A novel method of multiple alignment of biopolymer sequences

Trimodal GSTT1 and GSTM1 Genotyping Assay by Real-Time PCR

The GSTT1 and GSTM1 genes are characterized by the existence of a GST*0 null allele responsible for a lack of enzyme activity, with the respective null genotypes GSTT1*0/0 and GSTM1*0/0. The three resulting genotypes (GSTs*1/1, *1/0 and *0/0) are associated with a trimodal distribution of glutathione-conjugator activity. Previous epidemiological studies have only evaluated the cancer risk associated with the GST null genotype relative to the two GST carrier geno-® types (GSTs1*1/1 and *1/0). We developed GSTT1 and GSTM1 TaqMan real-time quantitative PCR assays to discriminate each of the three genotypes, with the albumin gene (ALB) as reference. The mean NGSTT1*1/1 value was 1.0 (95% confidence interval 0.80–1.20). The mean NGSTT1*1/0 value was 0.48 (95% CI 0.36–0.60). One (3.4%) of the 29 DNA samples yielded the GSTM1*1/1 genotype (NGSTM1*1/1 = 1), a frequency in keeping with the Hardy-Weinberg distribution. The mean NGSTM1*1/0 value was 0.50 (95% CI 0.42–0.58). All GSTT1*0/0 and GSTM1*0/0 samples yielded NGST values of 0 (Ct = 40); the frequencies of these genotypes (27.6% and 55.2%, respectively) were in keeping with published data. The GSTT1 and GSTM1 real-time PCR assays described here unambiguously discriminate each of the three existing genotypes which should be valuable for assessing the relative risk of cancer associated with each of the three GST genotypes.

The rearrangement of motif F in the flavivirus RNA-directed RNA polymerase

In the flavivirus genus, the non-structural protein NS5 plays a central role in RNA viral replication and constitutes a major target for drug discovery. One of the prime challenges in the study of NS5 protein is to investigate the interplay between the two protein domains, namely, the RNA-dependent RNA polymerase (RdRp) domain and the methyltransferase (MTase) domain. These investigations could clarify the multiple roles of NS5 protein in the virus life cycle. Here we present the results of sequence analyses and structural bioinformatics studies of NS5 protein, which suggest that the conserved motif F in the NS5 protein could act as a lock which controls the rearrangement of the domains and as a switch in the protein enzymatic activity.

Heavy metal contamination and metallothionein mRNA in blood and feathers of Black-tailed gulls (Larus crassirostris) from South Korea

The objectives of this study were to determine levels of heavy metal in the feathers and blood of Black-tailed gulls (Larus crassirostris), to evaluate metallothionein (MT) mRNA level in Black-tailed gulls on three independent islets, and to examine the correlation between heavy metal concentrations and MT mRNA expression. Eleven heavy metals (Al, Cd, Mn, Pb, Cr, Fe, Cu, Zn, Se, Hg, and As) were investigated in blood and feathers of 65 chicks from breeding colonies (Seomando, Hongdo, and Dokdo islet) of South Korea in 2010. Heavy metals were assayed by PerkinElmer NexION 300 inductively coupled plasma mass spectrometry. The mean concentrations of non-essential heavy metals were found to blood containing Cd (0.002 ~ 0.02 ppm), Pb (0.06 ~ 0.18) ppm, Hg (0.03 ~ 0.05) ppm, and As (0.26 ~ 0.48 ppm), and feather containing Cd (0.05 ~ 0.30 ppm), Pb (2.47 ~ 10.80 ppm), Hg (1.18 ~ 1.57 ppm), and As (0.15 ~ 0.44 ppm). Chicks on Seomando islet showed the highest levels of metals (Cd, Pb, Mn, Cr, Cu, and Se in blood; Al, As, Mn, Cr, Fe, Cu, and Se in feathers) among the colonies. Concentrations of Pb and Hg in feathers were the highest on Hongdo, and the levels of Cd and Zn in feathers were the highest on Dokdo islet. MT mRNA in the blood of Black-tailed gulls was relatively higher in gulls from Seomando than in gulls from Hongdo and Dokdo islet. MT mRNA level is thus positively correlated to heavy metal concentrations in Black-tailed gulls.

