Relationships Of Different Species Research Articles

Phylogenetic relationship and sequence diversity of candidate genes involved in anthocyanin biosynthesis pathway in Carthamus species with contrasting seed coat colors.

The morphological structure of seed such as coat color can be considered as effective parameters in the evaluation of resistance to pests. The present study is aimed at achieving these goals: first, to determine the phylogenetic relationship of different species of safflower with different seed coat colors based on three candidate genes in the anthocyanin biosynthesis pathway that encode the early steps (PAL: phenylalanine ammonia-lyase and CHS: chalcone synthase) and the final step (UFGT: flavonoid-3-O-glucosyltransferase); second, based on our previous study on the absence of cyanidin-3-O-glucoside (Cyd-3-glu) in white/brown-seeded genotypes, it can be determined whether the lack of production is related to the absence of genes or the lack ofexpression. In general, the detection of Cyd-3-glu upstream compounds in all studied safflower genotypes, regardless of the color of the seed coat, can be interpreted as the expression of genes responsible for the synthesis of these compounds in the anthocyanin synthesis pathway. In addition, these findings indicated that the accumulation pattern of the mentioned secondary metabolites could be varied in safflower genotypes according to the seed coat color pattern. Regarding the UFGT gene, the evidence showed that this gene is expressed in safflower genotypes with two different seed coat color patterns, but in each genotype the tendency to produce secondary metabolites is different. Consequently, it seems that UFGT may not only regulate Cyd-3-glu biosynthesis but also involved in biosynthesis offlavonol glucoside in black safflower. Additionally, UFGT only affected flavonol glycosides biosynthesis and had no effect on Cyd-3-glu biosynthesis in white- seeded safflower genotypes.

Comparison of the Chloroplast Genome Sequences of 13 Oil-Tea Camellia Samples and Identification of an Undetermined Oil-Tea Camellia Species From Hainan Province.

The comparison of chloroplast genome (cpDNA) sequences among different plant species is an important source of plant molecular phylogenetic data. In this paper, the cpDNA sequences of 13 different oil-tea camellia samples were compared to identify an undetermined oil-tea camellia species from Hainan Province. The cpDNA of the samples was sequenced and resequenced, and divergence hotspots and simple sequence repeat (SSR) variations were analyzed. Bayesian inference (BI) and maximum-likelihood (ML) phylogenetic trees were constructed based on the full cpDNA sequences. The cpDNA sequences were 156512∼157089 bp in length and had the circular tetrad structure typical of angiosperms. The inverted repeats (IRs) of different species included varying contractions and expansions. The cpDNA sequences of the samples of the undetermined species of oil-tea camellia from Hainan Province and Camellia gauchowensis from Xuwen County were identical. In total, 136 genes were annotated, including 91 protein-coding genes (PCGs), 37 tRNA genes and 8 rRNA genes. The GC content of the cpDNA was 37.3%. The small single-copy (SSC)/IR boundary was rich in variation. Divergence hotspots were mainly located in the intergenic space (IGS) and coding sequences (CDSs), and there were obvious differences in divergence hotspots among species. The same divergence hotspots were found in Camellia vietnamensis, Camellia gauchowensis and the undetermined species of oil-tea camellia from Hainan Province. A total of 191∼198 SSR loci were detected. Most of the SSRs included A or T, and the distribution of SSRs in the cpDNA was uneven. Different species shared common SSRs and exhibited unique SSRs. Based on the full cpDNA sequences, the evolutionary relationships of different species of Camellia were well identified. The thirteen samples were classified into 2 clades and 6 subclades, and the different sections of Camellia clustered on the same branch in 2 clades and 2 subclades. Camellia vietnamensis was more closely related to the undetermined species of oil-tea camellia from Hainan Province and the sample of Camellia gauchowensis from Xuwen County than to the sample of Camellia gauchowensis from Luchuan County. Camellia osmantha was closely related to Camellia gauchowensis and Camellia vietnamensis. In conclusion, the cpDNA of different oil-tea camellia species has a conserved tetrad structure with certain length polymorphisms. SSRs are expected to be developed as “barcodes” or “identity cards” for species identification. SSR variations and other factors result in abundant divergence hotspots in the CDSs and IGS (one non-CDS region), indicating that full cpDNA sequences can be used for the species identification and phylogenetic analysis of Camellia. Accordingly, the undetermined species of oil-tea camellia from Hainan Province is likely Camellia vietnamensis, Camellia vietnamensis and Camellia gauchowensis may be the same species, and additional genetic evidence is needed to determine whether Camellia osmantha is a new independent species. The previous division of related sections of Camellia may need readjustment based on full cpDNA sequences.

