Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of covariance in agronomy and crop research

Yang, R. -C. and Juskiw, P. 2011. Analysis of covariance in agronomy and crop research. Can. J. Plant Sci. 91: 621-641. Analysis of covariance (ANCOVA) is a statistical technique that combines the methods of the analysis of variance (ANOVA) and regression analysis. However, ANCOVA is an advanced topic that often appears towards the end of many textbooks, and thus, it is either taught cursorily or ignored completely in many statistics classes. Additionally, many elaborated applications of ANCOVA to agronomy and crop research along with uses of the latest statistical software are rarely described in textbooks or classes. The objectives of this paper are to provide an overview on conventional ANCOVA and to introduce more advanced uses of ANCOVA under mixed models. We describe three elaborate applications including (i) the use of ANCOVA for dissecting dosage responses for different treatments, (ii) stability of treatments across multiple environments and (iii) removal of spatial variation that is not effectively controlled by blocking. These analyses illustrate that ANCOVA is either a simpler analysis or provides more information than conventional statistical methods. We provide a technical appendix (Appendix A) on principles and theory underlying mixed-model analysis of ANCOVA along with SAS programs (Appendix B) for more uses and in-depth understanding of this powerful technique in agronomy and crop research.
Mycorrhiza and Common Mycorrhizal Network Regulate the Production of Signal Substances in Trifoliate Orange (Poncirus trifoliata)

Common mycorrhizal networks (CMNs) connecting two or more neighbouring plants are confirmed to transfer signals, whereas little information about CMNs effects on the signal substances production is known. In this study, a two-chambered rootbox separated by 37 µm nylon mesh was used to establish donor and receptor chambers. Two chambers both were planted with trifoliate orange (Poncirus trifoliata) and then only donor chamber inoculated with Diversispora versiformis, Paraglomus occultum and Rhizoglomus intraradices. The roots of the donor and receptor plants both were mycorrhizated suggesting that CMNs were established between donor and receptor seedlings. Moreover, the AMF association dramatically increased plant height, stem diameter, leaf numbers, and shoot and root biomass in both the donor and receptor seedlings. The AMF inoculation in the donor plants and the subsequent mycorrhizal colonization by CMNs in the receptor plants significantly increased root calmodulin (CaM) and salicylic acid (SA) concentrations, while considerably decreased root nitric oxide (NO) and jasmonic acid (JA) concentrations. This was accompanied by down-regulated expression of three JA synthetic genes (PtLOX, PtAOS and PtAOC), regardless of donor and receptor seedlings. These results thus suggest that CMNs between trifoliate orange seedlings manifestly promote plant growth and affect the production of signal substances.
Proteomic analysis of erythropoietin-induced changes in neuron-like SH-SY5Y cells

Abstract Objective Erythropoietin (EPO) is widely used for treatment of anemia associated with different diseases; however, its adverse effects limit its use in clinical practice. Therefore, understanding the effects of EPO at the molecular and cellular level is crucial to adjust treatment regimes, and to develop non-hematopoietic EPO derivatives. In this study, we used a proteomics approach to identify how EPO treatment modifies the cellular proteome. Methods SH-SY5Y neuroblastoma cells were used as the model system to analyze the effects of EPO treatment at different time points (24 h and 48 h). Proteomic analysis revealed changes in 74 proteins after EPO treatment. Following proteomics analysis, Reactome pathway analysis were carried out to identify the affected cellular pathways. Results According to results, EPO alters the levels of 74 protein species (40 were increased, 34 were decreased). The levels of 35 proteins were changed by 24 h EPO incubation, whereas 17 protein species were altered by 48 h EPO incubation. Levels of 22 protein species were altered by both of the incubation periods (24 h and 48 h). Conclusion Overall, our results suggest that EPO mainly affects protein species in glucose metabolism, protein and RNA metabolism, cytoskeletal proteins, and mitochondrial protein species.
Mechanical interpretation of infills-to-frame interaction: contributions to the global base shear for strut-based frame models

