“Paralogism”由谁推断,如何展开?关于《诗学》第二十四章中的一个译注

亚理士多德《诗学》第二十四章提出诗人应该借助“paralogism”获取艺术效果,并从《奥德赛》第十九卷选取例证。目前学界常见的《诗学》英译本和中译本中对此例证的解释存在分歧。分歧之一在于回答作品中“paralogism”由谁做出推断,一种认为是奥德修斯的妻子Penelo-pe,另一种认为是老仆Eurycleia。后一种观点不符合《诗学》关于诗人语言技艺的论述。分歧之二是“paralogism”如何展开,一种观点认为是借用了调换因果前后顺序的方法,另一种观点认为是“一果多因”不能逆推造成了“谬误判断”。后一种观点与亚理士多德的自叙初衷不够契合。

Historical relationships of the Mesoamerican highlands,with emphasis on tropical montane cloud forests:a temporal cladistic biogeographical analysis

The historical relationships of nine areas of endemism of the tropical montane cloud forests(TMCFs)were analysed based on a temporal cladistic biogeographical approach.Three cladistic biogeographical analyses were conducted based on 29cladograms of terrestrial taxa by partitioning them into three time-slices,namely,Miocene,Pliocene,and Pleistocene.The results showed different area relationships over time.For the Miocene and Pliocene time slices,the Isthmus of Tehuantepec acted as a geographic barrier that fragmented the TMCFs into two portions:west of the Isthmus and east of the Isthmus.In the case of the Pleistocene,the TMCFs were broken into two portions,one related to the Neotropical region and the other to the Nearctic region.Furthermore,the analyses allowed us to detect the influences of different geological and paleoclimatological events on the distribution of the TMCFs over time.Therefore,the TMCFs current distribution might have been driven by geological events during the Miocene-Pliocene,whereas climatic fluctuations have the highest impact during the Pleistocene.

检测番茄BAC序列中paralogs的blastn参数研究

并系同源(paralog)和直系同源(ortholog)是物种进化过程中产生的两种基本的同源序列类型。目前判断ortholog的方法已经基本确立,而paralog的判断却还没有统一的标准。番茄全基因组测序正在进行中,利用Gen-Bank中已有的番茄BAC序列进行一系列不同参数下的比对(blastn),根据比对结果确定了paralog预测的最佳参数,分别是E值为10-40,匹配序列长度为200bp,序列一致率为80%。这些参数值的确定为以后在番茄BAC序列中进行paralog预测提供了适用的参数。

Small ubiquitin-related modifier paralogs are indispensable but functionally redundant during early development of zebrafish

The Small ubiquitin-related modifier （SUMO） conjugation to a variety of proteins regulates diverse cellular processes, including transcription, cell cycle regulation and maintenance of genome integrity. To investigate in vivo biological function of SUMO paralogs, we inactivated them in the early development of zebrafish. While zebrafish embryos deficient for all three SUMO paralogs, as Ubc9-deficient ones, displayed severe defects, loss of individual SUMO paralog was compatible with a normal development. SUMO-deficient embryos can be rescued by a single human or zebrafish SUMO. While key structural basic lysine residues and N-terminal unstructured stretch of SUMO are critical for in vivo rescue, the consensus Kll sumoylation site of SUMO2 is dispensable, implying that chain formation on this potential site is unessential for normal development. Inactivation of all three SUMOs triggered p53- dependent apoptosis and further inactivation of p53 restored normal zebrafish development. Interestingly, we also demonstrate that the dominant negative truncated form of p53, Δ113p53, significantly blunts SUMO depletion-induced p53 activity in vivo. Taken together, our results suggest that SUMO paralogs are indispensable, but redundant, in the early development of zebrafish.

The impact of paralog genes:detection of copy number variation in spinal muscle atrophy patients

Spinal muscular atrophy(SMA)is caused by dysfunction of the alpha motor neurons of the spinal cord.It is an autosomal recessive disease associated to the SMN1 gene,located in the subtelomeric region of 5q13.A paralog SMN2 gene is located at the centromeric region of the same chromosome,which apparently originated by an ancestral inverted duplication occurring only in humans.The exon sequence differs in two nucleotides in exon 7 and exon 8,which leads to an SMN2 transcript that lacks exon 7 and results in a truncated protein.Part(10%)of the SMN2 transcripts avoids the splicing of exon 7 but most of the copies are dysfunctional.In a disease scenario,the more SMN2 copies the higher possibility to restore at least partly the effects of SMN1 deficiency.Some therapeutic approaches are being developed to increase the expression of SMN2.To determine the number of SMN1 and SMN2 copies,the methodology must distinguish accurately between both genes.In this work,we present the results obtained using multiplex ligation-dependent probe amplification(MLPA)in 60 SMA suspected patients/carriers derived from different regions of Argentina.In 32 of these DNA samples we found alterations in SMN1.Among these,16 presented a heterozygous deletion(carrier status)and 14 an homozygous deletion(patient status)in exon 7 and 8 of SMN1.In one case,exon 7 was found homozygously deleted but exon 8 presented a single copy,and in another case,exon 7 was found heterozygously deleted while exon 8 was normal.Almost half of the patients(7/15)presented a normal diploid number of SMN2 while the other half(8/15)presented an increased number.In this work we showed how a probe-based methodology such as MLPA was able to distinguish between the paralog genes and determine the amount of copies in DNA samples from suspected patients/carriers of SMA.

