Epigenetic Variations in Plant Hybrids and Their Potential Roles in Heterosis

Heterosis,one of the most important biological phenomena,refers to the phenotypic superiority of a hybrid over its genetically diverse parents with respect to many traits such as biomass,growth rate and yield.Despite its successful application in breeding and agronomic production of many crop and animal varieties,the molecular basis of heterosis remains elusive.The classic genetic explanations for heterosis centered on three hypotheses:dominance (Davenport,1908;Bruce,1910;Keeble and Pellew,1910;Jones,1917),overdominance (East,1908;Shull,1908) and epistasis (Powers,1944;Yu et al.,1997).However,these hypotheses are largely conceptual and not connected to molecular principles,and are therefore insufficient to explain the molecular basis of heterosis (Birchler et al.,2003).Recently,many studies have explored the molecular mechanism of heterosis in plants at a genome-wide level.These studies suggest that global differential gene expression between hybrids and parental lines potentially contributes to heterosis in plants (e.g.,Swanson-Wagner et al.,2006;Zhang et al.,2008;Wei et al.,2009;Song et al.,2010).Research suggests that genetic components,including cis-acting elements and trans-acting factors,are critical regulators of differential gene expression in hybrids (Hochholdinger and Hoecker,2007;Springer and Stupar,2007;Zhang et al.,2008).However,other research indicates that epigenetic components,the regulators of chromatin states and genome activity,also have the potential to impact heterosis (e.g.,Ha et al.,2009;He et al.,2010;Groszmann et al.,2011;Barber et al.,2012;Chodavarapu et al.,2012;Greaves et al.,2012a;Shen et al.,2012).     

Interaction between Bms1 and Rcl1,two ribosome biogenesis factors,is evolutionally conserved in zebrafish and human

正Ribosomes are large RNA and protein complexes that function as the machinery for translation protein synthesis(Boisvert et al.,2007;Ben-Shem et al.,2011;Henras et al.,2015;Khatter et al.,2015;McCann et al.,2015).The eukaryotic ribosome is composed of two subunits,the 60S large subunit(LSU)and the 40S small subunit(SSU),which collectively comprise of four different ribosomal RNA(rRNA)species and more than 70 proteins(Ben-Shem et al.,2011;Henras et al.,2015;Khatter et al.,2015).The LSU contains     

Resident endothelial cells generate hepatocytes through cell fusion in adult mouse liver

正Unravelling lineage plasticity and cellular contribution to hepatocytes provides valuable information for understanding sources that fuel homeostatic renewal of the liver(Miyajima et al.,2014).In the adult stage,hepatocytes are mainly self-renewed through cell division(Schaub et al.,2014;Tarlow et al.,2014;Yanger et al.,2014).Under severe injury or when hepatocyte proliferation is significantly impaired,cholangiocytes or biliary epithelial cells contribute to hepatocytes(Raven et al.,2017;Deng et al.,2018).It     

Synaptobrevin-2 facilitates the trafficking and function of atrial SK2 channel

正Dear Editor,Small conductance Ca2+-activated potassium (SK) channels are widely expressed in various tissues and play a unique role in regulating cell function by integrating cytosolic Ca2+ levels and membrane potential (Adelman et al., 2012). Xu et al. first identified SK channels in the heart and found that SK channels, particularly the SK2 channel, are preferentially expressed in human and mouse atrial myocytes but not in ventricular myocytes (Xu et al., 2003). This suggests that the SK     

Is bitter actually better? Targeting a soyasaponin acetyltransferase affects soybean seed germination

<正>Soyasaponins are a class of triterpenoid saponins that accumulate in soybean (Glycine max) seeds and give a bitter flavor to some soybean products (Berhow et al., 2006).Acetylated sugars at C22 in type-A soyasaponins are largely responsible for the undesirable bitterness in soybean-derived foods, as non-acetylated type-A soyasaponins are not bitter(Okubo et al., 1992; Takada et al., 2013; Chitisankul et al.,     

Using the inverse Poisson distribution to calculate multiplicity of infection and viral replication by a high-throughput fluorescent imaging system

正Dear Editor,For virologists,it is crucial to confidently determine the concentration of infectious particles that are utilized and produced in experiments(Dulbecco,1952;Bushar and Sagripanti,1990;La Barre and Lowy,2001;Gueret et al.,2002;Gao et al.,2009;Kutner et al.,2009;Grigorov et al.,2011;Knipe and Howley,2013).With respect to     

Understanding the pathogenic evolution of Zika virus

正Unlike the previous circulating strains that were not associated with significant human pathology,recent circulating Zika virus(ZIKV)strains isolated during the 2015–2016Brazilian Outbreak are highly suspected to cause neuropathology,including disorders of fetal brain development and Guillain-Barrésyndrome(Broutet et al.,2016).Studies have revealed that recent ZIKV strains can be spread through maternal-fetal(Calvet et al.,2016)and sexual(Hills et al.,2016)transmission,in addition to the traditional route     

Evolutionary selection on MDA5 and LGP2 in the chicken preserves antiviral competence in the absence of RIG-I

