A Robust Noninvasive Approach to Study Gut Microbiota Structure of Amphibian Tadpoles by Feces

The 16S rDNA amplicon high-throughput sequencing technique provides a robust and inexpensive approach to detect the gut microbiota of amphibians. Since different experimental protocols generate technical biases in drawing the gut microbiota profiles, the integrative analysis of gut microbiota produced by different studies must be performed with circumspection. In this study, we compared the efficacy of two DNA extraction methods(i.e., a phenol-chloroform method and TIANamp Stool DNA Kit) in describing intestinal and fecal bacterial communities of transplanted Asiatic toad(Bufo gargarizans) tadpoles. In terms of the DNA extraction quality(i.e., DNA purity and yield rate) and the consistency in between fecal and intestinal microbiota structures(i.e., α and β diversity indices), the phenol-chloroform method was more robust than this commercial stool kit in profiling gut microbiota of tadpoles with feces.     

Mutations in TP53, ZNF750, and RB1 typify ocular sebaceous carcinoma

<正>Sebaceous carcinoma(SC) of the eyelid is a rare but aggressive malignancy, accounting for 3%e5% of eyelid malignancies in the United States, and up to 35% in Asian populations(Deprez and Uffer, 2009; Xu et al., 2018; Yu et al., 2018). It is frequently mistaken for benign conditions or less aggressive malignancies such as basal cell carcinoma(Muqit et al., 2013), and the effects of delay in diagnosis can be devastating to patients. Aggressive surgical resection is the primary treatment of these tumors and often involves orbital     

Strengthening the functional research on the interaction between host genes and microbiota

正In recent years, many studies have focused on the interaction between host genes and microbiota and their mutual influence (Bonder et al., 2016; Goodrich et al., 2014; Rothschild et al., 2018; Wang et al., 2016; Zhang et al., 2019). Host genetic variation influences the composition of the microbial community, for instance in inflammatory bowel disease, host genetic susceptibilities induce pathological shifts in micro-     

A new strategy for high-throughput identification of human gut microbiota containing specific monosaccharide

<正>Dear Editor,The human gastrointestinal tract is colonized by trillions of microorganisms, the majority of which cannot be cultured(Wu et al., 2018). Numerous glycans are expressed on the surface of gut microbiota that are characteristic of different strains, and the diversity of these glycans is partially attributed to variations in their monosaccharides. More than 100distinct monosaccharides have been identified within the     

PIK-75 promotes homology-directed DNA repair

Homo!ogy-directed repair(HDR)is one of two major DNA repair pathways to mend the double-strand breaks(DSBs)formed in the genome(Liang et al.,1998;Pardo et al.,2009).Although less efficient compared with another DNA repair pathway,nonhomologous end joining(NHEJ),HDR is a type of precise repair to restore DNA damage and sustain genomic stability(Pardo et al.,2009;Ceccaldi et al.,2016).By contrast,NHEJ usually introduces mutations into the repaired site,thus probably harming the genomic integrity(Lieber et al.,2003).The error-free property enables HDR to be harnessed to correct a faulty mutation for therapeutic purpose in cells or in the body(Wu et al.,2013).In add让ion,HDR possesses great potential in the generation of genome-edited animals with precise genetic modifications,such as point mutation,DNA replacement,and DNA insertion in a specific genomic site(Wang et al.,2013).However,the low repair frequency mediated by HDR significantly limits让s application for efficient gene correction or establishment of various genetically modified animal models.Currently,multiple site-specific endonucleases have emerged as highly efficient tools to create targeted DSBs and markedly promote subsequent DNA repair either via HDR or NHEJ(Gaj et al.,2013).Nonetheless,the HDR-mediated modifications following the cleavage of engineering nucleases are still inefficient,usually with an efficiency less than 20%in cultured mammalian cells and embryos(Mali et al..2013;Wang et al.,2013;Yang et al.,2013).     

