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PubMed1988

Rapid production of full-length cDNAs from rare transcripts: amplification using a single gene-specific oligonucleotide primer.

We have devised a simple and efficient cDNA cloning strategy that overcomes many of the difficulties encountered in obtaining full-length cDNA clones of low-abundance mRNAs. In essence, cDNAs are generated by using the DNA polymerase chain reaction technique to amplify copies of the region between a single point in the transcript and the 3' or 5' end. The minimum information required for this amplification is a single short stretch of sequence within the mRNA to be cloned. Since the cDNAs can be produced in one day, examined by Southern blotting the next, and readily cloned, large numbers of full-length cDNA clones of rare transcripts can be rapidly produced. Moreover, separation of amplified cDNAs by gel electrophoresis allows precise selection by size prior to cloning and thus facilitates the isolation of cDNAs representing variant mRNAs, such as those produced by alternative splicing or by the use of alternative promoters. The efficacy of this method was demonstrated by isolating cDNA clones of mRNA from int-2, a mouse gene that expresses four different transcripts at low abundance, the longest of which is approximately 2.9 kilobases. After less than 0.05% of the cDNAs produced had been screened, 29 independent int-2 clones were isolated. Sequence analysis demonstrated that the 3' and 5' ends of all four int-2 mRNAs were accurately represented by these clones.

Animals↗

PubMed1994

Exact permutational tests for group sequential clinical trials.

An efficient numerical algorithm is developed for computing stopping boundaries for group sequential clinical trials. Patients arrive in sequence, and are randomized to one of two treatments. The data are monitored at interim time points, with a fresh block of patients entering the study from one monitoring point to the next. The stopping boundaries are derived from the exact joint permutational distribution of the linear rank statistics observed across all the monitoring times. Specifically, the algorithm yields the exact boundary generating function, Pr(W1 < b1, W2 < b2, ..., Wi-1 < bi-1, Wi = wi), where Wj is the linear rank statistic at the jth interim time point. The distribution theory is based on assigning ranks after pooling all the patients who have entered the study, and then permuting the patients to the two treatments independently within each block of newly arrived patients. The methods are applicable for an arbitrary number of monitoring times, which need not be specified at the start of the study. The data may be continuous or categorical, and censored or uncensored. The randomization rule for treatment allocation can be adaptive. The algorithm is especially useful during the early stages of a clinical trial, when very little data have been gathered, and stopping boundaries are based on the extreme tails of the relevant boundary generating function. In that case the corresponding large-sample theory is not very reliable. To illustrate the techniques we present a group sequential analysis of a recently completed study by the Eastern Cooperative Oncology Group.

Algorithms↗

PubMed1997

Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.

We have determined the structure of Pvu II methyltransferase (M. Pvu II) complexed with S -adenosyl-L-methionine (AdoMet) by multiwavelength anomalous diffraction, using a crystal of the selenomethionine-substituted protein. M. Pvu II catalyzes transfer of the methyl group from AdoMet to the exocyclic amino (N4) nitrogen of the central cytosine in its recognition sequence 5'-CAGCTG-3'. The protein is dominated by an open alpha/beta-sheet structure with a prominent V-shaped cleft: AdoMet and catalytic amino acids are located at the bottom of this cleft. The size and the basic nature of the cleft are consistent with duplex DNA binding. The target (methylatable) cytosine, if flipped out of the double helical DNA as seen for DNA methyltransferases that generate 5-methylcytosine, would fit into the concave active site next to the AdoMet. This M. Pvu IIalpha/beta-sheet structure is very similar to those of M. Hha I (a cytosine C5 methyltransferase) and M. Taq I (an adenine N6 methyltransferase), consistent with a model predicting that DNA methyltransferases share a common structural fold while having the major functional regions permuted into three distinct linear orders. The main feature of the common fold is a seven-stranded beta-sheet (6 7 5 4 1 2 3) formed by five parallel beta-strands and an antiparallel beta-hairpin. The beta-sheet is flanked by six parallel alpha-helices, three on each side. The AdoMet binding site is located at the C-terminal ends of strands beta1 and beta2 and the active site is at the C-terminal ends of strands beta4 and beta5 and the N-terminal end of strand beta7. The AdoMet-protein interactions are almost identical among M. Pvu II, M. Hha I and M. Taq I, as well as in an RNA methyltransferase and at least one small molecule methyltransferase. The structural similarity among the active sites of M. Pvu II, M. Taq I and M. Hha I reveals that catalytic amino acids essential for cytosine N4 and adenine N6 methylation coincide spatially with those for cytosine C5 methylation, suggesting a mechanism for amino methylation.