<正>The pattern recognition receptors (PRRs) act as the first line of defense against pathogens and are common molecular targets in the conflict between viruses and their host (Tan et al.,2018).The RIG-I-like receptors (RLRs),including RIG-I (Yoneyama et al.,2004),MDA5 (Andrejeva et al.,2004),and LGP2 (Saito et al.,2007),are PRRs and reside in the cytoplasm.These proteins recognize the RNA structures of different viral RNA species.All RLRs have an intermediate RNA helicase domain that catalyzes ATP hydrolysis and a C-terminal domain (CTD).RIG-I and MDA5,but not LGP2,contain tandem caspase recruitment domains at their N-termini     

Effect of pH,temperature and freezing-thawing on quantity changes and cellular uptake of exosomes

Exosomes are cup-shaped small(30-150 nm)extracellular vesicles with the structure of lipid bilayer membrane(Tkach and Thery,2016)containing proteins,mRNAs and micro-RNAs that mediate intercellular communication(Valadi et al.,2007).Unlike other extracellular vesicles,exosomes are released into the extracellular space when the multivesicular bodies(MVBs)fuse with the plasma membrane(Colombo et al.,2014).     

Insights from avian influenza surveillance of chickens and ducks before and after exposure to live poultry markets

<正>Dear Editor,Live poultry markets are the major trading system of poultry in China and many other countries, and are also thought to be important for the generation and spread of avian influenza viruses and other avian pathogens (Zhang et al., 2013; Shi et al., 2017; Quan et al., 2018). Surveillance studies indicate that the H7 avian influenza viruses were maintained and circulated for years in the New York live poultry markets(Suarez et al., 1999). H9N2 and H5N1 influenza viruses have been detected in poultry in China since 1994 and 1996, respectively, and vaccines have been developed and used in poultry to control these two subtypes of viruses (MOA,     

Engrafted newborn neurons could functionally integrate into the host neuronal network

The limited capability to regenerate new neurons following injuries of the central neural system (CNS) still remains a major challenge for basic and clinical neuroscience.Neural stem cells (NSCs) could nearly have the potential to differentiate into all kinds of neural cells in vitro.Previous studies verified that exogenous transplanted NSCs are capable of differentiating into neurons and projecting onto the host neurons in the rat brain (Tabar et al.,2005;Dong JR et al.,2012),which could lead to behavioral recovery from neuronal damages such as spinal cord injury (McDonald et al.,1999),Parkinson's disease (Gonzalez et al.,2015;Kim et al.,2002;Lindvall,2001),and stroke (Zhang et al.,2016).     

Persisting lung pathogenesis and minimum residual virus in hamster after acute COVID-19

Dear Editor,Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)has infected more than 200 million people,causing coronavirus disease 2019(COVID-19)worldwide.Lungs are the primary target organ of SARS-CoV-2 infection.The mild COVID-19 cases develop symptoms of fever,fatigue,muscle weakness,chest pain,headache and cough(Chen et al.,2020;Wang et al.,2020;Zhu et al.,2020),while severe COIVD-19 cases might have pneumonia,breathing difficulties,multiple organ failure and death(Chen et al.,2020;Wang et al.,2020;Zhu et al.,2020).Both the clinicians and researchers have largely focused on the acute phase of COVID-19,but the long-term health consequences of the COVID-19 patients after clinical recovery remain less investigated.Several clinical cohorts demonstrated that some patients discharged from hospital still experience symptoms including fatigue,muscle weakness,chest pain,cough and breathing difficulties(Carfi et al.,2020;Lim et al.,2020;Huang et al.,2021).Moreover,severely impaired pulmonary diffusion capacities and abnormal chest imaging manifestations were observed in some convalescent patients(Huang et al.,2021).Surprisingly,residual virus(An et al.,2020;Yao et al.,2020;Kim et al.,2021)were detected in some convalescent patients.     

A Brassinosteroid-Signaling Kinase Interacts withMultiple Receptor-Like Kinases in Arabidopsis

Dear Editor, Higher plants have evolved hundreds of genes encodingreceptor-like kinases （RLKs）, which function as cell surfacereceptors perceiving developmental and environmental sig-nals （Shiu et al., 2004）. Many RLKs have been shown to playspecific roles in hormone responses, developmental regula-tion, defense against pathogen infection, and adaptationto abiotic stresses （Chae et al., 2009; Antolin-Llovera et al.,2012）. The mechanisms that ensure specific signal transduc-tion from each RLK to target cellular responses remain poorlyunderstood. Recent studies revealed that many RLKs trans-duce signals by phosphorylating receptor-like cytoplasmickinases （RLCKs）, which lack the transmembrane domainsbut are anchored at the plasma membrane through lipidmodification （Tang et al., 2008; Zhang et al., 2010; Shi et al.,2013）. There are over 400 RLKs and only about 150 RLCKs inArabidopsis （Shiu et al., 2004）. One outstanding question iswhether each RLCK mediates signaling downstream of a spe-cific RLK, participates in multiple RLK pathways, or mediatescrosstalk between RLK pathways.     