Gene expression of ribosomal protein mRNA in Chironomus riparius: effects of endocrine disruptor chemicals and antibiotics

Ribosomal protein genes are essential for cellular development. To examine the effects of ribosomal protein genes under various cellular stress conditions in chironomids, ribosomal protein S3 (RpS3) and S6 (RpS6) cDNA from Chironomus riparius were characterized and their expression was analyzed during development. A comparative and phylogenetic study among different orders of insects was carried out by analysis of sequence databases. C. riparius RpS3 was highly conserved at the protein level and shared over 85% amino acid identity with homologous sequences from other insects. RpS6 also showed approximately 80% amino acid identity. The RpS3 and S6 transcripts were present during different developmental stages but were most abundant during the embryonic stage. Furthermore, expression of the previously reported ribosomal proteins RpL11, L13, and L15, as well as RpS3 and S6 was analyzed following exposure to various concentrations of three endocrine disruptor chemicals (EDCs), di(2-ethylhexyl) phthalate, bisphenol A, and 4-nonylphenol (4NP), and the veterinary antibiotics (VAs) fenbendazole, sulfathiazole, and lincomycin. Only RpS3 gene expression was up-regulated significantly in response to EDCs and fenbendazole. However, the C. riparius ribosomal proteins showed a limited response to cellular stress, following exposure to EDCs and VAs.

NS2B/NS3 protease: allosteric effect of mutations associated with the pathogenicity of tick-borne encephalitis virus

The sequences of the protease domain of the tick-borne encephalitis (TBE) virus NS3 protein have two amino acid substitutions, 16 R→K and 45 S→F, in the highly pathogenic and poorly pathogenic strains of the virus, respectively. Two models of the NS2B-NS3 protease complex for the highly pathogenic and poorly pathogenic strains of the virus were constructed by homology modeling using the crystal structure of West Nile virus NS2B-NS3 protease as a template; 20 ns molecular dynamic simulations were performed for both models, the trajectories of the dynamic simulations were compared, and the averaged distance between the two models was calculated for each residue. Conformational differences between two models were revealed in the identified pocket. The different conformations of the pocket resulted in different orientations of the NS2B segment located near the catalytic triad. In the model of the highly pathogenic TBE virus the identified pocket had a more open conformation compared to the poorly pathogenic model. We propose that conformational changes in the active protease center, caused by two amino acid substitutions, can influence enzyme functioning and the virulence of the virus.

Viral diseases of the giant fresh water prawn Macrobrachium rosenbergii: a review

The giant freshwater prawn Macrobrachium rosenbergii is cultivated essentially in Southern and South-eastern Asian countries such as continental China, India, Thailand and Taiwan. To date, only two viral agents have been reported from this prawn. The first (HPV-type virus) was observed by chance 25 years ago in hypertrophied nuclei of hepatopancreatic epithelial cells and is closely related to members of the Parvoviridae family. The second, a nodavirus named MrNV, is always associated with a non-autonomous satellite-like virus (XSV), and is the origin of so-called white tail disease (WTD) responsible for mass mortalities and important economic losses in hatcheries and farms for over a decade. After isolation and purification of these two particles, they were physico-chemically characterized and their genome sequenced. The MrNV genome is formed with two single linear ss-RNA molecules, 3202 and 1250 nucleotides long, respectively. Each RNA segment contains only one ORF, ORF1 coding for the RNA-dependant RNA polymerase located on the long segment and ORF2 coding for the structural protein CP-43 located on the small one. The XSV genome (linear ss-RNA), 796 nucleotides long, contains a single ORF coding for the XSV coat protein CP-17. The XSV does not contain any RdRp gene and consequently needs the MrNV polymerase to replicate.

