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PubMed2025

Whole genome sequencing-based detection of extensively drug-resistant tuberculosis from Ethiopia.

BACKGROUND: Rapid and accurate detection of extensively drug-resistant tuberculosis is crucial for effective intervention. Next-generation sequencing technologies have been recommended to rapidly and accurately detect resistance to second-line anti-TB drugs. We deployed whole-genome sequencing to detect mutations associated with drug resistance in pre-extensively drug-resistant tuberculosis and extensively drug-resistant tuberculosis strains in Ethiopia. METHODS: This report is part of the routine laboratory-based drug-resistance surveillance in Ethiopia. Among 15 pre-extensively drug-resistant tuberculosis and extensively drug-resistant tuberculosis isolates identified during the study period, eleven isolates were retrieved by Whole-genome sequencing. Illumina NextSeq 550 instruments were used to generate genomic data. Lineage and drug-resistance prediction were performed with Tuberculosis Profiler, while phylogeny was conducted by IQ-tree. RESULTS: Of the genotyped isolates, whole-genome sequencing identifies five extensively drug-resistant tuberculosis and four pre-extensively drug-resistant tuberculosis strains. It detects fluoroquinolone resistance mutations gyrA (Ala90Val, Asp94Tyr, Asp94Gly). Bedaquiline resistance mutations are found in atpE (Glu61Asp) and Rv0678 (139dupG, 141 and 142dupTC). Cross-resistance is identified between bedaquiline and clofazimine (n = 4) and delamanid and pretomanid (n = 1). Concordance result is observed between phenotypic drug-susceptibility testing and whole-genome sequencing for eight cases, while three cases are discordant (fluoroquinolones, delamanid, and pretomanid). Phylogenetic analysis reveals three major lineages: Lineage 4 (Euro-American, n = 6 isolates), Lineage 3 (East African-Indian, n = 3 isolates), and Lineage 1 (Indo-Oceanic, n = 2 isolates). CONCLUSIONS: Whole-genome sequencing identifies dominant mutations in genes such as gyrA, atpE, and Rv067 that are associated with resistance to second-line anti-tuberculosis drugs. Significant cross-resistance is observed between key second-line drugs, bedaquiline and clofazimine, as well as delamanid and pretomanid. This finding highlights the need for routine genomic surveillance to detect drug resistance early, improve treatment outcomes, and prevent transmission.

Journal Article↗

PubMed1995

Second-generation octarellins: two new de novo (beta/alpha)8 polypeptides designed for investigating the influence of beta-residue packing on the alpha/beta-barrel structure stability.

The sequence of octarellin I, the first de novo (beta/alpha)8 polypeptide, was revised according to several criteria, among others the symmetry of the sequence, beta-residue volume and hydrophobicity, and charge distribution. These considerations and the overall conclusions drawn from the first design led to two new sequences, corresponding to octarellins II and III. Octarellin II retains perfect 8-fold symmetry. Octarellin III has the same sequence as octarellin II, except for the beta-strands which exhibit a 4-fold symmetry. The two proteins were produced in Escherichia coli. Infrared and CD spectral analyses of octarellins II and III reveal a high secondary structure content. Non-denaturing gel electrophoresis, molecular sieve chromatography and analytical ultracentrifugation suggest that both of these second-generation artificial polypeptides exist as a mixture of a monomer and a dimer form. Octarellins II and III are at least 10 times more soluble than octarellin I. Urea-induced unfolding followed by fluorescence emission suggests that the tryptophan residues, designed to be buried in the (beta/alpha)8, are indeed packed in the hydrophobic core of both proteins. However, octarellin III displays a higher stability towards urea denaturation, indicating that introducing 4-fold symmetry into the beta-barrel might be important for stability of the overall folding.

Amino Acid Sequence↗

PubMed1995

Complex sensory-motor sequence learning based on recurrent state representation and reinforcement learning.

