Detection of the HLA-B*40:78 allele in a Taiwanese individual.

One nucleotide substitution in codon 136 of HLA-B*40:02:01:01 results in a novel allele, HLA-B*40:78.

Characterisation of the novel HLA-C*01:262 allele by sequencing-based typing.

HLA-C*01:262 differs from HLA-C*01:02:01:01 by one nucleotide substitution in codon 150 in exon 3.

Characterisation of the novel HLA-DQA1*01:02:24 allele by sequencing-based typing.

HLA-DQA1*01:02:24 differs from HLA-DQA1*01:02:01:03 by one nucleotide substitution in codon 167 in exon 3.

Identification of the novel HLA-B*49:01:01:22 allele in an Indian renal transplant donor by next generation sequencing.

HLA-B*49:01:01:22 differs from HLA-B*49:01:01:01 by a single nucleotide C->G change in intron 5 at gDNA 2451.

MiR-495-3p promotes cardiac hypertrophy by targeting Pum2.

Pathological cardiac hypertrophy (CH) may lead to heart failure and sudden death. MicroRNAs (miRNAs) have been documented to play crucial parts in CH. The objective of this research was to discuss the potential along with molecule mechanism of miR-495-3p in CH. In vivo CH model was induced by aortic banding (AB) in rats. Cellular hypertrophy in H9c2 rat cardiomyocytes was stimulated by angiotensin II (Ang II) treatment. Haematoxylin and eosin (HE), echocardiography and immunofluorescence staining were used to examine the alterations in cardiac function. The outcomes showed that miR-495-3p expression was high in rat model as well as in Ang II-stimulated cardiomyocytes. Besides, silenced miR-495-3p attenuated CH both in vitro and in vivo. Mechanically, miR-495-3p bound to pumilio RNA binding family member 2 (Pum2) 3'UTR and silenced its expression. Rescue assays further notarized that Pum2 silence abrogated the inhibitory impacts of miR-495-3p inhibitor on CH. In a word, the present research uncovered that miR-495-3p promoted CH by targeting Pum2. Therefore, miR-495-3p may be a novel therapeutic molecule for this disease.

Characterisation of the novel HLA-B*18:37:03 allele, first identified in a Brazilian individual.

The novel HLA-B*18:37:03 allele, first described in a potential bone marrow donor from Brazil.

Characterisation of the novel HLA-DQB1*05:305 allele using next-generation sequencing.

HLA-DQB1*05:305 shows one single nucleotide substitution at position 664 compared with HLA-DQB1*05:03:01:01.

Characterisation of the novel HLA-DRB3*02:202 allele by sequencing-based typing.

HLA-DRB3*02:202 differs from DRB3*02:112 by one nucleotide substitution in codon 51 in exon 2.

Characterisation of the novel HLA-A*26:247 allele by sequencing-based typing.

HLA-A*26:247 differs from HLA-A*26:01:01:01 by one nucleotide substitution in codon 245 in exon 4.

Complete genome sequence of an umbravirus from white snakeroot (Ageratina altissima).

Complete genome sequencing of a virus from a white snakeroot plant (Ageratina altissima (L.) King & H. Rob.) collected in the Great Smoky Mountains National Park, USA, revealed a quadricistronic organization resembling that of umbraviruses. ORFs 1 and 2 are putatively translated via a -1 ribosomal frameshift mechanism as a single polypeptide with a role in viral replication, whereas the 3'-proximal and extensively overlapping ORFs 3 and 4 code for proteins involved in long distance trafficing and cell-to-cell movement within the host. Sequence comparisons and phylogenetic analysis strongly suggested that this virus is a previously undescribed member of the genus Umbravirus (family Tombusviridae), for which the name "white snakeroot virus A" (WSVA) is proposed. In addition, we identified and initiated characterization of its possible helper virus, a putative new member of the genus Luteovirus.

Programming gel automata shapes using DNA instructions.

The ability to transform matter between numerous physical states or shapes without wires or external devices is a major challenge for robotics and materials design. Organisms can transform their shapes using biomolecules carrying specific information and localize at sites where transitions occur. Here, we introduce gel automata, which likewise can transform between a large number of prescribed shapes in response to a combinatorial library of biomolecular instructions. Gel automata are centimeter-scale materials consisting of multiple micro-segments. A library of DNA activator sequences can each reversibly grow or shrink different micro-segments by polymerizing or depolymerizing within them. We develop DNA activator designs that maximize the extent of growth and shrinking, and a photolithography process for precisely fabricating gel automata with elaborate segmentation patterns. Guided by simulations of shape change and neural networks that evaluate gel automata designs, we create gel automata that reversibly transform between multiple, wholly distinct shapes: four different letters and every even or every odd numeral. The sequential and repeated metamorphosis of gel automata demonstrates how soft materials and robots can be digitally programmed and reprogrammed with information-bearing chemical signals.

The subcellular distribution of miRNA isoforms, tRNA-derived fragments, and rRNA-derived fragments depends on nucleotide sequence and cell type.