Epigenetic modification cooperates with Zeb1 transcription factor to regulate Bmp4 to promote chicken PGCs formation.

BMP4 is the critical gene of primordial germ cell formation in mammal, however, the mechanism of PGCs formation in chicken still unknown. In this research, we compared the evolution relationship of different species. Although the protein sequence is highly conservative between mouse, human and chicken, promotors vary among avian and mammal species. Therefore, it is easily to predict that there would be different regulation mechanism of Bmp4 expression in chicken. Here, we elucidate the function of chicken Bmp4 during PGCs formation. In vivo, Bmp4 can promote PGCs development and migration, and increase the expression of key genes (Cvh, c-kit, cxcr4, etc.). Whereas, the expression of these genes will decrease after knocking out Bmp4. After over-expression and knockout Bmp4 in vitro, we found that overexpression of Bmp4 could promote the formation of embryoid bodies (EB) and up-regulate the key genes of PGCs formation and migration, while knockout Bmp4 could inhibit the formation of embryoid bodies and decrease the expression of related genes. Flow and indirect immunofluorescence also indicated the same result. These all results proved that chicken Bmp4 could also promote the formation of PGCs. Furthermore, dual-luciferase activity detection showed that the promotor activity of Bmp4 was positively regulated by transcription factor Zeb1. Overexpression of Zeb1 can also increase the mRNA and protein expression of Bmp4. At the same time, DNA methylation inhibited Bmp4 transcription and histone methylation was able to promote its transcription. In conclusion, this study established that chicken Bmp4 can promote the formation of chicken PGCs. This gene is regulated by DNA, histone methylation and transcription factor Zeb1. These results lay a theoretical foundation for exploring the function and molecular mechanism of Bmp4 in the process of PGCs formation.

Potential effects of temperature levels on soil bacterial community structure

Soil microorganisms play a crucial role in the response to global warming in terrestrial ecosystems. Soils with higher microbial diversity have more ecological functions, higher resistance to environmental stress and higher crop production capacity. At present, the research on the effect of temperature change on soil microorganisms mostly adopts the methods of outdoor infrared temperature measurement or exchange and transplantation of soil with different temperature zones. Here, we investigate how temperature gradients potentially affect soil bacterial communities to change. For this reason, we used indoor precise temperature control treatment and combined high-throughput sequencing with bioinformatics to systematically analyze the diversity and species composition of soil bacteria under different temperature gradients, and to clarify the variation trend and interaction relationships of different species with temperature gradients. The results showed that temperature significantly affected the Alpha diversity of soil bacterial communities (P<0.05).Soil bacteria has different sensitivity and adaptability to temperature. In the range of 0-40℃, insensitive bacteria includes Proteobacteria, Gemmatimonadetes and Chloroflexi. Sensitive bacteria includes Sphingomonas, Ellin6055 and norank_f_67-14. The main reaction types of two bacteria showed four trends: ① Proteobacteria and Sphingomonas showed an “arch” variation; ② Gemmatimonadetes and Chloroflexi showed “inverted arch”. ③ Norank_f_67-14 showed an “inverted S type” change; ④ Ellin6055 shows a” parabolic ” shape. In different classification levels such as phylum and genus, the higher the classification level is, the higher degree it is weakened by temperature on, and the lower the classification level is, the stronger effect temperature has on it. In short, when temperature changes, soil bacteria can respond positively or negatively according to their ability to adapt to temperature, and accordingly form certain regular changes.

