Analysis of genetic effects and correlations for nutrient quality traits of indica rice in different environments

Understanding the variation for the expressionof genes in different environments is one of themajor goals in qualitative genetics. In this pa-per, the genetic models for quantitative traitsof endosperm in cereal crops were used to eval-uate the seed, cytoplasm and maternal geneticeffects as well as the genotype × environment(GE) interaction effects, and to predict thebreeding value of parents and genotypic corre-lation for nutrient quality traits of indica rice (Oryza sativa L.).

Rise of quantum correlations in non-Markovian environments in continuous-variable systems

We investigate the time evolution of quantum correlations, which are measured by Gaussian quantum discord in a continuous-variable bipartite system subject to common and independent non-Markovian environments. Considering an initial two-mode Gaussian symmetric squeezed thermal state, we show that quantum correlations can be created during the non-Markovian evolution, which is different from the Markovian process. Furthermore, we find that the temperature is a key factor during the evolution in non-Markovian environments. For common reservoirs, a maximum creation of quantum correlations may occur under an appropriate temperature. For independent reservoirs, the non-Markovianity of the total system corresponds to the subsystem whose temperature is higher. In both common and independent environments, the Gaussian quantum discord is influenced by the temperature and the photon number of each mode.

Controlling transfer of quantum correlations among bi-partitions of a composite quantum system by combining different noisy environments

The correlation dynamics are investigated for various bi-partitions of a composite quantum system consisting of two qubits and two independent and non-identical noisy environments. The two qubits have no direct interaction with each other and locally interact with their environments. Classical and quantum correlations including the entanglement are initially prepared only between the two qubits. We find that contrary to the identical noisy environment case, the quantum correlation transfer direction can be controlled by combining different noisy environments. The amplitude- damping environment determines whether there exists the entanglement transfer among bi-partitions of the system. When one qubit is coupled to an amplitude-damping environment and the other one to a bit-flip one, we find a very interesting result that all the quantum and the classical correlations, and even the entanglement, originally existing between the qubits, can be completely transferred without any loss to the qubit coupled to the bit-flit environment and the amplitude-damping environment. We also notice that it is possible to distinguish the quantum correlation from the classical correlation and the entanglement by combining different noisy environments.

Correlation Study on Grain Size Characteristics and Geotechnical Properties of Surface Sediments in Qingdao Offshore Area

The comprehension of sediment grain size parameters and the corresponding sedimentary environment holds paramount importance in elucidating the engineering geological attributes of the subaqueous seabed.This study delineated the sedimentary environment zoning in the northern sea area of Qingdao through cluster analysis of grain size parameters derived from 123 surface sediment samples.The study analyzed the correlation between sediment geotechnical indices and grain size parameters across diverse sedimentary environments.A correlation equation was established for samples exhibiting a strong correlation.The study found four distinct sedimentary environments in the study area:coastal,transitional,shallow sea,and residual.Within the same sedimentary environment,the average grain size and sorting coefficient exhibit significant correlations with geotechnical indices such as water content,density,shear strength,plastic limit,liquid limit,and plastic index.However,notable disparities in the correlation between grain size parameters and geotechnical indices emerge across different sedimentary environments.

Identification of Light-Harvesting Chlorophyll a/b-Binding Protein Genes of Zostera marina L.and Their Expression Under Different Environmental Conditions

Photosynthesis includes the collection of light and a/b-binding （LHC） proteins. In high plants, the LHC gene family constituting the light-harvesting complex ofphotosystems I and II. the transfer of solar energy using light-harvesting chlorophyll includes LHCA and LHCB sub-families, which encode proteins Zostera marina L. is a monocotyledonous angiosperm and inhab- its submerged marine environments rather than land environments. We characterized the Lhca and Lhcb gene families of Z. marina from the expressed sequence tags （EST） database. In total, 13 unigenes were annotated as ZmLhc, 6 in Lhca family and 7 in ZmLhcb family. ZmLHCA and ZmLHCB contained the conservative LHC motifs and amino acid residues binding chlorophyll. The average similarity among mature ZmLHCA and ZmLHCB was 48.91% and 48.66%, respectively, which indicated a high degree of diver- gence within ZmLHChc gene family. The reconstructed phylogenetic tree showed that the tree topology and phylogenetic relation- ship were similar to those reported in other high plants, suggesting that the Lhc genes were highly conservative and the classification of ZmLhc genes was consistent with the evolutionary position of Z. marina. Real-time reverse transcription （RT） PCR analysis showed that different members of ZmLhca and ZmLhcb responded to a stress in different expression patterns. Salinity, temperature, light intensity and light quality may affect the expression of most ZmLhca and ZmLhcb genes. Inorganic carbon concentration and acidity had no obvious effect on ZmLhca and ZmLhcb gene expression, except for ZmLhca6.

