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PubMed1997

Characterization of two rice MADS box genes that control flowering time.

Plants contain a variety of the MADS box genes that encode regulatory proteins and play important roles in both the formation of flower meristem and the determination of floral organ identity. We have characterized two flower-specific cDNAs from rice, designated OsMADS7 and OsMADS8. The cDNAs displayed the structure of a typical plant MADS box gene, which consists of the MADS domain, I region, K domain, and C-terminal region. These genes were classified as members of the AGL2 gene family based on sequence homology. The OsMADS7 and 8 proteins were most homologous to OM1 and FBP2, respectively. The OsMADS7 and 8 transcripts were detectable primarily in carpels and also weakly in anthers. During flower development, the OsMADS genes started to express at the young flower stage and the expression continued to the late stage of flower development. The OsMADS7 and 8 genes were mapped on the long arms of the chromosome 8 and 9, respectively. To study the functions of the genes, the cDNA clones were expressed ectopically using the CaMV 35S promoter in a heterologous tobacco plant system. Transgenic plants expressing the OsMADS genes exhibited the phenotype of early flowering and dwarfism. The strength of the phenotypes was proportional to the levels of transgene expression and the phenotypes were co-inherited with the kanamycin resistant gene to the next generation. These results indicate that OsMADS7 and 8 are structurally related to the AGL2 family and are involved in controlling flowering time.

Amino Acid Sequence↗

PubMed1995

Editing DNA replication and recombination by mismatch repair: from bacterial genetics to mechanisms of predisposition to cancer in humans.

A hereditary form of colon cancer, hereditary non-polyposis colon cancer (HNPCC), is characterized by high instability of short repeated sequences known as microsatellites. Because the genes controlling microsatellite stability were known in bacteria and yeast, as was their evolutionary conservation, the search for human genes responsible for HNPCC became a 'targeted' search for known sequences. Mismatch-repair deficiency in bacteria and yeast produces multiple phenotypes as a result of its dual involvement in the editing of both replication errors and recombination intermediates. In addition, mismatch-repair functions are specialized in eukaryotes, characterized by specific mitotic (versus meiotic) functions, and nuclear (versus mitochondrial) localization. Given the number of phenotypes observed so far, we predict other links between mismatch-repair deficiency and human genetic disorders. For example, a similar type of sequence instability has been found in HNPCC tumours and in a number of neuro-muscular genetic disorders. Several human mitochondrial disorders display genomic instabilities reminiscent of yeast mitochondrial mismatch-repair mutants. In general, the process of mismatch repair is responsible for the constant maintenance of genome stability and its faithful transmission from one generation to the next. However, without genetic alteration, species would not be able to adapt to changing environments. It appears that nature has developed both negative and positive controls for genetic diversity. In bacteria, for example, an inducible system (sos) exists which generates genetic alterations in response to environmental stress (e.g. radiation, chemicals, starvation). Hence, the cost of generating diversity to adapt to changing conditions might be paid as sporadic gene alterations associated with disease.

Amino Acid Sequence↗

PubMed2000

Development of rapid one-step immunochromatographic assay.

An analytical system for a one-step immunoassay has been constructed using the concept of immunochromatography. The system employed two different antibodies that bound distinct epitopes of an analyte molecule: an antibody labeled with a signal generator (e.g., colloidal gold), which was placed in the dry state at a predetermined site on a glass-fiber membrane, and another antibody immobilized on the surface of a nitrocellulose membrane. Three membranes, one with the tracer, one with immobilized antibody, and a cellulose membrane as the absorbent of medium (in a sequence from the bottom), were attached to a plastic film and cut into strips. Aqueous medium containing analyte absorbed from the bottom end of the immunostrip dissolved the labeled antibody, and the antigen-antibody binding complex formed was transported into the next nitrocellulose membrane by the flow caused by capillary action. The complex subsequently reacted with the immobilized antibody, which generated a signal in proportion to the analyte concentration. The convective mass transfer of the immunoreactant to the binding partner allowed the assay to be performed with no handling of reagents. The reaction, however, was carried out under nonequilibrium conditions, which resulted in decreased sensitivity as compared with assays performed in an equilibrium mode (e.g., ELISA). To minimize such sacrifice, major factors that control system performance were identified and the system was then devised under optimal conditions.