Analysis of mutations that influence pre-mRNA splicing

A rapidly increasing number of human diseases are now recognized as being caused by the selection of wrong splice sites. In most cases, these changes in alternative splice site selection are due to single nucleotide exchanges in splicing regulatory elements. This chapter describes the use of bioinformatics tools to predict the influence of a mutation on alternative pre-mRNA splicing and the experimental testing of these predictions. The bioinformatic analysis determines the influence of a mutation on splicing enhancers and silencers, splice sites and RNA secondary structures. This approach generates hypotheses that are tested using splicing reporter constructs, which are then analyzed in transfection assays. We describe a recombination-based system that allows for the generation of splicing reporter constructs in the first week and their subsequent analysis in the second week.

[Liver cirrhosis patogenetics: polymorphism of glutation S-transferase genes]

Association of deletion polymorphism in GSTT1 and GSTM1 genes and polymorphic variant A313G of GSTP1 gene with cirrhosis diseases and 4-year survival rate for the Tomsk region (West Siberia) patients were tested. Homozygous deletion of GSTM1 gene (null genotype) was a protective factor for alcoholic and mixed (HCV, HBV and alcohol) liver cirrhosis development. The patients from the joint group (all etiology forms) as well as having alcoholic and mixed cirrhosis had lower frequency of GSTM1 null genotype (39.2, 39.0, and 34.2%, respectively) in comparison with the control group (64.6%). The GSTM1 null genotype and GSTP1 gene A313G polymorphic variant correlated with the patients' survival rate. The patients survived in comparison with the dead had higher frequency of a GSTM1 null genotype (46.6 vs. 30.2%) and GSTP1 AA genotype (63.1 vs. 40.5%), and lower frequency of GSTP1 AG (A313G) genotype (31.1 vs. 51.2%). A survival rate was 2.5 times higher for patients having GSTP1 AA genotype in comparison with the GG and AG genotype carriers and 2 times higher for patients having GSTM1 null genotype than the gene carriers. A 4-year fatal case probability was 2.3 times higher among the patients having heterozygous AG GSTP1 genotype in comparison with homozygous AA and GG genotype carriers.

Sequence-function analysis of the Sendai virus L protein domain VI

The large (about 2200 amino acids) L polymerase protein of nonsegmented negative-strand RNA viruses (order Mononegavirales) has six conserved sequence regions (“domains”) postulated to constitute the specific enzymatic activities involved in viral mRNA synthesis, 5′-end capping, cap methylation, 3′ polyadenylation, and genomic RNA replication. Previous studies with vesicular stomatitis virus identified amino acid residues within the L protein domain VI required for mRNA cap methylation. In our recent study we analyzed four amino acid residues within domain VI of the Sendai virus L protein and our data indicated that there could be differences in L protein sequence requirements for cap methylation in two different families of Mononegavirales — rhabdoviruses and paramyxoviruses. In this study, we conducted a more comprehensive mutational analysis by targeting the entire SeV L protein domain VI, creating twenty-four L mutants, and testing these mutations for their effects on viral mRNA synthesis, cap methylation, viral genome replication and virus growth kinetics. Our analysis identified several residues required for successful cap methylation and virus replication and clearly showed the importance of the K-D-K-E tetrad and glycine-rich motif in the SeV cap methylation. This study is the first extensive sequence analysis of the L protein domain VI in the family Paramyxoviridae, and it confirms structural and functional similarity of this domain across different families of the order Mononegavirales.

Molecular effects of endocrine-disrupting chemicals on the Chironomus riparius estrogen-related receptor gene

Endocrine-disrupting chemicals (EDCs) mimic the action of endogenous estrogen hormones; consequently, they can interfere with the endocrine systems of a variety of organisms. There is global concern regarding the potential impacts of EDCs on the aquatic environment. To evaluate the effects of EDCs on the estrogen-related receptors (ERR) of Chironomus, we characterized full-length cDNA sequences of the ERR gene from Chironomus riparius. The complete cDNA sequence of the ERR gene was found to be 1332bp in length. The results of our phylogenetic analysis demonstrated that C. riparius ERR was most closely related to that of mosquitoes. The basal level of ERR mRNA was expressed abundantly during different life-history stages, with the exception of adult males. Additionally, ERR gene expression was upregulated significantly in C. riparius exposed to bisphenol A (BPA) and 4-nonylphenol (NP) at all concentrations assayed after 24h of exposure. The ERR gene was significantly upregulated following short periods of exposure to di(2-ethylhexyl)phthalate (DEHP) concentrations of only 50mgL(-1). However, under long-term exposure conditions, ERR expression was induced to a significant degree after BPA, NP, and DEHP exposure at all concentrations assayed. Furthermore, the luciferase reporter gene assay revealed increased ERR expression following exposure to these compounds. Collectively, these findings indicate that EDCs influence the expression of ERR in Chironomus species.