The built environment correlates of objectively measured physical activity in Norwegian adults:A cross-sectional study

Background: Built environments that are designed to provide accessible, attractive, and convenient locales promote regular physical activity(PA).Norway has great variability in its geographic, natural, and built environment features. Urban areas have well-developed built environment features, whereas the rural areas are less walkable and this may influence the mode of transport. In general, active transport is more common in urban centers. Further, public transportation is more developed in urban areas, whereas motorized transport may be more widespread in the rural areas. Despite this, in Sogn & Fjordane, a rural county in western Norway, high PA levels are frequently observed. Thus, the aims of this study were to(1) explore perceived built environment features and characterize their associations with objectively measured PA levels in Norwegian adults and(2) explore the differences in these correlates between Sogn & Fjordane and the rest of Norway.Methods: In this cross-sectional study, participants used questionnaires to rate perceptions of their built environments, and their PA was objectively measured for 7 consecutive days using the Acti Graph GT1 M accelerometer. There were 972 Norwegian adults who were included in the study. The average age was 46.9 ± 6.5 years and 43.8% of participants were men. Data were analyzed using multiple linear regression.Results: Total PA and moderate-to-vigorous physical activity(MVPA) were both associated with perceived walkability, the community perception score, and active transport for commuting(all p ≤ 0.004). We also observed geographic-area-specific associations: the community perception score was negatively associated with total PA and MVPA in the rest of Norway(p ≤ 0.012) but not in Sogn & Fjordane. Public transport for commuting was positively associated with MVPA in Sogn & Fjordane(p = 0.03) but not in the rest of Norway.Conclusion: Total PA level and MVPA were associated with built environment factors, such as perceptions of community, perceived walkability,and engaging in active transport for commuting. Geographic differences in the PA correlates were observed, and thus, locally customized environmental population approaches aimed at increasing PA levels may be essential complements to individual behavior and lifestyle strategies.Further, objective measures of Norwegian built environments, such as geographic information system data, and validated walk-and bike-scores would advance the field.

Gene-gene,gene-environment,gene-nutrient interactions and single nucleotide polymorphisms of inflammatory cytokines

Inflammation plays a significant role in the etiology of type 2 diabetes mellitus(T2DM).The rise in the pro-inflammatory cytokines is the essential step in glucotoxicity and lipotoxicity induced mitochondrial injury,oxidative stress and beta cell apoptosis in T2 DM.Among the recognized markers are interleukin(IL)-6,IL-1,IL-10,IL-18,tissue necrosis factor-alpha(TNF-α),C-reactive protein,resistin,adiponectin,tissue plasminogen activator,fibrinogen and heptoglobins.Diabetes mellitus has firm genetic and very strong environmental influence; exhibiting a polygenic mode of inheritance.Many single nucleotide polymorphisms(SNPs) in various genes including those of pro and antiinflammatory cytokines have been reported as a risk for T2 DM.Not all the SNPs have been confirmed by unifying results in different studies and wide variations have been reported in various ethnic groups.The inter-ethnic variations can be explained by the fact that gene expression may be regulated by gene-gene,gene-environment and gene-nutrient interactions.This review highlights the impact of these interactions on determining the role of single nucleotide polymorphism of IL-6,TNF-α,resistin and adiponectin in pathogenesis of T2 DM.

