Dissecting Disease Inheritance Modes in a Three-Dimensional Protein Network Challenges the “Guilt-by-Association” Principle

To better understand different molecular mechanisms by which mutations lead to various human diseases, we classified 82,833 disease-associated mutations according to their inheritance modes (recessive versus dominant) and molecular types (in-frame [missense point mutations and in-frame indels] versus truncating [nonsense mutations and frameshift indels]) and systematically examined the effects of different classes of disease mutations in a three-dimensional protein interactome network with the atomic-resolution interface resolved for each interaction. We found that although recessive mutations affecting the interaction interface of two interacting proteins tend to cause the same disease, this widely accepted “guilt-by-association” principle does not apply to dominant mutations. Furthermore, recessive truncating mutations in regions encoding the same interface are much more likely to cause the same disease, even for interfaces close to the N terminus of the protein. Conversely, dominant truncating mutations tend to be enriched in regions encoding areas between interfaces. These results suggest that a significant fraction of truncating mutations can generate functional protein products. For example, TRIM27, a known cancer-associated protein, interacts with three proteins (MID2, TRIM42, and SIRPA) through two different interfaces. A dominant truncating mutation (c.1024delT [p.Tyr342Thrfs^∗30]) associated with ovarian carcinoma is located between the regions encoding the two interfaces; the altered protein retains its interaction with MID2 and TRIM42 through the first interface but loses its interaction with SIRPA through the second interface. Our findings will help clarify the molecular mechanisms of thousands of disease-associated genes and their tens of thousands of mutations, especially for those carrying truncating mutations, often erroneously considered “knockout” alleles.     

Molecular characterization of myostatin (MSTN) gene and association analysis with growth traits in the bighead carp (Aristichthys nobilis)

Myostatin (MSTN) is a member of the transforming growth factor-β superfamily and functions as a negative regulator of skeletal muscle development and growth. In this study, the bighead carp MSTN gene (AnMSTN for short) was cloned and characterized. The 3,769 bp genomic sequence of AnMSTN consisted of three exons and two introns, and the full length cDNA (2,141 bp) of the gene had an open reading frame encoding a polypeptide of 375 amino acids. The deduced amino acid sequence of AnMSTN showed 67.1-98.7 % homology with MSTNs of avian, mammalian and teleostean species. Sequence comparison and phylogenetic analysis confirmed the MSTNs were conserved throughout the vertebrates and AnMSTN belonged to MSNT-1 isoform. AnMSTN was expressed in various tissues with the highest expression in muscle. Two single nucleotide polymorphisms, g.1668T > C in intron 2 and g.2770C > A in 3' UTR, were identified in AnMSTN by sequencing PCR fragments, and genotyped by SSCP. Association analysis showed that g.2770C > A genotypes were significantly associated with total length, body length and body weight (P < 0.01). These results suggest that AnMSTN involves in the regulation of growth, and this polymorphism would be informative for further studies on selective breeding in bighead carp.     

Use of a bovine genome chip to identify new biological pathways for beef quality in cattle

The accumulation of muscle is largely influenced by the genetic background of cattle. Muscle tissue was collected from the longissimus muscle of Lilu beef cattle at 12, 18, 24 and 30?months old. Using meat quality analysis, we found that the Lilu beef cattle have good production and slaughter performance, the performance meets the criterion of beef cattle. Microarray analysis was able to identify a total of 4,219 genes that are differentially expressed (P?≤?0.01) between the two groups of cattle (12 vs 18; 18 vs 24; 24 vs 30). Bioinformatics analysis results suggested that most of the differentially expressed genes are involved in the metabolic pathways and neuroactive ligand–receptor interaction pathways. In the future study that aims to look for genes relating to growth and meat quality, we will focus on the genes that have been shown to have a significant variation between groups and are involved in the two pathways.     

