The systematic position of Fritillaria hupehensis has been in dispute. Phylogentic analyses were conducted on sequences of ITS, rpl16, matK sequences for species of F. hupehensis and allies. Lilium davidii was designed as outgroup. The analyses were performed using MP and ML methods. Conclusions could be achieved as follow. The topologies of MP and ML are consistent. The samples of F. hepehensis from different places form a supported clade with a strong bootstrap. And then form a strongly supported clade with F. anhuiensis, F. monantha. The results suggests that although F. hupehensis has a closet relation with the two ones, it exists some difference.
DNA, Plant ; chemistry ; genetics ; DNA, Ribosomal Spacer ; genetics ; Endoribonucleases ; genetics ; Fritillaria ; classification ; genetics ; Molecular Sequence Data ; Nucleotidyltransferases ; genetics ; Phylogeny ; Plant Leaves ; genetics ; Ribosomal Proteins ; genetics ; Sequence Analysis, DNA ; Species Specificity

OBJECTIVETo study the phylogeny relationship and molecular identification of 10 species from Huperzia (Huperziaceae) based on matK gene sequences data.

METHODTotal DNA of nine species from Huperzia was extracted; matK gene sequence was amplified by PCR. PCR product was directly sequenced after purification.

RESULTThe chloroplast matK gene nucleotide sequences from 9 species of Huperzia species were sequenced. The matK gene nucleotide sequences length was 1 589 bp. Analysis with Huperzia lucidula matK gene nucleotide sequences (download from GenBank) and taking Lycopodiella cernua as outgroup, Maximum Parsimony, Neighbor-Joining analyses and genetic distances were conducted using MEGA 3.1 software. 35 variable sites and 35 parsimony informative sites have been found. Pairwise genetic distances among 10 species of Huperzia was 1.59% - 0.25%.

CONCLUSIONThe results were consistent with the taxonomy in morphological of Huperzia. But H. longipetiolata and H. serrata were resolved into in different clade. There are 19 different sites of matK gene sequences between H. longipetiolata and H. serrata, the genetic distances is 0.121%. It is suggested H. longipetiolata should be as an independent species.

DNA, Chloroplast ; genetics ; DNA, Plant ; chemistry ; genetics ; Endoribonucleases ; genetics ; Huperzia ; classification ; enzymology ; genetics ; Molecular Sequence Data ; Nucleotidyltransferases ; genetics ; Phylogeny ; Plant Proteins ; genetics ; Plants, Medicinal ; classification ; enzymology ; genetics ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; Species Specificity

The study of antiviral pathways to reveal methods for the effective response and clearance of virus is closely related to understanding interferon (IFN) signaling and its downstream target genes, IFN-stimulated genes. One of the key antiviral factors induced by IFNs, 2'-5' oligoadenylate synthase (OAS), is a well-known molecule that regulates the early phase of viral infection by degrading viral RNA in combination with RNase L, resulting in the inhibition of viral replication. In this review, we describe OAS family proteins from a different point of view from that of previous reviews. We discuss not only RNase L-dependent (canonical) and -independent (noncanonical) pathways but also the possibility of the OAS family members as biomarkers for various diseases and clues to non-immunological functions based on recent studies. In particular, we focus on OASL, a member of the OAS family that is relatively less well understood than the other members. We will explain its anti- and pro-viral dual roles as well as the diseases related to single-nucleotide polymorphisms in the corresponding gene.
2',5'-Oligoadenylate Synthetase/*genetics/*metabolism ; Animals ; Biomarkers ; *Disease Susceptibility ; Endoribonucleases/metabolism ; Genetic Predisposition to Disease ; Humans ; Multigene Family ; Polymorphism, Single Nucleotide ; Signal Transduction

AIMTo provide more molecular evidences for species relationship between Chuanxiong (Ligusticum chuanxiong Hort.) from China and Japanese Chuanxiong (Senkyu in Japanese) (Cnidium officinale Makino).

METHODSTo sequence such two genes as internal transcribed spacer (ITS) from nuclear rDNA and maturase for lysine (matK) in tRNA(lys) (UUU) intron from chloroplast DNA of both Ligusticum chuanxiong and Cnidium officinale using PCR direct sequencing and to analyze the sequence variation of two genes between these two species.

RESULTSThe matK gene sequence of Ligusticum chuanxiong and Cnidium officinale is 1268 bp in length, coding 422 amino acids of maturase protein. ITS gene sequence 699 bp, consisting of 54 bp of 18S rRNA-3', 215 bp of ITS1, 162 bp of 5.8S rRNA, 222 bp of ITS2, 46 bp of 26S rRNA-5'. Multiple sequence alignment shows that the sequence of two genes between dried crude drug and fresh voucher material of Ligusticum chuanxiong and Cnidium officinale, there is 1 variable site (T-->C) in matK (upstream at 595 nt) and ITS (ITS1 at 54 nt) between Ligusticum chuanxiong and Cnidium officinale.

CONCLUSIONBased on homology analysis of two genes plastid matK and nuclear ITS, the origin of Chuanxiong from China and Japan ought to be identical, the scientific name Cnidium officinale of Japanese Chuanxiong should be changed to Ligusticum chuanxiong.