Overexpression of OsSPL9 enhances accumulation of Cu in rice grain and improves its digestibility and metabolism

正Copper(Cu)is an essential trace mineral element for all forms of life,and is an important structural component and co-factor for a variety of metalloenzymes(Pen~a et al.,1999;Bertinato and L'Abbe,2004).In humans,Cu deficiency is not common because of the ubiquitous occurrence of Cu and ease of gastrointestinal absorption(Zidar et al.,1977;Uauy et al.,1998).However,because of the low Cu content in most sources of feed,the use of Cu as a growth promoter to maximize animal production has been well documented in animal feeding(Braude,1945;Lu et al.,2010).Pre-     

Clinical utility of whole genome sequencing for the detection of mitochondrial genome mutations

正Genetic mitochondrial disorders are a heterogenous group of multi-system disorders caused by an imbalance in mitochondrial function (Moggio et al.,2014;Wallace,2018).In contrast to the nuclear genome,each cell contains hundreds,or even thousands,of mtDNA molecules (Veltri et al.,1990;Calvo et al., 2006).Thus,a mixture of different mtDNA sequences can co-exist within the same individual,a situation referred to as he terop las my.The level of heteroplasmy in an individual often affects the penetrance and phenotypic severity of the diseases.Consequently,detection of sequence heteroplasmy is essential for the proper clinical interpretation of mitochondrial diseases (Stewart and Chinnery,2015).     

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).     

The effect of clinical-grade retinal pigment epithelium derived from human embryonic stem cells using different transplantation strategies

Dear Editor, Many forms of sight-threatening diseases, including retinitis pigmentosa (RP) and age-related macular degeneration (AMD), are caused by the dysfunction, degeneration and loss of the retinal pigment epithelium (RPE)(Strauss, 2005). RPE cell transplantation may potentially recover or halt disease progression, in which human embryonic stem cells (hESCs) could serve as an unlimited donor source for RPE differentiation, and a few clinical trials have shown the safety and effective of transplantation of hESCs-derived RPE (hESC-RPE) for AMD patients (Schwartz et al., 2012;Schwartz etal., 2015;Song etal., 2015;da Cruz et al., 2018;Kashani et al., 2018;Liu et al., 2018).     

Genomic characterizations of H4 subtype avian influenza viruses from live poultry markets in Sichuan province of China, 2014–2015

正Dear Editor,Avian influenza viruses (AIVs) have posed a serious threat to poultry production and public health. To date, more than fourteen AIV subtypes that are able to infect human beings have been documented. Also, it is suggested that new subtypes may be reported in the future, owing to the migration of wild birds and live poultry transportation (Gao, 2018).Poultry may act as a potential incubator for novel subtypes of avian influenza virus (Bi et al., 2016a; Bi et al., 2016b; Liu et al., 2014a; Su et al., 2017). Up to date, the H7N9 AIV emerged in February 2013 has caused 1,567 human cases,with a fatality rate of 39.2%(http://www.who.int/influenza/     

Molecular evolution of pancreatic ribonuclease gene(RNase1) in Rodentia

<正>Pancreatic ribonuclease,which is encoded by RNase1,is a digestive enzyme secreted by the pancreas of vertebrates,and has been recognized to be a classic example for molecular evolutionary studies due to the frequent occurrence of gene duplication and functional divergence in organisms(Zhang et al.,2002,2006;Yu and Zhang,2006;Yu et al.,2010;Xu et al.,2013;Liu et al.,2014).RNase1 has been extensively studied in many mammals,including     

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).     