The psoriasis drug monomethylfumarate is a potent nicotinic acid receptor agonist

Nicotinic acid has been used for several decades to treat dyslipidemia. In mice, the lipid-lowing effect of nicotinic acid is mediated by the Gi coupled receptor PUMA-G. In humans, high (GPR109A) and low (GPR109B) affinity nicotinic acid receptors have been characterized. Here we identify monomethylfumarate as a GPR109A agonist. Monomethylfumarate is the active metabolite of the psoriasis drug Fumaderm. We show that monomethylfumarate activates GPR109A in a calcium based aequorin assay, cAMP assay and demonstrate competitive binding with nicotinic acid. We show that GPR109A is highly expressed in neutrophils and epidermal keratinocytes, and that its expression is increased in human psoriatic lesions. Our findings provide evidence that GPR109A is a target for the drug Fumaderm and suggest that niacin should be investigated to treat psoriasis in addition to its role in treating lipid disorders.     

三倍体白鲫的生物学特性

由人工诱导的异源四倍体白鲫雄鱼与正常的二倍体白鲫雌鱼交配获得的异源三倍体白鲫,其主要生物学特性同二倍体白鲫进行比较研究表明,三倍体白鲫具有体形较大、相对体高和相对尾柄高较高、侧线上下鳞数目较多的形态特征,仍保留着二倍体白鲫以浮游植物为主的植食性营养方式,雌雄均不育,比二倍体生长快,网箱养殖１１２天后,体重比二倍体平均增加３２．３８％。试验证实三倍体白鲫是一个具有养殖生产前景的新对象。     

Cas12a-based on-site,rapid detection of genetically modified crops

A CRISPR/LbCas12a-based nucleic acid detection method that uses crude leaf extracts as samples and is rapid (≤40 min for a full run) and highly sensitive (0.01%) can be used to monitor genetically modified organisms in the field.     

Factors affecting the survival,fertilization, and embryonic development of mouse oocytes after vitrification using glass capillaries

Cryopreservation of mammalian oocytes is an important way to provide a steady source of materials for research and practice of parthenogenetic activation, in vitro fertilization, and nuclear transfer. However, oocytes cryopreservation has not been common used, as there still are some problems waiting to be solved on the repeatability, safety, and validity. Then, it is necessary to investigate the damage occurred from vitrification and find a way to avoid or repair it. In this study, mouse mature oocytes were firstly pretreated in different equilibrium media, such as 5% ethylene glycol (EG) + 5% dimethyl sulfoxide (DMSO), 10% EG + 10% DMSO, and 15% EG + 15% DMSO in TCM199 supplemented with 20% fetal calf serum (FCS), for 1, 3, and 5 min, respectively, and then oocytes were transferred into vitrification solution (20% EG, 20% DMSO, 0.3 M sucrose, and 20% FCS in TCM199, M2, Dulbecco’s phosphate buffered saline, and 0.9% saline medium, respectively) and immediately loaded into glass capillaries to be plunged into liquid nitrogen. After storage from 1 h to 1 wk, they were diluted in stepwise sucrose solutions. The surviving oocytes were stained for cortical granule, meiotic spindles, and chromosomes. Oocytes without treatments were used as controls. The results showed that oocytes pretreated in 5% EG +5% DMSO group for 3–5 min or in 10% EG + 10% DMSO group for 1–3 min were better than other treatments. Oocytes vitrified in TCM199 as basic medium showed higher survival and better subsequent embryonic development than other groups. When the concentration of FCS in vitrification solution reduced below 15%, the rates of survival, fertilization, and developing to blastocyst declined dramatically. The inner diameter (0.6 mm) of glass capillaries and amount of vitrification solution (1–3 μl) achieved more rapid cooling and warming and so reduce the injury to oocytes. Cropreservation led to the exocytosis of cortical granule of oocytes (about 10%) and serious disturbance of microtubules and chromosomes. With 2 h incubation, the microtubules could repolymerize and the rate of fertilization in vitro was much higher than those of 1 and 3 h incubation groups. In conclusion, the protection of basic medium and FCS to oocytes during cryopreservation and sufficient cooling and warming rates using glass capillaries have profound effects on oocytes survival and subsequent embryonic development competence. The appropriate time for fertilization in vitro may be related to the recovery of spindles after incubation and avoiding ageing in the whole process.     