BACKGROUND: MicroRNA isoforms (isomiRs), tRNA-derived fragments (tRFs), and rRNA-derived fragments (rRFs) represent most of the small non-coding RNAs (sncRNAs) found in cells. Members of these three classes modulate messenger RNA (mRNA) and protein abundance and are dysregulated in diseases. Experimental studies to date have assumed that the subcellular distribution of these molecules is well-understood, independent of cell type, and the same for all isoforms of a sncRNA. RESULTS: We tested these assumptions by investigating the subcellular distribution of isomiRs, tRFs, and rRFs in biological replicates from three cell lines from the same tissue and same-sex donors that model the same cancer subtype. In each cell line, we profiled the isomiRs, tRFs, and rRFs in the nucleus, cytoplasm, whole mitochondrion (MT), mitoplast (MP), and whole cell. Using a rigorous mathematical model we developed, we accounted for cross-fraction contamination and technical errors and adjusted the measured abundances accordingly. Analyses of the adjusted abundances show that isomiRs, tRFs, and rRFs exhibit complex patterns of subcellular distributions. These patterns depend on each sncRNA's exact sequence and the cell type. Even in the same cell line, isoforms of the same sncRNA whose sequences differ by a few nucleotides (nts) can have different subcellular distributions. CONCLUSIONS: SncRNAs with similar sequences have different subcellular distributions within and across cell lines, suggesting that each isoform could have a different function. Future computational and experimental studies of isomiRs, tRFs, and rRFs will need to distinguish among each molecule's various isoforms and account for differences in each isoform's subcellular distribution in the cell line at hand. While the findings add to a growing body of evidence that isomiRs, tRFs, rRFs, tRNAs, and rRNAs follow complex intracellular trafficking rules, further investigation is needed to exclude alternative explanations for the observed subcellular distribution of sncRNAs.

Characterisation of the novel HLA-B*51:411 allele by sequencing-based typing.

HLA-B*51:411 differs from HLA-B*51:01:01:01 by one nucleotide substitution in codon 235 in exon 4.

Characterisation of the novel HLA-DPB1*1618:01 allele by sequencing-based typing.

HLA-DPB1*1618:01 differs from HLA-DPB1*18:01:01:01 by one nucleotide substitution in codon 215 in exon 4.

Detection of the HLA-B*51:01:44 allele in a Taiwanese individual.

Nucleotide substitution in codon 221 of HLA-B*51:01:01:01 results in a novel allele, HLA-B*51:01:44.

A novel HLA-DQB1*03 variant allele, HLA-DQB1*03:01:01:64, identified by next-generation sequencing.

The HLA-DQB1*03:01:01:64 allele differs from HLA-DQB1*03:01:01:03 by a single nucleotide substitution in intron 2.

A novel HLA-DQB1*06 variant allele, HLA-DQB1*06:02:01:40, identified by next-generation sequencing.

The HLA-DQB1*06:02:01:40 allele differs from HLA-DQB1*06:02:01:01 by a single nucleotide substitution in intron 2.

Complete genome sequence of lima bean endornavirus 1: a putative new member of the genus Alphaendornavirus (family Endornaviridae).

In this study, we completely sequenced the genome of a new member of the genus Alphaendornavirus, family Endornaviridae, from lima bean (Phaseolus lunatus), for which we propose the name "lima bean endornavirus 1" (LbEV1). The complete genome of LbEV1 consists of 15,265 nucleotides, including a stretch of 12 cytosine residues at its 3' end, and contains a long single open reading frame (ORF) coding for a 4980-aa-long polyprotein. Analysis of the polyprotein sequence revealed the presence of four conserved functional domains (in order from the N- to C-terminus): viral helicase 1, peptidase _C97, glycosyltransferase_GTB-type, and viral RNA-dependent RNA polymerase (RdRP). The LbEV1 polyprotein showed the highest amino acid sequence similarity (63% identity and 98% coverage) to Phaseolus vulgaris endornavirus 3 (PvEV3) and also showed 42% identity (95% coverage) to Geranium carolinianum endornavirus. Phylogenetic analysis based on the viral RdRp domain showed that LbEV1 belongs to a subclade within the genus Alphaendornavirus that includes three other viruses infecting plants of the genus Phaseolus.

Homology-based characterization of the cis-regulatory elements modulate flavone induction of CYP321A1 in Helicoverpa armigera.

Xenobiotic response element (XRE) to flavone was the cis- regulatory elements that mediates the induction of the allelochemical-metabolizing CYP321A1 gene from Helicoverpa zea. However, it was unknown whether the XRE-Fla element existed in other species. Recently we have identified and cloned the CYP321A1 gene with promoter region in a related species, Helicoverpa armigera. Sequence similarity of two orthologous CYP321A1 genes was 97.27%, but the promoter sequence similarity was only 56.32%. Sequence alignment showed the XRE-Fla like element owns three mutations in H. armigera compared with H. zea. Progressive 5' deletions and internal mutation indicated that H. armigera XRE-Fla was the essential element of CYP321A1 gene in response to flavone. XRE-Fla mutations and EMSA analysis confirmed that the H. armigera XRE-Fla element binding factor was stronger than H. zea. The findings indicate the XRE element mutations mainly contribute to the differences between the flavone-induced expressions of two CYP321A1 genes, which improve the flexibility and adaptability for allelochemical response of H. armigera.

A novel HLA-C*07 variant allele, HLA-C*07:01:01:141, identified by next-generation sequencing.

Characterisation of the novel HLA-C*07:01:01:141 allele in a 23-year-old Greek bone marrow donor.