Animals↗

PubMed1992

Expression of antisense or sense RNA of an ankyrin repeat-containing gene blocks chloroplast differentiation in arabidopsis.

The Arabidopsis AKR gene that encodes a protein with four ankyrin repeats (a 33-amino acid motif that appears in the 89K domain of the human protein ankyrin) was isolated and characterized. A short sequence outside the ankyrin repeats is similar to that of the protein of the Drosophila muscle segment homeobox (msh) gene. The expression of the AKR gene is light dependent, and transgenic Arabidopsis plants with two or more copies of an antisense or sense AKR construct became chlorotic in a developmentally regulated manner. The chlorotic phenotype was genetically transmitted to the next generation, although most chlorotic plants produced much less seed. Reduced presence of thylakoid membranes and loss of grana are found in the plastids of chlorotic leaves, indicating that antisense or sense AKR has blocked chloroplast differentiation. This study indicates the importance of ankyrin repeat-containing proteins, not only in yeast and animals, but in plants as well.

Amino Acid Sequence↗

PubMed2004

Coupling generation of cytomegalovirus deletion mutants and amplification of viral BAC clones.

Human cytomegalovirus (HCMV) genome manipulation has always been difficult. Recently, the introduction of full-length HCMV DNA into Escherichia coli as an artificial bacterial chromosome (BAC) clone has allowed reliable targeted mutagenesis. Here, we show the next generation of improvement in designing recombinant HCMV, which will also be applicable to other viral BAC clones. An inducible origin of replication linked with an antibiotic resistance marker was used as a cassette for targeted replacement of sequences within a HCMV BAC clone, TowneBAC. The origin of replication allowed for the induction of increased amounts BAC DNA that improved recovery, ease of use and transfections for mutant viruses. By specific deletion of UL147 and the recombinant GFP gene, we have shown that targeted deletion of a gene and selection for a recombinant genome are coupled with the ability to amplify the BAC clone DNA. These HCMV BAC clones were amplified approximately 10-fold. In the case of the removal of GFP from the clone TowneBAC shown in this study, the resulting BAC DNA preparation following amplification was used for successful primary cell transfection. Both parental and deletion BAC clone transfections gave similar levels of recombinant HCMV, and the GFP deletion virus replicated the same as the TowneBAC in a multi-step growth curve analysis.

Cells, Cultured↗

PubMed1989

Age differences in learning serial patterns: direct versus indirect measures.

Adult age differences in learning and retention of a nonverbal sequence were examined using the serial reaction-time task of Nissen and Bullemer (1987), with 20 younger and 20 older Ss. An asterisk appeared in one of 4 spatial locations, and the Ss responded with a corresponding key press. The first 4 blocks each contained 10 repetitions of a 10- or 16-element spatial sequence, and the 5th block contained a random sequence. The difference between response time on Blocks 5 and 4 served as an indirect measure of pattern learning. The direct measure was accuracy in a final generation block in which the Ss predicted which location would appear next. Results were similar to those with verbal materials; the indirect measure revealed age similarity for patterns of both lengths, but the direct measure yielded age differences favoring the young. For both ages and types of measures, the long patterns led to poorer learning than did the short patterns.

Adult↗

PubMed1997

A radiation hybrid map of human chromosome 5 with integration of cytogenetic, genetic, and transcript maps.