Can environmental sustainability be decoupled from economic growth? Empirical evidence from Eastern Europe using the common correlated effect mean group test

The European Union(EU) and Organisation for Economic Co-operation and Development(OECD) aim to develop long-term policies for their respective member countries. Having observed increasing dangers to the environment posed by rising economic growth, they are seeking pathways to enable policy action on economic growth and environmental sustainability. Given the facts in theoretical and empirical studies, this study assessed the validity of the decoupling hypothesis by investigating asymmetricity in the relationship between environmental sustainability and economic growth in nine Eastern European countries from 1998 to 2017 using the cross-section augmented Dickey-Fuller(CADF) unit root, panel corrected standard error(PCSE), common correlated effect mean group(CCEMG), and Dumitrescu Hurlin causality approaches. Both population growth and drinking water are used as controlled variables. The outcomes establish strong cointegration among all the variables of interest. According to the results of CCEMG test, economic growth exerts short-term environmental degradation but has long-term environmental benefits in Eastern Europe;and population growth and drinking water exert a positive effect on environmental sustainability in both the short-and long-run. The results of Dumitrescu Hurlin causality test indicate that environmental sustainability is unidirectionally affected by economic growth. Based on these outcomes, we suggest the following policies:(1) the EU and OECD should implement member-targeted policies on economic growth and fossil-fuel use towards regulating industrial pollution, water use, and population control;and(2) the EU and OECD member countries should invest in environmental technologies through green research and development(R&D) to transform their dirty industrial processes and ensure productive energy use.

Developmental Changes of GH Gene in Tan Sheep and Correlation Analysis with Slaughter Traits

[ Objective] The paper was to study the differential expression of growth hormone （GH） gene in different ages and different tissues of Tan sheep. [ Method] Using real-time fluorescent quantitative PCR （RT-PCR） assay, specific primers were designed according to the GH gene sequence published on Gen- Bank. With the total RNA of Tan sheep tissue as the template, the expression levels of GH gene in pectoral muscle, leg muscle and longissimus dorsi muscle at dif- ferent ages were analyzed. [ Result] In three types of muscle tissues, the expression patterns of GH gene in different tissues at the same month of age were pectoral muscle 〉 leg muscle 〉 longissimus dorsi muscle. The expression levels of GH gene were positively correlated with live weight before slaughter, carcass weight and net meat weight, and had significant positive correlation only with net meat weight （ P 〈 0.05 ）. [ Conclusion ] The content of GH gene in different tissues gradually increased with the increasing months of age, and there were extremely significant differences in expression level of GH gene among different months of age or different sites （P〈0. 01）.

Gene-environment interaction and male reproductive function

As genetic factors can hardly explain the changes taking place during short time spans, environmental and lifestyle-related factors have been suggested as the causes of time-related deterioration of male reproductive function. However, considering the strong heterogeneity of male fecundity between and within populations, genetic variants might be important determinants of the individual susceptibility to the adverse effects of environment or lifestyle. Although the possible mechanisms of such interplay in relation to the reproductive system are largely unknown, some recent studies have indicated that specific genotypes may confer a larger risk of male reproductive disorders following certain exposures. This paper presents a critical review of animal and human evidence on how genes may modify environmental effects on male reproductive function. Some examples have been found that support this mechanism, but the number of studies is still limited. This type of interaction studies may improve our understanding of normal physiology and help us to identify the risk factors to male reproductive malfunction. We also shortly discuss other aspects of gene-environment interaction specifically associated with the issue of reproduction, namely environmental and lifestyle factors as the cause of sperm DNA damage. It remains to be investigated to what extent such genetic changes, by natural conception or through the use of assisted reproductive techniques, are transmitted to the next generation, thereby causing increased morbidity in the offspring.

Gene×environment interaction in major depressive disorder

Major depressive disorder(MDD)is a multifactorial disorder,where multiple susceptibility genes interact with environmental factors,predisposing individuals to the development of the illness.In this article,we reviewed different gene×environment interaction(G×E)studies shifting from a candidate gene to a genome-wide approach.Among environmental factors,childhood adversities and stressful life events have been suggested to exert crucial impacts on MDD.Importantly,the diathesis-stress conceptualization of G×E has been challenged by the differential susceptibility theory.Finally,we summarized several limitations of G×E studies and suggested how future G×E studies might reveal complex interactions between genes and environments in MDD.

