Yongqiang Liu

Ocean University of China

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Zeng-jie Yang

Chinese Academy of Medical Sciences & Peking Union Medical College

Renata E. Gordon

Janssen (United States)

Tom Curran

Mercy Research

Larra W. Yuelling

Temple University Health System

Jessica M.Y. Ng

Yale University

Eric H. Lee

Temple University Health System

Fang Du

University of Jinan

Andrey Korshunov

German Cancer Research Center

Stefan M. Pfister

University Hospital Heidelberg

Jinhua Wu

Zhejiang Medicine (China)

Cooperative Institutions

Ocean University of China

Qingdao National Laboratory for Marine Science and Technology

Chinese Academy of Sciences

Chinese Academy of Medical Sciences & Peking Union Medical College

Shanghai Jiao Tong University

Capital Medical University

Chinese Academy of Agricultural Sciences

University of Chinese Academy of Sciences

Ministry of Agriculture and Rural Affairs

Sun Yat-sen University

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Supplementary Figure S2 from Nestin Mediates Hedgehog Pathway Tumorigenesis

Peng Li Eric H. Lee Fang Du Renata E. Gordon Larra W. Yuelling

ptch1-deficient GNPs develop MB upon transplantation

Nestin

10.1158/0008-5472.22411698

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Citations (0)

Supplementary Figure S5 from Nestin Mediates Hedgehog Pathway Tumorigenesis

Peng Li Eric H. Lee Fang Du Renata E. Gordon Larra W. Yuelling

Proliferation and Hh signaling in MB cells at 24hrs after Nestin depletion

Nestin

10.1158/0008-5472.22411689

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Diversity of Pleurostomatid Ciliates: Morphology, Taxonomy and Molecular Phylogeny of Freshwater Isolates Found in a Northern China Wetland, with a Description of Two New Species

Diversity (2024)

Gongaote Zhang Yongqiang Liu Hongbo Pan Yujie Liu Honggang Ma

Ciliates of the order Pleurostomatida play essential functions in microbial food webs from a variety of habitats and have been thought to possess a high level of diversity. Due to undersampling and often absent molecular data, the actual diversity and phylogenetic relationships within this group remain unclarified. To help address this deficiency, a survey of freshwater pleurostomatid ciliates was undertaken in Lake Weishan Wetland, northern China. Here, two new Amphileptus species, Amphileptus sinicus sp. nov. and Amphileptus piscinarius sp. nov., were investigated using modern morphological and molecular techniques. Amphileptus sinicus sp. nov. is characterized by possessing a comparatively large cell size of 330–490 μm, contractile vacuoles on both ventral and dorsal margins, and 8–10 left and 42–61 right kineties. Amphileptus piscinarius sp. nov. is characterized by possessing a cell size of 140–210 μm, a large distinctly developed apical extrusome group, 3–4 contractile vacuoles on the ventral margin, and 6–8 left and 24–28 right kineties. Phylogenetic results based on the 18S rRNA gene data of these two species group them with other congeners, with these data suggesting the genus Amphileptus is paraphyletic.

Paraphyly

Molecular Phylogenetics

10.3390/d16050294

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Citations (1)

Supplementary Figure S7 from Nestin Mediates Hedgehog Pathway Tumorigenesis

Peng Li Eric H. Lee Fang Du Renata E. Gordon Larra W. Yuelling

Nestin expression in human MB

Nestin

10.1158/0008-5472.22411683.v1

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Citations (0)

Additional file 5 of Frameshift and wild-type proteins are often highly similar because the genetic code and genomes were optimized for frameshift tolerance

Figshare (2022)

Xiaolong Wang Quanjiang Dong Gang Chen Jianye Zhang Yongqiang Liu

Additional file 5: Table S5. FSSs of different usages of codon pairs. (1) The summary of codon pair usages and their weighted mean FSSs (Table 7). (2) The codon pair usages and their weighted mean FSSs of humans. (3) The codon pair usages and their weighted mean FSSs of mouse. (4) The codon pair usages and their weighted mean FSSs of xenopus. (5) The codon pair usages and their weighted mean FSSs of zebrafish. (6) The codon pair usages and their weighted mean FSSs of fruit fly. (7) The codon pair usages and their weighted mean FSSs of nematode. (8) The codon pair usages and their weighted mean FSSs of Arabidopsis. (9) The codon pair usages and their weighted mean FSSs of yeast. (10) The codon pair usages and their weighted mean FSSs of E. coli. (11) The equal codon pair usages and their weighted mean FSSs.

Code (set theory)

10.6084/m9.figshare.19976804

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Supplementary Figure S4 from Nestin Mediates Hedgehog Pathway Tumorigenesis

Peng Li Eric H. Lee Fang Du Renata E. Gordon Larra W. Yuelling

Nestin knockdown in MB cells by Nestin shRNA

Nestin

10.1158/0008-5472.22411692

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Figure S2 from Astrocytes Promote Medulloblastoma Progression through Hedgehog Secretion

Yongqiang Liu Larra W. Yuelling Yuan Wang Fang Du Renata E. Gordon

MB cells can not maintain Gli1 expression in vitro

10.1158/0008-5472.22415867

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Supplementary Figure S1 from Nestin Mediates Hedgehog Pathway Tumorigenesis

Peng Li Eric H. Lee Fang Du Renata E. Gordon Larra W. Yuelling

Nestin expression in Hh type MB

Nestin

10.1158/0008-5472.22411701

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Citations (0)

Study on time-varying viscosity of cement and sodium silicate grout under seawater condition

Construction and Building Materials (2020)

P. Li C.Q. Wang Guoxi Fan Yongqiang Liu Jie Xiong

Grout

10.1016/j.conbuildmat.2020.121223

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Citations (18)

Frameshift and wild-type proteins are highly similar because the genetic code and genomes were optimized for frameshift tolerance

bioRxiv (Cold Spring Harbor Laboratory) (2016)

Xiaolong Wang Quanjiang Dong Gang Chen Jianye Zhang Yongqiang Liu

Abstract Frameshift protein sequences encoded by alternative reading frames of coding genes have been considered meaningless, and frameshift mutations have been considered of little importance for the molecular evolution of coding genes and proteins. However, functional frameshifts have been found widely existing. It was puzzling how a frameshift protein kept its structure and functionality while its amino-acid sequence was changed substantially. Here we show that frame similarities between frameshifts and wild types are higher than random similarities and are defined at the genetic code, gene, and genome levels. In the standard genetic code, frameshift codon substitutions are more conservative than random substitutions. The frameshift tolerability of the standard genetic code ranks in the top 2.0-3.5% of alternative genetic codes, showing that the genetic code is nearly optimal for frameshift tolerance. Furthermore, frameshift-resistant codons (codon pairs) appear more frequently than expected in many genes and certain genomes, showing that the frameshift optimality is reflected not only in the genetic code but more importantly, in its allowance of further optimizing the frameshift tolerance of a particular gene or genome, which shed light on the role of frameshift mutations in molecular and genomic evolution.

Genetic Code

Stop codon

Translational frameshift

Coding region

10.1101/067736

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Citations (10)