Amino Acid Sequence↗

PubMed2005

Theoretically modeling microarray with the chemical equilibrium and thermodynamics.

To date, the idea that microarray may shed the light on cellular processes by identifying groups of genes that appear to be co-expressed seems to remain a dream. This is partly because that there are some blank (meaning the knowledge is unavailable) or even erroneous areas in the fundamental theory in this field. This paper attempts to present the digest of microarray hybridization system with chemical thermodynamics, theoretically clarifying some misunderstandings and looking for answers to some critical questions around this technology, such as the mechanisms and conditions of quantitative measuring by hybridization reaction, the reasons of inconsistency of the data and the analysis results and the solutions, how to analyze the data, etc. A theoretical model for the next generation of microarray is proposed. We believe that this model is universal, laying the foundation for microarray technology from array design through the data analysis.

Computer Simulation↗

PubMedDate not supplied

Toward the next-generation drug delivery vehicle: synthesis of a dendrimer with four orthogonally reactive groups.

The synthesis of a dendrimer based on melamine that displays multiple copies of four orthogonally reactive groups, three on the surface and one on the interior, is described. The three groups on the surface are nucleophilic and include four free hydroxyl groups, four hydroxyl groups masked as tert-butyldiphenylsilyl (TBDPS) ethers, and 16 amines masked as tert-butoxycarbonyl (BOC) groups. The core of the dendrimer displays two electrophilic monochlorotriazines. The dendrimer is available in seven linear steps (eight total steps) at 55% overall yield for the longest linear sequence.

Amines↗

PubMed1993

[Depressed mothers: the impact of depression on early interactions. An analysis of Anglo-Saxon studies].

Maternal depression remains a public health problem as indicated by many studies focusing on depression in mothers of young children. Although the high prevalence of depression in mothers of infants and young children is now a recognized fact, the detection and management of maternal depression in everyday practice still raises significant problems. This initial review centers on studies providing diagnostic guidelines. The problem of maternal depression and of its impact on the offspring is relevant to the issue of how qualities, abilities, and vulnerabilities are transmitted from one generation to the next. Psychoanalysts, infant psychiatrists, and developmental psychologists show great interest in this field. The current review was restricted to recent Anglo-Saxon studies on depression-related changes in early maternal behavior. The most striking findings are as follows: although depression affects maternal behavior overall, there is considerable variation across mothers; timing alterations (in terms of micro and macro sequences) in mother-child interactions occur in every case and are among the obstacles to harmony and synchronization; subtle alterations in the mother's response to her baby's signals preclude flexibility and anticipation.

Adult↗

PubMed2005

Transcription of the murine gammaherpesvirus 68 ORF73 from promoters in the viral terminal repeats.

Gammaherpesviruses persist as latent episomes in a dynamic lymphocyte pool. The regulated production of an episome maintenance protein is therefore crucial to their survival. The transcription initiation site of the murine gammaherpesvirus 68 episome maintenance protein, ORF73, was mapped to the viral terminal repeats, more than 10 kb distant from the open reading frame (ORF) itself. A 5' non-coding exon in the terminal repeats was spliced to the right end of the viral unique sequence, and then across ORFs 75a, 75b, 75c and 74 to ORF73. The right-hand portion of a single repeat unit was sufficient for constitutive promoter activity. The unique left end of the viral genome further enhanced ORF73 transcription. This, together with the large size of the predominant ORF73 mRNA, suggested that transcription initiates in distal repeat units and then splices between repeats to generate an extensive 5' untranslated region. A second promoter in the left-hand portion of the proximal terminal repeat unit generated a transcript which overlapped that of ORF73, but failed to splice to the ORF73 coding exon and so transcribed ORF75a. In distal repeat copies, however, transcription from this promoter would enter the next repeat unit to become an ORF73 mRNA. There was a third promoter just upstream of ORF73 itself. These data indicate that ORF73 transcription is highly complex, and support the idea that the terminal repeats of gamma-2-herpesviruses constitute a vital component of episomal persistence.

Animals↗

PubMed2006

Conjecture: imines as unidirectional photodriven molecular motors-motional and constitutional dynamic devices.