Genetic relationship of rapeseed yield-related traits revealed by elite lines under multiple environments

To provide a theoretical basis for further improvement of Brassica napus yield, additive dominance with additive - by - additive epistatic effects （ ADAA） genetic model and a 6 X 8 partial dial- lel cross design were used to analyze the genetic effects and correlations of five yield related traits of 14 excellent Brassica napus parental lines and their 46 and F2 populations. The results showed that silique density （SD） , siliques per plant （SPP） , seeds per silique （SPS） and thousand - seed weight （TSW） exhibited not only additive and dominant effects, but also significant epistatic effects. The dominant effects of all five yield - related traits were obviously greater than their additive effects and epistatic effects. Yield per plant （YPP） showed significant genetic correlation with SD, SPP and SPS, and the main component of the genetic correlation was the dominance correlation. SPP and SPS both showed a significant negative correlation with TSW. The SD of rapeseed was genetically correlated with all three components of yield to a certain extent, and there were different components of genetic effects positively correlated with the three yield components, indicating that SD is a potential trait to reconcile the conflict between TSW and SPP as well as SPS.

A correlation study between ITGA6 gene,chromosome 8q24,MSMB genes and prostate cancer

Objective To explore the correlation between IT-GA6 gene ( rs12621278, G ) , MSMB gene ( rs10993994,T) ,chromosome 8q24 9 ( rs10086908, T) and prostate cancer ( PCa) in Beijing residents,and to explore the correlation between genotype and pheno-

A clinical analysis of multilocular cystic renal cell carcinoma and its correlation with mutation of the von Hippel-Lindau gene

Objective To discuss the diagnosis and surgical management of multilocular cystic renal cell carcinoma ( MCRCC) and to evaluate the gene function of the mutation of von Hippel-Lindau ( VHL) gene in MCRCC. Methods Seventeen MCRCC cases ( 11 men and

Relationship between Storage Environment and Fruit Quality of a Pear Cultivar Xinli No.7 at Different Picking Time

[Objective] This study aimed to study the effects of different picking time and storage environment on fruit quality of a pear cultivar Xinlin No.7 and the relationship between storage environment and fruit quality, so as to provide a theoretical basis for storage and preservation of Xinli No.7. [Method] The fruits of Xinli NO.7 were picked up in August （optimal） and September respectively and then stored in room, cellar and freezer, respectively. The dynamics in temperature, humidity, CO2 concentration, fruit weight loss rate, pericarp chlorophyll content and fruit interior quality were determined. [Result] The environment differed significantly among different storage methods. In room and cellar, the temperature showed a downward trend, and the humidity decreased after early-mid October. The CO2 concentration changed steadily, and increased rapidly in cellar after December. In freezer, the temperature and humidity changed steadily, and the CO2 concentration increased after October. The changes in quality of the fruits harvested in August and September were similar. There was a certain correlation between storage environment and fruit quality of Xinli No.7. In room and cellar, the variation trends of tem- perature and humidity were consistent with those of chlorophyll content, fruit hardness and titratable acid content with positive correlations, but were opposite from those of fruit weight loss rate, soluble solids content and soluble sugar content with negative correlations. In freezer, the CO2 concentration was closely related to the changes in fruit quality. Its variation trend was consistent with those of fruit weight loss rate and soluble solids content, but was opposite from those of pericarp chlorophyll content, fruit firmness, soluble sugar content and titratable acid content. The differences in some of the traits reached significant levels （P〈0.05, P〈0.01）. [Conclusion] With the extension of storage time, the temperature, humidity and CO2 concentration changed according to different patterns among different storage methods. The changes in fruit quality of Xinli NO.7 were related to the storage environment, especially to the temperature, to a certain extent.