The presence of infills has substantial effects on the behaviour of frame structural systems, both in the linear and non-linear behaviour. Different effects might arise at global (increase in strength and stiffness, modification of the plastic mechanism) and local level (e.g. triggering of shear failures in the columns). The global effects can be captured by adopting numerical macro-models (e.g. representing the infill panels as equivalent struts), while local effects can be typically better captured by using FEM micro-modelling. Focusing on single- or multiple-strut macro-modelling strategies, in this paper a mechanically-based procedure to decouple the frame and infills contributions to the overturning moment (and hence base shear) capacity for any value of the global displacement is proposed. The method is applicable regardless of the distribution of the infills and of the non-linear Axial loadAxial strain relationship of the equivalent struts. For these reasons, such procedure can be applied to post-process the results of non-linear pushover or time-history analyses of different types of infilled frames (material-wise) as well as be adopted as a simplified analytical approach, such as SLaMA (Simple Lateral Mechanism Analysis), to derive the capacity curve of an infilled frame whilst capturing the proper internal actions. An application of the method on an experimentally-tested one-storey one-bay masonry infilled frame is used to calibrate the adopted numerical model. Furthermore, the method is applied to the pushover analysis of a two-storey one-bay masonryinfilled RC frame, with uniform or “pilotis” infill distributions, modelled by means of a single-strut approach. The results confirm the suitability of the proposed method in decoupling the frame and infills contributions to the total overturning moment.
Variability of Natural Populations of Atriplex Halimus L. in Morocco as Investigated by RAPD Markers

Atriplex halimus L. (Chenopodiaceae) is a monoecious C 4 perennial shrub native to the Mediterranean Basin, used as fodder shrub for livestock and useful for rehabilitation of degraded rangelands. To assess the levels and patterns of genetic diversity of this species, 99 samples of 11 populations collected throughout the natural range in Morocco plus 9 samples obtained from one population originating from USA, were analyzed using RAPD method and markers. A number of 157 reproducible amplified bands were obtained with 17 primers. Out of 157 amplified bands, 146 (93%) were polymorphic, and only 11 (7%) monomorphic. Global AMOVA analysis showed that the most genetic variation was within populations (66.57%), with the reminder occurring between populations (33.43%). Hierarchical AMOVA analysis revealed that variation among regions (Morocco versus USA) accounted only for 5.87% of the total genetic variation, suggesting that there is not a significant genetic differentiation of populations located at the opposite sides of the Atlantic Ocean. The actual genetic structure could have arisen by a combination of genetic drift effect and limited level of gene flow (0.50). The genetic diversity maintained by this species (0.238) was somewhat higher in comparison to other species with similar life histories and ecological traits. A neighbour- joining dendrogram based on Dice's coefficient resolved five major groups of populations correlated in part with bioclimatic type. Nevertheless, geographic distance did not explain the genetic differentiation among populations (r = 0.103, P = 0.646). The data obtained in this study should have important implications for the conservation and management strategies of genetic variation of Atriplex halimus in Morocco.
Pentraxin -Carbonic anhydrase CA VI: A novel multidomain protein

