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Summary To further analyze the structural requirements responsible for the enhanced activity of the newly developed, highly active benzylpyrimidine K-130, a series of trimethoprim analogues with various 4-anilinoalkoxy moieties has been synthesized and tested against dihydrofolate reductase (DHFR) derived from various species (Mycobacterium lufu, Escherichia coli, Candida albicans and rats). The importance of the secondary amino group for binding affinity could be shown by varying the substituent in the para position to the sec-amino moiety. This finding could be supported by multiple linear regression and comparative molecular field analysis (CoMFA). The polarized SO2 group, which was thought to be responsible for the increased activity of K-130, seems not to be the only group important for receptor binding. Additionally, a high selectivity of the new compounds for DHFR derived from the various bacteria and C albicans compared with DHFR derived from rat liver is shown by PC analysis.

The onion is a widely distributed vegetable crop, which takes an important place in the vegetable production in Serbia. The traditional planting method is the one from sets. Old cultivars and populations and, in recent years, foreign cultivars are grown. The large variety of genotypes, including both domestic populations and cultivars, comprises the significant gene pool of this region. The onion collection of the Institute of Field and Vegetable Crops in Novi Sad is based on the populations and cultivars from the territory of the former Yugoslavia. This paper reviews 30 onion genotypes on the basic IPGRI descriptors (ANNEX I). Variability of the reviewed characteristics was determined by PC analysis. High variability values have been established for bulb skin color, bulb flesh color, bulb hearting and bulb skin thickness. The genotypes varied in bulb skin color as well as in bulb flesh color from white to dark violet. These two characteristics had the largest impact on clustering, with a single genotype being heterogeneous exactly for these two characteristics. Crni luk je široko rasprostranjena povrtarska vrsta, čija proizvodnja zauzima značajno mesto u setvenoj strukturi povrća u Srbiji. Tradicionalni način ove proizvodnje je iz arpadžika, gde su zastupljene stare sorte, populacije i sve prisutniji strani sortiment. Bogatstvo genotipova crnog luka, kako gajenih domaćih populacija tako i sorata, predstavlja značajan gen fond sa ovog područja. U Institutu za ratarstvo i povrtarstvo u Novom Sadu, osnovu kolekcije čine domaće populacije i sorte koje se gaje u širem region, sa prostora bivše Jugoslavije. U radu su prikazane osnovne osobine 30 genotipova crnog luka prema deskriptoru IPGRI (ANNEX I.). Varijabilnost ispitivanih osobina je utvrđena PC analizom, gde je ustanovljena visoka varijabilnost za boju lukovice, boju sočnih listova lukovice, broj gnezda i debljinu listova lukovice. Genotipovi su imali boju lukovice od bele do tamno ljubičaste, a takođe i boja sočnih listova. Ove dve osobine su imale najveći uticaj na grupisanje genotipova, tako su formirane dve grupe, uz izdvajanje jednog genotipa koji je heterogen upravo za ove osobine.

This article aims was to compare two sugarcane genotypes under elevated atmospheric carbon dioxide (CO2) concentration and soil water deficit, through an approach based on statistical analysis of plant growth multiple characteristics. For that, Pearson's correlation, dissimilarity and principal components (PC) analysis were performed, of some parameters such as stem length (culm) and roots length, number of leaves, dry mass of plant tissues, among other characteristics. Biometric attributes have a positive and significant correlation with each other. However, the dry mass values ​​have a negative correlation with the other parameters, meaning, therefore, there is a growth reduction as there is also a decrease in plants water conditions subjected to stress. Based on the dissimilarity and PC analysis, observed that genotypes genetically diverge and the imposed environmental condition influences growth responses. This preliminary study is an indication that this approach is essential for understanding the variations between the sugarcane genotypes responses. In addition, is evident (due to divergence) that analyses about the physiological and molecular responses of these genotypes in this environmental condition will contribute to the identification of regulated biological processes and possible tolerance mechanisms. El objetivo del trabajo fue comparar dos genotipos de caña de azúcar ante la alta concentración atmosférica de dióxido de carbono (CO2) y la deficiencia de agua en el suelo, mediante un enfoque basado en el análisis estadístico de múltiples características del crecimiento vegetal. Para ello, se realizó la correlación de Pearson, análisis de disimilitud y componentes principales (ACP), de algunos parámetros como la longitud del tallo y raíces, número de hojas, masa seca de tejidos vegetales, entre otras características. Los atributos biométricos tienen una correlación positiva y significativa entre sí. Sin embargo, los valores de masa seca tienen una correlación negativa con el resto de parámetros, es decir, por lo tanto, hay una reducción del crecimiento ya que también hay una disminución de las condiciones hídricas de las plantas sometidas a estrés. Con base en los análisis de disimilitud y ACP, se observa que los genotipos divergen genéticamente y la condición ambiental impuesta influye en las respuestas de crecimiento. Este estudio preliminar es una indicación de que este enfoque es esencial para comprender las variaciones entre las respuestas de los genotipos de la caña de azúcar. Además, es evidente (debido a la divergencia) que análisis sobre las respuestas fisiológicas y moleculares de estos genotipos en esta condición ambiental contribuirán a la identificación de procesos biológicos regulados y posibles mecanismos de tolerancia. O objetivo do trabalho foi comparar dois genótipos de cana-de-açúcar frente à elevada concentração atmosférica de dióxido de carbono (CO2) e deficiência hídrica no solo, através de uma abordagem baseada em análises estatísticas de múltiplas características do crescimento vegetal. Para isso, realizou-se a correlação de Pearson, análise de dissimilaridade e componentes principais (ACP), de alguns parâmetros como o comprimento do caule (colmo) e das raízes, número de folhas, massa seca de tecidos da planta, entre outras características. Os atributos biométricos apresentam correlação positiva e significativa entre si. Entretanto, os valores de massa seca possuem correlação negativa com os demais parâmetros, significando, portanto, haver uma redução do crescimento à medida que também ocorre um decréscimo nas condições hídricas das plantas submetidas ao estresse. Com base nas análises de dissimilaridade e ACP, observa-se que os genótipos divergem geneticamente e a condição ambiental imposta influencia nas respostas de crescimento. Esse estudo preliminar é um indicativo de que essa abordagem é fundamental para o entendimento das variações existentes entre as respostas de genótipos de cana-de-açúcar. Além disso, fica evidente (devido à divergência) que análises acerca das respostas fisiológicas e moleculares desses genótipos nessa condição ambiental contribuirão para a identificação dos processos biológicos regulados e possíveis mecanismos de tolerância.

AimThe novel SARS-CoV-2 virus, which causes the COVID-19 disease, has infected more than 10 million people and caused 500K deaths worldwide. In Europe, over 2 million confirmed cases have been reported, while nearly 200K people have died from the disease. Despite strict containment measures in Spain and Italy after the first reported COVID-19 patient, these two countries have remained in the top five European nations with the highest mortality rate for over two months. We hypothesised that a genetic mechanism could partially explain the poor survival outcome observed in these two countries.MethodsAn extensive literature search to identify human candidate genes linked to SARS-CoV infection, host immune evasion and disease aggressiveness was carried out. Pathway analysis (IPA) was performed to select the most significantly associated canonical signalling pathways with the genes of interest. The genetic variants’ at these genes with ±1Mb flanking region was extracted (GRCh37/hg19 built). Over 80 million single nucleotide polymorphisms (SNPs) were analysed in genome-wide data of 2,504 individuals (1000 genomes, phase III, https://www.internationalgenome.org/). Principal component (PC) analysis was performed, ancestry by the whole genome was inferred and subsets of the regions of interest were extracted (PLINK v1.9b, http://pngu.mgh.harvard.edu/purcell/plink/). PC1 to PC20 values from five European ancestries, including the Spanish and Italian populations, were used for PC analysis. Gene function predictions were run with our genes of interest as a query to the GeneMANIA Cytoscape plugin (https://genemania.org/).ResultsA total of 437 candidate genes associated with SARS were identified, including 21 correlated with COVID-19 aggressiveness. The two most significant pathways associated with all 437 genes (Caveolar-mediated Endocytosis and MSP-RON Signalling) did not show any segregation at the population level. However, the most significant canonical pathway associated with genes linked to COVID-19 aggressiveness, the Hepatic Fibrosis and Hepatic Stellate Cell Activation, showed population-specific segregation. Both the Spanish and Italian populations clustered together from the rest of Europe. This was also observed for the Finnish population but in the opposite direction. These results suggest some of the severe COVID-19 cases reported in Spain and Italy could be partially explained by a pre-existing liver condition (especially liver cancer) and/or may lead to further COVID-19 related liver complications.

