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Jason A Reuter, Damek V Spacek, Reetesh K Pai, Michael P Snyder
Paired DNA and RNA profiling is increasingly employed in genomics research to uncover molecular mechanisms of disease and to explore personal genotype and phenotype correlations. Here, we introduce Simul-seq, a technique for the production of high-quality whole-genome and transcriptome sequencing libraries from small quantities of cells or tissues. We apply the method to laser-capture-microdissected esophageal adenocarcinoma tissue, revealing a highly aneuploid tumor genome with extensive blocks of increased homozygosity and corresponding increases in allele-specific expression...
October 10, 2016: Nature Methods
Manreet Kaur, Deepa Panikkath, Xiaofei Yan, Zhenqiu Liu, Dror Berel, Dalin Li, Eric A Vasiliauskas, Andrew Ippoliti, Marla Dubinsky, David Q Shih, Gil Y Melmed, Talin Haritunians, Phillip Fleshner, Stephan R Targan, Dermot P B McGovern
BACKGROUND: Perianal Crohn's Disease (pCD) is a particularly severe phenotype associated with poor quality of life with a reported prevalence of 12%-40%. Previous studies investigating the etiology of pCD have been limited in the numbers of subjects and the intensity of genotyping. The aim of this study was to identify clinical, serological, and genetic factors associated with pCD. METHODS: We performed a case-control study comparing patients with (pCD+) and without perianal (pCD) involvement in CD; defined as the presence of perianal abscesses or fistulae...
April 2016: Inflammatory Bowel Diseases
Brandon S Carpenter, Renee L Barry, Kristen J Verhey, Benjamin L Allen
GLI transport to the primary cilium and nucleus is required for proper Hedgehog (HH) signaling; however, the mechanisms that mediate these trafficking events are poorly understood. Kinesin-2 motor proteins regulate ciliary transport of cargo, yet their role in GLI protein function remains unexplored. To examine a role for the heterotrimeric KIF3A-KIF3B-KAP3 kinesin-2 motor complex in regulating GLI activity, we performed a series of structure-function analyses using biochemical, cell signaling and in vivo approaches that define novel specific interactions between GLI proteins and two components of this complex, KAP3 and KIF3A...
March 1, 2015: Journal of Cell Science
Pamela Metten, Ovidiu D Iancu, Stephanie E Spence, Nicole A R Walter, Denesa Oberbeck, Christina A Harrington, Alexandre Colville, Shannon McWeeney, Tamara J Phillips, Kari J Buck, John C Crabbe, John K Belknap, Robert J Hitzemann
BACKGROUND: Data from C57BL/6J (B6) × DBA/2J (D2) F2 intercrosses (B6xD2 F2 ), standard and recombinant inbred strains, and heterogeneous stock mice indicate that a reciprocal (or inverse) genetic relationship exists between alcohol consumption and withdrawal severity. Furthermore, some genetic studies have detected reciprocal quantitative trait loci (QTLs) for these traits. We used a novel mouse model developed by simultaneous selection for both high alcohol consumption/low withdrawal and low alcohol consumption/high withdrawal and analyzed the gene expression and genome-wide genotypic differences...
December 2014: Alcoholism, Clinical and Experimental Research
Joost R Broekhuis, Kristen J Verhey, Gert Jansen
Primary cilia are important sensory organelles. They exist in a wide variety of lengths, which could reflect different cell-specific functions. How cilium length is regulated is unclear, but it probably involves intraflagellar transport (IFT), which transports protein complexes along the ciliary axoneme. Studies in various organisms have identified the small, conserved family of ros-cross hybridizing kinases (RCK) as regulators of cilium length. Here we show that Intestinal Cell Kinase (ICK) and MAPK/MAK/MRK overlapping kinase (MOK), two members of this family, localize to cilia of mouse renal epithelial (IMCD-3) cells and negatively regulate cilium length...
2014: PloS One
Branch Craige, George B Witman
Cilia and flagella are assembled and maintained by the motor-driven, bidirectional traffic of large protein complexes in a process termed intraflagellar transport (IFT). In this issue of Developmental Cell, Liang et al. (2014) report that IFT is regulated in part by the phosphorylation status of the kinesin-II subunit FLA8/KIF3B.
September 8, 2014: Developmental Cell
Yinwen Liang, Yunong Pang, Qiong Wu, Zhangfeng Hu, Xue Han, Yisheng Xu, Haiteng Deng, Junmin Pan
The assembly and maintenance of cilia depends on intraflagellar transport (IFT). Activated IFT motor kinesin-II enters the cilium with loaded IFT particles comprising IFT-A and IFT-B complexes. At the ciliary tip, kinesin-II becomes inactivated, and IFT particles are released. Moreover, the rate of IFT entry is dynamically regulated during cilium assembly. However, the regulatory mechanism of IFT entry and loading/unloading of IFT particles remains elusive. We show that the kinesin-II motor subunit FLA8, a homolog of KIF3B, is phosphorylated on the conserved S663 by a calcium-dependent kinase in Chlamydomonas...