Molecular basis of COVID-19 relationships in different species: a one health perspective

Outside the Hubei province, China, the mild form of infection and the progressive recover of the COVID-19 patients suggest the intervention of “unconventional” biological mechanisms worthy of attention. Based on the high-homology between the Spike protein epitopes of taxonomically-related coronaviruses, we hypothesized that past contact with infected dogs shield humans against the circulating SARS-CoV-2. Elseways, the recurrent virus exposure over a short time-lapse might result in the Antibody Dependent Enhancement, triggering the violent immune reaction responsible for the severe clinical outcomes observed in the Hubei province. Nevertheless, further experimental studies are desired for a confidential evaluation of the postulated hypotheses.

Amphibians in agricultural landscapes: the habitat value of crop areas, linear plantings and remnant woodland patches

AbstractMitigating the negative impacts of agriculture on amphibians requires knowledge of how different land uses affect species distribution and community composition. In the case of frogs, there is currently insufficient information on their use of terrestrial habitats in cropping landscapes to inform conservation planning. We examined how four different farmland types (linear plantings, cereal crops, grazing paddocks and woody mulch) and crop harvesting influenced amphibian abundance, richness, body condition and movement. We found the abundance of frogs was significantly higher in linear plantings compared to grazing paddocks and adjacent patches of remnant woodland vegetation. However, species richness and abundance of three individual species did not vary significantly between farmland types. For the most common frog Uperoleia laevigata, body condition was higher at the edges of the woody debris treatment (coupled with higher abundance) and lower in farmland with debris and linear plantings. The body condition of Limnodynastes tasmaniensis and L. interioris was not influenced by farmland type. Frog abundance and condition was largely unaffected by crop harvesting. However, frogs were less common after harvesting at the edges of farmland and within remnant patches. Movement patterns did not suggest mass movement out of crops after harvest, where almost half of all individuals recaptured remained within the farmland. These results suggest that some generalist frog species may have an affinity for habitats within agricultural paddocks, particularly when key habitat features like plantings are present. However, we found overall frog richness was low and did not differ between remnant patches, edges and farmland which may be an indication of habitat degradation within terrestrial habitats across the landscape. Although protection of remnant native vegetation is important, conservation strategies for the protection of amphibians will be ineffective if they do not consider the variety of land uses and the relationships of different species and their microhabitats within and outside of patches.

On the information content of discrete phylogenetic characters.

Phylogenetic inference aims to reconstruct the evolutionary relationships of different species based on genetic (or other) data. Discrete characters are a particular type of data, which contain information on how the species should be grouped together. However, it has long been known that some characters contain more information than others. For instance, a character that assigns the same state to each species groups all of them together and so provides no insight into the relationships of the species considered. At the other extreme, a character that assigns a different state to each species also conveys no phylogenetic signal. In this manuscript, we study a natural combinatorial measure of the information content of an individual character and analyse properties of characters that provide the maximum phylogenetic information, particularly, the number of states such a character uses and how the different states have to be distributed among the species or taxa of the phylogenetic tree.

Changes in Anthocyanin Production during Domestication of Citrus.

Mandarin (Citrus reticulata), citron (Citrus medica), and pummelo (Citrus maxima) are important species of the genus Citrus and parents of the interspecific hybrids that constitute the most familiar commercial varieties of Citrus: sweet orange, sour orange, clementine, lemon, lime, and grapefruit. Citron produces anthocyanins in its young leaves and flowers, as do species in genera closely related to Citrus, but mandarins do not, and pummelo varieties that produce anthocyanins have not been reported. We investigated the activity of the Ruby gene, which encodes a MYB transcription factor controlling anthocyanin biosynthesis, in different accessions of a range of Citrus species and in domesticated cultivars. A white mutant of lemon lacks functional alleles of Ruby, demonstrating that Ruby plays an essential role in anthocyanin production in Citrus Almost all the natural variation in pigmentation by anthocyanins in Citrus species can be explained by differences in activity of the Ruby gene, caused by point mutations and deletions and insertions of transposable elements. Comparison of the allelic constitution of Ruby in different species and cultivars also helps to clarify many of the taxonomic relationships in different species of Citrus, confirms the derivation of commercial varieties during domestication, elucidates the relationships within the subgenus Papeda, and allows a new genetic classification of mandarins.