Calponin gene expression in Chironomus riparius exposed to di(2-ethylhexyl) phthalate

Di(2-ethylhexyl) phthalate, which is a ubiquitous environmental contaminant because of its extensive use as a plasticizer, is a potential nongenotoxic carcinogen. To assess the effects of DEHP exposure on the cytoskeleton of Chironomus, we characterized full-length cDNA sequences of the calponin gene from Chironomus riparius. The expression of the calponin gene was analyzed during different life-history stages and under various DEHP concentrations for short and long periods. A phylogenetic investigation was then conducted to compare different orders of insects using sequence database analysis. The complete cDNA sequence of the calponin gene was found to be 555 bp in length. The results of phylogenetic analysis revealed that C. riparius calponin is most closely related to that of beetles. The basal level of calponin mRNA was highly expressed during different life-history stages. In addition, calponin gene expression decreased within 1 h of short-term exposure to DEHP, regardless of the concentration. We also investigated expression of the calponin gene following long-term exposure (10 days). Calponin gene expression was found to decrease significantly in C. riparius that were exposed to a low dose of DEHP, and this response was found to occur in a dose-dependent manner. Taken together, these results suggest that DEHP affects the functions of Ca(2+) binding muscle proteins such as calponin in Chironomus species.

Ecotoxicological multilevel-evaluation of the effects of fenbendazole exposure to Chironomus riparius larvae

Veterinary antibiotics may find their way into the aquatic environment through direct or indirect pathways due to their widespread use. Fenbendazole is a benzimidazole anthelmintic that is widely used in veterinary medicine. To evaluate the potential ecological risk of fenbendazole, we examined the molecular and biochemical responses of biomarker genes such as heat shock proteins (HSPs), cytochrome P450 (CYP450), glutathione S-transferases (GSTs) and hemoglobins (Hbs) in Chironomus riparius for long periods. The expression of HSP70, HSP40, HSP90 and CYP450 in C. riparius increased significantly after exposure to all concentrations of fenbendazole evaluated, while the levels of GST and HbA only increased in C. riparius exposed to relatively high concentrations of fenbendazole (30 microg L(-1)). HbB expression did not differ significantly between the control and treatment groups. Exposure to 30 microg L(-1) fenbendazole had significant effects on the survival, growth, sex balance of emergent adults and development of mouthpart deformity in C. riparius. These results should constitute an important contribution to the understanding of the toxicology of fenbendazole in C. riparius. Moreover, the responses of the biomarker genes also provide valuable information that will aid in understanding the effects of fenbendazole in aquatic ecosystems.

Alcohol dehydrogenase gene expression in Chironomus riparius exposed to di(2-ethylhexyl) phthalate

Di(2-ethylhexyl) phthalate (DEHP) is an industrial additive that is widely used as a plasticizer. Due to its widespread use, DEHP is often found in freshwater ecosystems and many freshwater species have been exposed to various levels of DEHP in natural aquatic systems. Alcohol dehydrogenase (ADH) is a metabolizing enzyme produced in response to exposure to DEHP. To evaluate the effects of DEHP exposure on the ADH metabolizing process of Chironomus, the full-length cDNA of ADH from Chironomus riparius was determined through molecular cloning and rapid amplification of cDNA ends (RACE). The expression of ADH was then analyzed during different life-cycle developmental stages and under various DEHP concentrations. In addition, a comparative and phylogenetic study among different orders of insects and vertebrates was conducted through analysis of sequence databases. The complete cDNA sequence of the ADH gene was 1134 bp in length. The amino acid sequence of C. riparius ADH was found to have a low degree of homology (around 70%) with other insects available in the databases. ADH mRNA was highly expressed during various developmental stages. ADH gene expression by C. riparius increased significantly after short-term exposure (24 h) to DEHP, regardless of the exposure concentration. ADH gene expression also increased in C. riparius following exposure to DEHP for 7 days. These results suggest that DEHP affects the metabolism associated with ADH in Chironomus species.

