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Genes, Volume 8, Issue 9

2017 September - 27 articles

Cover Story: Zebrafish are an emerging model for cancer research, enabling high-resolution in vivo imaging. Using xenotransplantation of fluorescent glioma cells, we validated the effect of silencing RECQ1 helicase, an enzyme involved in DNA repair and upregulated in some brain tumours, on tumour progression in zebrafish embryos. Measurements of tumour growth in the zebrafish brain confirmed the effects of RECQ1 helicase silencing in experiments in vitro. These results may help improve glioma treatment by targeting DNA-repair in tumour cells. View this paper
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Articles (27)

  • Review
  • Open Access
30 Citations
10,462 Views
29 Pages

Zebrafish in Translational Cancer Research: Insight into Leukemia, Melanoma, Glioma and Endocrine Tumor Biology

  • Aurora Irene Idilli,
  • Francesca Precazzini,
  • Maria Caterina Mione and
  • Viviana Anelli

20 September 2017

Over the past 15 years, zebrafish have emerged as a powerful tool for studying human cancers. Transgenic techniques have been employed to model different types of tumors, including leukemia, melanoma, glioblastoma and endocrine tumors. These models p...

  • Communication
  • Open Access
59 Citations
7,433 Views
18 Pages

Chloroplast Genome Sequence of Clusterbean (Cyamopsis tetragonoloba L.): Genome Structure and Comparative Analysis

  • Tanvi Kaila,
  • Pavan K. Chaduvla,
  • Hukam C. Rawal,
  • Swati Saxena,
  • Anshika Tyagi,
  • S. V. Amitha Mithra,
  • Amolkumar U. Solanke,
  • Pritam Kalia,
  • T. R. Sharma and
  • Kishor Gaikwad
  • + 1 author

19 September 2017

Clusterbean (Cyamopsis tetragonoloba L.), also known as guar, belongs to the family Leguminosae, and is an annual herbaceous legume. Guar is the main source of galactomannan for gas mining industries. In the present study, the draft chloroplast genom...

  • Review
  • Open Access
35 Citations
6,908 Views
24 Pages

Circulating microRNAs and Bioinformatics Tools to Discover Novel Diagnostic Biomarkers of Pediatric Diseases

  • Antonella Baldassarre,
  • Cristina Felli,
  • Giorgio Prantera and
  • Andrea Masotti

19 September 2017

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at the post-transcriptional level. Current studies have shown that miRNAs are also present in extracellular spaces, packaged into various membrane-bound vesicles, or associated...

  • Article
  • Open Access
37 Citations
6,523 Views
20 Pages

Genome-Wide Analysis of the Biosynthesis and Deactivation of Gibberellin-Dioxygenases Gene Family in Camellia sinensis (L.) O. Kuntze

  • Cheng Pan,
  • Kunhong Tian,
  • Qiuyan Ban,
  • Leigang Wang,
  • Qilu Sun,
  • Yan He,
  • Yuanfei Yang,
  • Yuting Pan,
  • Yeyun Li and
  • Changjun Jiang
  • + 1 author

19 September 2017

Gibberellins (GAs), a class of diterpenoid phytohormones, play a key role in regulating diverse processes throughout the life cycle of plants. Bioactive GA levels are rapidly regulated by Gibberellin-dioxygenases (GAox), which are involved in the bio...

  • Article
  • Open Access
18 Citations
6,816 Views
9 Pages

Effects of Cellular Methylation on Transgene Expression and Site-Specific Integration of Adeno-Associated Virus

  • Diptiman Chanda,
  • Jonathan A. Hensel,
  • Jerome T. Higgs,
  • Rajat Grover,
  • Niroop Kaza and
  • Selvarangan Ponnazhagan

18 September 2017

DNA methylation is a major epigenetic event that affects not only cellular gene expression but that also has the potential to influence bacterial and viral DNA in their host-dependent functions. Adeno-associated virus (AAV) genome contains a high deg...

