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PubMed2003

A pollen-expressed gene for a novel protein with an F-box motif that is very tightly linked to a gene for S-RNase in two species of cherry, Prunus cerasus and P. avium.

This study describes a novel F-box protein gene in the S-locus of sour cherry (Prunus cerasus) and sweet cherry (P. avium). The gene showed an S-haplotype-specific sequence polymorphism and the expression was specific to pollen. Genomic DNA blot analysis of eight sweet cherry cultivars with the probe for the F-box protein gene under low stringency conditions yielded RFLP bands specific to the S-haplotypes of each cultivar. We discuss the possibility of the gene for the F-box protein being a candidate for the male determinant of gametophytic self-incompatibility in PRUNUS:

Amino Acid Sequence↗
PubMed2003

Systematic reverse genetic screening of T-DNA tagged genes in rice for functional genomic analyses: MADS-box genes as a test case.

We have generated 47 DNA pools and 235 subpools from 21,049 T-DNA insertion lines of rice. DNA pools of 500-1,000 lines were adequate for screening a T-DNA insertion within a 2-kb region. To examine the efficacy of the DNA pools, we selected MADS-box genes, which play an important role in controlling various aspects of plant development. A total of 34 MIKC-type MADS-box genes have now been identified from rice sequence databases. Our PCR screening for T-DNA insertions within 12 MADS-box genes resulted in the identification of five insertions in four different genes. These DNA pools will be valuable when isolating T-DNA insertional mutants in various rice genes. The DNA pool screening service and the mutant seeds are available upon request to genean@postech.ac.kr.

DNA, Bacterial↗
PubMed1994

Mutational analysis of the N-capping box of the alpha-helix of chymotrypsin inhibitor 2.

The N-terminus of the helix of the chymotrypsin inhibitor 2 from barley (CI2) has an N-capping box (Ser at the first position in the helix and Glu at position 4) as well as a frequently found Glu at position 3. The energetic importance of this motif has been studied by determining the free energy of unfolding of the wild-type and protein mutants derived from those residues using guanidinium chloride-induced denaturation and differential scanning microcalorimetry. Mutating N-cap residue Ser31 to either Ala or Gly destabilizes CI2 by 0.8-1 kcal mol-1. Truncation of the box in the mutants SA31EA33EA34 or SG31EA33EA34 destablizes the protein by 1.5-2 kcal mol-1. The N-capping box is an important motif in stabilizing proteins and delineating the beginning of alpha-helices in the pathway of protein folding.

Calorimetry, Differential Scanning↗
PubMed1995

An approach to protein homology modelling based on an ensemble of NMR structures: application to the Sox-5 HMG-box protein.

A new approach has been developed to reduce multiple protein structures obtained from NMR structure analysis to a smaller number of representative structures which still reflect the structural diversity of the data sets. The method, based on the clustering of similar structures, has been tested in the homology model building of the structure of Sox-5, a sequence-specific DNA-binding protein belonging to the high mobility group (HMG) nuclear proteins family. Sox (SRY box) genes are the autosomal genes related to the sex-determining SRY, Y chromosomal gene. The Sox-5 protein, encoded by one of the SRY-related genes, displays a 29% sequence identity with the HMG1 B-box domain whose structure, determined previously by NMR, has been used in our study to predict the structure of Sox-5. Two independent ensembles of HMG1 structures, each represented by closely related coordinate sets, were used. Nine representative structures for HMG1 were subsequently selected as starting points for the modelling of Sox-5. The model of the protein shows close similarity to the HMG1 fold, with differences at the secondary structure level located mainly in alpha-helices 1 and 3. A left-handed, three residue per turn polyproline II helix, forming a conserved polyproline II/alpha-helix supersecondary motif, was identified in the N-terminal region of Sox-5 and other HMG boxes.

Algorithms↗
PubMed2001

ngl9: a third MADS box gene expressed in alfalfa root nodules.