Amino Acid Sequence ; Base Sequence ; China ; Cnidium ; genetics ; DNA, Plant ; analysis ; DNA, Ribosomal Spacer ; genetics ; Endoribonucleases ; genetics ; Japan ; Ligusticum ; genetics ; Molecular Sequence Data ; Nucleotidyltransferases ; genetics ; Phylogeny ; RNA, Ribosomal, 18S ; genetics ; Sequence Analysis ; Sequence Homology ; Terminology as Topic

To efficiently produce non-specific nuclease (NU) of Serratia marcescens through recombinant overexpression approach and to characterize the purified NU. The nuclease gene was amplified from the genomic DNA of Serratia marcescens by PCR and fused into vector pMAL-c4X with maltose binding protein (MBP) tag. The recombinant vector verified by DNA sequencing was transformed into Escherichia coli BL21. The expressed MBP-NU was purified through the amylose resin and its catalytic characters were analyzed. The results showed the NU gene had 97% identities with the reported S. marcescens nuclease gene and intracellularly expressed in E. coli BL21. The optimal expression conditions were 37 degrees C, 0.75 mmol/L IPTG with 1.5 h induction. The purified MBP-NU exhibited non-specific nuclease activity, able to degrade various nucleic acids, including RNA, single-stranded DNA and double-stranded DNA that was circular or linear. Its optimal temperature was 37 degrees C and optimal pH 8.0. From 1 L culture broth 10.8 mg NU could be purified with a specific activity of 1.11x10(6) U/mg. The catalytic activity of NU was not inhibited by reagents such as EDTA (0.5 mmol/L), PMSF (1 mmol/L) and KCl (150 mmol/L) commonly used in protein purification.
Base Sequence ; Endodeoxyribonucleases ; biosynthesis ; genetics ; Endoribonucleases ; biosynthesis ; genetics ; Escherichia coli ; genetics ; metabolism ; Maltose-Binding Proteins ; genetics ; Molecular Sequence Data ; Recombinant Fusion Proteins ; biosynthesis ; genetics ; isolation & purification ; Serratia marcescens ; enzymology

The aim of this study was to analyze the use of 12 single-nucleotide polymorphisms in genes ELAC2, RNASEL and MSR1 as biomarkers for prostate cancer (PCa) detection and progression, as well as perform a genetic classification of high-risk patients. A cohort of 451 men (235 patients and 216 controls) was studied. We calculated means of regression analysis using clinical values (stage, prostate-specific antigen, Gleason score and progression) in patients and controls at the basal stage and after a follow-up of 72 months. Significantly different allele frequencies between patients and controls were observed for rs1904577 and rs918 (MSR1 gene) and for rs17552022 and rs5030739 (ELAC2). We found evidence of increased risk for PCa in rs486907 and rs2127565 in variants AA and CC, respectively. In addition, rs627928 (TT-GT), rs486907 (AG) and rs3747531 (CG-CC) were associated with low tumor aggressiveness. Some had a weak linkage, such as rs1904577 and rs2127565, rs4792311 and rs17552022, and rs1904577 and rs918. Our study provides the proof-of-principle that some of the genetic variants (such as rs486907, rs627928 and rs2127565) in genes RNASEL, MSR1 and ELAC2 can be used as predictors of aggressiveness and progression of PCa. In the future, clinical use of these biomarkers, in combination with current ones, could potentially reduce the rate of unnecessary biopsies and specific treatments.
Aged ; Aged, 80 and over ; Cohort Studies ; Disease Progression ; Endoribonucleases/*genetics ; Gene Frequency ; Genetic Markers/genetics ; Genetic Predisposition to Disease ; Humans ; Male ; Middle Aged ; Neoplasm Proteins/*genetics ; *Polymorphism, Single Nucleotide ; Prognosis ; Prostate/metabolism/*pathology ; Prostatic Neoplasms/*diagnosis/*genetics ; Scavenger Receptors, Class A/*genetics

BACKGROUNDThe role of epigenetics in gene expression regulation and development significantly enhances our understanding of carcinogenesis. All the tumor related genes may be the target of epigenetical or genetic regulation. We selected some epigenetically regulated genes for cDNA array analysis and observed variability in the expression of the DICER1 gene in distinct stages of gastric cancer. The aim of this study was to assess the correlation between the expression of DICER1, an epigenetically regulated gene, and gastric cancer.

METHODSTo detect the expression of 506 tumor-associated genes, including DICER1, in the matched cancerous mucosa, pre-malignant lesion (adjacent mucosa), non-cancerous gastric mucosa and distant lymphocyte metastatic lesion in 3 cases of gastric cancers using cDNA array. DICER1 mRNA expression and DICER1 protein expression were further analyzed by Real-time PCR and Western blot in 32 cases of progressive gastric cancer. DICER1 protein expression was also detected in 33 early and 30 progressive gastric cancers by the immunohistochemistry (IHC) method.