One of the major goals of the human genome project is to establish a physical map of each human chromosome with a density of sequence-tagged site (STS) markers exceeding one every 100 kb. We report here the generation of a human chromosome 5-specific radiation hybrid (RH) map that includes 556 markers. Of these markers, 132 loci are ordered with a maximum likelihood ratio of >1000:1 compared with the next most likely order. An additional 113 loci were ordered relative to these backbone markers with a maximum likelihood ratio of >10:1 but <1000:1. Together, these 245 loci form an ordered framework map for the chromosome. Using this framework, >300 more markers were localized based on two-point analysis with the ordered set. On average, there are 50 markers in common with the RH map presented here and other chromosome 5 maps included in the current whole genome cytogenetic, genetic, and physical maps. The accuracy of all the maps is evident in that there are no more than two discrepancies between any one of them and these data. All of the maps encompassing chromosome 5 complement each other providing excellent STS coverage with >2200 loci combined. The chromosome 5-specific RH map contains 20% of these independent loci. In addition, our RH map contains STSs derived from clones suitable for fluorescent in situ hybridization, allowing alignment to the cytogenetic map. Together, these maps will assist in the assembly of sequence-ready contigs and will aid in the identification of disease loci on chromosome 5 by positional cloning and positional candidate approaches.

Centromere↗

PubMed1986

Human cDNA clones for four species of G alpha s signal transduction protein.

lambda gt11 cDNA libraries derived from human brain were screened with oligonucleotide probes for recombinants that code for alpha subunits of G signal transduction proteins. Eleven alpha s clones were detected with both probes and characterized. Four types of alpha s cDNA were cloned that differ in nucleotide sequence in the region that corresponds to amino acid residues 71-88. The clones differ in the codon for alpha s amino acid residue 71 (glutamic acid or aspartic acid), the presence or absence of codons for the next 15 amino acid residues, and the presence or absence of an adjacent serine residue. S1 nuclease protection experiments revealed at least two forms of alpha s mRNA. A mechanism for generating four species of alpha s mRNA by alternative splicing of precursor RNA is proposed.

Amino Acid Sequence↗

PubMed1986

Minus-strand initiation by brome mosaic virus replicase within the 3' tRNA-like structure of native and modified RNA templates.

An RNA-dependent RNA polymerase (replicase) extract from brome mosaic virus-infected barley leaves has been shown to initiate synthesis of (-) sense RNA from (+) sense virion RNA. Initiation occurred de novo, as demonstrated by the incorporation of [gamma-32P]GTP into the product. Sequencing using cordycepin triphosphate to terminate (-) strands during their synthesis by the replicase generated sequence ladders that confirmed that copying was accurate, and that initiation occurred very close to the 3' end. The precise site of initiation was further defined by testing the replicase template activity after stepwise removal of 3'-terminal nucleotides. Whereas removal of the terminal A did not decrease template activity, removal of the next nucleotide (C-2) did. Thus, initiation almost certainly occurs opposite the penultimate 3'-nucleotide (C-2) in vitro. The structure of the double-stranded replicative form of RNA isolated from brome mosaic virus-infected leaves was consistent with such a mechanism occurring in vivo, in that it lacked the 3'-terminal A found on virion RNAs. The specific site of (-) strand initiation and normal template activity were retained for RNAs with as many as 15 to 30 A residues added to the 3' end. However, only limited oligonucleotide 3' extensions can be present on active templates. In order to assess the 5' extent of sequences required for an active template, a 134-nucleotide-long fragment of brome mosaic virus RNA, corresponding to the tRNA-like structure, was generated. This RNA had high template activity, but a shorter 3' (85-nucleotide) fragment was inactive. RNAs with various heterologous sequences 5' to position 134 also showed high template activity. Thus, the 3'-terminal tRNA-like structure common to all four brome mosaic virus virion RNAs contains all of the signals required for initiation of replication, and sequences 5' to it do not play a role in template selection.

Base Sequence↗

PubMed1994

Proinsulin processing in the regulated and the constitutive secretory pathway.