Expression of MADS box genes has previously been localized to the infected cells of alfalfa (Medicago sativa) root nodules. These genes represent the first putative transcription factors to be identified in nodules and are hypothesized to be involved in a signal transduction pathway initiated by the intracellular bacterium. The eventual activation of specific target genes defines pertinent characteristics of this nitrogen-fixing differentiated cell. In this study, we identify a third nodule MADS box gene, ngl9, and demonstrate that the DNA-binding activity of its protein product is dependent on the presence of a second MADS box protein, NMH7. Despite previous results to the contrary, both genes are expressed in the early stages of flower development, further strengthening the premise that nodule developmental programming may capitalize upon existing developmental cascades.

Amino Acid Sequence↗
PubMed2002

A GC-box within the proximal promoter region of the rat cathepsin L gene activates transcription in Sertoli cells of sexually mature rats.

It has been proposed that stage-specific gene expression in Sertoli cells results from sequential activation and repression of transcription. However, the exact molecular mechanisms are unknown. As a first step in addressing this fundamental issue, we recently demonstrated that a 3-kilobase (kb) genomic fragment immediately upstream of the rat cathepsin L translation start site directed stage-specific expression of a reporter gene only in Sertoli cells of transgenic mice in a manner comparable to that of the endogenous gene (predominantly in stages VI-VIII tubules). Supporting the activation/repression model of regulation, an upstream domain that mediated an inhibitory effect by male germ cells was identified within this 3-kb promoter region. In the present study, we localized and characterized the regulatory elements that activate transcription. Analyses of a series of 5' deletion constructs demonstrated that a 120-base pair (bp) region that spans the transcription start site of the rat cathepsin L gene was sufficient to activate transcription in Sertoli cells isolated from sexually mature rats. Within this region, electrophoretic mobility shift assays showed that one member of the Sp/XKLF family of factors, Sp3, specifically bound to a GC-box. Furthermore, Sp1-binding activity was not detected in nuclear extracts from Sertoli cells of sexually mature rats. Finally, the GC-box was shown to be essential for promoter activity since mutating this binding motif abolished promoter activity. Collectively, these results suggest that the GC-box is a critical regulatory element for the cathepsin L promoter in mature Sertoli cells.

Animals↗
PubMed1998

Mammalian male and female germ cells express a germ cell-specific Y-Box protein, MSY2.

Here we report the isolation and characterization of mouse testicular cDNAs encoding the mammalian homologue of the Xenopus germ cell-specific nucleic acid-binding protein FRGY2 (mRNP3+4), hereafter designated MSY2. MSY2 is a member of the Y box multigene family of proteins; it contains the cold shock domain that is highly conserved among all Y box proteins and four basic/aromatic islands that are closely related to the other known germline Y box proteins from Xenopus, FRGY2, and goldfish, GFYP2. Msy2 undergoes alternative splicing to yield alternate N-terminal regions upstream of the cold shock domain. Although MSY2 is a member of a large family of nucleic acid-binding proteins, Southern blotting detects only a limited number of genomic DNA fragments, suggesting that Msy2 is a single copy gene. By Northern blotting and immunoblotting, MSY2 appears to be a germ cell-specific protein in the testis. Analysis of Msy2 mRNA expression in prepubertal and adult mouse testes, and in isolated populations of germ cells, reveals maximal expression in postmeiotic round spermatids, a cell type with abundant amounts of stored messenger ribonucleoproteins. In the ovary, MSY2 is present exclusively in diplotene-stage and mature oocytes. MSY2 is maternally inherited in the one-cell-stage embryo but is not detected in the late two-cell-stage embryo. This loss of MSY2 is coincident with the bulk degradation of maternal mRNAs in the two-cell embryo.

Alternative Splicing↗
PubMed1997

The value of additional carpal box radiographs in suspected scaphoid fracture.

