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Genes, Volume 8, Issue 4

2017 April - 22 articles

Cover Story: "Bambara groundnut (Vigna subterranea (L.) Verdc.) is an African drought-tolerant legume, grown widely at low levels in sub-Saharan Africa. Khan et al. use a soybean microarray to evaluate leaf gene expression. ‘Nodal’ points are identified through a co-expression network analysis—probably transcription factors that turn on a cascade of genes. Genotypic differences were observed, and there is also initial intriguing evidence that bambara groundnut may be ‘primed’ for drought stress." View this paper
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Articles (22)

  • Article
  • Open Access
14 Citations
5,961 Views
25 Pages

Gene Expression Analysis before and after Treatment with Adalimumab in Patients with Ankylosing Spondylitis Identifies Molecular Pathways Associated with Response to Therapy

  • Marzia Dolcino,
  • Elisa Tinazzi,
  • Andrea Pelosi,
  • Giuseppe Patuzzo,
  • Francesca Moretta,
  • Claudio Lunardi and
  • Antonio Puccetti

24 April 2017

The etiology of Ankylosing spondylitis (AS) is still unknown and the identification of the involved molecular pathogenetic pathways is a current challenge in the study of the disease. Adalimumab (ADA), an anti-tumor necrosis factor (TNF)-alpha agent,...

(This article belongs to the Section Human Genomics and Genetic Diseases)
  • Brief Report
  • Open Access
6 Citations
5,704 Views
10 Pages

Functional Analysis of the rs774872314, rs116171003, rs200231898 and rs201107751 Polymorphisms in the Human RORγT Gene Promoter Region

  • Marcin Ratajewski,
  • Marcin Słomka,
  • Kaja Karaś,
  • Marta Sobalska-Kwapis,
  • Małgorzata Korycka-Machała,
  • Anna Sałkowska,
  • Jarosław Dziadek,
  • Dominik Strapagiel and
  • Jarosław Dastych

21 April 2017

RAR-related orphan receptor gamma RORγT, a tissue-specific isoform of the RORC gene, plays a critical role in the development of naive CD4+ cells into fully differentiated Th17 lymphocytes. Th17 lymphocytes are part of the host defense against numero...

(This article belongs to the Section Human Genomics and Genetic Diseases)
  • Review
  • Open Access
29 Citations
8,610 Views
19 Pages

20 April 2017

The etiology and pathophysiology of type 1 diabetes remain largely elusive with no established concepts for a causal therapy. Efforts to clarify genetic susceptibility and screening for environmental factors have identified the vitamin D system as a...

(This article belongs to the Special Issue Genetics and Functional Genomics of Diabetes Mellitus)
  • Article
  • Open Access
38 Citations
8,765 Views
18 Pages

K-mer Content, Correlation, and Position Analysis of Genome DNA Sequences for the Identification of Function and Evolutionary Features

  • Aaron Sievers,
  • Katharina Bosiek,
  • Marc Bisch,
  • Chris Dreessen,
  • Jascha Riedel,
  • Patrick Froß,
  • Michael Hausmann and
  • Georg Hildenbrand

19 April 2017

In genome analysis, k-mer-based comparison methods have become standard tools. However, even though they are able to deliver reliable results, other algorithms seem to work better in some cases. To improve k-mer-based DNA sequence analysis and compar...

(This article belongs to the Section Technologies and Resources for Genetics)
  • Review
  • Open Access
75 Citations
14,344 Views
20 Pages

19 April 2017

Over 35 years ago, c-MYC, a highly pleiotropic transcription factor that regulates hepatic cell function, was identified. In recent years, a considerable increment in the number of publications has significantly shifted the way that the c-MYC functio...

(This article belongs to the Special Issue MYC Networks)
  • Article
  • Open Access
53 Citations
8,821 Views
20 Pages

19 April 2017

Notopterygium H. de Boissieu (Apiaceae) is an endangered perennial herb endemic to China. A good knowledge of phylogenetic evolution and population genomics is conducive to the establishment of effective management and conservation strategies of the...