A novel neural network model is presented that learns by trial-and-error to reproduce complex sensory-motor sequences. One subnetwork, corresponding to the prefrontal cortex (PFC), is responsible for generating unique patterns of activity that represent the continuous state of sequence execution. A second subnetwork, corresponding to the striatum, associates these state-encoding patterns with the correct response at each point in the sequence execution. From a neuroscience perspective, the model is based on the known cortical and subcortical anatomy of the primate oculomotor system. From a theoretical perspective, the architecture is similar to that of a finite automaton in which outputs and state transitions are generated as a function of inputs and the current state. Simulation results for complex sequence reproduction and sequence discrimination are presented.

Animals↗

PubMed1982

Efficient algorithms for folding and comparing nucleic acid sequences.

Fast algorithms for analysing sequence data are presented. An algorithm for strict homologies finds all common subsequences of length greater than or equal to 6 in two given sequences. With it, nucleic acid pieces five thousand nucleotides long can be compared in five seconds on CDC 6600. Secondary structure algorithms generate the N most stable secondary structures of an RNA molecule, taking into account all loop contributions, and the formation of all possible base-pairs in stems, including odd pairs (G.G., C.U., etc.). They allow a typical 100-nucleotide sequence to be analysed in 10 seconds. The homology and secondary structure programs are respectively illustrated with a comparison of two phage genomes, and a discussion of Drosophila melanogaster 55 RNA folding.

Animals↗

PubMed1984

Apple II PASCAL programs for molecular biologists.

A collection of PASCAL programs designed for the Apple II microcomputer is presented. These DNA sequence handling and analysis programs are interactive and may be used even by people with no computer experience. The package allows the user to enter a sequence from the keyboard, to modify it, to generate the reverse complement, to create new sequences from parts of other ones, to display or print sequences in various formats. Some analysis tasks are also performed: Translation, searches for restriction sites, for homology with subsequences, either perfect or with an adjustable match percentage. In addition, two programs are also included: The first one allows DNA data sequences generated with a BASIC program under the CP/M operating system to be used with these PASCAL programs. The second one is designed for the automatic assembly of DNA fragments sequences, obtained with the GILBERT-MAXAM or M13 techniques, into a complete sequence.

Amino Acid Sequence↗

PubMed1986

The chromosomal gene structure and two mRNAs for human granulocyte colony-stimulating factor.

Two different cDNAs for human granulocyte colony-stimulating factor (G-CSF) were isolated from a cDNA library constructed with mRNA prepared from human squamous carcinoma cells, which produce G-CSF constitutively. The nucleotide sequence analysis of both cDNAs indicated that two polypeptides coded by these cDNAs are different at one position where three amino acids are deleted/inserted. When the two cDNAs were introduced into monkey COS cells under the SV40 early promoter, both of them produced proteins having authentic G-CSF activity and some difference in the specific activity was suggested. A human gene library was then screened with the G-CSF cDNA and the DNA fragment containing the G-CSF chromosomal gene was characterized by the nucleotide sequence analysis. The human G-CSF gene is interrupted by four introns and a comparison of the structures of the two G-CSF cDNAs with that of the chromosomal gene indicated that the two mRNAs are generated by alternative use of two 5' splice donor sequences in the second intron of the G-CSF gene. When the G-CSF chromosomal gene was expressed in monkey COS cells by using the SV40 enhancer two mRNAs were detected by S1 mapping analysis.

Amino Acid Sequence↗

PubMed1984

Centrally programmed patterns of muscle activity in voluntary motor behavior of humans.