Background: Orthodontic science centers primarily on the growth, development and advancement of the craniofacial structures. Geometric morphometrics (GMM) is a new approach for shape identification in forensic sciences. Purpose: The aim of this study was to examine the shape variation in the Indian sample in order to assess sexual dimorphism by application of two-dimensional GMM. Materials and Methods: The sample comprised a total of 105 lateral cephalograms (54 males–51 females) of Angle's Class I malocclusion patients that were later subjected to principal component (PC) analysis and discriminant analysis. Results: The PC analysis showed over 96% of shape variation. The initial three PCs were statistically significant that depicted as 58.37% of total shape variability, with PC1 represent for the most significant variance 28.48%, PC2 described 18.83% and PC3 11.06%. Conclusion: Sex of an individual was clearly associated with occlusion of teeth and showed considerable variation. GMM is an alternative research tool and can be utilized for diagnosing individual characterization and classification of malocclusion.

Heat shock protein 90 (Hsp90) has been an attractive target of potential drug design for antitumor treatment. The current work integrates molecular dynamics (MD) simulations, calculations of binding free energy, and principal component (PC) analysis with scanning of inhibitor–residue interaction to probe the binding modes of inhibitors YK9, YKJ and YKI to Hsp90 and identify the hot spot of the inhibitor–Hsp90 binding. The results suggest that the introductions of two groups G1 and G2 into YKJ and YKI strengthen the binding ability of YKJ and YKI to Hsp90 compared to YK9. PC analysis based MD trajectories prove that inhibitor bindings exert significant effects on the conformational changes, internal dynamics and motion modes of Hsp90, especially for the helix α2 and the loops L1 and L2. The calculations of residue-based free energy decomposition and scanning of the inhibitor–Hsp90 interaction suggest that six residues L107, G108, F138, Y139, W162 and F170 construct the common hot spot of the inhibitor–residue interactions. Moreover the substitutions of the groups G1 and G2 in YKJ and YKI lead to two additional hydrogen bonding interactions and multiple hydrophobic interactions for bindings of YKJ and YKI to Hsp90. This work is also expected to contribute theoretical hints for the design of potent inhibitors toward Hsp90.

Knowledge about the extent of variability and the association among traits are of a high value for any breeding efforts. The objective of this investigation is to evaluate the agro-morphological traits in a set of durum wheat genotypes under supplemental irrigation and dry land conditions. Results showed that principal component (PC) analysis had grouped the measured traits into four main components that altogether accounted for 77% of the total variation under non-stressed condition and 87% under water-stressed condition. With regard to the first four PCs, peduncle length, agronomic score, grain yield, vigority, test weight, days to physiological maturity and thousand kernel weight have shown to be the most important variables affecting the performance of durum wheat under non-stressed condition. In the first four PCs at the water- stressed condition, agronomic score, grain yield, vigority, days to physiological maturity, test weight and peduncle length have been shown to be the important variables under water-stressed condition. The results of factor analysis relatively confirmed the results of PC analysis. Our findings indicated that a selection strategy should take into consideration of agronomic score and days to physiological maturity under non-stressed condition while plant height and spike length under water-stressed condition. Therefore, the above-mentioned traits could be used as indirect selection criteria for genetic improvement of grain yield in durum wheat, especially in early generations of breeding programmes

Background. VNTR-polymorphism at 5 HTTLPR regulatory region of human serotonin transporter gene SLC6A4, which is associated with some psychiatric diseases and personality traits, is presented by two alleles, S and L, affecting the gene transcription level. A correlation between the S allele frequency in populations of European and Asian origin and a Hofstede’s individualism-collectivism index was revealed and a hypothesis of culture-gene coevolution was suggested (Chiao, Blizinsky, 2010). Methods. As another reason for the correlation we examined underlying population genetic substructure, which may affect genetic association level. Results. We have experimentally established the 5 HTTLPR genotypes for 2144 individuals to calculate S and L allele frequencies in 21 populations of Eurasia and Africa. In contrast to Eurasia populations, we have found low S allele frequencies in all four African populations studied, although the collectivism index in the populations was high. The total set of Eurasian and African populations analysis does not confirm the correlation (R= 0.263, p=0.146). We have applied principal component (PC) analysis to check a correlation between S allele frequency distribution and a frequency distribution for alleles which are supposed to be neutral. PC analysis for 68 alleles of five CODIS STR loci revealed correlation between PC2 and S allele frequency (R= 0.820, p0.0001). The correlation means that S allele frequency distribution corresponds to general genetic variability distribution in the human populations studied. The correlation between the Hofestede’s index and frequency of four out of 68 STR alleles is even higher than the correlation with S allele frequency in the same populations. Conclusion. Our findings do not support the hypothesis on culture-gene coevolution of “individualism-collectivism” and the S allele frequency of serotonin transporter gene.

Wheat yields in Chile have increased significantly during the last four decades as a consequence of plant improvement and better crop husbandry. Central Chile is characterised by high-yield Mediterranean conditions, where precipitation received by the crop in most years does not represent a major limitation to productivity. This study assesses the changes in agronomic and physiological traits of spring cultivars released in the country between 1920 and 2000. A total of 95 spring bread wheat accessions, representing 20 old and 75 modern cultivars (released before and after 1960, respectively) were tested in a humid Mediterranean-type climate, with irrigation. Modern genotypes exhibited higher grain yield, harvest index, number of grains per ear and sedimentation values and lower height, test weight, wet gluten content and hardness index. No differences were found for days to heading, and ear length, whereas kernel weight decreased with the Green Revolution. Principal component (PC) analysis using ten agronomic traits clearly separated modern from old cultivars. Grain yield, a trait not included in PC analysis, was highly correlated with the first PC ( r = 0.80, P

To study the morphological diversity of the popular ornamental crop Calibrachoa, traded since the 1990s, floral and vegetative characters of 91 commercial cultivars were compared to those of natural species. Floral colours were classified according to the ISCC-NBS system and the CIE LAB system. The numerical data obtained by measuring 19 floral and vegetative characters was tested with principal component (PC) analysis. Floral colour classes of commercial cultivars were divided into 37 groups according the ISCC-NBS system, whereas those of natural species were divided into 9 groups. These tendencies were readily observable in the scatter diagrams of the a* vs. b* values and the C* vs. L* values. As the result of PC analysis, six PCs were obtained. For PC4, which negatively correlated with the degree of nocturnal corolla limb closure, the majority of natural species showed negative scores whereas the majority of cultivars had positive PC4 scores. In terms of PC2 (flower size), PC3 (growth form), PC5 (floral shape) and PC6 (leaf shape), natural species were dispersed in a range wider than the cultivars. These results suggest that Calibrachoa cultivars possess more highly variable floral colour than natural species, and breeding programmes to diversify the floral colour seem to have progressed rapidly. The tendency of natural species to close the corolla limb toward evening has been removed almost completely from the cultivars. The floral size, growth form, floral shape and leaf shape of the cultivars were rather uniform compared to those of natural species.