A new method to analyze protein sequence similarity using Dynamic Time Warping

Sequences similarity analysis is one of the major topics in bioinformatics. It helps researchers to reveal evolution relationships of different species. In this paper, we outline a new method to analyze the similarity of proteins by Discrete Fourier Transform (DFT) and Dynamic Time Warping (DTW). The original symbol sequences are converted to numerical sequences according to their physico-chemical properties. We obtain the power spectra of sequences from DFT and extend the spectra to the same length to calculate the distance between different sequences by DTW. Our method is tested in different datasets and the results are compared with that of other software algorithms. In the comparison we find our scheme could amend some wrong classifications appear in other software. The comparison shows our approach is reasonable and effective.

ISSR Fingerprinting to Ascertain the Genetic Relationship of <i>Curcuma sp.</i> of Tripura

Molecular fingerprints of four different species of Curcuma, viz., C. amada, C. caesia, C. longa and C. zedoaria, found in Tripura were developed using Inter Simple Sequence Repeats. Twenty ISSR primers generated 116 loci amplified in the range of 200 - 5000 bp with an average of 5.8 alleles and 1.6 effective alleles per locus. The percentage of polymorphic band was found to be 86.29 with an average of 5.15 per primer. Based on UPGMA algorithm these four species are placed in two different clusters that validate the classification based on external and internal morphological characters. The polymorphic ISSR markers generated from this study will be useful for understanding the genetic relationship of different species of the genus Curcuma.

Assessment of genetic relationship in Persea spp by traditional molecular markers.

Currently, the reclassification of the genus Persea is under discussion with molecular techniques for DNA analysis representing an alternative for inter- and intra-specific differentiation. In the present study, the traditional random-amplified polymorphic DNA (RAPD) and the inter simple sequence repeat (ISSR) markers were used to determine the genomic relationship of different species and hybrids representative of the subgenera Eriodaphne and Persea in a population conserved in a germplasm bank. The data were analyzed statistically using multivariate methods. In the RAPD analysis, a total of 190 polymorphic bands were produced, with an average of 23.7 bands per primer, the percentage contribution of each primer was from 7.66 to 19.63; the polymorphic information content (PIC) ranged from 0.23 to 0.45, with an average of 0.35. In the ISSR analysis, a total of 111 polymorphic bands were considered, with an average of 18.5 bands per primer, the percentage contribution of each was from 11.83 to 19.57; the PIC ranged from 0.35 to 0.48, with an average of 0.42. The phenograms obtained in each technique showed the relationship among the accessions through the clusters formed. In general, both the techniques grouped representatives of the Persea americana races (P. americana var. drymifolia, P. americana var. guatemalensis, and P. americana var. americana). However, it was not possible to separate the species of Persea used as reference into independent clades. In addition, they tended to separate the representatives of subgenera Eriodaphne and Persea.

Transcriptome-wide identification of Camellia sinensis WRKY transcription factors in response to temperature stress.

Tea plant [Camellia sinensis (L.) O. Kuntze] is a leaf-type healthy non-alcoholic beverage crop, which has been widely introduced worldwide. Tea is rich in various secondary metabolites, which are important for human health. However, varied climate and complex geography have posed challenges for tea plant survival. The WRKY gene family in plants is a large transcription factor family that is involved in biological processes related to stress defenses, development, and metabolite synthesis. Therefore, identification and analysis of WRKY family transcription factors in tea plant have a profound significance. In the present study, 50 putative C. sinensis WRKY proteins (CsWRKYs) with complete WRKY domain were identified and divided into three Groups (Group I-III) on the basis of phylogenetic analysis results. The distribution of WRKY family transcription factors among plantae, fungi, and protozoa showed that the number of WRKY genes increased in higher plant, whereas the number of these genes did not correspond to the evolutionary relationships of different species. Structural feature and annotation analysis results showed that CsWRKY proteins contained WRKYGQK/WRKYGKK domains and C2H2/C2HC-type zinc-finger structure: D-X18-R-X1-Y-X2-C-X4-7-C-X23-H motif; CsWRKY proteins may be associated with the biological processes of abiotic and biotic stresses, tissue development, and hormone and secondary metabolite biosynthesis. Temperature stresses suggested that the candidate CsWRKY genes were involved in responses to extreme temperatures. The current study established an extensive overview of the WRKY family transcription factors in tea plant. This study also provided a global survey of CsWRKY transcription factors and a foundation of future functional identification and molecular breeding.