Characterization of heat shock protein 40 and 90 in Chironomus riparius larvae: effects of di(2-ethylhexyl) phthalate exposure on gene expressions and mouthpart deformities

Di(2-ethylhexyl) phthalate (DEHP) is a widely distributed phthalate that organisms are frequently exposed to due to its wide range of commercial and manufacturing uses as a plasticizer. Indeed, DEHP is often found in freshwater systems that receive domestic waste water discharges. Therefore, we evaluated the effects of DEHP on the mRNA levels of heat shock protein (HSP) 40 and 90 in chironomids. In addition, we evaluated the effects of exposure to DEHP on the induction of morphological deformities in chironomids. To accomplish this, partial sequences of HSP 40 and 90 from Chironomus riparius larvae were amplified and sequenced. The inferred amino acid sequences were then aligned with those of other insect HSP 40 and 90 genes. The results of this alignment revealed that there was a high degree of similarity among the homologues. In addition, the HSP 40 and 90 mRNA expressions were significantly upregulated in response to short and long-term exposure to DEHP at concentrations of 1, 10, and 30 microgL(-1). Furthermore, the occurrence of mouthpart deformities was significantly higher in chironomids that were treated with DEHP (12-20%) than in controls (3-5%). Taken together, these results indicate that HSP 40 and 90 play important roles in the physiological changes related to metabolism and cell protection that occur in C. riparius larvae that have been exposed to DEHP.

Expression of Chironomus riparius serine-type endopeptidase gene under di-(2-ethylhexyl)-phthalate (DEHP) exposure

Environmental stressors can induce changes in gene expression that can be useful as biomarkers. To identify potential biomarkers of water quality, we characterized full-length cDNA sequences of the serine-type endopeptidase (SP) gene from Chironomus riparius. Their expression was analyzed during different life-history stages and in response to treatment with various concentrations of di(2-ethylhexyl) phthalate (DEHP) for short and long periods of time. A comparative molecular and phylogenetic investigation was then conducted among different orders of insects using sequence database analysis. The sequence of the C. riparius SP gene was found to be most closely related to the sequence of SPs isolated from Aedes aegypti. In addition, the basal level of C. riparius SP mRNA was more highly expressed in larvae than in other life-history stages. However, the expression of C. riparius SP was primarily limited to the gut in larvae. When the effects of short-term exposure to DEHP were evaluated, C. riparius SP gene expression decreased within 1 h of treatment, regardless of dose. We also investigated expression of the C. riparius SP gene following long-term DEHP exposure (10 days) and found that it decreased significantly across all DEHP dosages. Finally, the response of the SP gene was more sensitive in C. riparius that were exposed to low concentrations of DEHP than in those that were exposed to high concentrations. These results show that suppression of the C. riparius SP gene by DEHP is as a potential biomarker that could be useful for monitoring aquatic quality.

The myotonic dystrophy type 2 protein ZNF9 is part of an ITAF complex that promotes cap-independent translation