Proinsulin is converted to insulin in beta-cell granules. Conversion involves endoproteolytic cleavage at the two pairs of basic residues linking the insulin A- and B-chains to C-peptide. The sequence of events leading to complete conversion differs from one proinsulin species to the next. In man, the structure of the proinsulin molecule is such as to favour cleavage at the B-chain/C-peptide junction leading to the generation of des-31,32 split proinsulin as the predominant, naturally occurring conversion intermediate. Under normal circumstances, proinsulin conversion is largely completed before secretion, and neither the intact prohormone nor conversion intermediates are thus encountered in large quantities in the circulation. In some pathological situations, including non-insulin-dependent diabetes, insulinoma and familial hyperproinsulinaemia, unusually high ratios of des-31,32 split proinsulin and/or proinsulin to insulin have been reported. As we understand the biochemistry of proinsulin conversion in increasingly fine molecular detail, it should become possible to make use of such unusual ratios to provide insight into lesions underlying altered beta-cell function in disease states.

Animals↗

PubMed2000

Cbfa1, an essential transcription factor for bone formation, is expressed in testis from the same promoter used in bone.

Cbfa1 is an essential transcription factor for bone formation, but its transcripts have also been detected in thymus and testis. To elucidate the expression of Cbfa1 in testis, we isolated Cbfa1 cDNA from mouse testis. First we examined the length of the transcripts expressed in mouse testis by Northern hybridization. Using a cDNA probe that can detect both Type-I and Type-II Cbfa1 (Type-I: originally reported as Pebp2alphaA by Ogawa et al.; Type-II: originally reported as til-1 by Stewart et al.), 1.8-kb transcripts were detected in testis, and larger transcripts (6.3 kb and 7.4 kb) in T-cell lines, thymus and bone. Using a Type-II specific probe (bone isoform-specific probe), surprisingly, 1.8-kb testis transcript(s) were detected as well as those (6.3 kb) found in bone. In addition, the transcription start site in mouse testis coincides with one of three start sites identified in bone. These results suggest that the testis transcript is generated from the same promoter of Type-II Cbfa1, which is thought to be active only in osteoblasts and some chondrocytes. Next, to define the difference in length of transcripts, we isolated the Cbfa1 cDNA from mouse testis. Sequence analysis of the cDNA showed that alternative splicing around exon 2 and poly-adenylation within exon 8 occurred in the testis isoform, which produce the smaller transcripts. These data revealed that testis Cbfa1 mRNA is transcribed from same promoter used in bones, but the post-transcriptional regulation is different between testis and skeletal tissues.

Animals↗

PubMed2006

How lifetimes shape epigenotype within and across generations.

Despite our detailed characterization of the human genome at the level of the primary DNA sequence, we are still far from understanding the molecular events underlying phenotypic variation. Epigenetic modifications to the DNA sequence and associated chromatin are known to regulate gene expression and, as such, are a significant contributor to phenotype. Studies of inbred mice and monozygotic twins show that variation in the epigenotype can be seen even between genetically identical individuals and that this, in some cases at least, is associated with phenotypic differences. Moreover, recent evidence suggests that the epigenome can be influenced by the environment and these changes can last a lifetime. However, we also know that epigenetic states in real-time are in continual flux and, as a result, the epigenome exhibits instability both within and across generations. We still do not understand the rules governing the establishment and maintenance of the epigenotype at any particular locus. The underlying DNA sequence itself and the sequence at unlinked loci (modifier loci) are certainly involved. Recent support for the existence of transgenerational epigenetic inheritance in mammals suggests that the epigenetic state of the locus in the previous generation may also play a role. Over the next decade, many of these processes will be better understood, heralding a greater capacity for us to correlate measurable molecular marks with phenotype and providing the opportunity for improved diagnosis and presymptomatic healthcare.

Animals↗

PubMed1997

Interrelating of ventricular pressure and intracellular calcium in intact hearts.