Compounds containing the C==N group, such as imines and their derivatives, may undergo syn-anti isomerization by two different routes: 1) photochemically, by out-of-plane rotation around the carbon-nitrogen double bond through a "perpendicular" form, and 2) thermally, by in-plane nitrogen inversion through a "linear" transition state. When the two interconversions occur in sequence, a full, closed process is accomplished, restoring the initial state of the system along two different steps. In a chiral imine-type compound, for example, with an asymmetric center next to the C==N function, photoinduced rotation may be expected to occur in one sense in preference to the opposite one. Thus, photoisomerization followed by thermal isomerization in a chiral imine compound generates unidirectional molecular motion. Generally, imine-type compounds represent unidirectional molecular photomotors converting light energy into mechanical motion. As they are also able to undergo exchange of the carbonyl and amine partners, they present constitutional dynamics. Thus, imine-type compounds are double dynamic, motional, and constitutional devices.

Imines↗

PubMed1988

Regulation of Mu element copy number in maize lines with an active or inactive Mutator transposable element system.

In the progeny of an active Mutator plant, the number of Mu elements increases on self-pollination and maintains the average parental Mu content on outcrossing to a non-Mutator line; both patterns of transmission require an increase in the absolute number of Mu elements from one generation to the next. The same average copy number of Mu elements is transmitted through the male and female, but there is wide variation in the absolute copy number among the progeny. In inactive Mutator plants-defined both by the loss of somatic instability at a reporter gene (bronze2-mu1) and by modification of the HinfI sites in the terminal inverted repeat sequences of Mu elements - the absolute copy number of Mu elements is fixed in the parent. Thus, in outcrosses Mu element number is halved, and on self-pollination Mu copy number is constant. Reactivation of somatic mutability at cryptic bz2-mu1 alleles in inactive individuals by crossing to an active line seems not to involve an increase in Mu element copy number transmitted by the inactive individual. These and other results suggest that increases in Mu copy number occur late in plant development or in the gametophyte rather than after fertilization.

DNA Transposable Elements↗

PubMed2006

vasa mRNA accumulates at the posterior pole during blastoderm formation in the flour beetle Tribolium castaneum.

The correct specification of germ cells during embryogenesis is a fundamental step in life that ensures the existence of the next generation. Although different species display various cellular modes of generating germ cells, the product of the vasa gene proves to be a reliable marker of primordial germ cells in metazoans [Extavour and Akam (2003) 130:5869-5884; Raz (2000) 1:1017]. Here, I report the isolation of the vasa ortholog from the red flour beetle Tribolium castaneum, named Tc-vasa, and describe its sequence, its genomic organisation and its expression pattern during early embryogenesis. Unlike in Drosophila where vasa messenger RNA (mRNA) is ubiquitously distributed in the egg, Tc-vasa mRNA gradually accumulates at the posterior egg pole during blastoderm formation. Shortly before gastrulation, Tc-vasa mRNA marks a group of intra-blastodermal cells at the posterior pole. In the germ rudiment, a ball-like group of vasa-positive cells adheres to the growth zone at the posterior end of the embryo. These vasa-positive cells likely represent the primordial germ cells that have not been described in Tribolium prior to gonad formation. At the beginning of germ growth, a small band of vasa-positive cells starts to migrate along the dorsal side of the growth zone. vasa transcription ceases during further germ band extension. In contrast to Drosophila, Tc-vasa transcripts cannot be detected in the germ cells within the gonadal anlage after segmentation is completed.

Amino Acid Motifs↗

PubMed2002

Evolvability of random polypeptides through functional selection within a small library.

A directed evolution with phage-displayed random polypeptides of about 140 amino acid residues was followed until the sixth generation under a selection based on affinity to a transition state analog for an esterase reaction. The experimental design deliberately limits the observation to only 10 clones per generation. The first generation consists of three soluble random polypeptides and seven arbitrarily chosen clones from a previously constructed library. The clone showing the highest affinity in a generation was selected and subjected to random mutagenesis to generate variants for the next generation. Even within only 10 arbitrarily chosen polypeptides in each of the generations, there are enough variants in accord to capacity of binding affinity. In addition, the binding capacity of the selected polypeptides showed a gradual continuous increase over the generation. Furthermore, the purified selected random polypeptides exhibited a gradual but significant increase in esterase activity. The ease of the functional development within a small sequence variety implies that enzyme evolution is prompted even within a small population of random polypeptides.

Amino Acid Sequence↗

PubMed2005

One hundred years of physiology education in Singapore.