Rapid voluntary limb movements are accompanied by a triphasic electromyogram (EMG): the agonist muscle discharges briefly to generate the initial limb displacement and then, in sequence, an antagonist and second agonist burst occur. The origins of these bursts of EMG have been attributed to both peripheral and central sources. We attempted to determine in human subjects whether somesthetic afferent inputs related to passive muscle stretch or joint rotation were necessary for the appearance of the three bursts. EMGs were recorded while subjects performed rapid isotonic movements before and after forearm afferent function was blocked by ischemia. EMG patterns were also studied during phasic and sustained isometric contractions of forearm muscles. When the forearm was ischemically deafferented the triphasic EMG pattern persisted though the amplitudes of the three bursts were modified. In separate experiments, a similar three burst pattern was also observed while phasic isometric contractions were performed but not when rapid-onset sustained isometric contractions were executed. These data support the view that somesthetic afferent information related to muscle length or joint rotation is not necessary for the occurrence of the three burst pattern during rapid motor behaviors. Since bursts of EMG activity were observed when torque rose and fell quickly during fast isotonic movements and phasic isometric contractions, the triphasic pattern appears to be a fundamental property of the central program underlying such rapid motor behaviors.

Adult↗

PubMed1978

DNA sequence at the integration sites of the insertion element IS1.

We have detected two independent occurrences of insertion mutations in the lacl gene of E. Coli, and have used small plasmids carrying the l gene to purify large amounts of DNA containing these insertions. Analyses with restriction endonucleases and DNA sequencing techniques establish that both insertions involve the previously characterized element IS1. In each case, the integration of IS1 into the l gene DNA is associated with a directly repeated sequence of 9 nucleotides appearing at each end of the insertion element. Since one of these sequences was present in the wild-type gene, the second sequence either preexisted in the IS1 before integration, or else was generated by the process of insertion itself. The 9 base repeat is different in both cases. We discuss the relevance of these findings to the mechanism of integration of transposable elements.

Base Sequence↗

PubMed1990

Introduction of specific point mutations into RNA polymerase II by gene targeting in mouse embryonic stem cells: evidence for a DNA mismatch repair mechanism.

We have introduced two specific point mutations, located 20 base pairs apart, into the endogenous murine gene that encodes the largest subunit of RNA polymerase II (RPII215). The first mutation conferred resistance to the mushroom toxin alpha-amanitin (amar), and the second mutation generated a restriction fragment length polymorphism without altering the protein sequence. Targeted amar clones were generated at a frequency of 1 in 30 totipotent embryonic stem cells that expressed stably integrated DNA vectors after electroporation. Thirty to 40% of these clones had acquired both mutations, whereas, surprisingly, the remaining clones had acquired the specific amar point mutation but lacked the restriction fragment length polymorphism. We suggest that the latter clones were generated by independent DNA mismatch repair rather than by double crossover or gene conversion. These results demonstrate that it is possible to introduce specific point mutations into an endogenous gene in embryonic stem cells. Thus it should be possible to introduce single base substitutions into other cellular genes, including nonselectable genes, by optimizing the efficiency of gene transfer and/or the sensitivity of screening for targeted clones.

Amino Acid Sequence↗

PubMed1987

The nucleotide sequence of the gene encoding the F protein of canine distemper virus: a comparison of the deduced amino acid sequence with other paramyxoviruses.

The nucleotide sequence of the gene encoding the fusion protein of canine distemper virus was determined from cDNA clones derived from virus genome RNA and poly(A)+ RNA extracted from infected cells. The mRNA encoding the F protein is about 2300 nucleotides in length including the 3' poly(A) tail. There is a large open reading frame from nucleotides 86 to 2071 which begins at the first AUG codon in the F mRNA. This reading frame encodes a protein of 662 amino acid residues with a calculated mol. wt. of 73001. The first major hydrophobic domain in the amino acid sequence of the deduced protein (residues 104 to 130) may represent all or part of a signal sequence for cleavage of the N terminal part of the F2 protein. There are four potential N glycosylation sites in the F protein located within the F2 part of the molecule or the putative signal sequence, and one in the F1 portion. A second hydrophobic region corresponds to the proteolytic cleavage site which generates the F2 and F1 subunits. This stretches from residue 225 to 262 and the N terminal part of the F1 protein shows sequence conservation with the other paramyxoviruses. A third major hydrophobic domain near the C terminus of the F protein probably represents the membrane anchor for the F protein (residues 602 to 630). The F1 proteins of six paramyxoviruses are compared and shown to have substantial conservation of those residues important in the maintenance of tertiary structure of this protein.