Climatic response of three tree species growing at different elevations in the Lüliang Mountains of Northern China

In this study, we present the results of a dendroclimatological investigation of three coniferous tree species, Larix principis-rupprechtii, Picea meyeri and Pinus tabulaeformis, growing along an altitudinal gradient at the Lüliang Mountains in Northern China. Totally five tree-ring width chronologies were developed to explore the climate-growth responses of these tree species. No obviously regular trend associated with the increase of elevation was found by comparing the statistical characteristics of the chronologies. Correlation analysis indicated that the chronologies from lowerest to middle-high sites (SZ, BWD, BDGL and BDGP, respectively) were highly correlated, and different species from the same site showed the highest correlation. Growth–climate analysis indicated that the chronology of Larix principis-rupprechti at the uppermost site near the tree line (XWS) did not exhibit a significant response to the seasonal climatic factors, whereas the other four lower chronologies were consistently and significantly influenced by both the mean temperature from May to July and the total precipitation from March to June, regardless of tree species and elevation. The similarity of the tree growth–climate relationships of different species growing at different elevations (except that from the tree line) suggests that the trees in this region can provide common regional climate information, and combinations of multiple species (RC) are more successful in reconstructing the climate data than single species. The results of this research are very crucial for the future forest management and dendroclimatological sampling strategy in the arid to semi-arid area of northern China.

New graphical representation of a DNA sequence based on the ordered dinucleotides and its application to sequence analysis

AbstractGraphical representation of a DNA sequence is a powerful tool for basic biological research. Based on the ordered dinucleotides, we propose a novel three dimensional (3D) graphical representation without circuit or degeneracy. Simultaneously, we derive the projection curve of the 3D graph. These two curves have good visualization for longer DNA sequences. The utility of the proposed curves is illustrated by mutation analysis, similarity analysis, and evolutionary relationships of different species. The results indicate that our method is efficient and powerful. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

COMPARISON OF HUMAN AND RODENT LUNG DOSIMETRY MODELS FOR PARTICLE CLEARANCE AND RETENTION

Interspecies differences in the kinetics and/or mechanisms of particle retention can influence the amount and location of particle retention in the lungs, which can also influence the tissue response to a given particle burden. Dosimetric models may be used to adjust for differences in the exposure-dose relationships in different species, thus allowing for comparison of lung responses at equivalent doses. Although the rat is one of the most frequently used animal models for assessing the risk of exposures to hazardous substances in humans, few data are available for comparison of human and animal responses to inhaled particles. A biologically-based human dosimetric lung model was developed to describe the fate of respirable particles in the lungs of humans, using data from U.S. coal miners and assumptions about the overloading of alveolar clearance from studies in rats. This model includes alveolar, interstitial, and hilar lymph node compartments. The form of the model that provides the best fit to the lung dust burden data in these coal miners includes a first-order interstitialization process and either no dose-dependent decline in alveolar clearance or much less decline than expected from rodent studies. These findings are consistent with the particle retention patterns observed previously in the lungs of primates. This human lung dosimetry model is useful for investigating the factors that may influence the relationships between the airborne particle exposure, lung dust burden, and fibrotic lung disease.

Systematic relationship of several controversial Cunninghamella taxa inferred from sequence comparisons of ITS2 of rDNA

The ITS2 of rDNA of eight strains representing five controversial species and a variety of Cunninghamella , i.e. C. bertholletiae, C. blakesleeana, C. elegans, C. phaeospora var. phaeospora, C. phaeospora var. multiverticillata , and C. polymorpha , were amplified through PCR. The PCR products were purified and their sequences determined. Sequence variations among the three strains of C. elegans and between the two strains each of C. bertholletiae and C. polymorpha are less than 5%, while those among the other three strains each representing a different taxon as well as among these strains and the above mentioned five strains representing two different species are 14–32%. Sequence variations between each of the eight Cunninghamella strains and Rhizopus stolonifer var. lyococcos , used as outgroup, are more than 70%. These results confirm the value of sequence analyses of ITS2 rDNA in the taxonomy of Cunninghamella. C. polymorpha is proven to be synonymous with C. bertholletiae , while the others are considered to be distinct taxa. Phylogenetic analyses of the sequence data by the neighbour-joining method generally reflect the systematic relationship of different species based on morphologic studies made by our research group. The three strains of C. elegans , and the two strains each of C. bertholletiae and C. polymorpha (a synonym of C. bertholletiae ) are respectively clustered in the same clade with high confidence, while the strains representing the two varieties of C. phaeospora are also clustered in the same clade though with relatively low bootstrap value and long distance which supports the establishment of the distinct varieties.