(This article belongs to the Special Issue Evolution and Biodiversity of the Plant Genome Architecture)
  • Article
  • Open Access
33 Citations
6,871 Views
19 Pages

A Transcriptomic Comparison of Two Bambara Groundnut Landraces under Dehydration Stress

  • Faraz Khan,
  • Hui Hui Chai,
  • Ishan Ajmera,
  • Charlie Hodgman,
  • Sean Mayes and
  • Chungui Lu

18 April 2017

The ability to grow crops under low-water conditions is a significant advantage in relation to global food security. Bambara groundnut is an underutilised crop grown by subsistence farmers in Africa and is known to survive in regions of water deficit...

(This article belongs to the Section Plant Genetics and Genomics)
  • Review
  • Open Access
25 Citations
10,343 Views
11 Pages

MYC, Cell Competition, and Cell Death in Cancer: The Inseparable Triad

  • Simone Di Giacomo,
  • Manuela Sollazzo,
  • Simona Paglia and
  • Daniela Grifoni

17 April 2017

Deregulation of MYC family proteins in cancer is associated with a global reprogramming of gene expression, ultimately promoting glycolytic pathways, cell growth, and proliferation. It is well known that MYC upregulation triggers cell-autonomous apop...

(This article belongs to the Special Issue MYC Networks)
  • Article
  • Open Access
58 Citations
7,182 Views
16 Pages

Identification of Drought-Responsive MicroRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing

  • Yue Li,
  • Liqiang Wan,
  • Shuyi Bi,
  • Xiufu Wan,
  • Zhenyi Li,
  • Jing Cao,
  • Zongyong Tong,
  • Hongyu Xu,
  • Feng He and
  • Xianglin Li

13 April 2017

Alfalfa, an important forage legume, is an ideal crop for sustainable agriculture and a potential crop for bioenergy resources. Drought, one of the most common environmental stresses, substantially affects plant growth, development, and productivity....

(This article belongs to the Section Plant Genetics and Genomics)
  • Review
  • Open Access
19 Citations
8,168 Views
24 Pages

11 April 2017

The transcription factor and cell growth regulator MYC is potently oncogenic and estimated to contribute to most cancers. Decades of attempts to therapeutically target MYC directly have not resulted in feasible clinical applications, and efforts have...

(This article belongs to the Special Issue MYC Networks)
  • Review
  • Open Access
12 Citations
11,657 Views
13 Pages

Eukaryotic Replicative Helicase Subunit Interaction with DNA and Its Role in DNA Replication

  • Matthew P. Martinez,
  • Amanda L. Wacker,
  • Irina Bruck and
  • Daniel L. Kaplan

6 April 2017

The replicative helicase unwinds parental double-stranded DNA at a replication fork to provide single-stranded DNA templates for the replicative polymerases. In eukaryotes, the replicative helicase is composed of the Cdc45 protein, the heterohexameri...

(This article belongs to the Special Issue Protein-DNA Interactions)
  • Review
  • Open Access
164 Citations
20,345 Views
23 Pages

5 April 2017

c-MYC is one of the most essential transcriptional factors, regulating a diverse array of cellular functions, including proliferation, growth, and apoptosis. Dysregulation of c-MYC is essential in the pathogenesis of a number of B-cell lymphomas, but...

(This article belongs to the Special Issue MYC Networks)
  • Review
  • Open Access
18 Citations
7,985 Views
20 Pages

Role of MYC in B Cell Lymphomagenesis

  • Petra Korać,
  • Snježana Dotlić,
  • Maja Matulić,
  • Matea Zajc Petranović and
  • Mara Dominis

4 April 2017

B cell lymphomas mainly arise from different developmental stages of B cells in germinal centers of secondary lymphoid tissue. There are a number of signaling pathways that affect the initiation and development of B cell lymphomagenesis. The function...

(This article belongs to the Special Issue MYC Networks)
  • Review
  • Open Access
32 Citations
15,311 Views
20 Pages

Targeting MYC Dependence by Metabolic Inhibitors in Cancer

  • Himalee S. Sabnis,
  • Ranganatha R. Somasagara and
  • Kevin D. Bunting

31 March 2017

Abstract: MYC is a critical growth regulatory gene that is commonly overexpressed in a wide range of cancers. Therapeutic targeting of MYC transcriptional activity has long been a goal, but it has been difficult to achieve with drugs that directly bl...