September 8, 2014: Developmental Cell
Clayton D Albracht, Katherine C Rank, Steven Obrzut, Ivan Rayment, Susan P Gilbert
KIF3AB is an N-terminal processive kinesin-2 family member best known for its role in intraflagellar transport. There has been significant interest in KIF3AB in defining the key principles that underlie the processivity of KIF3AB in comparison with homodimeric processive kinesins. To define the ATPase mechanism and coordination of KIF3A and KIF3B stepping, a presteady-state kinetic analysis was pursued. For these studies, a truncated murine KIF3AB was generated. The results presented show that microtubule association was fast at 5...
October 3, 2014: Journal of Biological Chemistry
Yang Lu, Qi Wang, Da-Hui Wang, Hong Zhou, Yan-Jun Hu, Wan-Xi Yang
BACKGROUND: Spermatogenesis represents the transformation process at the level of cellular development. KIF3A and KIF3B are believed to play some roles in the assembly and maintenance of flagella, intracellular transport of materials including organelles and proteins, and other unknown functions during this process. During spermatogenesis in Eriocheir sinensis, if the sperm shaping machinery is dependent on KIF3A and KIF3B remains unknown. METHODOLOGY/PRINCIPAL FINDINGS: The cDNA of KIF3A and KIF3B were obtained by designing degenerate primers, 3'RACE, and 5'RACE...
2014: PloS One
Xiaodong Huang, Fang Liu, Changlai Zhu, Jing Cai, Hua Wang, Xinxiu Wang, Song He, Cheng Liu, Li Yao, Zongmei Ding, Yixin Zhang, Tianyi Zhang
BACKGROUND: Human hepatocellular carcinoma (HCC) is one of the most common fatal cancers and an important health problem worldwide, but its mechanism is still unclear. Microtubule (MT) kinesin motor proteins orchestrate a variety of cellular processes (e.g. mitosis, motility and organelle transportation) and have been involved in human carcinogenesis. KIF3B, the kinesin superfamily of proteins (KIFs), plays an important role in the regulation of mitotic progression. AIM: The expression of KIF3B and its involvement in HCC was investigated...
April 2014: Digestive Diseases and Sciences
Hui-Qun Phang, Jing-Ling Hoon, Soak-Kuan Lai, Yukai Zeng, Keng-Hwee Chiam, Hoi-Yeung Li, Cheng-Gee Koh
The kinesin motors are important in the regulation of cellular functions such as protein trafficking, spindle organization and centrosome separation. In this study, we have identified POPX2, a serine-threonine phosphatase, as an interacting partner of the KAP3 subunit of the kinesin-2 motor. The kinesin-2 motor is a heterotrimeric complex composed of KIF3A, KIF3B motor subunits and KAP3, the non-motor subunit, which binds the cargo. Here we report that the phosphatase POPX2 is a negative regulator of the trafficking of N-cadherin and other cargoes; consequently, it markedly influences cell-cell adhesion...
February 15, 2014: Journal of Cell Science
H T Nguyen, M Geens, A Mertzanidou, K Jacobs, C Heirman, K Breckpot, C Spits
Gain of 20q11.21 is a chromosomal abnormality that is recurrently found in human pluripotent stem cells and cancers, strongly suggesting that this mutation confers a proliferative or survival advantage to these cells. In this work we studied three human embryonic stem cell (hESC) lines that acquired a gain of 20q11.21 during in vitro culture. The study of the mRNA gene expression levels of the loci located in the common region of duplication showed that HM13, ID1, BCL2L1, KIF3B and the immature form of the micro-RNA miR-1825 were up-regulated in mutant cells...
February 2014: Molecular Human Reproduction
Judith M Neugebauer, Adam B Cadwallader, Jeffrey D Amack, Brent W Bisgrove, H Joseph Yost
As cells integrate molecular signals from their environment, cell surface receptors require modified proteoglycans for the robust activation of signaling pathways. Heparan sulfate proteoglycans (HSPGs) have long unbranched chains of repetitive disaccharide units that can be sulfated at specific positions by heparan sulfate O-sulfotransferase (OST) families. Here, we show that two members of the 3-OST family are required in distinct signaling pathways to control left-right (LR) patterning through control of Kupffer's vesicle (KV) cilia length and motility...
September 2013: Development
Jarema Malicki, Joseph C Besharse
This review focuses on recent advances in the understanding of kinesin-2 family motors in vertebrate photoreceptor development. Zebrafish photoreceptors develop by the 3rd day of embryogenesis, making it possible to study mutant phenotypes without the use of conditional alleles. Recent work using a zebrafish kif3b mutant allele validates the concept that the heterotrimeric kinesin II motor is generally required for ciliogenesis. In zebrafish photoreceptors, however, loss of kif3b function delays but does not block cilium formation...