Recent advances in computational tools for quantitative genetics have allowed the genetic analysis of complex, polygenic morphological traits (Barton and Keightly 2002; Doerge 2002; Glazierm et al. 2002; Darvasi 2005). We used these tools in conjunction with molecular genotyping to analyze the genetic basis of variation in the canine skeleton (Chase et al. 2002, 2004; Carrier et al. 2005; Trut et al. 2006; Lark et al. 2006a, 2006b). The dog, Canis familiaris, is one of the most morphologically diverse mammals (Hart 1995; Coppinger and Coppinger 2001; Young and Bannasch 2006). Sizes range from 2 kg (Chihuahua) to 80 kg (Bull Mastiff) and shapes can vary from Basset Hounds and Boxers to Greyhounds and Great Danes. Previously, we analyzed independent combinatorial aspects of skeletal variation using principal component (PC) analysis (Chase et al. 2002; Carrier et al. 2005). PCs vary in a quantitative manner and can be subjected to genetic analysis. PC analysis reduces correlated sets of traits to independent (orthogonal) vectorial components, each of which can be characterized by the projection of the vector onto each of the traits (Venables and Ripley 2002). These “loadings” present the extent and direction (+ or −) of the trait’s contribution to the resulting vector. In previous publications, we used this approach to identify variation in heritable constellations of canine skeletal traits (reviewed by Lark et al. 2006a). A surprising result of this analysis was the discovery that removal of the covariation involved in size (PC1) revealed variation in independent components of shape, suites of functionally integrated traits, each of which were controlled by genetic loci. Quantitative trait loci (QTLs) are regions of the genome that contain one or more genes that regulate PC variation (Darvasi 2005). Thus, genetic analysis of the Portuguese Water Dog led to identification of QTLs responsible for variation in shape defined by canine skeletal PCs composed of groups of functionally related traits. Each of these groupings appeared to vary along a trade-off axis forming a functional compromise between high production of force (as exemplified by the Pit Bull) and energy-efficient speed (as exemplified by the Greyhound). Examples include trade-offs between the skull and postcranial skeleton (Chase et al. 2002) as well as changes in the pelvis and limb bones (Carrier et al. 2005). Using phenotypic data derived from radiograms and polymorphic molecular markers (Simple Sequence Repeats or SSRs), we identified QTLs for these trade-offs. Data from foxes indicated that these trade-offs were ancient and could be identified in the silver fox (Vulpes vulpes), the silver color phase of the red fox, and a member of the outgroup species for the evolutionary lineages of modern canids that separated from C. familiaris 10 million years ago (Wayne 1993; Bardeleben et al. 2005). Here we compare PCs derived from metrics of the forelimbs and hind limbs of Portuguese Water Dogs and silver foxes. We show that both species exhibit similar constellations of traits that affect very small amounts of variation along trade-off axes that partition function between the forelimbs and hind limbs. In most cases, these trade-offs though small in magnitude are heritable in both species and genetic loci regulating these trade-offs have been identified in the Portuguese Water Dog.

This study evaluated associations between craniofacial candidate genes and skeletal variation in patients with malocclusion. Lateral cephalometric radiographs of 269 untreated adults with skeletal classes I, II, and III malocclusion were digitized with 14 landmarks. Two-dimensional coordinates were analyzed using Procrustes fit and principal component (PC) analysis to generate continuous malocclusion phenotypes. Skeletal class classifications (I, II, or III) were used as a categorical phenotype. Individuals were genotyped for 198 single-nucleotide polymorphisms (SNPs) in 71 craniofacial genes and loci. Phenotype-genotype associations were tested via multivariate linear regression for continuous phenotypes and multinomial logistic regression for skeletal malocclusion class. PC analysis resulted in 4 principal components (PCs) explaining 69% of the total skeletal facial variation. PC1 explained 32.7% of the variation and depicted vertical discrepancies ranging from skeletal deep to open bites. PC1 was associated with a SNP near PAX5 ( P = 0.01). PC2 explained 21.7% and captured horizontal maxillomandibular discrepancies. PC2 was associated with SNPs upstream of SNAI3 ( P = 0.0002) and MYO1H ( P = 0.006). PC3 explained 8.2% and captured variation in ramus height, body length, and anterior cranial base orientation. PC3 was associated with TWIST1 ( P = 0.000076). Finally, PC4 explained 6.6% and detected variation in condylar inclination as well as symphysis projection. PC4 was associated with PAX7 ( P = 0.007). Furthermore, skeletal class II risk increased relative to class I with the minor alleles of SNPs in FGFR2 (odds ratio [OR] = 2.1, P = 0.004) and declined with SNPs in EDN1 (OR = 0.5, P = 0.007). Conversely, skeletal class III risk increased versus class I with SNPs in FGFR2 (OR 2.2, P = 0.005) and COL1A1 (OR = 2.1, P = 0.008) and declined with SNPs in TBX5 (OR = 0.5, P = 0.014). PAX5, SNAI3, MYO1H, TWIST1, and PAX7 are associated with craniofacial skeletal variation among patients with malocclusion, while FGFR2, EDN1, TBX5, and COL1A1 are associated with type of skeletal malocclusion.

Patterns of flowering and seed set were explored by principal component (PC) analysis of counts of fresh flowers, total flowers and seeds at four observation times. This pattern analysis was attempted because of the complicated rhythms of flowering and seed set over an extended period. The approach was considered superior to regressions (over time) for this data because of these pattern complexities, and because these were few time-nodes. Also it avoided the need to find optimum regression functions. Parsimony was achieved with a two-component ordination based on truncation at 70% of the total variance. The results for all characters showed that the first component concentrated on the middle period of flowering/seed set, and de-emphasized the early phase. The second component emphasized the extremities of the flowering/seed set span. The first component accounted for a large proportion of total variance (45.5% to 69.2%), which indicated its importance. The general meaning of the first component was ‘median flowering’, ‘general flower production’ and ‘median-to-late seed set’ for these characters fresh flowers, total flowers and seed set, respectively. The results showed that PC analysis successfully summarized the complex patterns of flowering/seed set and revealed the pattern differences between plants. It was apparent that no particular pattern of general flowering and seed set could be regarded as ‘typical’ in meadowfoam. It was confirmed that the population was diverse, this being typical of segregating plants within a randomly fertilized population.

Summary Ownership of intellectual and tangible property (IP/TP) rights in agricultural biotechnology (ag-biotech) and transgenic plants has become critically important. For scientists in all institutions, whether industrialized or developing country, public or private sector, an understanding of IP/TP rights is fundamental in both research and development. Transgenic plants and ag-biotech products embody numerous components and processes, each of which may have IP/TP rights attached. To identify these rights, a transgenic plant or ag-biotech product must be dissected into its essential components and processes, with each ‘piece’ analysed under the IP/TP ‘microscope’. This product deconstruction is an integral step in product clearance (PC) analysis leading to freedom to operate (FTO). To facilitate a PC analysis, the following points are important: (1) knowing what one has and where it’s from, (2) organizing material transfer agreements and licences, (3) researching scientific and patent databases and relevant literature, (4) instituting a laboratory notebook policy, (5) keeping track of ownership of germplasm and plant genetic resources, and (6) promoting ongoing IP/TP management, awareness and training. However, a FTO opinion does not solve the IP/TP issues of releasing a transgenic plant or ag-biotech product; rather, it is a management tool for assessing the risks of litigation. When transferring transgenic plants or ag-biotech to developing nations, scientists from industrialized countries have the heightened responsibility of verifying that IP/TP issues are fully addressed and documented. Successful technology transfer goes beyond research, development and licensing; it is an holistic package leading to long-term partnerships in international development. Managing IP/TP requires capacity-building in scientists and technology transfer offices, in both industrialized and developing countries.

A collection of more than 3000 accessions of triticale ( x Triticosecale Wittmack), called the North American Triticale Genetic Resources Collection (NATGRC), was assembled from 10 active and inactive breeding programs in the USA, Canada, and Mexico for the purposes of conservation, characterization, evaluation, and documentation. Since triticale has no wild ancestors and hybrid parentage is often unknown, preservation of unique gene combinations is essential for continued utilization. The origin groups that comprised the whole collection were evaluated in field plots for 2 yr at Davis, CA. Accessions were predominantly secondary hexaploid triticales having spring growth habit. The collection was classified for spike type and 38% had spikes typical of complete (Beagle type) and 30% were substituted (Armadillo type) triticale. The Shannon-Weaver diversity index (H'), computed for seven qualitative traits, was 1.275 for the whole collection. The most diverse group was from Manitoba (1.404) and the least diverse groups were from Oregon (0.822) and CIMMYT (0.867). Overtrait mean coefficients of variation for eight quantitative traits gave similar diversity ratings as H' for each of the origin groups (r = 0.74*), suggesting that simply scored traits may be useful for assessing overall diversity in large genetic resource collections. Principal components (PC) analysis of quantitative traits showed differentiation, but considerable commonality, among the Canada, Mexico, and USA groups. The CA-Davis group included hybrid derivatives from CA-Jenkins x CIMMYT groups that clustered intermediate to those groups, suggesting a genetic basis for the phenotypic clustering. The PC analysis showed that the Beagle and Armadillo types differed in several quantitative traits, showing that this classification is a useful descriptor for hexaploid triticale. The NATGRC is conserved at USDA, Aberdeen, ID, and CIMMYT, Mexico. Researchers are urged to use and contribute to this collection. The formation of a European-based collection emphasizing winter growth habit is recommended.

