also contains the extracellular matrix produced by fibroblasts, which provide the boundary and isolation of antigen. Their etiology may classify granulomatous diseases as infectious and noninfectious. However, recent studies demonstrate that pathogenic microorganisms may cause the granuloma formation in diseases previously considered as noninfectious. In some cases, differentiation between infectious and noninfectious processes may be problematic. This chapter aims to highlight the multiformity of granulomatous diseases, characterize the pathologic features of different infectious and noninfectious granulomatosis, and delineate the diagnostic approach

Additional heat loss of jamb in enclosing structures

One of the urgent problems today is to increase the energy efficiency of civil buildings. There is a need at the design stage to choose structures and design solutions that will compensate for the increasing consumption of energy resources in civil engineering. This article compares different building envelopes used in the construction of residential buildings: a volumetric block and a wall made of aerated concrete blocks. To determine the most energy efficient design solution construction is compared in different climatic regions. One of the most vulnerable places of a wall, from the point of view of energy efficiency, is a window jamb. In this article, an analysis is carried out to determine the construction with the lowest heat loss window jambs. Using the ELCUT software temperature fields and additional heat flux densities are calculated. According to the calculation, the proportion of heat loss due to window slope from heat loss according to the surface of the structure was determined. The heat flux density of the homogeneous section of the wall of the volume block is 1.28 times higher on average than in the aerated concrete wall. Regardless of the climatic conditions, the junction of the window jamb in buildings made of insulated panels of volumetric blocks is more energy efficient than the same junction in a building with aerated concrete walls

Genomic and phenotypic analysis of Vavilov's historic landraces reveals the impact of environment and genomic islands of agronomic traits.

The Vavilov Institute of Plant Genetic Resources (VIR), in St. Petersburg, Russia, houses a unique genebank, with historical collections of landraces. When they were collected, the geographical distribution and genetic diversity of most crops closely reflected their historical patterns of cultivation established over the preceding millennia. We employed a combination of genomics, computational biology and phenotyping to characterize VIR's 147 chickpea accessions from Turkey and Ethiopia, representing chickpea's center of origin and a major location of secondary diversity. Genotyping by sequencing identified 14,059 segregating polymorphisms and genome-wide association studies revealed 28 GWAS hits in potential candidate genes likely to affect traits of agricultural importance. The proportion of polymorphisms shared among accessions is a strong predictor of phenotypic resemblance, and of environmental similarity between historical sampling sites. We found that 20 out of 28 polymorphisms, associated with multiple traits, including days to maturity, plant phenology, and yield-related traits such as pod number, localized to chromosome 4. We hypothesize that selection and introgression via inadvertent hybridization between more and less advanced morphotypes might have resulted in agricultural improvement genes being aggregated to genomic 'agro islands', and in genotype-to-phenotype relationships resembling widespread pleiotropy

Non-linear regression models for time to flowering in wild chickpea combine genetic and climatic factors

Background: Accurate prediction of crop flowering time is required for reaching maximal farm efficiency. Several models developed to accomplish this goal are based on deep knowledge of plant phenology, requiring large investment for every individual crop or new variety. Mathematical modeling can be used to make better use of more shallow data and to extract information from it with higher efficiency. Cultivars of chickpea, Cicer arietanum, are currently being improved by introgressing wild C. reticulatum biodiversity with very different flowering time requirements. More understanding is required for how flowering time will depend on environmental conditions in these cultivars developed by introgression of wild alleles. Results: We built a novel model for flowering time of wild chickpeas collected at 21 different sites in Turkey and grown in 4 distinct environmental conditions over several different years and seasons. We propose a general approach, in which the analytic forms of dependence of flowering time on climatic parameters, their regression coefficients, and a set of predictors are inferred automatically by stochastic minimization of the deviation of the model output from data. By using a combination of Grammatical Evolution and Differential Evolution Entirely Parallel method, we have identified a model that reflects the influence of effects of day length, temperature, humidity and precipitation and has a coefficient of determination of R 2=0.97. Conclusions: We used our model to test two important hypotheses. We propose that chickpea phenology may be strongly predicted by accession geographic origin, as well as local environmental conditions at the site of growth. Indeed, the site of origin-by-growth environment interaction accounts for about 14.7% of variation in time period from sowing to flowering. Secondly, as the adaptation to specific environments is blueprinted in genomes, the effects of genes on flowering time may be conditioned on environmental factors. Genotype-by-environment interaction accounts for about 17.2% of overall variation in flowering time. We also identified several genomic markers associated with different reactions to climatic factor changes. Our methodology is general and can be further applied to extend existing crop models, especially when phenological information is limited

Dynamical climatic model for time to flowering in Vigna radiata

Background: Phenology data collected recently for about 300 accessions of Vigna radiata (mungbean) is an invaluable resource for investigation of impacts of climatic factors on plant development. Results: We developed a new mathematical model that describes the dynamic control of time to flowering by daily values of maximal and minimal temperature, precipitation, day length and solar radiation. We obtained model parameters by adaptation to the available experimental data. The models were validated by cross-validation and used to demonstrate that the phenology of adaptive traits, like flowering time, is strongly predicted not only by local environmental factors but also by plant geographic origin and genotype. Conclusions: Of local environmental factors maximal temperature appeared to be the most critical factor determining how faithfully the model describes the data. The models were applied to forecast time to flowering of accessions grown in Taiwan in future years 2020-2030