An enriched environment increases the expression of fibronectin type Ⅲ domain-containing protein 5 and brain-derived neurotrophic factor in the cerebral cortex of the ischemic mouse brain

Many studies have shown that fibronectin type III domain-containing protein 5(FDNC5) and brain-derived neurotrophic factor(BDNF) play vital roles in plasticity after brain injury. An enriched environment refers to an environment that provides animals with multi-sensory stimulation and movement opportunities. An enriched environment has been shown to promote the regeneration of nerve cells, synapses, and blood vessels in the animal brain after cerebral ischemia;however, the exact mechanisms have not been clarified. This study aimed to determine whether an enriched environment could improve neurobehavioral functions after the experimental inducement of cerebral ischemia and whether neurobehavioral outcomes were associated with the expression of FDNC5 and BDNF. This study established ischemic mouse models using permanent middle cerebral artery occlusion(pMCAO) on the left side. On postoperative day 1, the mice were randomly assigned to either enriched environment or standard housing condition groups. Mice in the standard housing condition group were housed and fed under standard conditions. Mice in the enriched environment group were housed in a large cage, containing various toys, and fed with a standard diet. Sham-operated mice received the same procedure, but without artery occlusion, and were housed and fed under standard conditions. On postoperative days 7 and 14, a beam-walking test was used to assess coordination, balance, and spatial learning. On postoperative days 16–20, a Morris water maze test was used to assess spatial learning and memory. On postoperative day 15, the expression levels of FDNC5 and BDNF proteins in the ipsilateral cerebral cortex were analyzed by western blot assay. The results showed that compared with the standard housing condition group, the motor balance and coordination functions(based on beam-walking test scores 7 and 14 days after operation), spatial learning abilities(based on the spatial learning scores from the Morris water maze test 16–19 days after operation), and memory abilities(based on the memory scores of the Morris water maze test 20 days after operation) of the enriched environment group improved significantly. In addition, the expression levels of FDNC5 and BDNF proteins in the ipsilateral cerebral cortex increased in the enriched environment group compared with those in the standard housing condition group. Furthermore, the Pearson correlation coefficient showed that neurobehavioral functions were positively associated with the expression levels of FDNC5 and BDNF(r = 0.587 and r = 0.840, respectively). These findings suggest that an enriched environment upregulates FDNC5 protein expression in the ipsilateral cerebral cortex after cerebral ischemia, which then activates BDNF protein expression, improving neurological function. BDNF protein expression was positively correlated with improved neurological function. The experimental protocols were approved by the Institutional Animal Care and Use Committee of Fudan University, China(approval Nos. 20160858 A232, 20160860 A234) on February 24, 2016.

The impact of the environmental factors on the photosynthetic activity of common pine (Pinus sylvestris) in spring and in autumn in the region of Eastern Siberia

The taiga coniferous forests of the Siberian region are the main carbon sinks in the forest ecosystems.Quantitatively, the size of the carbon accumulation is determined by the photosynthetic productivity, which is strongly influenced by environmental factors. As a result,an assessment of the relationship between environmental factors and photosynthetic productivity makes it possible to calculate and even predict carbon sinks in coniferous forests at the regional level. However, at various stages of the vegetative period, the force of the connection between environmental conditions and the productivity of photosynthesis may change. In this research, correlations between the photosynthetic activity of Scots pine(Pinus sylvestris L.) with the environmental conditions were compared in spring and in autumn. In spring, close positive correlation of the maximum daily net photosynthesis was identified with only one environmental factor. For different years, correlations were for soil temperature(rs= 0.655,p = 0.00315) or available soil water supply(rs= 0.892,p = 0.0068). In autumn within different years, significant correlation was shown with two(temperature of air and soil; rs= 0.789 and 0.896, p = 0.00045 and 0.000006,respectively) and four factors: temperature of air(rs=0.749, p = 0.00129) and soil(rs= 0.84, p = 0.00000),available soil water supply(rs= 0.846, p = 0.00013) and irradiance(rs= 0.826, p = 0.000001). Photosynthetic activity has a weaker connection with changes in environmental factors in the spring, as compared to autumn.This is explained by the multidirectional influence of environmental conditions on photosynthesis in this period and by the necessity of earlier photosynthesis onset, despite the unfavorable conditions. This data may be useful for predicting the flow of carbon in dependence on environmental factors in this region in spring and in autumn.

