Full-length cDNA sequences from Rhesus monkey placenta tissue: analysis and utility for comparative mapping

<p>Abstract</p> <p>Background</p> <p>Rhesus monkeys (<it>Macaca mulatta</it>) are widely-used as experimental animals in biomedical research and are closely related to other laboratory macaques, such as cynomolgus monkeys (<it>Macaca </it><it>fascicularis</it>), and to humans, sharing a last common ancestor from about 25 million years ago. Although rhesus monkeys have been studied extensively under field and laboratory conditions, research has been limited by the lack of genetic resources. The present study generated placenta full-length cDNA libraries, characterized the resulting expressed sequence tags, and described their utility for comparative mapping with human RefSeq mRNA transcripts.</p> <p>Results</p> <p>From rhesus monkey placenta full-length cDNA libraries, 2000 full-length cDNA sequences were determined and 1835 rhesus placenta cDNA sequences longer than 100 bp were collected. These sequences were annotated based on homology to human genes. Homology search against human RefSeq mRNAs revealed that our collection included the sequences of 1462 putative rhesus monkey genes. Moreover, we identified 207 genes containing exon alterations in the coding region and the untranslated region of rhesus monkey transcripts, despite the highly conserved structure of the coding regions. Approximately 10% (187) of all full-length cDNA sequences did not represent any public human RefSeq mRNAs. Intriguingly, two rhesus monkey specific exons derived from the transposable elements of AluYRa2 (SINE family) and MER11B (LTR family) were also identified.</p> <p>Conclusion</p> <p>The 1835 rhesus monkey placenta full-length cDNA sequences described here could expand genomic resources and information of rhesus monkeys. This increased genomic information will greatly contribute to the development of evolutionary biology and biomedical research.</p

The enhancer activity of long interspersed nuclear element derived microRNA 625 induced by NF-κB

Transposable elements (TEs) are DNA sequences that cut or introduced into the genome, and they represent a massive portion of the human genome. TEs generate a considerable number of microRNAs (miRNAs) are derived from TEs (MDTEs). Numerous miRNAs are related to cancer, and hsa-miRNA-625 is a well-known oncomiR derived from long interspersed nuclear elements (LINEs). The relative expression of hsa-miRNA-625-5p differs in humans, chimpanzees, crab-eating monkeys, and mice, and four primers were designed against the 3′UTR of GATAD2B to analyze the different quantities of canonical binding sites and the location of miRNA binding sites. Luciferase assay was performed to score for the interaction between hsa-miRNA-625 and the 3′UTR of GATAD2B, while blocking NF-κB. In summary, the different numbers of canonical binding sites and the locations of miRNA binding sites affect gene expression, and NF-κB induces the enhancer activity of hsa-miRNA-625-5p by sharing the binding sites

Suppression of magnetic ordering in XXZ-type antiferromagnetic monolayer NiPS3

How a certain ground state of complex physical systems emerges, especially in two-dimensional materials, is a fundamental question in condensed-matter physics. A particularly interesting case is systems belonging to the class of XY Hamiltonian where the magnetic order parameter of conventional nature is unstable in two-dimensional materials leading to a Berezinskii-Kosterlitz-Thouless transition. Here, we report how the XXZ-type antiferromagnetic order of a magnetic van der Waals material, NiPS3, behaves upon reducing the thickness and ultimately becomes unstable in the monolayer limit. Our experimental data are consistent with the findings based on renormalization group theory that at low temperatures a two-dimensional XXZ system behaves like a two-dimensional XY one, which cannot have a long-range order at finite temperatures. This work provides experimental examination of the XY magnetism in the atomically thin limit and opens new opportunities of exploiting these fundamental theorems of magnetism using magnetic van der Waals materials.Comment: 57 pages, 24 figures (including Supplementary Information

Selection of internal reference genes for SYBR green qRT-PCR studies of rhesus monkey (Macaca mulatta) tissues