(This article belongs to the Special Issue MYC Networks)
  • Review
  • Open Access
163 Citations
18,431 Views
27 Pages

The MYCN Protein in Health and Disease

  • María Victoria Ruiz-Pérez,
  • Aine Brigette Henley and
  • Marie Arsenian-Henriksson

30 March 2017

MYCN is a member of the MYC family of proto-oncogenes. It encodes a transcription factor, MYCN, involved in the control of fundamental processes during embryonal development. The MYCN protein is situated downstream of several signaling pathways promo...

(This article belongs to the Special Issue MYC Networks)
  • Review
  • Open Access
16 Citations
7,454 Views
12 Pages

Anatomy of Mammalian Replication Domains

  • Shin-ichiro Takebayashi,
  • Masato Ogata and
  • Katsuzumi Okumura

28 March 2017

Genetic information is faithfully copied by DNA replication through many rounds of cell division. In mammals, DNA is replicated in Mb-sized chromosomal units called “replication domains.” While genome-wide maps in multiple cell types and disease stat...

(This article belongs to the Special Issue DNA Replication Controls)
  • Article
  • Open Access
81 Citations
8,223 Views
25 Pages

28 March 2017

Sucrose synthase (SS) is widely considered as the key enzyme involved in the plant sugar metabolism that is critical to plant growth and development, especially quality of the fruit. The members of SS gene family have been identified and characterize...

(This article belongs to the Section Plant Genetics and Genomics)
  • Review
  • Open Access
57 Citations
11,379 Views
24 Pages

DNA Replication Origins and Fork Progression at Mammalian Telomeres

  • Mitsunori Higa,
  • Masatoshi Fujita and
  • Kazumasa Yoshida

28 March 2017

Telomeres are essential chromosomal regions that prevent critical shortening of linear chromosomes and genomic instability in eukaryotic cells. The bulk of telomeric DNA is replicated by semi-conservative DNA replication in the same way as the rest o...

(This article belongs to the Special Issue DNA Replication Controls)
  • Review
  • Open Access
18 Citations
7,443 Views
27 Pages

24 March 2017

Duchenne muscular dystrophy (DMD) is caused by defects in the DMD gene and results in progressive wasting of skeletal and cardiac muscle due to an absence of functional dystrophin. Cardiomyopathy is prominent in DMD patients, and contributes signific...

(This article belongs to the Special Issue Therapeutic Alternative Splicing: Mechanisms and Applications)
  • Communication
  • Open Access
33 Citations
6,706 Views
10 Pages

Development of 44 Novel Polymorphic SSR Markers for Determination of Shiitake Mushroom (Lentinula edodes) Cultivars

  • Hwa-Yong Lee,
  • Suyun Moon,
  • Donghwan Shim,
  • Chang Pyo Hong,
  • Yi Lee,
  • Chang-Duck Koo,
  • Jong-Wook Chung and
  • Hojin Ryu

24 March 2017

The shiitake mushroom (Lentinula edodes) is one of the most popular edible mushrooms in the world and has attracted attention for its value in medicinal and pharmacological uses. With recent advanced research and techniques, the agricultural cultivat...

(This article belongs to the Section Molecular Genetics and Genomics)
  • Review
  • Open Access
30 Citations
10,898 Views
19 Pages

Modeling and Targeting MYC Genes in Childhood Brain Tumors

  • Sonja Hutter,
  • Sara Bolin,
  • Holger Weishaupt and
  • Fredrik J. Swartling

23 March 2017

Brain tumors are the second most common group of childhood cancers, accounting for about 20%–25% of all pediatric tumors. Deregulated expression of the MYC family of transcription factors, particularly c-MYC and MYCN genes, has been found in many of...

(This article belongs to the Special Issue MYC Networks)
  • Article
  • Open Access
52 Citations
9,761 Views
15 Pages

23 March 2017

Smokeless tobacco (ST) products vary significantly in their oral carcinogenicity. Much is known about the differences in the chemical, but not the bacterial, constituents of these products. In this study, we explored the composition and function of t...

(This article belongs to the Section Microbial Genetics and Genomics)
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Genes - ISSN 2073-4425