Physiology is the study of normal function in the body and how genes, proteins, organ systems interact to maintain health. It provides a foundation for the health sciences profession and life science research. Physiology education in Singapore began soon after the establishment of the Federated States Government Medical School in 1905. The importance of Physiology to medical education was recognised by the appointment of a separate lecturer in Physiology in 1906, followed by the appointment of Professor James Argyll Campbell as the first King Edward VII professor and endowed Chair in Physiology in 1912. The teaching of Physiology in the early days was focused on the basics of normal function with little correlation to clinical problems and application. However, by the 1970s, first-year medical students were given the opportunity to visit hospitals where they were tutored by clinicians to help them apply Basic Physiology to clinical problems. Curriculum changes in the subsequent years emphasised a reduction in content, integration among preclinical subjects, independent learning and clinical relevance. Physiology is taught not only to medical but also dental, pharmacy and life science students. The teaching of Physiology to science students is a collaborative effort between the Department of Physiology, Faculty of Medicine and the Department of Biological Sciences, Faculty of Science. A lot of the teaching of Physiology to life science students occurs not in classrooms but in the laboratories, where students work closely with research supervisors and mentors on research projects. There has been a very significant increase in the number of students doing research projects in Physiology in recent years, especially in the areas of Cell Physiology, Immunology and Neurobiology. The completion of the human genome sequence poses new challenges to understand function, especially how genes, proteins and organ systems interact to sustain function. Physiology education will be increasingly important in the undergraduate and graduate life science and medical curriculum. Further, the country's vision of being the biomedical R&D and healthcare hub for the region means that Physiology education must remain at the forefront to prepare the next generation of doctors, clinician-scientists, researchers and entrepreneurs.

Education, Medical, Undergraduate↗

PubMed1996

The Ikaros gene encodes a family of lymphocyte-restricted zinc finger DNA binding proteins, highly conserved in human and mouse.

The Ikaros gene is an essential regulator in the development and homeostasis of the mouse lymphopoietic system. To study the role of the Ikaros gene in the human lymphopoietic system, we cloned and characterized human Ikaros cDNAs. In the human, as in the mouse, differential splicing of Ikaros primary transcripts generates a family of lymphoid-restricted zinc finger DNA binding proteins, highly conserved in sequence composition and relative expression to the mouse homologues. Expression of Ikaros isoforms is highly restricted to the lymphopoietic system and is particularly enriched in maturing thymocytes. The Ikaros gene maps at a syntenic locus located on the short arm of human chromosome 7 and on mouse chromosome 11 next to the epidermal growth factor receptor (Egfr). The high degree of conservation of the Ikaros gene at the genetic and expression levels strongly suggests that it plays a fundamental role in the ontogeny of the lymphopoietic system across species.

3T3 Cells↗

PubMed2002

The mutation of two amino acid residues in the N-terminus of tyrosine hydroxylase (TH) dramatically enhances the catalytic activity in neuroendocrine AtT-20 cells.

The sequence Arg37-Arg38 of tyrosine hydroxylase (TH) is known to play a significant role in the feedback inhibition by the end product DA. To clarify how deeply the sequence Arg37-Arg38 and the phosphorylated Ser40 of human TH type 1 (hTH1) are involved in the regulation of this feedback inhibition in mammalian cells, we generated the following mutants: (i) RR-GG, Arg37-Arg38 replaced by Gly37-Gly38; (ii) RR-EE, Arg37-Arg38 replaced by Glu37-Glu38; (iii) S40D, Ser40 replaced by Asp40; and (iv) S40A, Ser40 replaced by Ala40. In a cell-free system, the level of the DA inhibition of the RR-EE mutant enzyme was to the same or smaller degree than that of the phosphorylation-mimicking S40D. Next, AtT-20 neuroendocrine cells were transfected with wild-type and mutated TH genes because these cells were earlier shown to be capable of fully converting L-3,4-dihydroxyphenylalanine into DA, whereby the catalytic activity of TH would be expected to be inhibited by the end product DA accumulating in the cells. The level of DA accumulation in AtT-20 cells expressing the TH gene was in the order: RR-EE > S40D > S40A = RR-GG > wild-type, which was in accordance with the observations for the cell-free system. These results suggest that the sequence Arg37-Arg38 of hTH1 is a more potent determinant of the efficient production of DA in mammalian cells than is the phosphorylated Ser40-hTH1.

3,4-Dihydroxyphenylacetic Acid↗

PubMed1999

How the worm was won. The C. elegans genome sequencing project.