Genome-wide association study in accessions of the mini-core collection of mungbean (Vigna radiata) from the World Vegetable Gene Bank (Taiwan)

Background: Mungbean (Vigna radiata (L.) R. Wilczek, or green gram) is important tropical and sub-tropical legume and a rich source of dietary protein and micronutrients. In this study we employ GWAS to examine the genetic basis of variation in several important traits in mungbean, using the mini-core collection established by the World Vegetable Center, which includes 296 accessions that represent the major market classes. This collection has been grown in a common field plot in southern European part of Russia in 2018. Results: We used 5041 SNPs in 293 accessions that passed strict filtering for genetic diversity, linkage disequilibrium, population structure and GWAS analysis. Polymorphisms were distributed among all chromosomes, but with variable density. Linkage disequilibrium decayed in approximately 105 kb. Four distinct subgroups were identified within 293 accessions with 70% of accessions attributed to one of the four populations. By performing GWAS on the mini-core collection we have found several loci significantly associated with two important agronomical traits. Four SNPs associated with possibility of maturation in Kuban territory of Southern Russia in 2018 were identified within a region of strong linkage which contains genes encoding zinc finger A20 and an AN1 domain stress-associated protein. Conclusions: The core collection of mungbean established by the World Vegetable Center is a valuable resource for mungbean breeding. The collection has been grown in southern European part of Russia in 2018 under incidental stresses caused by abnormally hot weather and different photoperiod. We have found several loci significantly associated with color of hypocotyl and possibility of maturation under these stressful conditions. SNPs associated with possibility of maturation localize to a region on chromosome 2 with strong linkage, in which genes encoding zinc finger A20 and AN1 domain stress associated protein (SAP) are located. Phenotyping of WorldVeg collection for maturation traits in temperate climatic locations is important as phenology remains a critical breeding target for mungbean. As demand rises for mungbean, production in temperate regions with shorter growing seasons becomes crucial to keep up with needs. Uncovering SNPs for phenology traits will speed breeding efforts

A Pipeline for Classifying Deleterious Coding Mutations in Agricultural Plants

The impact of deleterious variation on both plant fitness and crop productivity is not completely understood and is a hot topic of debates. The deleterious mutations in plants have been solely predicted using sequence conservation methods rather than function-based classifiers due to lack of well-annotated mutational datasets in these organisms. Here, we developed a machine learning classifier based on a dataset of deleterious and neutral mutations in Arabidopsis thaliana by extracting 18 informative features that discriminate deleterious mutations from neutral, including 9 novel features not used in previous studies. We examined linear SVM, Gaussian SVM, and Random Forest classifiers, with the latter performing best. Random Forest classifiers exhibited a markedly higher accuracy than the popular PolyPhen-2 tool in the Arabidopsis dataset. Additionally, we tested whether the Random Forest, trained on the Arabidopsis dataset, accurately predicts deleterious mutations in Orýza sativa and Pisum sativum and observed satisfactory levels of performance accuracy (87% and 93%, respectively) higher than obtained by the PolyPhen-2. Application of Transfer learning in classifiers did not improve their performance. To additionally test the performance of the Random Forest classifier across different angiosperm species, we applied it to annotate deleterious mutations in Cicer arietinum and validated them using population frequency data. Overall, we devised a classifier with the potential to improve the annotation of putative functional mutations in QTL and GWAS hit regions, as well as for the evolutionary analysis of proliferation of deleterious mutations during plant domestication; thus optimizing breeding improvement and development of new cultivars

Mechanisms of gap gene expression canalization in the Drosophila blastoderm

<p>Abstract</p> <p>Background</p> <p>Extensive variation in early gap gene expression in the <it>Drosophila </it>blastoderm is reduced over time because of gap gene cross regulation. This phenomenon is a manifestation of canalization, the ability of an organism to produce a consistent phenotype despite variations in genotype or environment. The canalization of gap gene expression can be understood as arising from the actions of attractors in the gap gene dynamical system.</p> <p>Results</p> <p>In order to better understand the processes of developmental robustness and canalization in the early <it>Drosophila </it>embryo, we investigated the dynamical effects of varying spatial profiles of Bicoid protein concentration on the formation of the expression border of the gap gene <it>hunchback</it>. At several positions on the anterior-posterior axis of the embryo, we analyzed attractors and their basins of attraction in a dynamical model describing expression of four gap genes with the Bicoid concentration profile accounted as a given input in the model equations. This model was tested against a family of Bicoid gradients obtained from individual embryos. These gradients were normalized by two independent methods, which are based on distinct biological hypotheses and provide different magnitudes for Bicoid spatial variability. We showed how the border formation is dictated by the biological initial conditions (the concentration gradient of maternal Hunchback protein) being attracted to specific attracting sets in a local vicinity of the border. Different types of these attracting sets (point attractors or one dimensional attracting manifolds) define several possible mechanisms of border formation. The <it>hunchback </it>border formation is associated with intersection of the spatial gradient of the maternal Hunchback protein and a boundary between the attraction basins of two different point attractors. We demonstrated how the positional variability for <it>hunchback </it>is related to the corresponding variability of the basin boundaries. The observed reduction in variability of the <it>hunchback </it>gene expression can be accounted for by specific geometrical properties of the basin boundaries.</p> <p>Conclusion</p> <p>We clarified the mechanisms of gap gene expression canalization in early <it>Drosophila </it>embryos. These mechanisms were specified in the case of <it>hunchback </it>in well defined terms of the dynamical system theory.</p