Additional index words. electrophoresis, flowering dogwood, principal component analysis, population genetics Abstract. Starch gel electrophoresis and principal component (PC) analysis were used to determine the levels of genetic variation and the relationship between morphology and geographic origin for Cornus florida (flowering dogwood) populations in a Michigan provenance plantation. The populations are representative of the species' geographic distribution, ranging from Texas to Georgia and north to Connecticut and Michigan. Allelic variation at 11 loci encoded by 5 enzymes was very low in comparison to other plant species. On average, populations displayed 1.16 alleles per locus, 9.89% of loci polymorphic, with an observed heterozygosity value of 0.048. Genetic identify values ranged from 0.961 to 1.00 and displayed no relationship with geographic origin. While the isozyme analysis revealed little genetic variation, the PC analysis revealed a considerable amount of morphological variation. Most variation (83.3%) in leaf and flower bud morphology was explained by three PCs. Leaf characters revealed no relationship with geographic origin. However, flower bud size and number of florets decreased with changes in latitude from northern, central, and southern populations, respectively. The relationship between flower bud size and latitude suggests an adaptive response to photoperiod throughout the species' geographic range. variation among populations while reducing variation within popu- lations (Loveless and Hamrick, 1984). This paper presents results of an isozyme and morphological evaluation of native C. florida trees in a provenance plantation. The objectives of the study were to determine the levels of genetic variation in native populations and assess the relationships among geographic origin, allelic profiles, and morphometric traits.

Studies of bone genetics have addressed an array of related phenotypes, including various measures of biomechanical performance, bone size, bone, shape, and bone mineral density. These phenotypes are not independent, resulting in redundancy of the information they provide. Principal component (PC) analysis transforms multiple phenotype data to a new set of orthogonal “synthetic” phenotypes. We performed PC analysis on 17 femoral biomechanical, anatomic, and body size phenotypes in a reciprocal intercross of HcB-8 and HcB-23, accounting for 80% of the variance in 4 PCs. Three of the 4 PCs were mapped in the cross. The linkage analysis revealed a quantitative trait locus (QTL) with LOD = 4.7 for PC2 at 16 cM on chromosome 19 that was not detected using the directly measured phenotypes. The chromosome 19 QTL falls within a ~ 10 megabase interval, with Osf1 as a positional candidate gene. PC QTLs were also found on chromosomes 1, 2, 4, 6, and 10 that coincided with those identified for directly measured or calculated material property phenotypes. The novel chromosome 19 QTL illustrates the power advantage that attends use of PC phenotypes for linkage mapping. Constraint of the chromosome 19 candidate interval illustrates an important advantage of experimental crosses between recombinant congenic mouse strains.

Raman microspectroscopy is used to probe the age and milieu parameters for suspensions of bacteria for their detection in water backgrounds. No studies have been reported on the fate of Raman signatures over time for biologicals stored in water matrices. A FALCON II Raman Chemical Imaging System (ChemImage, Pittsburgh, PA) and 532 nm laser excitation source acquired the Raman spectra. MATLAB principal components (PC) analysis software was employed for data reduction. Suspensions of Bacillus atrophaeus, Bacillus thuringiensis , and three strains of E. coli (EC) were prepared in distilled and recipe tap water. Aliquots at 5 min, 5 hr, and 1, 2, and 7 days at 25 C were dried on microscope slides in replicate. Adequate spectral differences were observed for all three organism species. Microscope analysis showed that freshly suspended Bacillus spores and EC vegetative cells, in both water matrices, remained as spores after seven days. Agar plate growth procedures showed that the bacteria were still viable even after seven days resting in both water matrices. All three bacterial species were separated based on PC analysis; however, the three EC strains coalesced. The water matrix parameter was inconsistent in its ability to separate the Raman spectra in PC plots of the five bacteria. Within each group, the time parameter poorly separated the bacterial resting suspensions as the aging proceeded. A Mahalanobis linkage distance analysis (dendrogram) for all three species and strains in both water matrices confirmed a random order for all five suspension times.

The study was aimed at determining cardiorespiratory coordination under the influence of acute hypoxia in athletes with different levels of sports qualifications. Eighteen runners aged 17 to 25 were exposed to acute (10% O2) hypoxia for 10 min. Respiration, gas exchange, and heart rate were measured during normoxia and hypoxia. The principal component (PC) analysis was used to assess cardiorespiratory coordination; the stability of PCs under the influence of hypoxia was evaluated by the Tucker’s Congruence Coefficient. The analysis was performed on a time series of 10 min of normoxia and hypoxia with the inclusion of heart rate, minute ventilation, the expired fraction of O2 and CO2. According to the level of qualification, athletes were divided into two groups: highly trained (HT, no less than category I, n = 9) and medium-trained (MT, category II, n = 9). Under normoxia, cardiorespiratory coordination in athletes of both groups was higher than in normobaric hypoxia (p = 0.001): during normoxia, the model included one PC from coordinated variables according to the Kaiser criterion in 44% of the athletes; during hypoxia, the model consisted of two PCs in 100% of the athletes. During hypoxia, the percentage of total variance explained by PC2 increased significantly (p < 0.001), regardless of the level of qualification. In hypoxia, there was a change in the variable contributions to PC1 and PC2, more pronounced in the MT group: the contribution of heart rate to PC1 increased, and the expired fraction of CO2 decreased (p < 0.001). The congruence coefficient of the first PC between normoxia and hypoxia in the HT group showed a high level of similarity (median = 0.88; 25/75% = 0.84/0.93) and was significantly (p < 0.05) higher than in MT (0.82; 0.46/0.94). Thus, highly qualified athletes have the higher cardio-respiratory stability under hypoxic exposure. This can be an additional predictive sign of good athletic performance.

WOS: 000261230700005 In the north of Turkey, pinto bean (Phaseolus vulgaris) is one of the most important crops. Forty-four analysed Populations of pinto bean were collected from Samsun province in northern Turkey. The variability of the 44 self-pollinated populations of pinto bean was evaluated on morphological, reproductive, and agronomical traits during 2003-2004. Individual data for 24 traits (14 quantitative and 10 qualitative) related to earliness and yield, and plant, pod, and seed structure were analysed using Principal Component (PC) analysis which revealed differences among the populations. The PC analysis showed that the first four PC axes explained 83.3% of the total multivariate variation. Characters with high coefficients in the first PC (earliness and yield traits), and the second PC (pod length, pod width, and pod form) were considered the most important since these axes explain nearly half of the total variation. Data were subjected to cluster analysis and several groups Were identified with most of the Populations. Clustered into six groups, a dendrogram was prepared to evaluate morphological differences among Populations. It revealed high variation. The results provide information on the diversity and breeding values of Turkish pinto bean germplasm. Ondokuz Mayis University Research FoundationOndokuz Mayis University [Z-405] We thank Ondokuz Mayis University Research Foundation (Z-405) for financial support.

The goal of this paper is to investigate the effect of using principal components as a data reduction method for expression data in linkage analysis. We used 45 probes normalized using the Affymetrix Global Scaling that had evidence of high heritability to estimate the first 10 principal components (PC). A genome-wide linkage scan was performed on the 45 expression values and the 10 PCs using 2272 single-nucleotide polymorphisms. Our conclusions were: 1) PC analyses under-performed the single-probe analysis for known signals; 2) the PC that best reproduced the single-probe analysis was primarily composed of that probe; 3) no new signals were detected in the PC analysis; 4) no new pleiotropic effects were detected in the PC analysis.

Intraspecific morphological variation in Clarias gariepinus was studied in three water bodies. Twenty-three morphometric characteristics and seven meristic were used. Principal component (PC) analysis showed that morphometric traits of River Osun and Ogbese were somewhat related while that of Aago showed no relatedness, there were no difference among the meristic counts of the populations. PC1, and PC2 accounted for 93% and 4% of the variation observed in the populations. High positive correlation was observed in Aago (r = 0.872, b = 2.10) and Ogbese population while low correlation and negative allometric growth (r = 0.425 and b= 1.38) was observed in Asejire population. Cluster analysis revealed that three studied populations are separated into two major clusters, with samples from Asejire and Ogbese population found within the same cluster but different sub- clusters, similarly some of samples from Aago were also within the same cluster while samples 10 were found on a separate and major cluster. The study confirms the variability among individual species within each population, indicates the presence of genetic diversity among the populations of C. gariepinus and the Pre-anal distance and dorsal fin ray count could be employed in the identification of populations of catfish. Key words: morphometric traits, meristic characters, populations, allometric