RATIONALE AND OBJECTIVES: Carpal Box (CB) radiographs, transverse and longitudinal, produce elongated and magnified views of the carpus. These radiographs can be used after carpal injury, in addition to conventional scaphoid x-rays. In this study, the use of CB radiographs was evaluated in patients with possible scaphoid fracture. METHODS: Seventy-one consecutive patients who presented at the First Aid department from May 1994 to May 1995 were included. All patients were examined for scaphoid fracture after a fall on the out-stretched hand. If a scaphoid fracture was seen on the scaphoid x-rays, patients were immobilized. If the x-rays remained negative or dubious for fracture, additional transverse and longitudinal CB radiographs were obtained. If CB radiographs remained negative or inconclusive, patients were referred for three-phase bone scintigraphy. The results of independent and masked judgment by three different observers were used for an inter- and intraobserver analysis. RESULTS: Twenty of 71 patients initially showed a scaphoid fracture on the conventional scaphoid x-rays, 41 were negative, and 10 inconclusive. All 41 negative patients remained negative on CB radiograph; however, the bone scintigraphy was positive for scaphoid fracture in 11 patients and in 9 patients a hot spot elsewhere in the carpus was found. Of the 10 patients with inconclusive x-rays, 2 showed a clear fracture of the scaphoid on CB radiograph, 5 were negative, and 3 remained inconclusive. The agreement between observers, calculated in kappa values, was highest in CB radiographs. CONCLUSIONS: In the diagnosis of scaphoid fracture, Carpal Box radiography is of limited value in patients with clinically suspected scaphoid fracture. In two of 10 patients with initial dubious scaphoid x-ray, bone scintigraphy can be avoided. Furthermore, the reliability of the interpretation of the radiographs is increased by additional Carpal Box radiography.

Adolescent↗
PubMed1992

Use of a microprocessor-equipped tablet box in monitoring compliance with antihypertensive treatment.

Compliance with antihypertensive therapy is usually monitored by questionnaire, tablet counts, or estimation of drug levels in blood or in urine. The aim of this study was to examine patient compliance by means of an "electronic monitor." After 2 weeks of run-in on placebo, 34 moderately hypertensive patients were included in an open, randomized, crossover trial examining the efficacy and tolerance of nitrendipine, 20 mg as a single daily dose (morning or evening) for 1 month. We analyzed the results in 26 patients. Patients were supplied with tablet boxes equipped with a microprocessor (MENS) that registered the timing and duration of opening of the box over both the placebo and nitrendipine periods. Compliance (%) was calculated as the ratio of the number of days that the pill box was opened to the number of days between visits. The compliance was analyzed for each treatment group, namely placebo and nitrendipine morning and evening, over 1 month. Compliance (mean + SD) was 96.5 +/- 7.4% on placebo and 94.4 +/- 10.7% in the morning and 90.6 +/- 15.4% in the evening. Nitrendipine was taken in the morning at 0700 h +/- 2 h and in the evening at 1859 h +/- 2 h 12 min. The frequency of 24 h +/- 1 h intervals between medication was 83.5% on placebo. This frequency was 72.6% for morning dosage and 71.8% for evening dosage on nitrendipine. There were no differences in compliance between the morning and evening groups when analyzed according to age and sex. There was a negative correlation with time (r = -0.57, p less than 0.001).(ABSTRACT TRUNCATED AT 250 WORDS)

Blood Pressure↗
PubMed2001

Telemedicine in a box: overcoming complexity and high-cost telemedicine barriers using self-contained videoconferencing units.

This report describes our experience using low-and moderate-cost videoconferencing systems for telemedicine. After determining that low-cost systems using a standard personal computer and personal computer camera were unsatisfactory, a demonstration project was carried out using a $4000 self-contained videoconferencing unit (telemedicine in a box), using eight simulated telemedicine consultation scenarios. The quality of the videoconferencing was good for all eight scenarios. All eight consultation simulations demonstrated different ways of improving patient care. Two of the major problems hindering the broad proliferation of telemedicine (high cost and high complexity) are solved by the telemedicine in a box concept. Focussing on the telemedicine in a box concept when planning a telemedicine system will improve its feasibility in the real world of health care.

Humans↗
PubMed2006

Surplus nest boxes and the potential for polygyny affect clutch size and offspring sex ratio in house wrens.

Females of many species can gain benefits from being choosy about their mates and even exhibit context-dependent investment in reproduction in response to the quality of their breeding situation. Here, we show that if a male house wren is provided with surplus nest boxes in his territory, his mate lays a larger clutch with a significantly higher proportion of sons. This response to a territory characteristic directly associated with male competitive ability, and ultimately to male reproductive success, suggests that male competition over access to high-quality territories with surplus nest boxes (i.e. those able to support polygyny) may influence female reproductive investment decisions. The results of this study have interesting implications, particularly considering the important role that studies of cavity nesting birds utilizing nest boxes have played in advancing our understanding of behaviour, ecology and evolution.