  • Article
  • Open Access
4 Citations
5,461 Views
15 Pages

18 September 2017

DNA shape readout is an important mechanism of transcription factor target site recognition, in addition to the sequence readout. Several machine learning-based models of transcription factor–DNA interactions, considering DNA shape features, have bee...

  • Article
  • Open Access
25 Citations
4,993 Views
13 Pages

Transcription Factors Responding to Pb Stress in Maize

  • Yanling Zhang,
  • Fei Ge,
  • Fengxia Hou,
  • Wenting Sun,
  • Qi Zheng,
  • Xiaoxiang Zhang,
  • Langlang Ma,
  • Jun Fu,
  • Xiujing He and
  • Yaou Shen
  • + 2 authors

18 September 2017

Pb can damage the physiological function of human organs by entering the human body via food-chain enrichment. Revealing the mechanisms of maize tolerance to Pb is critical for preventing this. In this study, a Pb-tolerant maize inbred line, 178, was...

  • Article
  • Open Access
36 Citations
6,054 Views
15 Pages

Salt-Stress Response Mechanisms Using de Novo Transcriptome Sequencing of Salt-Tolerant and Sensitive Corchorus spp. Genotypes

  • Zemao Yang,
  • Ruike Lu,
  • Zhigang Dai,
  • An Yan,
  • Qing Tang,
  • Chaohua Cheng,
  • Ying Xu,
  • Wenting Yang and
  • Jianguang Su

18 September 2017

High salinity is a major environmental stressor for crops. To understand the regulatory mechanisms underlying salt tolerance, we conducted a comparative transcriptome analysis between salt-tolerant and salt-sensitive jute (Corchorus spp.) genotypes i...

  • Article
  • Open Access
41 Citations
6,998 Views
17 Pages

Isoform Sequencing Provides a More Comprehensive View of the Panax ginseng Transcriptome

  • Ick-Hyun Jo,
  • Jinsu Lee,
  • Chi Eun Hong,
  • Dong Jin Lee,
  • Wonsil Bae,
  • Sin-Gi Park,
  • Yong Ju Ahn,
  • Young Chang Kim,
  • Jang Uk Kim and
  • Hojin Ryu
  • + 5 authors

15 September 2017

Korean ginseng (Panax ginseng C.A. Meyer) has been widely used for medicinal purposes and contains potent plant secondary metabolites, including ginsenosides. To obtain transcriptomic data that offers a more comprehensive view of functional genomics...

  • Review
  • Open Access
76 Citations
10,694 Views
21 Pages

Emerging Estrogenic Pollutants in the Aquatic Environment and Breast Cancer

  • Sylvain Lecomte,
  • Denis Habauzit,
  • Thierry D. Charlier and
  • Farzad Pakdel

15 September 2017

The number and amount of man-made chemicals present in the aquatic environment has increased considerably over the past 50 years. Among these contaminants, endocrine-disrupting chemicals (EDCs) represent a significant proportion. This family of compo...

  • Article
  • Open Access
81 Citations
7,792 Views
13 Pages

13 September 2017

Scutellaria baicalensis Georgi (Lamiaceae) is the source of the well-known traditional Chinese medicine “HuangQin” (Radix Scutellariae). Natural sources of S. baicalensis are rapidly declining due to high market demand and overexploitation. Moreover,...

  • Article
  • Open Access
31 Citations
4,867 Views
11 Pages

Identification of the Ovine Keratin-Associated Protein 26-1 Gene and Its Association with Variation in Wool Traits

  • Shaobin Li,
  • Huitong Zhou,
  • Hua Gong,
  • Fangfang Zhao,
  • Jiang Hu,
  • Yuzhu Luo and
  • Jon G. H. Hickford

13 September 2017

Keratin-associated proteins (KAPs) are structural components of wool and hair fibres, and are believed to play a role in defining the physico-mechanical properties of the wool fibre. In this study, the putative ovine homologue of the human KAP26-1 ge...