Background and aims: Carbonic anhydrases (CAs) participate in the maintenance of pH homeostasis catalyzing the reversible hydration of carbon dioxide CO2 + H2O HCO3− + H+. CAs is fundamental to a wide array of physiological processes in species and driving the diversification of CA isoforms in different environments. The CA VI is a secreted protein, found in saliva and breast milk. In some species, such as frogs, fish and chicken a part called pentraxin is attached to CA VI – protein. A function of this pentraxin is not known. In the present study, we investigated the characteristics of CA VI in different species. The alignment of sequences, the structure of protein and conservation among different species were observed using bioinformatics methods. The other focus on this study was to build a construct for zebrafish CA VI protein production in bacterial and insect cells and to observe the knockdown zebrafish embryonic development in early states using molecular biology and histological methods. Methods: The CA VI protein sequences found in the databases aligned and studied with bioinformatics methods. The molecular biology methods used to build the construct for the protein production of zebrafish CA VI and to study the knockdown effect in zebrafish embryos. Results: The alignment and the analysis of CA VI structure showed the regions of conserved amino acids in different species. One of these regions included the N-glycosylation site found in most of the studied sequences. The study of the 3D structure showed strong conservation at the active site of the protein. The construct has built for the zebrafish CA VI protein production. The template sequence of the construct verified with sequencing. The samples from the CA6 knockdown zebrafish embryos and fry showed changes in morphology of the swim bladder and the stomach area. Conclusions: The analysis confirms that the CA VI is a secreted protein having a signal peptide, and the N-glycosylation site predictions gave novel information about the conserved Nglycosylation site found in different species sequences. The visualizing tool proved to be very helpful of showing the conserved regions in 3D structure. The function of the attached pentraxin part remains unknown. A construct for zebrafish CA VI protein production was produced. The sequencing results verified with bioinformatics methods that the template codes the correct CA VI protein. The morphology results showed the malformation of the swim bladder and stomach area of the CA6 knockdown zebrafish.
Influence of vegetation type and prescribed fire on Peromyscus abundance in a longleaf pine ecosystem

Prescribed fire temporarily can alter food and cover resources for ground-dwelling wildlife, potentially leading to changes in animal abundance. Small mammals are an important ecosystem component in many terrestrial communities and depend on ground-level vegetation most commonly affected by prescribed fire. In this complex system of food and cover availability where easier access to food might compromise cover, and vice versa, it is imperative to study postfire habitat use by mice and other grounddwelling wildlife. We evaluated effects of time since burn and vegetation type on Peromyscus spp. abundance in a longleaf pine (Pinus palustris) ecosystem in Fort Bragg Military Installation, North Carolina, USA, during 2011 and 2012. We trapped in 5 vegetation types and captured 208 individual Peromyscus. Peromyscus abundance did not differ among 1, 2, and 3 years postburn upland pine vegetation types, although we noted a trend of decreasing abundance as time since burn increased; however, abundance was greater in the lowland hardwood vegetation type than in open areas (i.e., military drop zones). The lack of an effect of time since burn could be due to the short fire-return interval at the study site, which limited the time for postburn shifts in the composition of the understory from herbaceous to woody plant species. Therefore, we suggest future research in the longleaf pine ecosystem incorporate a wider time frame to assess shortand long-term effects of fire on small mammal populations. 2017 The Wildlife Society.
What variables make a forest stand vulnerable to browsing damage occurrence

Ungulate browsing results in important damages on the forests, affecting their structure, composition and development. In the present paper, we examine the occurrence of browsing damage in Norwegian forests, using data provided by the National Forest Inventory along several consecutive measurements (entailing the period 1995–2014). A portfolio of variables describing the stand, site and silvicultural treatments are analyzed using classification trees to retrieve combinations related to browsing damage. Our results indicate that the most vulnerable forest stands are young with densities below 1400 trees ha–1 and dominated by birch, pine or mixed species. In addition, stand diversity and previous treatments (e.g. thinnings) increase the damage occurrence and other variables, like stand size, could play a role on forest susceptibility to browsing occurrence although the latter is based on weaker evidence. The methods and results of our study can be applied to implement management measures aiming at reducing the browsing damages of forests.
Investigating the conservation of shikimate kinase-like 1 function in Solanum lycopersicum and Physcomitrella patens

A shikimate kinase (SK) gene duplicate annotated as shikimate kinase-like 1 (SKL1) has been identified in higher plants. Physcomitrella patens is one of the most ancient land plants, and is also the most ancient SKL1 ortholog. This suggests that the SK-SKL1 gene duplication event occurred during the emergence of land plants roughly 400-500MYA. SKL1 is required for plastid biogenesis and so has neofunctionalized since the gene duplication event. However, many questions remain to be answered such as the conservation of function across land plants and the time of SKL1 neofunctionalization. In order to investigate the conservation of SKL1 function in land plants, virus induced SKL1 silencing as well as RNAi and knockout mutant generation will be employed in Solanum lycopersicum and Physcomitrella patens respectively. Additionally, experimentation using Physcomitrella patens will provide us the opportunity to investigate the time of SKL1 neofunctionalization.
Effect of Casein/Fat Ratio on Milk Fat Recovery in Cheddar Cheese