The jute mallow (C. olitorius L.) is an important nutritious green leafy vegetable in the tropical region of Africa. This study assesses the extent of genetic diversity and intra-specific relationships among 16 cultivated jute mallows of Nigeria (14), [Ghana (1) and Togo (1), used as checks, evaluating 16 dark jute SSR markers and 16 morphological traits (quantitative and qualitative). The study reveals moderate to high variation among the cultivars in the number of pods, pod yield and plant height traits. Based on the principal component (PC) analysis of the quantitative traits, the pod length, pod width, number of pods, pod yield and plant height are important traits composing PC1. On the other hand, the pod pedicel length and days of 50% flowering traits are highly correlated variables in PC2. Pod length, pod width, pod pedicel length and plant height account for the total diversity. Two main groups (I and II) and an outgroup are identified among the 16 cultivars based on the quantitative traits. among the cultivars, leaf shapes identified are ovate (38% of cultivars), lanceolate (6%), oblanceolate (25%) and palmately lobed (31%). Three markers which have monomorphic alleles are excluded and thirteen markers are used to analyse the genetic diversity. A total of 41 alleles are amplified using the 13 polymorphic markers with an average of 2.75 per locus. The mean polymorphism information content (PIC) value is 0.42, ranging from 0.06 to 0.73. The mean gene diversity or expected heterozygosity = 0.05 (from 0.06 to 0.76). The observed heterozygosity (Ho) ranges from 0.00 to 0.88, with a mean of 0.60. The mean genetic dissimilarity is 0.35. Thus, the SSR data indicate a moderate genetic dissimilarity within jute mallow under study. Clustering using the neighbour-joining dendrogram predicated on the SSR data separates the cultivars into three major groups in which the two cultivars from Ghana and Togo show distinctiveness from the cultivars from Nigeria. Principal coordinate analysis of SSR data is consistent with neighbour-joining groupings. The study based on a set of dark jute markers and morphological traits reveals that the extent of genetic diversity of cultivated jute mallow and could be used in germplasm evaluation. In addition to the knowledge of the high genetic variability observed in the number of pod and the yield of some of the studied cultivars, further efforts are needed to characterise the cultivar pods’ nutritive values for human health.

ObjectiveTo validate the role of the dopamine transporter (DAT) imaging as a biomarker in multiple system atrophy (MSA), we analyzed the association between spatial patterns of [18F]fluoro-propyl-carbomethoxy-iodophenyl-tropane ([18F]FP-CIT) PET and the clinical characteristics of MSA.MethodsSixty-five patients with MSA who underwent [18F]FP-CIT PET between 2009 and 2018 were retrospectively enrolled. To identify spatial patterns of [18F]FP-CIT PET, principal component (PC) analysis was used and correlated with the clinical presentation.ResultsOf the 65 patients, 42 presented with parkinsonian subtype of MSA, and 23 presented with cerebellar subtype of MSA (mean age 63.7 ± 9.3 years; disease duration, 1.8 ± 1.8 years). Each PC represents a specific pattern of degeneration: PC1 and PC2 were associated with the DAT binding of the entire putamen and the posterior putamen, respectively. PC3 was associated with increased [18F]FP-CIT uptake of the caudate and decreased uptake of the dorsal pons. PC2 was significantly correlated with the presence of parkinsonism (p = 5.34 × 10−5) and a positive levodopa response (p = 0.044), with age as a cofactor. PC3 was correlated with the presence of urinary incontinence (p = 0.036). Onset age was significantly correlated with both PC2 (R = 0.48, p = 5.0 × 10−5) and PC3 (R = −0.39, p = 0.0013).ConclusionsThe spatial pattern of DAT binding can reflect distinct clinical features of MSA and provides insight into the underlying pathophysiology of a broad spectrum of clinical features in MSA.

Background: The one-carbon (1C) metabolism cycle consists of a network of interrelated biochemical reactions that provide 1C units required for critical intracellular processes. Polymorphisms in MTHFR and DMNT3b, genes central to the 1C metabolism cycle, and colorectal cancer risk have been reported. Variation in the expression of genes may be attributable to functional polymorphisms; but, it is increasingly clear that epigenetic variation also affects gene expression. DNA methylation, which involves the covalent addition of a methyl group to cytosine residues that precede guanine (CpG), is the most commonly studied epigenetic mechanism. This research investigated the relationship between DNA methylation in the MTHFR and DNMT3b genes, and colorectal adenoma risk; higher methylation was hypothesized to decrease gene expression and contribute to colorectal adenoma risk. Methods: A cross-sectional study recruited 272 patients aged 40-65 undergoing a screening colonoscopy. DNA methylation in the MTHFR and DNMT3b genes was quantified in DNA isolated from blood leukocytes using the Sequenom EpiTYPER® technology. Genomic regions of interest of each gene were selected based on location of CpG islands (1000-2000 base pairs) around the transcriptional start site. Raw data consisted of methylation ratios for 53 and 82 CpG units (a unit consists of either an individual CpG site or aggregates of multiple CpG sites) for MTHFR and DNMT3b, respectively; methylation ratio equals the percentage of methylated cytosines at a specific CpG unit of a gene, divided by the total number of copies of that CpG unit in the sample. Methylation data was cleaned to remove CpG units with potentially unreliable methylation ratios and those with little variability (SD Logistic regression was used to examine relationships between DNA methylation in MTHFR and DNMT3b on colorectal adenoma risk in separate sex- and age-adjusted models. Gene-specific DNA methylation for MTHFR and DNMT3b was conceptualized using two approaches: 1) a composite measure representing average methylation across all CpG units and; 2) unsupervised principal component (PC) analysis, a pattern derivation and data-reduction approach, to develop a smaller number of PCs which account for most of the variance in the methylation of CpG units. Composite and PC measures were categorized using equal-distant cut-points. Results: In our study population of 86 patients with colorectal adenoma and 174 patients with normal colonoscopies, no associations were observed between overall average DNA methylation in MTHFR or DNMT3b, and colorectal adenoma risk. Using unsupervised PC analysis, 3 PCs were derived accounting for 42% and 54% of the variance in the CpG units of MTHFR and DNMT3b, respectively. No association was observed in PC analysis for MTHFR. For DNMT3b, a higher score in PC1 was associated with colorectal adenoma risk (p=0.02); specifically, CpG units approximately 250 base pairs 5' and 3' of the transcriptional start site were found to load heavily onto PC1and higher methylation in this region was found to be associated with colorectal adenoma risk (OR=4.01 (95% CI: 1.17-13.78) when contrasting the highest versus lowest category of methylation). Conclusion: DNMT3b plays an important role in establishing and maintaining methylation patterns. Results of this novel investigation of epigenetic changes in 1C metabolism genes and colorectal adenoma risk suggest that alterations in methylation of the DNMT3b gene may be relevant to colorectal cancer etiology. Citation Format: Vikki Ho, Janet A. Ashbury, Sherryl Taylor, Stephen Vanner, Will D. King. The relationship between DNA methylation in one-carbon metabolism genes and colorectal adenoma risk. [abstract]. In: Proceedings of the Thirteenth Annual AACR International Conference on Frontiers in Cancer Prevention Research; 2014 Sep 27-Oct 1; New Orleans, LA. Philadelphia (PA): AACR; Can Prev Res 2015;8(10 Suppl): Abstract nr A09.

The diverse tumor cell populations may be the critical roles in relapse and resistance to treatment in prostate cancer patients. This study aimed to identify new marker genes and cell subtypes among castration-resistant prostate cancer (CRPC) cells. We downloaded single-cell RNA seq profiles (GSE67980) from the Gene Expression Omnibus (GEO) database. Principal component (PC) analysis and t-Distributed Stochastic Neighbor Embedding (TSNE) analysis were performed to identify marker genes. CRPC cells were clustered and annotated. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses among marker genes were performed. A total of 1500 genes with larger standardized variance were obtained. The top 20 genes were demonstrated in each identified 20 PCs. PC with P-value < 0.05 was selected, including PC1, PC7, PC8, and PC14. The TSNE analysis classified cells as two clusters. The top 6 genes in cluster 0 included HBB, CCL5, SLITRK4, GZMB, BBIP1, and PF4V1. Plus, the top 6 genes in cluster 1 included MLEC, CCT8, CCT3, EPCAM, TMPRSS2, EIF4G2. The GO analysis revealed that these marker genes were mainly enriched in RNA catabolic process, translational initiation, mitochondrial inner membrane, cytosolic part, ribosome, cell adhesion molecule binding, cadherin binding, and structural constituent of ribosome. The KEGG analysis showed that these marker genes mainly enriched in metabolism associated pathways, including carbon metabolism, cysteine and methionine metabolism, propanoate metabolism, pyruvate metabolism, and citrate cycle pathways. To conclude, our results provide essential insights into the spectrum of cellular heterogeneity within human CRPC cells. These marker genes, GO terms and pathways may be critical in the development and progression of human CRPC.