The genome sequence of the free-living nematode Caenorhabditis elegans is nearly complete, with resolution of the final difficult regions expected over the next few months. This will represent the first genome of a multicellular organism to be sequenced to completion. The genome is approximately 97 Mb in total, and encodes more than 19,099 proteins, considerably more than expected before sequencing began. The sequencing project--a collaboration between the Genome Sequencing Center in St Louis and the Sanger Centre in Hinxton--has lasted eight years, with the majority of the sequence generated in the past four years. Analysis of the genome sequence is just beginning and represents an effort that will undoubtedly last more than another decade. However, some interesting findings are already apparent, indicating that the scope of the project, the approach taken, and the usefulness of having the genetic blueprint for this small organism have been well worth the effort.

Animals↗

PubMed2001

The marks, mechanisms and memory of epigenetic states in mammals.

It is well recognized that there is a surprising degree of phenotypic variation among genetically identical individuals, even when the environmental influences, in the strict sense of the word, are identical. Genetic textbooks acknowledge this fact and use different terms, such as 'intangible variation' or 'developmental noise', to describe it. We believe that this intangible variation results from the stochastic establishment of epigenetic modifications to the DNA nucleotide sequence. These modifications, which may involve cytosine methylation and chromatin remodelling, result in alterations in gene expression which, in turn, affects the phenotype of the organism. Recent evidence, from our work and that of others in mice, suggests that these epigenetic modifications, which in the past were thought to be cleared and reset on passage through the germline, may sometimes be inherited to the next generation. This is termed epigenetic inheritance, and while this process has been well recognized in plants, the recent findings in mice force us to consider the implications of this type of inheritance in mammals. At this stage we do not know how extensive this phenomenon is in humans, but it may well turn out to be the explanation for some diseases which appear to be sporadic or show only weak genetic linkage.

Agouti Signaling Protein↗

PubMed2004

The compensation of head motion artifacts using an infrared tracking system and a new algorithm for fMRI.

We aim to provide a next generation Magnetic Resonance Imaging (MRI) technology with an integrated solution for reducing motion artifacts in brain imaging applications. New developments in the field of MRI are revolutionizing the diagnostic capabilities e.g. of functional (fMRI) of the technique. Unfortunately, motion artifacts are eminent problems in cerebral MRI images, especially in difficult patient populations (e.g. chronic pain, children, neonates). Patient motion artifacts are present in 2D sequences, but are extremely detrimental in multi-slice 3D sequences often employed in fMRI. The problem of motion compensation in MRI technology deals with: Identification of the source as well as pattern of motion. Obtaining a mathematical model of motion that can be used to identify and then compensate the motion effects. Optimizing the image acquisition sequence in order to minimize, or even eliminate, the effect of motion. We propose a method to obtain a quantitative measure of the movement of the head between different data acquisition points in both MRI, and functional MRI examination.

Algorithms↗

PubMed1984

The biological significance of meiosis.

Four possible biological functions of meiosis are considered. First, the conventional view that it generates by recombination and sexual reproduction the genetic diversity on which natural selection can act. Second, that recombination at meiosis plays an important role in the repair of genetic defects in germ line cells. Third, that it is essential, at least in animals, for the reprogramming of gametes which give rise to the fertilized egg. Fourth, that it helps maintain the immortality of the germ line, possible by a process of rejuvenation involving the removal of faulty RNA and protein molecules, or by the elimination of defective meiocytes. A unified hypothesis is proposed which attempts to link these diverse functions. Evidence is now available which strongly indicates that the control of gene activity in higher organisms depends in part on the pattern of cytosine methylation in DNA, and that this pattern is inherited through the activity of a maintenance methylase. Epigenetic defects may arise by the loss of methyl groups which the methylase is unable to replace in somatic and also germ line cells, if de novo methylation cannot occur. There is also evidence that recombination at meiosis is largely confined to structural genes or adjacent DNA. It is proposed that the absence of a functionally important methyl group in a promotor or operater region produces a recombinator or signal for the initiation of recombination. The formation of hybrid DNA in this region then allows the lost methyl groups to be replaced by maintenance methylase activity. The removal of epigenetic defects by recombination during meiosis therefore becomes an essential part of a reprogramming and rejuvenation process. Assuming some epigenetic defects are nevertheless transmitted to the next generation, sexual reproduction and outbreeding would be advantageous because they provide the opportunity for their removal at the next meiosis. Inbreeding would be disadvantageous, because it increases the probability that epigenetic defects would become homozygous and could no longer be removed by recombination.

5-Methylcytosine↗