Effect of Casein/Fat Ratio on Milk Fat Recovery in Cheddar Cheese by Nana A. Yiadom-Farkye, Master of Science Utah State University, 1984 Major Professor: C.A. Ernstrom Department: Nutr i tion and Food Sciences vii Cheddar cheese was made by the traditional 4.5-h method from three experimental lots of mi lk, each standardized to casein/fat ratios of approximately 0.64, 0.67 and 0.70. The effect of casein/fat ratio on milk fat recovery was determined. The effects of milk composition on curd firmness at cutting, cheese composition and resulting yield of cheese were evaluated. Correlations between milk constituents and various cheese components were obtained. Milk fat recovery was unaffected by casein/fat ratios within the limits of 0.64 and 0.71. Average milk fat recovery was 91.58 ± 1.73%. Cheese yield was a function of milk protein, milk fat and cheese moisture; and a modified Van Slyke equation predicted cheese yield better than the original equation within the limits of casein/fat ratio studied. Strong negative correlations were observed between casein/fat ratio and cheese fat and cheese fat in the dry matter whereas positive correlations were observed between casein/fat ratio and cheese protein. At constant protein levels curd firmness increased directly with the amount of fat in cheese milk.
First record of Hexaglandula corynosoma (Travassos, 1915) Petrochenko, 1958 (Acanthocephala: Polymorphidae) in intermediate and definitive hosts in Mexico

Members of Polymorphidae, including Hexaglandula corynosoma, are acanthocephalans commonly found as intestinal parasites in marine mammals, fish-eating birds and waterfowl. Hexaglandula corynosoma is distributed throughout the Southeastern U. S. and southwards to Puerto Rico and Brazil. An acanthocephalan (and its larvae) resembling H. corynosoma were found parasitizing intermediate (decapod crustaceans, Uca spinicarpa) and definitive hosts (yellow-crowned night herons, Nyctanacea violacea) from various localities in Mexico. A morphological and genetic study, in combination with previous studies, confirmed that the larvae and adults were conspecific and corresponded to H. corynosoma. This is the first record of H. corynosoma in Mexico parasitizing intermediate and definitive hosts.
Acibenzolar-S-methyl on Meloidogyne javanica control in lettuce

ABSTRACT Nematodes are among the main limiting factors of the vegetables productivity, especially due to management restriction this crop to obtain an efficient control of pathogen. Resistance induction using acibenzolar-S-methyl (ASM) has presented promising results in the management of diseases, but to plant-parasitic nematodes the time required to activate latent defense mechanisms is a limiting factor, which can be prevented with the treatment of seedlings in trays. Thus, the present study aimed to assess different times of ASM application to Meloidogyne javanica control in lettuce. Lettuce seedlings were produced in trays, transplanted to pots 25 days after germination and inoculated with 2000 eggs of the nematode. The seedlings were pulverized on shoots with ASM 10 or 5 days before of transplant (DBT), on the day of transplant (DT), 5 or 10 days after transplant (5 or 10 DAT), 10 DBT + DT and 10 DBT + 5 DAT. The untreated plants formed the control group. Fifty days later, these plants were collected and evaluated the nematological and vegetative parameters. The treatments promoted a decrease in M. javanica population higher than 60% when applied until 5 DAT and generally did not interfere with the vegetative parameters of lettuce, and ASM can be adopted as an alternative for the root-knot nematodes management.
Extensive Heteroplasmy and Evidence for Fragmentation in the Callinectes sapidus Mitochondrial Genome