Breeding for yield and quality requires the assessment of the seed metrics and vigour traits. This study, therefore, assessed the variability and inter-dependence of grain yield (GY), seed morphometric and vigour traits in hybrid maize. Seeds of 75 early maturing hybrid maize varieties were evaluated for morphometric traits and quality in four replicates. A field trial laid out in a randomised complete block design with three replicates was also conducted in Ibadan, Nigeria, to determine the grain yield of the hybrids. Data collected on the GY, seed dimension and quality were subjected to analysis of variance. The least significant difference was used to separate means. Relationships among the GY, seed morphometric and vigour traits were determined using correlation coefficients, while principal component (PC) analysis was performed for variability among the hybrids. Significant differences (P

The current research work was carried out to evaluate the genetic diversity associated with thirty cocoa accessions resistant to Phytophthora. The cluster analysis and principal component analysis evaluated the genetic variability among the different genotypes. The highest number of genotypes were observed in cluster III (8) when qualitative traits were considered. In quantitative cluster analysis, most of the genotypes were placed in separate clusters due to high variability in the germplasm. Principal component (PC) analysis showed that the first three PCs with more than one Eigen-value contributed to 79.9 per cent of variability for different traits. When qualitative and quantitative characters were considered along with resistant reaction, clusters with genotypes highly resistant to Phytophthora pod rot were observed. Hybridization programme involving these resistant hybrids belonging to diverse clusters will result in high yielding hybrids with ample resistance.

Fusarium wilt (Fusarium oxysporum f. sp. cumini) is a major constraint to production of cumin. To identify sources of resistance to Fusarium wilt, 64 accessions were screened in a field plot heavily infested with Fusarium wilt, in two years. Disease severity, infection type, disease incidence, plant height, days to flowering initiation, seed yield and yield components were measured. The results revealed significant differences among accessions for all studied traits across both experimental years. There was significant variability for resistance to Fusarium wilt disease among cumin accessions. Ten accessions, G1, G2, G3, G6, G7, G8, G15, G16, G17, and G49, were highly resistant with low dead plants. According to principal component (PC) analysis, the first three components explained about 78% of genetic variation in the first year while the first four components explained 83% of total variation in the second year. In the PC1 of both year, disease severity, infection type, disease incidence, biological yield, seed yield and number of umbellets per umbel were the most effective traits. Based on cluster analysis, 64 accessions were divided into five clusters in both years, whereas clusters I and II showed maximum seed yield and some yield components while clusters IV and V indicated maximum disease resistance variables.

Alzheimer’s disease (AD) biomarkers represent several neurodegenerative processes, such as synaptic dysfunction, neuronal inflammation and injury, as well as amyloid pathology. We performed an exome-wide rare variant analysis of six AD biomarkers (β-amyloid, total/phosphorylated tau, NfL, YKL-40, and Neurogranin) to discover genes associated with these markers. Genetic and biomarker information was available for 480 participants from two studies: EMIF-AD and ADNI. We applied a principal component (PC) analysis to derive biomarkers combinations, which represent statistically independent biological processes. We then tested whether rare variants in 9576 protein-coding genes associate with these PCs using a Meta-SKAT test. We also tested whether the PCs are intermediary to gene effects on AD symptoms with a SMUT test. One PC loaded on NfL and YKL-40, indicators of neuronal injury and inflammation. Four genes were associated with this PC: IFFO1, DTNB, NLRC3, and SLC22A10. Mediation tests suggest, that these genes also affect dementia symptoms via inflammation/injury. We also observed an association between a PC loading on Neurogranin, a marker for synaptic functioning, with GABBR2 and CASZ1, but no mediation effects. The results suggest that rare variants in IFFO1, DTNB, NLRC3, and SLC22A10 heighten susceptibility to neuronal injury and inflammation, potentially by altering cytoskeleton structure and immune activity disinhibition, resulting in an elevated dementia risk. GABBR2 and CASZ1 were associated with synaptic functioning, but mediation analyses suggest that the effect of these two genes on synaptic functioning is not consequential for AD development.

We examined chloroplast pigment variation in holm oak (Quercus ilex L.) leaves for two periods under two climatic conditions, at midday during summer. We compared variation between control (unburned) plants and plants burned the preceding summer, since post-fire resprouts show higher photosynthetic rates and lower thermal energy dissipation. Principal component (PC) analysis was performed on nine pigment-content variables for the two periods separately. Two PC factors (PC1 and PC2) explained 83 and 84% of the variance of the data for each period. In both periods, PC1 was marked by positive loading of pigments associated with light absorption or structural function namely neoxanthin, lutein, β-carotene, chlorophyll a, and chlorophyll b. These pigments were only affected by leaf age. In contrast, PC2 was marked by high loadings of xanthophyll-cycle pigments (associated with photoprotection), and lutein-5,6-epoxide. Leaf content of these pigments was affected by climatic conditions. In the situations considered in PC analysis (leaf types, periods), the lutein-5,6-epoxide content presented a variation pattern similar to that of violaxanthin, and was significantly correlated with thermal dissipation of excess energy (represented by non-photochemical quenching or NPQ). These results suggest a relationship of lutein and lutein-5,6-epoxide with photoprotection., This research was supported by funds from DGYCIT (PB94–0930) (I. Fleck) and PB97–1176 (J. Abadía).

Osteoporosis is the most common metabolic bone disease. A low peak bone mass is regarded a risk factor for osteoporosis. Heredity, physical activity, and nutrition are regarded important measures for the observed variance in peak bone mass. Lp(a) lipoprotein is a well-known risk factor for atherosclerosis. Serum insulin-like growth factor I (IGF-I) has been found to be increased in males with early cardiovascular disease. In this study, we evaluated the association between bone mass, body constitution, muscle strength, Lp(a), and IGF-I in 47 Caucasian male adolescents (mean age, 16.9 yr). Bone mineral density (BMD) and body composition were measured by dual x-ray absorptiometry, muscle strength of thigh using an isokinetic dynamometer, IGF-I by RIA, and Lp(a) by enzyme-linked immunosorbent assay. IGF-I was only associated with Lp(a) (r = 0.38, P < 0.01). Lp(a) was related to total body (r= 0.40, P < 0.01), skull (r = 0.45, P < 0.01), and femoral neck BMD (r = 0.44, P < 0.01). Lp(a) was also related to fat mass (r = 0.34, P < 0.05) and muscle strength (r = 0.30–0.42, P < 0.05). After multiple regression and principal component (PC) analysis, the so-called PC body size (weight, fat mass, lean body mass, and muscle strength) was the most significant predictor of BMD (β = 0.28–0.51, P < 0.05–0.01), followed by the so-called PC physical activity (β = 0.28–0.38, P < 0.05–0.01, weight-bearing locations). However, the PC analysis confirmed that Lp(a) was an independent predictor of total body, skull, and femoral neck BMD (β = 0.33–0.36, P < 0.01).The present investigation confirms that BMD, body size, and muscle strength are closely related and that the level of physical activity is a major determinant of BMD. However, the positive relation of Lp(a), a major risk factor for cardiovascular disease, to BMD has not previously been described. The importance of this observation has to be further investigated.

In the present study, the biochemical composition and shape and dimensional traits of 25 rosehip (Rosa canina) genotypes were investigated. The shape and dimensional traits were determined by image processing technique. Seed-propagated rosehip genotypes belonging to R. canina were collected from the natural flora of Mesudiye (Ordu) and Talas (Kayseri) districts. Antioxidant activity (39.510–72.673 mmol · kg−1), total flavonoids (287.80–1,686.20 mg quercetin equivalent (QE) · kg−1) and total phenolics (38,519.40–79,080.60 mg gallic acid equivalent · kg−1) of the genotypes exhibited large variations. Width (12.2 mm) and thickness (12.5 mm) of fruits averages were found to be close to each other. The genotypes exhibited fruit lengths between 12.0 mm and 29.5 mm. Average projected area at horizontal orientation (179.7 mm2) was greater than the projected area at vertical orientation (120.4 mm2). Sphericity average was calculated as 71.4%. According to principal component (PC) analysis, the most important dimensional traits discriminating genotypes from each other were identified as surface area, geometric mean diameter and volume. In terms of shape attributes, distinctive differences were observed in sphericity, circularity, elongation and surface closure rates (SCR) of the genotypes. According to elliptic Fourier analysis (EFA), genotypes look like a sphere. In terms of shape, there were long, spherical, flat bottomed, pointed bottomed and asymmetric-looking genotypes indicating how environment and genotype affect the fruit shape. The greatest shape variation was transverse contraction and expansion. According to the clustering analysis for shape attributes, rosehip genotypes were classified into six groups. Dendrogram, scatter plots of linear discriminant analysis and paired comparison test results put forth the shape differences of the genotype successfully.