  • Review
  • Open Access
10 Citations
8,929 Views
15 Pages

Advances in Genomic Profiling and Analysis of 3D Chromatin Structure and Interaction

  • Binhua Tang,
  • Xiaolong Cheng,
  • Yunlong Xi,
  • Zixin Chen,
  • Yufan Zhou and
  • Victor X. Jin

8 September 2017

Recent sequence-based profiling technologies such as high-throughput sequencing to detect fragment nucleotide sequence (Hi-C) and chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) have revolutionized the field of three-dimensiona...

  • Article
  • Open Access
26 Citations
6,251 Views
15 Pages

8 September 2017

The multigene universal stress protein (USP) family is evolutionarily conserved. Members play indispensable roles in plant tolerance to abiotic stresses. Although relatively well-characterized in model plants, such as Arabidopsis thaliana and Oryza s...

  • Article
  • Open Access
34 Citations
6,888 Views
12 Pages

High-Throughput Study of the Effects of Celastrol on Activated Fibroblast-Like Synoviocytes from Patients with Rheumatoid Arthritis

  • Zhengyu Fang,
  • Dongyi He,
  • Bo Yu,
  • Feng Liu,
  • Jianping Zuo,
  • Yuxia Li,
  • Qi Lin,
  • Xiaodong Zhou and
  • Qingwen Wang

6 September 2017

Celastrol, a natural triterpene, exhibits potential anti-inflammatory activity in a variety of inflammatory diseases. The present study aimed to investigate its biological effect on activated fibroblast-like synoviocytes (FLSs) from patients with rhe...

  • Article
  • Open Access
13 Citations
6,196 Views
11 Pages

RECQ1 Helicase Silencing Decreases the Tumour Growth Rate of U87 Glioblastoma Cell Xenografts in Zebrafish Embryos

  • Miloš Vittori,
  • Barbara Breznik,
  • Katja Hrovat,
  • Saša Kenig and
  • Tamara T. Lah

6 September 2017

RECQ1 helicase has multiple roles in DNA replication, including restoration of the replication fork and DNA repair, and plays an important role in tumour progression. Its expression is highly elevated in glioblastoma as compared to healthy brain tiss...

  • Article
  • Open Access
6 Citations
6,208 Views
11 Pages

Quantification of Pseudouridine Levels in Cellular RNA Pools with a Modified HPLC-UV Assay

  • Jialin Xu,
  • Alice Y. Gu,
  • Naresh R. Thumati and
  • Judy M.Y. Wong

5 September 2017

Pseudouridine (Ψ) is the most abundant post-transcriptionally modified ribonucleoside. Different Ψ modifications correlate with stress responses and are postulated to coordinate the distinct biological responses to a diverse panel of cellular stresse...

  • Review
  • Open Access
14 Citations
7,017 Views
17 Pages

Zebrafish Xenograft: An Evolutionary Experiment in Tumour Biology

  • Rachael A. Wyatt,
  • Nhu P. V. Trieu and
  • Bryan D. Crawford

5 September 2017

Though the cancer research community has used mouse xenografts for decades more than zebrafish xenografts, zebrafish have much to offer: they are cheap, easy to work with, and the embryonic model is relatively easy to use in high-throughput assays. Z...

  • Article
  • Open Access
11 Citations
5,718 Views
10 Pages

1 September 2017

The cell microenvironment consists of multiple types of biophysical and biochemical factors, and represents a complex integrated system that is variable in both time and space. Studies show that changes in biochemical and biophysical factors in cell...