Amino Acid Sequence↗

PubMed1995

A truncated herpes simplex virus thymidine kinase phosphorylates thymidine and nucleoside analogs and does not cause sterility in transgenic mice.

Dividing eukaryotic cells expressing the herpes simplex virus type 1 thymidine kinase (TK) gene are sensitive to the cytotoxic effect of nucleoside analogs such as acyclovir or ganciclovir (GCV). Transgenic mice with cell-targeted expression of this conditional toxin have been used to create animals with temporally controlled cell-specific ablation. In these animal models, which allow the study of the physiological importance of a cell type, males are sterile. In this study, we showed that this phenomenon is due to testis-specific high-level expression of short TK transcripts initiated mainly upstream of the second internal ATG of the TK gene. This expression is DNA methylation independent. To obtain a suicide gene that does not cause male infertility, we generated and analyzed the properties of a truncated TK (delta TK) lacking the sequences upstream of the second ATG. We showed that when expressed at sufficient levels, the functional properties of delta TK are similar to those of TK in terms of thymidine or GCV phosphorylation. This translated into a similar GCV-dependent toxicity for delta TK- or TK-expressing cells, both in vitro and in transgenic mice. However, delta TK behaved differently from TK in two ways. First, it did not cause sterility in delta TK transgenic males. Second, low-level delta TK RNA expression did not confer sensitivity to GCV. The uses of delta TK in cell-specific ablation in transgenic mice and in gene therapy are discussed.

Animals↗

PubMed1994

Glomerulopathy induced by IgG3 anti-trinitrophenyl monoclonal cryoglobulins derived from non-autoimmune mice.

We have previously shown that murine IgG3 monoclonal autoantibodies with cryoglobulin activity, derived from lupus-prone mice, are able to induce glomerular lesions resembling the "wire-loop" lesion typically described for human lupus nephritis. In the present study, we have further assessed the nephritogenic potential of four IgG3 anti-hapten, trinitrophenyl (TNP), monoclonal antibodies (mAb) obtained from non-autoimmune mice immunized with TNP-conjugated foreign antigens. Our results showed that two of four IgG3 anti-TNP monoclonal cryoglobulins were capable of inducing glomerular lesions, characterized by voluminous intracapillary thrombi and mesangial deposition of PAS-positive materials, which differed from "wire-loop" lesions generated by IgG3 monoclonal cryoglobulins with autoantibody activities. These anti-TNP monoclonal cryoglobulins, however, failed to induce glomerular lesions when mice were kept at 37 degrees C after the mAb administration. This finding formally proves that the cryoglobulin activity is critically involved in the development of glomerular lesions induced by IgG3 anti-TNP mAb. In addition, we have demonstrated a remarkable difference in the nephritogenic activities of two IgG3 anti-TNP mAb, which exhibit a marked sequence homology in the variable regions of their heavy and light chains (91.5% and 99.1% at the amino acid level, respectively) and an identical isoelectric point. Our results indicate first, that IgG3 monoclonal cryoglobulins are able to generate two different kinds of glomerular lesions, and second, that a subtle difference in variable region sequences may determine not only the nephritogenic activities, but also the type of glomerular lesions mediated by IgG3 cryoglobulins.

Animals↗

PubMed1986

Two distinct but overlapping antibody binding sites in the pre-S(2) region of HBsAg localized within 11 continuous residues.