Extrapolation from animals to man. The integration of pharmacokinetics and pharmacodynamics.

This paper has focused on the difficulties of extrapolating toxicological or pharmacological data obtained from animals to those expected in man. For some drugs, under certain conditions, there may be no problem, but for many, this is clearly not the case. Differences in apparent activity are impossible to reconcile without "normalizing" the dose for differences in pharmacokinetics and metabolism. The increasing use of artificial intelligence and expert systems in drug investigations may provide a greater insight into why these differences may occur and allow prediction but, in the end, they must be tested in the experiments undertaken. The use of kinetic dynamic relationships in different species will certainly help in this regard and, wherever possible, should be included in experimental design to build up a database of experience since such information is sadly lacking. But we must interpret with caution the data produced by those that continue to extrapolate animal data to humans without some attempt to discuss in detail the validity of their assumptions.

Interelement relationships in leaves of tropical montane trees

Chemical concentrations in leaves are reported for 14 elements in 6 tree species of a montane rain forest in Sri Lanka. The plant taxa varied greatly in chemistry and a few taxa appeared to concentrate several elements in high amounts. The chemical variability among taxonomic units was examined by comparing element-by-element concentration ratios in leaves. Several species seemed to have typical patterns of concentration ratios for certain elements and the interelement relationships of different species seemed to be repeated across varying habitat conditions.

Control of ovulation, vaginal estrus, and behavioral receptivity in voles (Microtus)

Rodents of the genus Microtus provide an excellent focus for the study of the effects of environmental and behavioral influences on reproductive physiology. Despite some early reports, there is little definitive evidence of truly spontaneous ovulation in Microtus. Stimuli from copulation with males appear capable of triggering ovulation in all species: the requisite amount of stimulation for ovulation and a functional luteal phase varies with the species. In addition, however, a certain percentage of the females of some, but not all, species ovulate when placed in proximity to males when copulation is prevented. There are few reports of regular cycles of cell types in the vaginal smears of Microtus females; the relative preponderance of cornified, nucleated, and leukocytic cells varies with species and conditions. Behavioral receptivity is not invariably correlated with smear type. The complexity of environment-behavior relationships in different species suggests the need for a more comprehensive classification schema for systems of female reproductive physiology and a study of their adaptive significance.

Seeding year alfalfa population development as influenced by weed competition and density of establishment

The research in intraspecific competition within an alfalfa stand and interspecific competition between alfalfa and weeds was begun on the Michigan State University farm in East Lansing in 1972. Alfalfa seeding densities of 50, 400 and 800 seeds/m2 were used to determine intraspecific competition. Interspecific competition between alfalfa and weeds occurred mainly in noncontrolled alfalfa stands at various levels of seeding densities. Plant competition was evaluated with importance values and with relative crowding coefficients. Both measurements were found to be suitable for this kind of study. Importance values primarily indicated the quantity relationships of different species. Relative crowding coefficients mainly characterized the competitive ability of a species in a mixed stand. The importance of alfalfa exceeded the importance of weeds in noncontrolled and herbicide controlled stands at the seeding rates of 14 and 7 kg/ha respectively. Relative crowding coefficients show the competitive ability of alfalfa with regard to weeds. In the case of intraspecific competition there was no change in the crowding coefficient of alfalfa in respect of weeds when the seeding rate of alfalfa was increased beyond 9 kg/ha. The crowding coefficient of weeds presented equal values under all treatments thereby indicating the variability and plasticity of weeds. The maximum yield level was obtained in all treatments with the alfalfa seeding rate of 9 kg/ha. The total biomass production per unit area was equal in the noncontrolled system at all seeding densities and in the herbicide controlled system at seeding rates of 9 kg/ha or more.