Hox Gene Clusters of Early Vertebrates:Do They Serve as Reliable Markers for Genome Evolution?

Hox genes, responsible for regional specification along the anteroposterior axis in embryogenesis, are found as clusters in most eumetazoan genomes sequenced to date. Invertebrates possess a single Hox gene cluster with some exceptions of secondary cluster breakages, while osteichthyans （bony vertebrates） have multiple Hox clusters. In tetrapods, four Hox clusters, derived from the so-called two-round whole genome duplications （2R-WGDs）, are observed. Overall, the number of Hox gene clusters has been regarded as a reliable marker of ploidy levels in animal genomes. In fact, this scheme also fits the situations in teleost fishes that experienced an additional WGD. In this review, I focus on cyclostomes and cartilaginous fishes as lineages that would fill the gap between invertebrates and osteichthyans. A recent study highlighted a possible loss of the HoxC cluster in the galeomorph shark lineage, while other aspects of cartilaginous fish Hox clusters usually mark their conserved nature. In contrast, existing resources suggest that the cyclostomes exhibit a different mode of Hox cluster organization. For this group of species, whose genomes could have differently responded to the 2R-WGDs from jawed vertebrates, therefore the number of Hox clusters may not serve as a good indicator of their ploidy level.

Genic C-Methylation in Soybean Is Associated with Gene Paralogs Relocated to Transposable Element-Rich Pericentromeres

Most plants are polyploid due to whole-genome duplications （WGD） and can thus have duplicated genes. Following a WGD, paralogs are often fractionated （lost） and few duplicate pairs remain. Little attention has been paid to the role of DNA methylation in the functional divergence of paralogous genes. Using high- resolution methylation maps of accessions of domesticated and wild soybean, we show that in soybean, a recent paleopolyploid with many paralogs, DNA methylation likely contributed to the elimination of ge- netic redundancy of polyploidy-derived gene paralogs. Transcriptionally silenced paralogs exhibit partic- ular genomic features as they are often associated with proximal transposable elements （TEs） and are pref- erentially located in pericentromeres, likely due to gene movement during evolution. Additionally, we provide evidence that gene methylation associated with proximal TEs is implicated in the divergence of expression profiles between orthologous genes of wild and domesticated soybean, and within populations.

Paralog-divergent Features May Help Reduce Off-target Effects of Drugs:Hints from Glucagon Subfamily Analysis

Side effects from targeted drugs remain a serious conccrn. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which arc highly homologous in sequences and have similar structures and drug-binding pockets. To identify targctablc differences between paralogs, we analyzed two types （type-I and type-ll） of functional divergence between two paralogs in the known target protein receptor family G-protein coupled receptors （GPCRs） at the amino acid level. Paralogous protein receptors in glucagon-like subfamily, glucagon receptor （GCGR） and glucagon-like peptide-I receptor （GLP-I R）, exhibit divergence in ligands and are clinically validated drug targets for type 2 diabetes. Our data showed that type-ll alnino acids were significantly enriched in the binding sites of antagonist MK-0893 to GCGR. which had a radical shift in physicochemical properties between GCGR and GLP-1R. We also examined the role of type-I amino acids between GCGR and GLP-IR. The divergent features between GCGR and GLP-I R paralogs may be helpful in their discrimination, thus enabling the identification of binding sites to reduce undesirable side effects and increase the target specificity of drugs.

Evidence that Natural Selection is the Primary Cause of the Guanine-cytosine Content Variation in Rice Genes

Cereal genes are classified into two distinct classes according to the guanine-cytosine （GC） content at the third codon sites （GC3）. Natural selection and mutation bias have been proposed to affect the GC content. However, there has been controversy about the cause of GC variation. Here, we characterized the GC content of 1 092 paralogs and other single-copy genes in the duplicated chromosomal regions of the rice genome （ssp. indica） and classified the paralogs into GC3-rich and GC3-poor groups. By referring to out-group sequences from Arabidopsis and maize, we confirmed that the average synonymous substitution rate of the GC3-rich genes is significantly lower than that of the GC3-poor genes. Furthermore, we explored the other possible factors corresponding to the GC variation including the length of coding sequences, the number of exons in each gene, the number of genes in each family, the location of genes on chromosomes and the protein functions. Consequently, we propose that natural selection rather than mutation bias was the primary cause of the GC variation.