Animals↗
PubMed2002

The role of multiple SOS boxes upstream of the Mycobacterium tuberculosis lexA gene--identification of a novel DNA-damage-inducible gene.

Four potential binding sites for LexA were identified upstream of the Mycobacterium tuberculosis lexA gene. A mutational analysis of these sites in a lexA-lacZ reporter construct revealed that only one of these SOS boxes was required for DNA-damage-mediated regulation of lexA expression. A novel DNA-damage-inducible gene, Rv2719c, was identified that was divergently transcribed relative to lexA; the other three SOS boxes were found to be involved in regulating expression of this novel mycobacterial-specific gene. The SOS boxes lay in the respective promoter regions of the genes that they regulated.

Amino Acid Sequence↗
PubMed2006

The orchid MADS-box genes controlling floral morphogenesis.

Orchids are known for both their floral diversity and ecological strategies. The versatility and specialization in orchid floral morphology, structure, and physiological properties have fascinated botanists for centuries. In floral studies, MADS-box genes contributing to the now famous ABCDE model of floral organ identity control have dominated conceptual thinking. The sophisticated orchid floral organization offers an opportunity to discover new variant genes and different levels of complexity to the ABCDE model. Recently, several remarkable research studies done on orchid MADS-box genes have revealed the important roles on orchid floral development. Knowledge about MADS-box genes' encoding ABCDE functions in orchids will give insights into the highly evolved floral morphogenetic networks of orchids.

Flowers↗
PubMed1996

Discrimination between different E-box-binding proteins at an endogenous target gene of c-myc.

c-myc plans a key role in regulating mammalian cell proliferation and apoptosis. The gene codes for a transcription factor, Myc, that belongs to the helix-loop-helix/leucine zipper (HLH/LZ) family of proteins. Myc heterodimerizes with a partner protein termed Max; the heterodimeric complex binds to CAC(G/A)TG (E-box) sequences and activates transcription from these sites. However, several other HLH/LZ proteins, including USF and TFE-3, bind to and trans-activate from the same element, yet have no documented effect on cell proliferation or apoptosis. Therefore, it is likely that mechanisms exist that discriminate between these proteins for activation of natural target genes of Myc. We now show that trans-activation from the E-box in the rat prothymosin-alpha intron enhancer is indeed specific for Myc, and identify both the distance from the start site of transcription and a second E-box element adjacent to that recognized by Myc as critical determinants of specificity. Surprisingly, transcription activation domains required for Myc to activate from this distal enhancer position differ from previously mapped domains and closely correlate with those domains essential for transformation. As observed in transformation assays, Myc and Max strongly synergize in activation from a distal enhancer position. Our data suggest that trans-activation from the prothymosin intron enhancer is a faithful reflection of the transforming properties of the Myc protein.

Animals↗
PubMed2006

PER-dependent rhythms in CLK phosphorylation and E-box binding regulate circadian transcription.

Transcriptional activation by CLOCK-CYCLE (CLK-CYC) heterodimers and repression by PERIOD-TIMELESS (PER-TIM) heterodimers are essential for circadian oscillator function in Drosophila. PER-TIM was previously found to interact with CLK-CYC to repress transcription, and here we show that this interaction inhibits binding of CLK-CYC to E-box regulatory elements in vivo. Coincident with the interaction between PER-TIM and CLK-CYC is the hyperphosphorylation of CLK. This hyperphosphorylation occurs in parallel with the PER-dependent entry of DOUBLE-TIME (DBT) kinase into a complex with CLK-CYC, where DBT destabilizes both CLK and PER. Once PER and CLK are degraded, a novel hypophosphorylated form of CLK accumulates in parallel with E-box binding and transcriptional activation. These studies suggest that PER-dependent rhythms in CLK phosphorylation control rhythms in E-box-dependent transcription and CLK stability, thus linking PER and CLK function during the circadian cycle and distinguishing the transcriptional feedback mechanism in flies from that in mammals.