ABSTRACT Heteroplasmy is the presence of multiple genotypes in an individual and is commonly associated with mitochondria where thousands of copies of the genome can be present in a single organelle. Even in low frequencies, it can cause severe illness or death and strong selective pressures usually result in a low occurrence. Despite this, cloning and sequencing of a portion of the open reading frames of the nad2, nad4, and coI mitochondrial loci in the blue crab Callinectes sapidus (Rathbun, 1896) revealed abnormally high levels of heteroplasmy at all loci with as many as 24 haplotypes in a single individual and the dominant haplotype accounting for as little as 43.9% of the total sequences. A minimum spanning network comparing these individuals at each locus demonstrated an overlap of haplotypes between the female and themegalopa with almost no overlap of themale sequences. Illumina sequencing ofmuscle and testes froma single individual usingmultiple differentDNA-based amplificationmethods as well as cDNA amplification confirmed heteroplasmic circular mitochondrial DNA templates with portions of the reads containing unmapped highly repetitive regions at specific sequence positions in both tissue types. Thus, the blue crab appears to possess a highly degenerate and possibly fragmented mitochondrial genome that is present in germline tissue and linearly inherited. A general lack of fragmentation present in the cDNA sequences as well as site-specific sequence changes argues for mitochondrial editing as a way of maintaining sequence integrity. This is the first evidence for mitochondrial editing in a crustacean and a potential explanation for observations of extremely high population diversity when using blue crab mitochondrial markers.
Quantitative Real-time PCR detection of putrescine-producing Gram-negative bacteria

Biogenic amines are indispensable components of living cells; nevertheless these compounds could be toxic for human health in higher concentrations. Putrescine is supposed to be the major biogenic amine associated with microbial food spoilage. Development of reliable, fast and culture-independent molecular methods to detect bacteria producing biogenic amines deserves the attention, especially of the food industry in purpose to protect health. The objective of this study was to verify the newly designed primer sets for detection of two inducible genes adiA and speF together in Salmonella enterica and Escherichia coli genome by Real-time PCR. These forenamed genes encode enzymes in the metabolic pathway which leads to production of putrescine in Gram-negative bacteria. Moreover, relative expression of these genes was studied in E. coli CCM 3954 strain using Real-time PCR. In this study, sets of new primers for the detection two inducible genes ( speF and adiA ) in Salmonella enterica and E. coli by Real-time PCR were designed and tested. Amplification efficiency of a Real-time PCR was calculated from the slope of the standard curves ( adiA , speF , gapA ). An efficiency in a range from 95 to 105 % for all tested reactions was achieved. The gene expression (R) of adiA and speF genes in E. coli was varied depending on culture conditions. The highest gene expression of adiA and speF was observed at 6, 24 and 36 h (R adiA ~ 3, 5, 9; R speF ~11, 10, 9; respectively) after initiation of growth of this bacteria in nutrient broth medium enchired with amino acids. The results show that these primers could be used for relative quantification analysis of E . coli .
Landscape genetic analysis of co-distributed white-footed mice (Peromyscus leucopus) and prairie deer mice (Peromyscus maniculatus bairdii) in an agroecosystem

Agricultural ecosystems are spatially and temporally dynamic systems that support wildlife populations in addition to food production for humans. The composition and configuration of land cover within agricultural systems, which often varies seasonally or annually, can have profound impacts on biodiversity. Specifically, landscape structure can influence animal dispersal and distribution. Depending on species-specific ecology, dispersal may be restricted, resulting in smaller, reproductively isolated populations. Few studies have characterized the spatial genetic structure of small mammal species in agricultural landscapes, despite their importance to crop pest management and food webs within agroecosystems. We characterized the spatial genetic structure of 2 co-distributed Peromyscus species (Peromyscus leucopus and Peromyscus maniculatus bairdii), and quantified relationships between spatial genetic structure based on interindividual relatedness resolved from 10 microsatellite loci, and landscape features hypothesized to influence dispersal. We found significant spatial autocorrelation in interindividual relatedness over interindividual distances of 1,800 m for P. leucopus and 300 m for P. maniculatus bairdii. We also identified distinct genetic clusters of interbreeding individuals for both species. Spatial genetic structure of P. leucopus was significantly related to the distribution of roads, indicating that highly fragmented landscapes could negatively affect dispersal and gene flow. Given the large and growing footprint of agriculture globally, it is important that studies of the effects that landscape features have on dispersal of wildlife species include human-dominated landscapes.