  • Article
  • Open Access
28 Citations
9,499 Views
16 Pages

X Chromosome Evolution in Cetartiodactyla

  • Anastasia A. Proskuryakova,
  • Anastasia I. Kulemzina,
  • Polina L. Perelman,
  • Alexey I. Makunin,
  • Denis M. Larkin,
  • Marta Farré,
  • Anna V. Kukekova,
  • Jennifer Lynn Johnson,
  • Natalya A. Lemskaya and
  • Alexander S. Graphodatsky
  • + 5 authors

31 August 2017

The phenomenon of a remarkable conservation of the X chromosome in eutherian mammals has been first described by Susumu Ohno in 1964. A notable exception is the cetartiodactyl X chromosome, which varies widely in morphology and G-banding pattern betw...

  • Article
  • Open Access
17 Citations
6,372 Views
10 Pages

Intrachromosomal Rearrangements in Rodents from the Perspective of Comparative Region-Specific Painting

  • Svetlana A. Romanenko,
  • Natalya A. Serdyukova,
  • Polina L. Perelman,
  • Svetlana V. Pavlova,
  • Nina S. Bulatova,
  • Feodor N. Golenishchev,
  • Roscoe Stanyon and
  • Alexander S. Graphodatsky

30 August 2017

It has long been hypothesized that chromosomal rearrangements play a central role in different evolutionary processes, particularly in speciation and adaptation. Interchromosomal rearrangements have been extensively mapped using chromosome painting....

  • Article
  • Open Access
7 Citations
9,706 Views
10 Pages

29 August 2017

Throughout the last four centuries, many anatomical museums across the world have collected teratological specimens that became precious objects. These can be regarded as spirits of the past which have captured the morphology of diseases through time...

  • Article
  • Open Access
23 Citations
6,474 Views
16 Pages

5′-UTR and 3′-UTR Regulation of MICB Expression in Human Cancer Cells by Novel microRNAs

  • Wipaporn Wongfieng,
  • Amonrat Jumnainsong,
  • Yaovalux Chamgramol,
  • Banchob Sripa and
  • Chanvit Leelayuwat

29 August 2017

The treatment of cancer through the induction of natural killer group 2, member D (NKG2D) ligands is of interest, but understanding of mechanisms controlling expression of individual ligand is limited. The major histocompatibility complex (MHC) class...

  • Article
  • Open Access
19 Citations
5,820 Views
18 Pages

25 August 2017

Auxin Response Factors (ARFs) are at the core of the regulation mechanism for auxin-mediated responses, along with AUX/IAA proteins.They are critical in the auxin-mediated control of various biological responses including development and stress. A wi...

  • Article
  • Open Access
13 Citations
5,404 Views
15 Pages

Two Archaeal RecJ Nucleases from Methanocaldococcus jannaschii Show Reverse Hydrolysis Polarity: Implication to Their Unique Function in Archaea

  • Gang-Shun Yi,
  • Yang Song,
  • Wei-Wei Wang,
  • Jia-Nan Chen,
  • Wei Deng,
  • Weiguo Cao,
  • Feng-Ping Wang,
  • Xiang Xiao and
  • Xi-Peng Liu

24 August 2017

Bacterial nuclease RecJ, which exists in almost all bacterial species, specifically degrades single-stranded (ss) DNA in the 5′ to 3′ direction. Some archaeal phyla, except Crenarchaea, also encode RecJ homologs. Compared with bacterial RecJ, archaea...

  • Article
  • Open Access
16 Citations
5,907 Views
14 Pages

Whole Genome Sequencing Revealed Mutations in Two Independent Genes as the Underlying Cause of Retinal Degeneration in an Ashkenazi Jewish Pedigree

  • Kevin Gustafson,
  • Jacque L. Duncan,
  • Pooja Biswas,
  • Angel Soto-Hermida,
  • Hiroko Matsui,
  • David Jakubosky,
  • John Suk,
  • Amalio Telenti,
  • Kelly A. Frazer and
  • Radha Ayyagari

24 August 2017

Retinitis pigmentosa (RP) causes progressive photoreceptor loss resulting from mutations in over 80 genes. This study identified the genetic cause of RP in three members of a non-consanguineous pedigree. Detailed ophthalmic evaluation was performed i...

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Genes - ISSN 2073-4425