RESULTSIn 3 cases of gastric cancer cDNA array showed dramatically decreased expression of DICER1 in pre-malignant lesion, cancerous mucosa and distant lymphocyte metastatic lesions compared with matched noncancerous gastric mucosa, pre-malignant lesion and cancerous mucosa. Real-time PCR results showed that the expression level of DICER1 mRNA in gastric cancer was significantly down-regulated compared to normal gastric tissue (P < 0.05). The IHC assay also showed that the expression of DICER1 was significantly decreased in progressive gastric cancer. Among the 63 cases of gastric cancers, 13/33 early (39.4%) and 19/30 (63.3%) progressive cancers showed negative expression of DICER1 (50.8%). The difference in expression of DICER1 between early and progressive gastric cancers was significant (P < 0.01). The result of Western blotting showed that DICER1 protein was down-regulated significantly in advanced gastric cancer (P < 0.05).

CONCLUSIONSDICER1 expression is decreased during the progression of gastric cancer, especially in progressive gastric cancers, which indicating DICER1 may play an important role in the development of cancer and the epigenetical regulation involved.

Blotting, Western ; DEAD-box RNA Helicases ; analysis ; genetics ; physiology ; Endoribonucleases ; analysis ; genetics ; physiology ; Epigenesis, Genetic ; Humans ; Immunohistochemistry ; Oligonucleotide Array Sequence Analysis ; Polymerase Chain Reaction ; Ribonuclease III ; Stomach Neoplasms ; chemistry ; etiology ; genetics

AIMTo provide molecular evidence for quality evaluation and GAP production of Pogostemon cablin (Blanco) Benth. cultivated in different regions in Guangdong and Hainan provinces, China, by comparing two sequences (1.2 kb of plastid matK gene and 1.8 kb of nuclear 18S rRNA gene) and two chemotypes (Pogostone-type and Patchouliol-type in essential oil composition).

METHODSPCR direct sequencing was applied to detemine the matK and 18S rRNA sequences for six samples of Pogostemon cablin from different localities.

RESULTSThe matK sequences of six samples of Pogostemon cablin from different regions of cultivation are 1,245 bp in length, which coding 415 amino acids of protein (maturase), and 18S rRNA sequences are 1,803-1,805 bp in size. Based on multiple sequence alignment, there are 47 variable sites in the matK sequence of these six samples, 17 in the 18S rRNA sequence. The cluster tree reconstructed by UPGMA method shows that the sequence divergence both in matK and 18S rRNA genes among six samples of Pogostemon cablin was well correlative with their regions of cultivation and intraspecific chemotypes of essential oil composition.

CONCLUSIONCombining with chemical and biogeographical data, DNA sequencing can become a powerful tool in the key technique-species identification of quality evaluation and GAP production of Pogostemon cablin.

Base Sequence ; DNA, Plant ; analysis ; Endoribonucleases ; genetics ; Genes, Plant ; Lamiaceae ; chemistry ; classification ; genetics ; Molecular Sequence Data ; Nucleotidyltransferases ; genetics ; Oils, Volatile ; analysis ; Polymorphism, Genetic ; Quality Control ; Sequence Analysis, DNA ; Species Specificity

In this study, Leishmania RNA virus 1-4 (LRV1-4) particles purified from host Leishmania guyanensis promastigotes were examined for capsid endoribonuclease. Temperature optimum for the endoribonulease activity was found to be at 37degrees C to 42degrees C and the activity was specifically inhibited by the aminoglycoside antibiotics, neomycin, kanamycin, and hygromycin and by 100 mM levels of NaCl or KCl. To determine the catalytic domain of the capsid endoribonuclease activity, three point-mutation at cysteine residues at C47S (P1), C128/ 133S (P2), and C194R (P3) were prepared and each gene was constructed into baculoviruses and expressed in Sf9 insect cells. LRV1-4 capsid N- terminus (N2 and N3) and C-terminus (C1 and C2) deletion mutants (Cadd et al., 1994) were also examined by in vitro RNA cleavage assay. The results showed that the capsid mutants; C1, C2, N3, P1, and P2 were capable of forming proper virus-like particles (VLPs) and they all possessed the specific endoribonuclease activity. However, two assembly-defective capsid mutants, N2 (N- terminus 24-amino acids deletion) and P3 mutants, did not retain the specific endoribonuclease activity. Taken together, the results suggest that at least 24 amino acids from the N-terminal region and C194 residue in LRV1-4 capsid protein are functionally important for LRV1-4 viral assembly and the capsid endoribonuclease activity may be dependent upon the properly assembled LRV1-4 virus particles.
Amino Acid Substitution ; Animals ; Anti-Bacterial Agents/pharmacology ; Baculoviridae ; Capsid/*enzymology ; Cell Line ; Cysteine/genetics ; Endoribonucleases/antagonists & inhibitors/chemistry/genetics/isolation & purification/*metabolism ; Enzyme Activation/drug effects ; Heat ; Insects ; Leishmania guyanensis/*virology ; RNA/chemistry ; RNA Viruses/*enzymology/genetics ; Recombinant Proteins/antagonists & inhibitors/genetics/isolation & purification/metabolism ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S. ; Substrate Specificity/genetics ; Transduction, Genetic