<p>Abstract</p> <p>Background</p> <p>The rhesus monkey (<it>Macaca mulatta</it>) is a valuable and widely used model animal for biomedical research. However, quantitative analyses of rhesus gene expression profiles under diverse experimental conditions are limited by a shortage of suitable internal controls for the normalization of mRNA levels. In this study, we used a systematic approach for the selection of potential reference genes in the rhesus monkey and compared their suitability to that of the corresponding genes in humans.</p> <p>Results</p> <p>Eight housekeeping genes (HKGs) (<it>GAPDH, SDHA, ACTB, RPL13A, RPL32, UBA52, PGK1Y</it>, and <it>YWHAZ</it>) from rhesus monkeys and humans were selected to test for normalization of expression levels in six different tissue types (brain, colon, kidney, liver, lung, and stomach). Their stability and suitability as reference genes were validated by <it>geNorm</it>, <it>NormFinder </it>and <it>BestKeeper </it>programs. Intriguingly, <it>RPL13A </it>and <it>RPL32 </it>were selected as ideal reference genes only in rhesus monkeys.</p> <p>Conclusion</p> <p>The results clearly indicated the necessity of using different reference genes for normalization of expression levels between rhesus monkeys and humans in various tissues.</p

Relationship between the Retinal Thickness Analyzer and the GDx VCC Scanning Laser Polarimeter, Stratus OCT Optical Coherence Tomograph, and Heidelberg Retina Tomograph II Confocal Scanning Laser Ophthalmoscopy

PURPOSE: To assess the relationship between the retinal thickness analyzer (RTA) parameters, and those of the GDx VCC scanning laser polarimeter (GDx VCC), Stratus OCT optical coherence tomography (Stratus OCT), and Heidelberg retinal tomograph II confocal scanning laser ophthalmoscopy (HRT II). METHODS: Twenty-nine primary open-angle glaucoma patients were retrospectively included in this study. Measurements were obtained using the RTA, GDx VCC, Stratus OCT, and HRT II. We calculated the correlation coefficients between the parameters of RTA and those of the other studies. RESULTS: Among the optic disc parameters of RTA, the cup volume was best correlated with Stratus OCT (R=0.780, p<0.001) and HRT II (R=0.896, p<0.001). Among the posterior pole retinal thickness parameters, the posterior pole abnormally thin area (PPAT) of the RTA and the inferior average of the GDx VCC were best correlated (R=-0.596, p=0.001). The PPAT of the RTA and the inferior maximum of the Stratus OCT were best correlated (R=-0.489, p=0.006). The perifoveal minimum thickness (PFMT) of the RTA and the cup shape measurement of the HRT II were best correlated (R=-0.565, p=0.004). CONCLUSIONS: Many RTA optic disc parameters were significantly correlated with those of the Stratus OCT and HRT II. The RTA posterior pole retinal thickness parameters were significantly correlated with those of the GDx VCC, Stratus OCT and HRT II. The RTA optic disc and posterior pole retinal thickness parameters may be valuable in the diagnosis of glaucomaope

Intron Retention and TE Exonization Events in ZRANB2

The Zinc finger, RAN-binding domain-containing protein 2 (ZRANB2), contains arginine/serine-rich (RS) domains that mediate its function in the regulation of alternative splicing. The ZRANB2 gene contains 2 LINE elements (L3b, Plat L3) between the 9th and 10th exons. We identified the exonization event of a LINE element (Plat L3). Using genomic PCR, RT-PCR amplification, and sequencing of primate DNA and RNA samples, we analyzed the evolutionary features of ZRANB2 transcripts. The results indicated that 2 of the LINE elements were integrated in human and all of the tested primate samples (hominoids: 3 species; Old World monkey: 8 species; New World monkey: 6 species; prosimian: 1 species). Human, rhesus monkey, crab-eating monkey, Africangreen monkey, and marmoset harbor the exon derived from LINE element (Plat L3). RT-PCR amplification revealed the long transcripts and their differential expression patterns. Intriguingly, these long transcripts were abundantly expressed in Old World monkey lineages (rhesus, crab-eating, and African-green monkeys) and were expressed via intron retention (IR). Thus, the ZRANB2 gene produces 3 transcript variants in which the Cterminus varies by transposable elements (TEs) exonization and IR mechanisms. Therefore, ZRANB2 is valuable for investigating the evolutionary mechanisms of TE exonization and IR during primate evolution