Joint Analysis Method for Major Genes Controlling Multiple Correlated Quantitative Traits

Based on the major gene and polygene mixed inheritance model for multiple correlated quantitative traits, the authors proposed a new joint segregation analysis method of major gene controlling multiple correlated quantitative traits, which include major gene detection and its effect and variation estimation. The effect and variation of major gene are estimated by the maximum likelihood method implemented via expectation-maximization （EM） algorithm. Major gene is tested with the likelihood ratio （LR） test statistic. Extensive simulation studies showed that joint analysis not only increases the statistical power of major gene detection but also improves the precision and accuracy of major gene effect estimates. An example of the plant height and the number of tiller of F2 population in rice cross Duonieai x Zhonghua 11 was used in the illustration. The results indicated that the genetic difference of these two traits in this cross refers to only one pleiotropic major gene. The additive effect and dominance effect of the major gene are estimated as -21.3 and 40.6 cm on plant height, and 22.7 and -25.3 on number of tiller, respectively. The major gene shows overdominance for plant height and close to complete dominance for number of tillers.

Host markers and correlated mutations in the overlapping genes of influenza viruses: M1, M2;NS1, NS2;and PB1, PB1-F2

The influenza A viruses have three gene segments, M, NS, and PB1, which code for more than one protein. The overlapping genes from the same segment entail their interdependence, which could be reflected in the evolutionary constraints, host distinction, and co-mutations of influenza. Most previous studies of overlapping genes focused on their unique evolutionary constraints, and very little was achieved to assess the potential impact of the overlap on other biological aspects of influenza. In this study, our aim was to explore the mutual dependence in host differentiation and co-mutations in M, NS, and PB1 of avian, human, 2009 H1N1, and swine viruses, with Random Forests, information entropy, and mutual information. The host markers and highly co-mutated individual sites and site pairs (P values < 0.035) in the three gene segments were identified with their relative significance between the overlapping genes calculated. Further, Random Forests predicted that among the three stop codons in the current PB1-F2 gene of 2009 H1N1, the significance of a mutation at these sites for host differentiation was, in order from most to least, that at 12, 58, and 88, i.e., the closer to the start of the gene the more important the mutation was. Finally, our sequence analysis surprisingly revealed that the full-length PB1-F2, if the three stop codons were all mutated, would function more as a swine protein than a human protein, although the PB1 of 2009 H1N1 was derived from human H3N2.

ADSL, AMPD1, and ATIC Expression Levels in Muscle and Their Correlations with Muscle Inosine Monophosphate Content in Dapulian and Hybridized Pig Species

We investigated the relationship between muscle inosine monophosphate (IMP) content and mRNA levels of ADSL, AMPD1, and ATIC in Dapulian (DPL), Landrace × Dapulian (LDPL), and Duroc × Landrace × Dapulian (DLDPL) hybridized pigs. Methods: The total RNA in longissimus dorsi was isolated from Dapulian (DPL), Landrace × Dapulian (LDPL) and Duroc × Landrace × Dapulian (DLDPL) hybridized pigs, weighed about 95.0 kg, n = 8/species. The internal genes with highest stability (YWHAZ and RPL4) were chosen from 11 common internal genes using Quantitative real-time PCR (qPCR) and geNorm software. The mRNA levels of ADSL, AMPD1 and ATIC genes were corrected with YWHAZ and RPL4 genes. The muscular IMP content was determined by HPLC. The muscular IMP content in DPL was higher than that in LDPL and DLDPL, 25.00% (p 0.05) and 15.56% (p > 0.05), respectively. The muscular mRNA level of ADSL gene in DPL and LDPL was higher than that in DLDPL, 24.14% and 12.07%, respectively (p 0.05). The muscular mRNA level of ATIC gene in DPL and LDPL was higher than that in DLDPL, 66.67% and 33.33%, respectively (p 0.05). The muscular mRNA level of AMPD1 gene in DPL and LDPL was higher than that in DLDPL, 14.49% and 33.26%, respectively. Furthermore, the IMP content was positively correlated with the mRNA level of ADSL, AMPD1 and ATIC genes, respectively (p 0.05). The mRNA level of ADSL gene was highly related to that of AMPD1 and ATIC gene, respectively (p 0.01), while that of AMPD1 gene was not strongly correlated with that of ATIC gene (p > 0.05). The muscular mRNA level of AMPD1, ADSL and ATIC genes and the muscular IMP content in DPL were highest, followed by those in LDPL and DLDPL. The muscular IMP content was positively correlated with the muscular mRNA level of ADSL, AMPD1 and ATIC genes, respectively.