Targeted gene disruption by CRISPR/xCas9 system in Drosophila melanogaster

Although the Cas9 protein from Streptococcus pyogenes (SpCas9) is the most widely used clustered regularly interspaced short palindromic repeats (CRISPR) variant in genome engineering experiments, it does have certain limitations. First, the stringent requirement for the protospacer adjacent motif (PAM) sequence limits the target DNA that can be manipulated using this method in insects. Second, its complementarity specifications are not very stringent, meaning that it can sometimes cause off-target effects at the target site. A recent study reported that an evolved SpCas9 variant, xCas9(3.7), with preference for various 5′-NG-3′ PAM sequences not only has the broadest PAM compatibility but also has much greater DNA specificity and lower genome-wide off-target activity than SpCas9 in mammalian cells. Here we applied the CRISPR/xCas9 system to target the white gene in Drosophila melanogaster, testing the genome-editing efficiency of xCas9 at different PAM sites. On the GGG PAM site, xCas9 showed less activity than SpCas9. For the non-NGG PAM site TGA, xCas9 could produce DNA cleavage and indel-mediated disruption on the target gene. However, for other non-NGG PAM sites, xCas9 showed no activity. These findings show that the evolved Cas9 variant with broad PAM compatibility is functional in Drosophila to induce heritable gene alterations, increasing the targeting range for the applications of genome editing in insects.     

Effects of chromium picolinate supplementation on the growth,carcass quality and gene expression of beef during the finishing period

Four groups of 12 young beef, as similar as possible with respect to age and weight, were fed a basic diet. The addition fed to four groups was 0, 200, 600, and 1,200 mg of organic chromium (chromium picolinate CrPic) per kg concentrated feed. The results showed that there was no effect on overall growth performance and dressing percentage and pure meat percentage when adding different CrPic content, but significant difference was found between 0 group and other three groups in percentage of high grade cuts (P < 0.05). The Cr content in Kidney, Musculus diaphragm, Semitendinosus muscles and Longissimusdorsi tissues have no difference in four groups (P > 0.05), but there was significant difference in liver tissues between 0, 200, 600 groups and 1200 group (P < 0.05). Gene expression analysis indicated that there were no differences in five genes expression in liver and muscle tissues in four groups (P > 0.05), but mRNA expression amount of FOX1, FSTL and MATR3 always had same trends whatever in liver or muscle tissues. However the RPLOP gene expression amount has large difference between liver and muscle.     

Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes

Much emphasis has been placed on the identification, functional characterization, and therapeutic potential of somatic variants in tumor genomes. However, the majority of somatic variants lie outside coding regions and their role in cancer progression remains to be determined. In order to establish a system to test the functional importance of non-coding somatic variants in cancer, we created a low-passage cell culture of a metastatic melanoma tumor sample. As a foundation for interpreting functional assays, we performed whole-genome sequencing and analysis of this cell culture, the metastatic tumor from which it was derived, and the patient-matched normal genomes. When comparing somatic mutations identified in the cell culture and tissue genomes, we observe concordance at the majority of single nucleotide variants, whereas copy number changes are more variable. To understand the functional impact of non-coding somatic variation, we leveraged functional data generated by the ENCODE Project Consortium. We analyzed regulatory regions derived from multiple different cell types and found that melanocyte-specific regions are among the most depleted for somatic mutation accumulation. Significant depletion in other cell types suggests the metastatic melanoma cells de-differentiated to a more basal regulatory state. Experimental identification of genome-wide regulatory sites in two different melanoma samples supports this observation. Together, these results show that mutation accumulation in metastatic melanoma is nonrandom across the genome and that a de-differentiated regulatory architecture is common among different samples. Our findings enable identification of the underlying genetic components of melanoma and define the differences between a tissue-derived tumor sample and the cell culture created from it. Such information helps establish a broader mechanistic understanding of the linkage between non-coding genomic variations and the cellular evolution of cancer.