The 5'-untranslated region of the ornithine decarboxylase (ODC) mRNA contains an internal ribosomal entry site (IRES). Mutational analysis of the ODC IRES has led to the identification of sequences necessary for cap-independent translation of the ODC mRNA. To discover novel IRES trans-acting factors (ITAFs), we performed a proteomics screen for proteins that regulate ODC translation using the wild-type ODC mRNA and a mutant version with an inactive IRES. We identified two RNA-binding proteins that associate with the wild-type ODC IRES but not the mutant IRES. One of these RNA-binding proteins, PCBP2, is an established activator of viral and cellular IRESs. The second protein, ZNF9 (myotonic dystrophy type 2 protein), has not been shown previously to bind IRES-like elements. Using a series of biochemical assays, we validated the interaction of these proteins with ODC mRNA. Interestingly ZNF9 and PCBP2 biochemically associated with each other and appeared to function as part of a larger holo-ITAF ribonucleoprotein complex. Our functional studies showed that PCBP2 and ZNF9 stimulate translation of the ODC IRES. Importantly these results may provide insight into the normal role of ZNF9 and why ZNF9 mutations cause myotonic dystrophy.

Human Homologs of the Putative G Protein-Coupled Membrane Progestin Receptors (mPRα, β, and γ) Localize to the Endoplasmic Reticulum and Are Not Activated by Progesterone

The steroid hormone progesterone exerts pleiotrophic functions in many cell types. Although progesterone controls transcriptional activation through binding to its nuclear receptors, it also initiates rapid nongenomic signaling events. Recently, three putative membrane progestin receptors (mPRα, β, and γ) with structural similarity to G protein-coupled receptors have been identified. These mPR isoforms are expressed in a tissue-specific manner and belong to the larger, highly conserved family of progestin and adiponectin receptors found in plants, eubacteria, and eukaryotes. The fish mPRα has been reported to mediate progesterone-dependent MAPK activation and inhibition of cAMP production through coupling to an inhibitory G protein. To functionally characterize the human homologs, we established human embryonic kidney 293 and MDA-MB-231 cell lines that stably express human mPRα, β, or γ. For comparison, we also established cell lines expressing the mPRα cloned from the spotted seatrout (Cynoscion nebulosus) and Japanese pufferfish (Takifugu rubripes). Surprisingly, we found no evidence that human or fish mPRs regulate cAMP production or MAPK (ERK1/2 or p38) activation upon progesterone stimulation. Furthermore, the mPRs did not couple to a highly promiscuous G protein subunit, Gαq5i, in transfection studies or provoke Ca2+ mobilization in response to progesterone. Finally, we demonstrate that transfected mPRs, as well as endogenous human mPRα, localize to the endoplasmic reticulum, and that their expression does not lead to increased progestin binding either in membrane preparations or in intact cells. Our results therefore do not support the concept that mPRs are plasma membrane receptors involved in transducing nongenomic progesterone actions.

Characterization of the Felix domesticus (cat) glaucoma-associated protein myocilin

The domestic cat (Felix domesticus) is a useful model for understanding the implications of long-term expression and function of normal and mutant myocilin. To better understand the role myocilin has in the cat eye, we isolated and characterized cat myocilin. Oligonucleotides designed against conserved nucleotide regions of myocilin mammalian orthologs were used to PCR amplify a partial cat myocilin cDNA clone. Rapid amplification of cDNA ends (5' and 3' RACE) was used to obtain full-length cat myocilin. The 2125 nucleotide cat myocilin cDNA contains a 490 amino acid open reading frame. Comparison of cat myocilin to human myocilin shows a 87% similarity, including conservation of the N-terminal leucine zipper, N-linked glycosylation site, C-terminal olfactomedin domain, and all five cysteine residues thought to be involved in disulfide bond formation. Expression in a transformed human trabecular cell line or in Crandall feline kidney cells showed cat myocilin was secreted from these cells, similar to human myocilin, suggesting cat myocilin contains a functional signal peptide sequence. In contrast, expression of cat myocilin containing a known human glaucoma-associated mutation (Y423H in cat; Y437H in human) was not secreted. Characterization of cat myocilin will enable long-term studies be performed in Felix domesticus to analyze changes to intraocular pressure and the aqueous outflow pathway following expression of myocilin and glaucoma causing mutations.