Although the mechanistic link between variations in intracellular calcium and its effects on myofilament regulatory proteins and subsequent impact on cardiac muscle force production have been known for some time, characterization of cardiac contractile properties are predominantly confined to phenomenological descriptions of the relationship between either muscle length and force or ventricular pressure and volume. However, as recognition of the limitations of these theories grow, investigators have begun to look toward more fundamental theories of cardiac contraction to explain whole heart function. The goal of the present study was first to explore, on a theoretical level, the degree of complexity required in a biochemical model necessary to adequately explain both equilibrium and twitch contraction behavior of cardiac muscle. Central to this analysis was a critical examination of the evidence for and against the importance of a calcium-free, force-generating state. Next, we determined whether such theories can actually account for the interrelationships between the experimentally measured time courses of pressure generation and the calcium transient measured from intact ventricles during both normal twitches as well as during complex contraction sequences. The results of this analysis provide strong support for a four-state model, including the calcium-free, force-generating state. These results will help guide the continuing quest for a mechanistic theory of ventricular function.

Aequorin↗

PubMed2006

Nuclear and mitochondrial markers reveal distinctiveness of a small population of bottlenose whales (Hyperoodon ampullatus) in the western North Atlantic.

Small populations at the edge of a species' distribution can represent evolutionary relics left behind after range contractions due to climate change or human exploitation. The distinctiveness and genetic diversity of a small population of bottlenose whales in the Gully, a submarine canyon off Nova Scotia, was quantified by comparison to other North Atlantic populations using 10 microsatellites and mitrochondrial DNA (mtDNA) control region sequences (434 bp). Both markers confirmed the distinctiveness of the Gully (n = 34) from the next nearest population, off Labrador (n = 127; microsatellites -F(ST)= 0.0243, P < 0.0001; mtDNA -Phi(ST) = 0.0456, P < 0.05). Maximum likelihood microsatellite estimates suggest that less than two individuals per generation move between these areas, refuting the hypothesis of population links through seasonal migration. Both males and females appear to be philopatric, based on significant differentiation at both genomes and similar levels of structuring among the sexes for microsatellites. mtDNA diversity was very low in all populations (h = 0.51, pi = 0.14%), a pattern which may be due to selective sweeps associated with this species' extreme deep-diving ecology. Whaling had a substantial impact on bottlenose whale abundance, with over 65 000 animals killed before the hunt ceased in the early 1970s. Genetic diversity was similar among all populations, however, and no signal for bottlenecks was detected, suggesting that the Gully is not a relic of a historically wider distribution. Instead, this unique ecosystem appears to have long provided a stable year-round habitat for a distinct population of bottlenose whales.

Animals↗

PubMed2026

Molecular biology and integrated strategies for activating cryptic biosynthetic gene clusters toward next-generation antibiotic discovery.

Antimicrobial resistance (AMR) has been identified as one of the 21st century's severest global public health crises. AMR led to an estimated 4.95 million deaths in 2019 and will claim 10 million lives a year by 2050 in the absence of targeted interventions. During the same period, the number of novel antibiotics discovered has decreased drastically as many researchers are rediscovering known antibiotics, non-model microorganisms are poorly understood or difficult to culture and antibiotic research and development investment has declined drastically. However, high-throughput whole genome sequencing and the subsequent application of bioinformatics in bacterial and fungal genomes have shown that a numerous of cryptic or silent biosynthetic gene clusters (BGCs) remain latent at ambient laboratory conditions since their genes are transcriptionally inactive. Cryptic BGCs represent a vast source of unique secondary metabolites, many of which may yield novel antibacterial, antifungal, anti-cancer and other potentially valuable natural products. This review discusses the biological relevance of cryptic BGCs, the major limiting factors that restricts their activation and novel strategies that have been employed to activate them and exploit their potential to produce novel natural products. The review focuses on biological approaches including CRISPR-Cas mediation for the activation of cryptic BGCs, promoter engineering, pathway refactoring, and heterologous expression; biochemical strategies such as Osman, OsMAC, Precursor Feeding, Chemical Elicitation, Epigenetic Regulation and Co-cultivation and technology-based strategies such as Genome mining, Microfluidic Cultivation systems, High-Throughput Screening, Metabolomics, Molecular Networking and Artificial Intelligence and Machine Learning based prediction of BGCs and their metabolites. The use of multi-omics technologies combined with synthetic biology to achieve better discovery, characterization and large-scale production of novel natural products is also discussed herein. Finally, we will talk about the ecological significance and evolutionary advantage of cryptic BGCs' role in interactions between microorganisms, such as competition, communication, symbiosis and environmental adaptability, so as to provide a useful background for accelerating next-generation antibiotics.