Unicellular volvocalean green algal Haematococcus pluvialis, known as astaxanthin rich microalgae, transforms into aplanospore stage from the flagellate stage when exposed to the stress environments. However, the mechanism of the formation of aplanospore cell wall, which hinders the extraction of astaxanthin and the genetic manipulation is still unclear. In this study, the cell wall components under salicylic acid and high light stresses were explored, and cellulose was considered the main component in the flagellates, which changed gradually into mannose in the aplanospore stages. During the period, the genes related to the cellulose and mannose metabolisms were identified based on the RNA-seq data, which presented a similar expression pattern. The positive correlations were observed among these studied genes by Pearson Correlation (PC) analysis, indicating the coordination between pathways of cellulose and mannose metabolism. The study firstly explored the formation mechanism of aplanospore cell wall, which might be of scientific significance in the study of H. pluvialis.

Pollens are nowadays recognized as one of the main atmospheric particles affecting public human health as well as the Earth's climate. In this context, an important issue concerns our ability to detect and differentiate among the existing pollen taxa. In this paper, the potential differences that may exist in light scattering by four of the most common pollen taxa, namely ragweed, birch, pine and ash, are analysed in the framework of the scattering matrix formalism at two wavelengths simultaneously (532 and 1064 nm). Interestingly, our laboratory experimental error bars are precise enough to show that these four pollens, when embedded in ambient air, exhibit different spectral and polarimetric light scattering characteristics, in the form of ten scattering matrix elements (five per wavelength), which allow identifying each separately. To end with, a simpler light scattering criterion is proposed for classifying among the four considered pollens by performing a principal component (PC) analysis, that still accounts for more than 99 % of the observed variance. We thus believe this work may open new insights for future atmospheric pollen detection.

There is a growing scientific and legislative consensus that fish are sentient, and therefore have the capacity to experience pain and suffering. The assessment of the welfare of farmed fish is challenging due to the aquatic environment and the number of animals housed together. However, with increasing global production and intensification of aquaculture comes greater impetus for developing effective tools which are suitable for the aquatic environment to assess the emotional experience and welfare of farmed fish. This study therefore aimed to investigate the use of Qualitative Behavioural Assessment (QBA), originally developed for terrestrial farmed animals, in farmed salmon and evaluate its potential for use as a welfare monitoring tool. QBA is a ‘whole animal’ approach based on the description and quantification of the expressive qualities of an animal’s dynamic style of behaving, using descriptors such as relaxed, agitated, lethargic, or confident. A list of twenty qualitative descriptors was generated by fish farmers after viewing video-footage showing behaviour expressions representative of the full repertoire of salmon in this context. A separate, non-experienced group of ten observers subsequently watched twenty-five video clips of farmed salmon, and scored the twenty descriptors for each clip using a Visual Analogue Scale (VAS). To assess intra-observer reliability each observer viewed the same twenty-five video clips twice, in two sessions 10 days apart, with the second clip set presented in different order. The observers were unaware that the two sets of video clips were identical. Data were analysed using Principal Component (PC) Analysis (correlation matrix, no rotation), revealing four dimensions that together explained 79% of the variation between video clips, with PC1 (tense/anxious/skittish – calm/mellow/relaxed) explaining the greatest percentage of variation (56%). PC1 was the only dimension to show acceptable inter- and intra-observer reliability, and mean PC1 scores correlated significantly to durations of slow and erratic physical movements measured for the same 25 video clips. Further refinements to the methodology may be necessary, but this study is the first to provide evidence for the potential of Qualitative Behavioural Assessment to serve as a time-efficient welfare assessment tool for juvenile salmon under farmed conditions.

The aim of this study was to evaluate the relationship between temperament in Nellore bulls with carcass and meat quality traits. In total, 1,400 bulls were studied, and temperament was assessed using two measurements: movement score (MOV) and flight speed test (FS). Both MOV and FS were measured at two time points, with background (MOVb and FSb) temperament measured at yearling age, ~550 d after birth, and the preslaughter (MOVps and FSps) temperament measured at the end of the feedlot period. The change of temperament resulting in an increase or decrease in reactivity was also used to measure meat quality. The traits used to define carcass and meat quality included carcass bruises (BRU), hot carcass weight (HCW, kg), ribeye area (REA, cm2), backfat thickness (BFT, cm), marbling score (MS), meat pH after thawing (pH), presence or absence of dark cutters, color parameters of luminosity (L*), redness (a*) and yellowness (b*), cooking loss (CL, %), and Warner–Bratzler shear force (WBSF, kg). A principal component (PC) analysis was initially applied to the carcass and meat quality traits, followed by logistic regression models and linear mixed models to evaluate the effects of temperament on carcass and meat quality. The risks of carcass bruises and dark cutters did not differ as a function of any temperament trait (P > 0.05). In turn, animals classified as high MOVb (reactive) had lower PC3 values (P = 0.05), CL (P = 0.02), and tended to have lower MS (P = 0.08). In addition, animals classified as high FSb (faster and reactive cattle) produced carcasses with smaller REA (P < 0.01), higher meat pH (P < 0.01), lower color gradients (L*, P = 0.04; b*, P < 0.01), and lower PC1 and PC4 scores (P < 0.01) when compared with the low FSb class. For preslaughter temperament, high MOVps was related to lower color a* (P = 0.04), whereas high FSps was related to lower HCW, MS, and PC2 (P < 0.01) than the calmer ones (low FSps). The reduction in MOV was related to more tender meat, and the reduction in FS to heavier carcass and brighter meat. We conclude that excitable temperament in Nellore cattle may have negative effects in some of the carcass and meat quality attributes assessed, mainly those related to muscle deposition on carcass and color gradients. Measurement of temperament before the cattle entered the feedlot was a better predictor of carcass and meat quality traits, compared with temperament assessment at the end of the feeding period.

The durum wheat breeding program in Field crops institute FCI - Chirpan started in 1928. In the last ten years, a number of varieties have been created to meet modern cultural requirements. Genetic distance is of great importance for the success of the combining breeding. In the study are included 13 varieties created over the last 10 years and 8 of the Institute's best advanced durum wheat breeding lines. The field experiment was conducted in experimental field of FCI-Chirpan during 2015-2017 year. A randomized block design in four replicated was used with a trial plot size of 15 m2. A standard farming technology for durum wheat in the country was applied. Tre traits: grain yield, plant height, heading date, test weight, 1000 kernel weight, protein content, wet gluten and vitreousness were observed. The means of three-year trials for all studied traits were calculated and genetic differences between genotypes were found. The coefficients of variation (CV%) obtained for the individual traits show that the heading date and grain yields are the most variable. The correlation analysis determines significant coeficients for 9 out of 28 possible combinations of traits. The multivariate methods for determining the genetic distance between the involved genotypes in the study were used. According to the dendrogram of the cluster analysis, the distances between the four main groups formed are determined. The applied graphical PC analysis shows the interrelations between the traits and the grouping of genotypes in terms of the genetic distance between them. These methods can help for faster breeding progress using the established genetic distance as the basis for deploying the breeding program.

The investigation included 24 durum wheat genotypes – varieties and breeding lines of different origin – Bulgaria - Field Crops Institute – Chirpan, Europe, CYMIT-Mexico and ICARDA-Syria. All genotypes were grown in field conditions in the competitive variety trials in three repetitions in harvesting years 2014/2016 and were analyzed for agronomically important traits and traits associated with grain quality. For statistical processing of the data were used variation analysis, analysis of variance and principle component analysis – PCA. Significant diversity of the studied traits based on the variation coefficients was found. In regard to the agronomic traits the greatest variation was determined for: yield, kernel weight per spike and kernel number per spike. For quality traits the highest variation was recorded for: SDS-value, gluten softening, bug damage degree. Correlation between some agronomic and quality traits was found, too. Based on the PC analysis the studied genotypes are divided into different groups. To the group with the highest SDS sedimentation belong 2 foreign varieties, 3 Bulgarian varieties and 3 breeding lines. The group characterized by the highest content of protein and wet gluten comprises 4 foreign varieties and the group with the highest yield includes 6 breeding lines.