Rapid breeding of pink-fruited tomato hybrids using the CRISPR/Cas9 system

<正>As one of the most important vegetables,tomato (Solanum lycopersicum) is extensively produced and consumed worldwide and substantially contributes to human nutrition and health (The Tomato Genome Consortium,2012).Although red tomatoes are the most common,pink tomatoes are more popular in Asia,particularly in China and Japan,because of their better taste (Ballester et al.,2010;Zhu et al.,2018).Compared with red tomatoes,pink tomatoes fail to accumulate the yellow-colored flavonoid pigment,naringenin chalcone (NarCh),in their peels,resulting in a colorless peel phenotype (Adato et al,2009;Ballester et al.,2010).Genetic     

A new record of the capped langur (Trachypithecus pileatus) in China

DEAR EDITOR, The distribution of the capped langur (Trachypithecus pileatus)in China has become controversial since Shortridge's langur (Trachypithecus shortridgei) was upgraded to a full species.The capped langur is considered to be distributed in northeast India,Bangladesh,Bhutan,and northwest Myanmar only (Brandon-Jones et al.,2004;Choudhury,2008,2014;Das et al.,2008;Groves,2001).In our field survey,however,we obtained photos of the capped langur,demonstrating its existence in China. Following the species promotion of Shortridge's langur (Brandon-Jones et al.,2004;Groves,2001) and the delimiting of its distribution range to northwestern Yunnan in China and northeastern Myanmar (Brandon-Jones et al.,2004;Cui et al.,2016;Das et al.,2008;Groves,2001;Htun et al.,2008),with a new record in southeastern Tibet (Wu et al.,2016),the capped langur has been deleted from the checklist of mammals in China (Jiang et al.,2015).Despite this,Dr.George Schaller has suggested that capped langurs might exist in the northeastern section of the Yarlung-Zangbo River (Choudhury,2008).     

Maternal heterozygous mutation in CHEK1 leads to mitotic arrest in human zygotes

Dear Editor,The first mitotic division in zygotes is crucial for the beginning of the life cycle for the human.After fertilization,zygotes reactivate cell cycle,both paternal and maternal genomes replicate and reprogram to become totipotent.In the meantime,the male and female pronucleus move to the center of the zygote and merge.Then zygotes enter the metaphase,and sister chromatids separate into two daughter cells(Eckersley-Maslin et al.,2018;Reichmann et al.,2018).This is a sensitive time window and many perturbances may cause the first mitosis to fail.     

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.,     

SOCS-3 contributes to bisphenol a exposure-induced insulin resistance in hepatocytes

<正>Dear Editor,Bisphenol A (BPA), a common and widely used monomer in the production of polycarbonate plastics and epoxy resin,(Healy et al., 2015; De Filippis et al., 2018) has been defined as an endocrine disrupting chemical (EDC) associated with the etiology of insulin resistance (IR)(Gioiosa et al., 2015;Wei et al., 2017) and metabolic disorders (Padmanabhan et al., 2010; Fang et al., 2015; Balistrieri et al., 2018). However,     

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     

Genome-Wide Analysis of Gene Expression in Stationary Phase and Genetic Characterization of Stationary-Phase-Dependent Halocin Gene Expression in the Haloarchaeon Haloferax mediterranei

The stationary phase of microbial growth is a very complex state regulated by various environmental and physiological factors.An intensive study of stationary phase could promote a comprehensive understanding of the complete life cycle of microorganisms,and may provide important insights into their adaptation to harsh and nutrient-depleted conditions.Although the underlying mechanisms have been well-studied in bacteria and yeasts (Herman,2002;Navarro Llorens et al.,2010),less is known about this growth phase in archaea yet.The haloarchaeon Haloferax mediterranei has served as a good model for studying haloarchaeal physiology and metabolism for several decades because of its accelerated growth,remarkable metabolic ability and genomic stability (Han et al.,2012).During stationary phase,H.mediterranei can produce halocin H4 (Cheung et al.,1997),synthesize gas vesicles (J(a)ger et al.,2002),secrete extracellular polysaccharide (Antón et al.,1988) and accumulate poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV)(Cai et al.,2012).Due to these specific features,we selected H.mediterranei as a model system to investigate the archaeal gene expression and regulation during the stationary phase.