CRISPR-Cas activation↗

PubMed1995

Multiple modes of ligand recognition: crystal structures of cyclin-dependent protein kinase 2 in complex with ATP and two inhibitors, olomoucine and isopentenyladenine.

Cyclin-dependent kinases (CDKs) are conserved regulators of the eukaryotic cell cycle with different isoforms controlling specific phases of the cell cycle. Mitogenic or growth inhibitory signals are mediated, respectively, by activation or inhibition of CDKs which phosphorylate proteins associated with the cell cycle. The central role of CDKs in cell cycle regulation makes them a potential new target for inhibitory molecules with anti-proliferative and/or anti-neoplastic effects. We describe the crystal structures of the complexes of CDK2 with a weakly specific CDK inhibitor, N6-(delta 2-isopentenyl)adenine, and a strongly specific inhibitor, olomoucine. Both inhibitors are adenine derivatives and bind in the adenine binding pocket of CDK2, but in an unexpected and different orientation from the adenine of the authentic ligand ATP. The N6-benzyl substituent in olomoucine binds outside the conserved binding pocket and is most likely responsible for its specificity. The structural information from the CDK2-olomoucine complex will be useful in directing the search for the next generation inhibitors with improved properties.

Adenine↗

PubMed2004

Identification of STAG1 as a key mediator of a p53-dependent apoptotic pathway.

A mutant version of p53 (p53-121F), in which phenylalanine replaces the 121st serine residue, can induce apoptosis more effectively than wild-type p53 (wt-p53). In view of this observation, we considered that one or more apoptosis-related p53-target genes might be preferentially induced by p53-121F. We carried out cDNA microarray analysis to identify such genes, using mRNAs isolated from LS174T colon-cancer cells infected by adenovirus vectors containing either p53-121F (Ad-p53-121F) or wt-p53 (Ad-p53). The STAG1 gene was one of the transcripts showing higher expression levels in cells infected with Ad-p53-121F as opposed to Ad-wtp53. The encoded product appears to contain a transmembrane domain, and binding motifs for SH3 and WW. In two other cancer cell lines, the expression of STAG1 mRNA was induced in response to various genotoxic stresses in a p53-dependent manner; moreover, enforced expression of STAG1 led to apoptosis in several additional cancer cell lines. Suppression of endogenous STAG1 using the RNA-interference method reduced the apoptotic response, whether induced by Ad-p53-121F or Ad-p53. These results suggest that STAG1, a novel transcriptional target for p53, mediates p53-dependent apoptosis, and might be a good candidate for next-generation gene therapy.

Amino Acid Substitution↗

PubMed2005

Generating highly ordered DNA nanostrand arrays.

Highly ordered arrays of stretched DNA molecules were generated over the millimeter scale by using a modified molecular combing method and soft lithography. Topological micropatterning on polydimethyl siloxane stamps was used to mediate the dynamic assembly of DNA molecules into arranged nonostrand arrays. These arrays consisted of either short nanostrands of several micrometers with fixed length and orientation or long nanostrands up to several hundred micrometers in length. The nanostrand arrays were transferred onto flat solid surfaces by contact printing, allowing for the creation of more complex patterns. This technique has potential applications for the construction of next-generation DNA chips and functional circuits of DNA-based 1D nanostructures.

DNA↗