The fine specificity of the humoral immune response to the pre-S(2) region of the hepatitis B surface antigen was studied. It was demonstrated that the murine antibody response to the pre-S(2) region is focused on residues 133 through 143, and two distinct but overlapping epitopes were identified within 11 continuous residues. One epitope, defined by p133-139, is group specific, and the other epitope, defined by p137-143, is influenced by a subtype-dependent amino acid substitution at residue 141. However, the influence of residue 141 was "covert" in that it was only detected when synthetic antigens of 19 amino acids or smaller were used as the solid-phase ligand. The minimum size of both epitopes (p133-139 and p137-143) was seven amino acids. The physical and chemical form of the immunogen (i.e., protein vs peptide; conjugated vs free peptide) influenced antibody fine specificity. In quantitative antibody inhibition studies it was demonstrated that antibodies with nonoverlapping as well as overlapping fine specificities were capable of mutual inhibition. Finally, human HBV-infected, patient sera were shown to possess anti-pre-S(2) region antibodies that recognized sequences in common with the murine antisera. These results have implications relevant to the design of synthetic and recombinant second generation HBV vaccines and diagnostic reagents.

Amino Acid Sequence↗

PubMed1987

The mechanism of transduction of proto-oncogene c-src by avian retroviruses.

Chicken c-src sequences have been transduced by avian leukosis viruses (ALV) and by partial src-deletion (td) mutants of Rous sarcoma virus in several independent events. Analyses of the recombination junctions in the genomes of src-containing viruses and the c-src DNA have shed light on the mechanism of transduction, which involves at least two steps of recombination. The initial recombination between a viral genome and the 5' region of c-src appears to occur at the DNA level. This step does not require extensive homology and can be mediated by stretches of sequences with only partial homology. The 5' recombination junction can also be formed by splicing between viral and c-src sequences. The second recombination is presumed to occur between the transducing ALV or td viral RNA and the viral-c-src hybrid RNA molecule generated from the initial recombination. This step involving recombination at the 3' ends of those molecules restores the 3' viral sequences essential for replication to the viral-c-src hybrid molecule. High frequency of c-src transduction by partial td mutants suggests that the second recombination is greatly enhanced when there is sequence homology between the transducing virus and the 3' region of c-src. Incorporation of the c-src sequences into an ALV genome results in greatly elevated expression of the gene. However, increased expression of c-src alone is insufficient to activate its transforming potential. Structural changes in c-src are necessary to convert it into a transforming gene. The changes can be as small as single nucleotide changes resulting in single amino aid substitutions at certain positions. Mutations can occur rapidly during viral replication after c-src is incorporated into the viral genome. Therefore, it is most likely that transduction of c-src by ALV is followed by subsequent mutation and selection for the sarcomagenic virus. In the case of transduction by td viruses that retain certain src sequences, joining of these sequences with the transduced c-src apparently is sufficient to activate its transforming potential.

Alpharetrovirus↗

PubMed1991

Enzymatic multiplex DNA sequencing.

The problem of reading DNA sequence films has been reformulated using an easily implemented, multiplex version of enzymatic DNA sequencing. By utilizing a uniquely tagged primer for each base-specific sequencing reaction, the four reactions can be pooled and electrophoresed in a single lane. This approach has been previously proposed for use with fluorescently labelled probes (1), and is analogous to the principle used in four-dye fluorescence sequencing except that the signals are resolved following electrophoresis (2). After transfer to a nylon membrane, images are obtained separately for each of the four reactions by hybridization using oligonucleotide probes. The images can then be superimposed to reconstitute a complete sequence pattern. In this way the correction of gel distortion effects and accurate band registration are considerably simplified, as each of the four base-specific ladders require very similar corrections. The methods therefore provide the basis for a second generation of more accurate and reliable film reading programs, as well as being useful for conventional multiplex sequencing. Unlike the original multiplex protocol (3), the approach described is suitable for small projects, as multiple cloning vectors are not used. Although more than one vector can be utilized, only a library of fragments cloned into any single phage, phagemid or plasmid vector is actually required, together with a set of tagged oligonucleotide primers.

Base Sequence↗

PubMed1993

Response of the 23Na-NMR double-quantum filtered signal to changes in Na+ ion concentration in model biological solutions and human erythrocytes.