Identification of Carnobacterium species by restriction fragment length polymorphism of the 16S-23S rRNA gene intergenic spacer region and species-specific PCR

The genus Carnobacterium is currently divided into the following eight species: Carnobacterium piscicola, C. divergens, C. gallinarum, C. mobile, C. funditum, C. alterfunditum, C. inhibens, and C. viridans. An identification tool for the rapid differentiation of these eight Carnobacterium species was developed, based on the 16S-23S ribosomal DNA (rDNA) intergenic spacer region (ISR). PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of this 16S-23S rDNA ISR was performed in order to obtain restriction profiles for all of the species. Three PCR amplicons, which were designated small ISR (S-ISR), medium ISR (M-ISR), and large ISR (L-ISR), were obtained for all Carnobacterium species. The L-ISR sequence revealed the presence of two tRNA genes, tRNA(Ala) and tRNA(Ile), which were separated by a spacer region that varied from 24 to 38 bp long. This region was variable among the species, allowing the design of species-specific primers. These primers were tested and proved to be species specific. The identification method based on the 16S-23S rDNA ISR, using PCR-RFLP and specific primers, is very suitable for the rapid low-cost identification and discrimination of all of the Carnobacterium species from other phylogenetically related lactic acid bacteria.

Soybean receptor-like protein kinase genes: paralogous divergence of a gene family

Receptor-like protein kinases (RLKs) in plants play major roles in cellular processes and stress responses. Three soybean (Glycine max) orthologs of Arabidopsis thaliana RLK were isolated and designated GmRLK1, GmRLK2, and GmRLK3. GmRLK1, GmRLK2, and GmRLK3 are similar in sequence, with GmRLK2 and GmRLK3 being nearly identical. The deduced amino acid sequences of GmRLK1, GmRLK2, and GmRLK3 possess characteristics of a transmembrane leucine-rich repeat RLK, AtCLV1. DNA fingerprinting and PCR analyses of a bacterial artificial chromosome library identified five GmRLK contigs (I-V): three for GmRLK1 (I, II, and V), one for GmRLK2 (III), and one for both GmRLK2 and GmRLK3 (IV). Phylogenetic analysis of the soybean RLKs together with other plant RLKs indicates that soybean and A. thaliana CLV1s generate a CLV1 branch, while soybean, A. thaliana, and rice RLKs generate an RLK branch. Thus, the AtCLV1 orthologs may have evolved later than the other pathogen-, environmental stress-, plant hormone-, and development-associated RLKs. A common ancestral GmRLK gene may have duplicated to give rise to GmRLK1, GmRLK2, and GmRLK3, or GmRLK2 and GmRLK3 may have resulted from a recent duplication event(s). Several amino acid replacements in the kinase domain of GmRLK1 compared with those of GmRLK2 and GmRLK3 may reflect evolutionary divergence of individual family members.

Forum domain in Drosophila melanogaster cut locus possesses looped domains inside

We have studied the relationship between chromosomal forum domains and looped domains in the cut locus of Drosophila melanogaster . Forum domains were earlier detected by separation in pulsed-field gels of 50-150 kb chromosomal DNA fragments obtained after spontaneous non-random degradation of chromosomes. We have localized the boundary region where cleavage sites are scattered between two forum domains in the regulatory region of the cut locus. We have sequenced a 13 kb region spanning few kilobases from distal domain, the boundary region and part of the proximal forum domain where several scaffold associated regions (SARs) were observed. We conclude that forum domains and looped domains are physically different types of domains and belong to different levels of organization in eukaryotic chromosomes. The boundary region between the neighboring forum domains in the cut locus possesses the Doc element insertion and a micro-satellite stretch and thus might remind a small island of heterochromatin and correspond to so-called intercalary heterochromatin that is known to be located in the 7B1-2 band where the major part of the cut locus is reside.

Combinatorial approaches to gene recognition

Recognition of genes via exon assembly approaches leads naturally to the use of dynamic programming. We consider the general graph-theoretical formulation of the exon assembly problem and analyze in detail some specific variants: multicriterial optimization in the case of non-linear gene-scoring functions; context-dependent schemes for scoring exons and related procedures for exon filtering; and highly specific recognition of arbitrary gene segments, oligonucleotide probes and polymerase chain reaction (PCR) primers.