December 15, 2012: Vision Research
Xiaowei Yu, Hai Wen, Jianhua Cao, Binbin Sun, Tao Ding, Ming Li, Hao Wu, Long Long, Xinghai Cheng, Guangfei Xu, Feng Zhang
The KIF3 subunit KIF3B was proved to be associated with mitosis. It has been known to be engaged in intracellular transport of neurons. To elucidate the certain expression and biological function in central nervous system, we performed an acute spinal cord contusion injury model in adult rats. Western blot analysis indicated a marked upregulation of KIF3B after spinal cord injury (SCI). Immunohistochemistry revealed wide distribution of KIF3B in spinal cord, including neurons and glial cells. Double immunofluorescent staining for proliferating cell nuclear antigen and phenotype-specific markers showed increases of KIF3B expression in proliferating microglia and astrocytes...
February 2013: Journal of Molecular Neuroscience: MN
Elia Aguado-Fraile, Edurne Ramos, David Sáenz-Morales, Elisa Conde, Ignacio Blanco-Sánchez, Konstantinos Stamatakis, Luis del Peso, Edwin Cuppen, Bernhard Brüne, María Laura García Bermejo
Ischemia/reperfusion (I/R) is at the basis of renal transplantation and acute kidney injury. Molecular mechanisms underlying proximal tubule response to I/R will allow the identification of new therapeutic targets for both clinical settings. microRNAs have emerged as crucial and tight regulators of the cellular response to insults including hypoxia. Here, we have identified several miRNAs involved in the response of the proximal tubule cell to I/R. Microarrays and RT-PCR analysis of proximal tubule cells submitted to I/R mimicking conditions in vitro demonstrated that miR-127 is induced during ischemia and also during reperfusion...
2012: PloS One
Chengtian Zhao, Yoshihiro Omori, Katarzyna Brodowska, Peter Kovach, Jarema Malicki
The differentiation of cilia is mediated by kinesin-driven transport. As the function of kinesins in vertebrate ciliogenesis is poorly characterized, we decided to determine the role of kinesin-2 family motors--heterotrimeric kinesin-II and the homodimeric Kif17 kinesin--in zebrafish cilia. We report that kif17 is largely dispensable for ciliogenesis; kif17 homozygous mutant animals are viable and display subtle morphological defects of olfactory cilia only. In contrast to that, the kif3b gene, encoding a heterotrimeric kinesin subunit, is necessary for cilia differentiation in most tissues, although exceptions exist, and include photoreceptors and a subset of hair cells...
February 14, 2012: Proceedings of the National Academy of Sciences of the United States of America
Ran Dang, Jun-Quan Zhu, Fu-Qing Tan, Wei Wang, Hong Zhou, Wan-Xi Yang
KIF3B is known for maintaining and assembling cilia and flagellum. To date, the function of KIF3B and its relationship with KIF3A during spermiogenesis in the cephalopod Octopus tankahkeei remains unknown. In the present study, we characterized a gene encoding a homologue of rat KIF3B in the O. tankahkeei testis and examined its temporal and spatial expression pattern during spermiogenesis. The cDNA of KIF3B was obtained with degenerate and RACE PCR and the distribution pattern of ot-kif3b were observed with RT-PCR...
May 2012: Molecular Biology Reports
Chiu-Jung Huang, Chih-Cheng Huang, Chih-Chun Chang
The Rnf33/Trim60 gene is temporally transcribed in the preimplantation embryo before being silenced at the blastocyst stage but Rnf33 expression is detected in adult testis of the mouse. The putative RNF33 protein is a tripartite motif (TRIM)/RBCC protein composed of a typical RING zinc finger, a B-box 2, two α-helical coiled-coil segments, and a B30.2 domain. As a first step towards the elucidation of the biologic function of RNF33, we aimed in this study to elucidate proteins that associate with RNF33. RNF33-interacting proteins were first derived by the yeast two-hybrid system followed by co-immunoprecipitation assays...
January 2012: Molecular and Cellular Biochemistry
Xiang-Ming Mao, Rong-Wei Xing, Xiao-Wei Jing, Qi-Zhao Zhou, Qing-Feng Yu, Wen-Bin Guo, Xiao-Qiang Wu, Qing-Jun Chu, Chun-Qiong Feng
OBJECTIVE: To study the differentially expressed genes in asthenospermia to gain a deeper insight into the molecular mechanisms of the disease. METHODS: We analyzed the differentially expressed genes in asthenospermia using GATHER, PANTHER and ToppGene online bioinformatics tools. RESULTS: Our bioinformatics mining and analyses revealed that the differentially expressed genes in asthenospermia played important roles in the cellular protein and macromolecular metabolism, protein modification, cell death, cell apoptosis and apoptosis induction...
August 2011: Zhonghua Nan Ke Xue, National Journal of Andrology
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