Double quantum filtered (DQF) 23Na-NMR signals were evaluated as a function of [Na+] at constant temperature in two model systems (bovine serum albumin (BSA) and Ficoll 400) and in human red blood cells (RBCs). In model systems, the ratio of double quantum filtered to single quantum (SQ) signal intensities was independent of [Na+], even over a wide range of Na+/K+ ratios. Varying the DQF preparation time affected only the DQF signal intensity. In contrast, in human red blood cells (RBCs) the shape and phase of the DQF intracellular Na+ signal (Na+in) varied as a function of preparation time. Similar observations in cartilage [Eliav, U., Shinar, H. and Navon, G. (1992) J. Magn. Reson. 28, 223-229] have been attributed to the generation of a second- and a third-rank tensor by the DQF pulse sequence, resulting from Na+ ion ordering. By using a DQF sequence which isolates the second-rank tensor only, this component was found to originate from the intracellular Na+ ion pool in human RBCs, as well as from interactions of Na+ ions with the extracellular face of the plasma membrane. The residual quadrupolar splitting for the signal originating from the former environment was shown to be less than the SQ linewidth, explaining its absence in SQ spectra, and this was confirmed by two-dimensional DQF 23Na-NMR experiments. By isolating the contribution from the third-rank tensor exclusively, the ratio of DQF:SQ signal intensities for Na+in in human RBCs was shown to be constant over a 4-fold change in [Na+in] produced by addition of an ionophore (nystatin). This indicates that such changes in physiological state do not alter the efficiency of DQF signal generation in human RBCs.

Animals↗

PubMed1995

Selection and characterization of RNAs replicated by Q beta replicase.

RNAs replicated by Q beta replicase were isolated from two random sequence RNA populations (one 56 nucleotides in length, the second 83) using a replication/dilution protocol. The selected molecules were cloned and sequenced, generating data set of 54 replicatable RNAs bound with higher affinity to Q beta replicase than did the random populations from which they were selected. Deletion analyses on two of the molecules indicated that internal regions of the RNAs were responsible for the specific binding of Q beta replicase. Truncated molecules representing the minimized RNA binding sites could inhibit replication of the full-length molecules, apparently by obstructing their binding to the replicase. The binding regions of the two RNAs were dominated by extended runs of pyrimidines. Similar C/U-rich regions existed in 85% of the sequences in the data set as well as in all of the previously published replicatable sequences. Mutation of the polypyrimidine domain of one of the replicatable sequences reduced the affinity of the molecule for Q beta replicase by 10-fold and completely abolished its ability to be replicated.

Base Sequence↗

PubMed1993

Post-transfusional anti-HCV-negative non-A non-B hepatitis (II) serological and polymerase chain reaction analysis for hepatitis C and hepatitis B viruses.

Hepatitis C virus (HCV) is a major etilogical agent of post-transfusional and sporadic acute and chronic hepatitis in various geographical areas. However, anti-HCV seroconversion was uncommon in a recent study of patients with post-transfusional hepatitis in Paris, France (N. Asar et al., companion paper). The aim of the present study was to detect viral markers, in particular HCV RNA and hepatitis B virus (HBV) DNA, in these patients. A combination of second-generation assays for anti-HCV antibodies and the polymerase chain reaction were used to identify HCV RNA and HBV DNA sequences in serum samples collected before and after transfusion from patients who developed non-A, non-B hepatitis. Eighteen cases of acute, post-transfusional, non-A, non-B hepatitis were identified in the prospective clinical survey. Only three of these 18 subjects developed anti-HCV antibodies in second-generation tests. HCV RNA was identified in the serum of these three subjects but in none of the others. Two patients who were anti-HCV-negative had polymerase chain reaction evidence of HBV DNA. Known viral markers were not identified in 13 of the 18 patients with acute post-transfusional non-A, non-B hepatitis. These results raise the issue of HCV strains or 'non-A, non-B, non-C' viruses not identified by current HCV and HBV markers and implicated in post-transfusional hepatitis in France.

Base Sequence↗