Animals↗
PubMed1988

The ubiquitous octamer-binding protein Oct-1 contains a POU domain with a homeo box subdomain.

The octamer motif ATGCAAAT is recognized indistinguishably by two mammalian transcription factors: one that is expressed ubiquitously and referred to here as Oct-1, and another, Oct-2, that is expressed in lymphoid cells. We report the cDNA cloning of the human oct-1 gene, which encodes Oct-1, by screening lambda gt11 recombinant phage in situ for octamer motif-specific DNA binding. One lambda gt11 recombinant expressed a beta-galactosidase-octamer-binding fusion protein with a DNA-binding specificity indistinguishable from human HeLa cell Oct-1 protein. As expected for a ubiquitously expressed protein, Oct-1 mRNA is expressed in all five human and two mouse cell lines tested. Polyclonal rabbit antiserum raised against the beta-galactosidase fusion protein shows that the DNA-binding domains of Oct-1 and Oct-2 proteins are related antigenically. Deletion analysis of the 743-amino-acid-long oct-1 open reading frame shows that the DNA-binding activity lies within a central highly charged domain of 160 amino acids. Comparison of the Oct-1 and Oct-2 sequences reveals that this domain is nearly identical between the two proteins. Highly similar domains are also present in the pituitary-specific transcription factor Pit-1 and the Caenorhabditis elegans unc-86 cell lineage gene product (see Herr et al. 1988). Within this shared POU (Pit-1, Oct-1 and Oct-2, unc-86) domain (pronounced 'pow') lie two subdomains: a POU-related homeo box and a POU-specific box. The Oct-1 protein is unique among the POU-related proteins and other homeo box proteins because it is expressed ubiquitously.

Amino Acid Sequence↗
PubMed2003

The Polycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1.

The Polycomb-group (PcG) proteins MEDEA, FERTILIZATION INDEPENDENT ENDOSPERM, and FERTILIZATION INDEPENDENT SEED2 regulate seed development in Arabidopsis by controlling embryo and endosperm proliferation. All three of these FIS-class proteins are likely subunits of a multiprotein PcG complex, which epigenetically regulates downstream target genes that were previously unknown. Here we show that the MADS-box gene PHERES1 (PHE1) is commonly deregulated in the fis-class mutants. PHE1 belongs to the evolutionarily ancient type I class of MADS-box proteins that have not yet been assigned any function in plants. Both MEDEA and FIE directly associate with the promoter region of PHE1, suggesting that PHE1 expression is epigenetically regulated by PcG proteins. PHE1 is expressed transiently after fertilization in both the embryo and the endosperm; however, it remains up-regulated in the fis mutants, consistent with the proposed function of the FIS genes as transcriptional repressors. Reduced expression levels of PHE1 in medea mutant seeds can suppress medea seed abortion, indicating a key role of PHE1 repression in seed development. PHE1 expression in a hypomethylated medea mutant background resembles the wild-type expression pattern and is associated with rescue of the medea seed-abortion phenotype. In summary, our results demonstrate that seed abortion in the medea mutant is largely mediated by deregulated expression of the type I MADS-box gene PHE1.

Arabidopsis↗
PubMed1990

Differential activation of Xenopus homeo box genes by mesoderm-inducing growth factors and retinoic acid.

What is the nature of positional information during embryogenesis? By using Xenopus homeo box genes as anteroposterior (A-P) markers, we confirm the findings of others that mesoderm-inducing growth factors and retinoic acid (RA) can provide positional information along the axis of the body. Xenopus tissue culture-mesoderm-inducing factor (XTC-MIF) selectively activates an anteriorly expressed homeo box gene (XlHbox 1), while basic fibroblast growth factor (bFGF) activates selectively a posteriorly expressed homeo box gene (XlHbox 6). RA activates expression of the posterior gene XlHbox 6, but not of XlHbox 1. This activation, however, requires exposure to growth factors. The data suggest that growth factors and RA may cooperate with each other to provide positional information in vertebrates.

Animals↗