Respiratory syncytial virus (RSV) is a major cause of lower respiratory tract infections and hospital visits during infancy and childhood. Although risk factors for RSV infection have been identified, the role of microbial species in the respiratory tract is only partially known. We aimed to understand the impact of interactions between the nasal microbiome and host transcriptome on the severity and clinical outcomes of RSV infection. We used 16 S rRNA sequencing to characterize the nasal microbiome of infants with RSV infection. We used RNA sequencing to interrogate the transcriptome of CD4+ T cells obtained from the same set of infants. After dimension reduction through principal component (PC) analysis, we performed an integrative analysis to identify significant co-variation between microbial clade and gene expression PCs. We then employed LIONESS (Linear Interpolation to Obtain Network Estimates for Single Samples) to estimate the clade-gene association patterns for each infant. Our network-based integrative analysis identified several clade-gene associations significantly related to the severity of RSV infection. The microbial taxa with the highest loadings in the implicated clade PCs included Moraxella, Corynebacterium, Streptococcus, Haemophilus influenzae, and Staphylococcus. Interestingly, many of the genes with the highest loadings in the implicated gene PCs are encoded in mitochondrial DNA, while others are involved in the host immune response. This study on microbiome-transcriptome interactions provides insights into how the host immune system mounts a response against RSV and specific infectious agents in nasal microbiota.

The main cause of death in newborn lambs is hypothermia, so is necessary to identify the factors affecting variations in body surface temperatures of sheep neonates because approximately 60% of their body heat losses occur through the skin. This study aimed to establish relationships among body surface thermography from different regions with rectal temperature (RT), birth weight (BW) and climatic variables in hair breed newborn lambs during early spring in an arid region. Data of body surface temperatures measured by infrared thermography (entire head, eye, muzzle, ear, entire body, shoulder, rump, loin, right flank, belly and leg), RT and BW were collected at 0, 12 and 24 h post-lambing in 85 lambs born in early spring. Relative humidity [RH], temperature [Te] and temperature-humidity index [THI] were also recorded. RT was not correlated with surface temperatures at 0 and 24 h, but it was at 12 h with all of them (0.36 ≤ r ≤ 0.44). BW and some surface temperatures were negatively correlated at 0 and 24 h (−0.24 ≤ r ≤ −0.30), but positively at 12 h (0.25 ≤ r ≤ 0.27). All surface temperatures were positively correlated (0.51 ≤ r ≤ 0.85) with Te and THI in the three sampling times. Principal component (PC) analysis showed that PC1 explained the majority of the variance (71–72%), followed by PC2 (8–9%) at 0, 12 and 24 h. Body surface temperatures increased as Te and THI also increased, but decreased with the increase in HR. In conclusion, under early spring environment (predominantly cold), the variations in body surface temperatures of hair sheep neonates were more closely related to climatic variables than to RT and BW. Thermography proved to be an effective tool to determine body heat loss by radiation in skin of neonate lambs.

Zeolites are hydrated alumino-silicates of alkali metals and alkaline earth cations which occur in sedimentary and volcano-sedimentary terrains. In this study, visible–near-infrared and shortwave infrared data of ASTER were evaluated in prospecting for zeolite in part of the green tuff belt of the Alborz Mountains, northern Iran. The study area is dominantly covered by sedimentary and volcano-sedimentary rocks, in which zeolite minerals occur only in the Late Eocene vitric tuff. Principal components (PC) analysis and spectral information divergence (SID) were used to discriminate and map the sedimentary and volcano-sedimentary units and the zeolite-rich areas, respectively. The X-ray diffraction and reflectance spectroscopy results indicated that clinoptilolite is the major type of zeolite mineral in this area. Comparing a color composite image, produced from PC images 1–3–5 as R–G–B, with the published geological map and the field investigations indicated that major sedimentary and volcano-sedimentary units as well as their alluvial deposits were discriminated efficiently. Results of the SID method, using an image-derived spectrum of clinoptilolite as a reference, showed good agreements with the field observations. The results of this study indicated that ASTER data are useful for discriminating various sedimentary and volcano-sedimentary units as well as clinoptilolite-type zeolite-rich areas in arid and semiarid terrains.

Heterophylly, or leaf morphological changes along plant shoot axes, is an important indicator of plant eco-adaptation to heterogeneous microenvironments. Despite extensive studies on the genetic control of leaf shape, the genetic architecture of heterophylly remains elusive. To identify genes related to heterophylly and their associations with plant saline tolerance, we conducted a leaf shape mapping experiment using leaves from a natural population of Populus euphratica. We included 106 genotypes grown under salt stress and salt-free (control) conditions using clonal seedling replicates. We developed a shape tracking method to monitor and analyze the leaf shape using principal component (PC) analysis. PC1 explained 42.18% of the shape variation, indicating that shape variation is mainly determined by the leaf length. Using leaf length along shoot axes as a dynamic trait, we implemented a functional mapping-assisted genome-wide association study (GWAS) for heterophylly. We identified 171 and 134 significant quantitative trait loci (QTLs) in control and stressed plants, respectively, which were annotated as candidate genes for stress resistance, auxin, shape, and disease resistance. Functions of the stress resistance genes ABSCISIC ACIS-INSENSITIVE 5-like (ABI5), WRKY72, and MAPK3 were found to be related to many tolerance responses. The detection of AUXIN RESPONSE FACTOR17-LIKE (ARF17) suggests a balance between auxin-regulated leaf growth and stress resistance within the genome, which led to the development of heterophylly via evolution. Differentially expressed genes between control and stressed plants included several factors with similar functions affecting stress-mediated heterophylly, such as the stress-related genes ABC transporter C family member 2 (ABCC2) and ABC transporter F family member (ABCF), and the stomata-regulating and reactive oxygen species (ROS) signaling gene RESPIRATORY BURST OXIDASE HOMOLOG (RBOH). A comparison of the genetic architecture of control and salt-stressed plants revealed a potential link between heterophylly and saline tolerance in P. euphratica, which will provide new avenues for research on saline resistance-related genetic mechanisms.

Biofortified potato could contribute a major role in food security for millions of people. It could help to alleviate worldwide micronutrient malnutrition. An experiment was carried out during 2019-2020 growing season with 49 accessions following randomized complete block design with three replications in order to evaluate and classify agro-morphological traits in Breeder seed production centre (BSPC), Debiganj, Panchagarh. Eight quantitative characters i.e. germination percent, foliage coverage, stem number per hill, plant height, plant vigor, tuber number per plant, tuber weight per plant, yield per plant were measured. Principal components (PC) analysis showed three components explained 72.16 % of the total variation among traits. The first PC assigned 35.22 % and the second PC assigned 58.47 % of total variation between traits. The first PC was more related to yield per plant and weight of tuber. Forty-nine germplasm was placed on three cluster based on cluster analysis using a hierarchical classification (HCA). All accessions were discriminated and high morphological variation was observed. Thus, the outcomes of principal component analysis used in the study have revealed the high level of genetic variation and the traits contributing to the variation were identified. CIP403, CIP404, CIP405, CIP413 and CIP445 accessions identified as superior based on cluster relationship and PCA bi-plot.

The protonation states of two aspartic acids in the catalytic strands of HIV-1 protease (PR) remarkably affect bindings of inhibitors to PR. It is requisite for the design of potent inhibitors towards PR to investigate the influences of Asp25/Asp25' protonated states on dynamics behaviour of PR and binding mechanism of inhibitors to PR. In this work, molecular dynamics (MD) simulations, MM-GBSA method and principal component (PC) analysis were coupled to explore the effect of Asp25/Asp25' protonation states on conformational changes of PR and bindings of Amprenavir and MKP97 to PR. The results show that the Asp25/Asp25' protonation states exert different impacts on structural fluctuations, flexibility and motion modes of PR. Dynamics analysis verifies that Asp25/Asp25' protonated states highly affect conformational dynamics of two flaps in PR. The binding free energy calculations results suggest that the Asp25/Asp25' protonated states obviously strengthen bindings of inhibitors to PR compared to the non-protonation state. Calculations of residue-based free energy decomposition indicate that the Asp25/Asp25' protonation not only disturbs the interaction network of inhibitors with PR but also stabilizes bindings of inhibitors to PR by cancelling the electrostatic repulsive interaction. Therefore, special attentions should be paid to the Asp25/Asp25' protonation in the design of potent inhibitors towards PR.