Rare variants in novel and known genes associated with primary angle closure glaucoma based on whole exome sequencing of 549 probands

<正>Primary angle closure glaucoma(PACG)is one of the most common causes of irreversible blindness in Asia and about 80%of PACG are present in Asia(Song et al.,2017).Genetics plays an important role in the development of PACG(Gramer et al.,2014).Recently,eight common SNPs were found to be strongly associated with PACG(Vithana et al.,2012;Khor et al.,2016)and mutations in MYRF cause high hyperopia accompanied with PACG(Xiao et al.,2019).However,the genetic defects underlying PACG are still     

Human evolution and human-influenced evolution of organisms in changing environments

Human evolution and human-influenced evolution of living organisms such as animals,plants,and microorganisms on our planet are among the most active and inspiring topics of scientific research.This is because the evolutionary processes influenced by humans can be detected within a quantifiable period of time,and the consequences of such evolutionary processes vary significantly in terms of their rates and diversification,compared to those under the conditions of no human influences (Hendry et al.,2008).For example,domesticated animals (e.g.,chicken and pig)and plant species (e.g.,rice and maize) have evolved relatively rapidly within the past 10 000 years,which has resulted in tremendous genetic diversity of these domesticates under human influences in different environments (Dorshorst et al.,2011;Huang et al.,2012;Rubin et al.,2012).However,the rapid evolution and changes in these organisms have had significant impacts on the environments that humans and these organisms inhabit.     

Identification of EGF as an Important Regulator for Promoting CYP3A4 Expression in Human Embryonic Stem Cell-Derived Hepatocytes Using TALEN-Based Gene Targeting

Functional human hepatocytes are one of the most significant tools for studying drug absorption, distribution, metabolism and excretion/toxicity （ADME/Tox）, especially for applications in preclinical drug development （Sahi et al., 2010; Godoy et al., 2013）. They provide the closest in vitro model to the human liver and the only model that mimics the drug metabolic profiles found in vivo. However, these cells lose their metabolic function rapidly and dramatically during the in vitro culture process, which largely hinders their wider application in drug development （Sahi et al., 2010; Godoy et al., 2013）. To overcome this obstacle, it is important to regulate the activities of key genes which are responsible for the detoxification metabolic function of human hepatocytes.     

Lack of an Additive Effect between the Deletions of Klf5 and Nkx3-1 in Mouse Prostatic Tumorigenesis

Prostate cancer is one of the most common malignancies.The development and progression of prostate cancer are driven by a series of genetic and epigenetic events including gene amplification that activates oncogenes and chromosomal deletion that inactivates tumor suppressor genes.Whereas gene amplification occurs in human prostate cancer,gene deletion is more common,and a large number of chromosomal regions have been identified to have frequent deletion in prostate cancer,suggesting that tumor suppressor inactivation is more common than oncogene activation in prostatic carcinogenesis (Knuutila et al.,1998,1999;Dong,2001).Among the most frequently deleted chromosomal regions in prostate cancer,target genes such as NKX3-1 from 8p21,PTENfrom 10q23 andATBF1 from 16q22 have been identified by different approaches (He et al.,1997;Li et al.,1997;Sun et al.,2005),and deletion of these genes in mouse prostates has been demonstrated to induce and/or promote prostatic carcinogenesis.For example,knockout of Nkx3-1 in mice induces hyperplasia and dysplasia (Bhatia-Gaur et al.,1999;Abdulkadir et al.,2002) and promotes prostatic tumorigenesis (Abate-Shen et al.,2003),while knockout of Pten alone causes prostatic neoplasia (Wang et al.,2003).Therefore,gene deletion plays a causal role in prostatic carcinogenesis (Dong,2001).     

Asthma-associated polymorphisms in 17q12-21 locus modulate methylation and gene expression of GSDMA in naive CD4~+ T cells

正The 17q12-21 locus harboring ORMDL sphingolipid biosynthesis regulator 3 (ORMDL3) and Gasdermin B (GSDMB) genes exhibits one of the most significant and replicated associations with asthma[MIM:600807](Stein et al.,2018).Several studies explored the complex interactions between SNPs,gene expression and epigenetic modifications at this locus,primarily focusing on the levels of expressed ORMDL3 and GSDMB (Stein et al.,2018).Given that DNA methylation and gene expression signals are cell-type specific(Reinius et al.,2012),isolated materials such as lymphocytes from blood and,to a lesser extent,bronchial epithelial cells from biopsies of bronchi or bronchoalveolar lavages have been used in a number of studies to investigate such interactions (Stein et al.,2018).None     

Narrow distribution of cyanophage psbA genes observed in two paddy waters of Northeast China by an incubation experiment

正Dear Editor,Cyanophages are viruses that infect cyanobacteria.They play an important role in shaping the genetic and functional diversity of themselves and their hosts through genetic exchange and shuffling(Lindell et al.,2005;Singh et al.,2012).The psb A gene of cyanophages is a"hostderived"gene,and its encoded D1 protein is capable of