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Atm-, p53-, and Gadd45a-deficient mice show an increased frequency of homologous recombination at different stages during development.

Atm, p53, and Gadd45a form part of a DNA-damage cellular response pathway; the absence of any one of these components results in increased genomic instability. We conducted an in vivo examination of the frequency of spontaneous homologous recombination in Atm-, p53-, or Gadd45a-deficient mice. In the absence of p53, we observed the greatest increase in events, a lesser increase in the absence of Atm, and only a modest increase in the absence of Gadd45a. The striking observation was the difference in the time at which the spontaneous events occurred in atm and trp53 mutant mice. The frequency of homologous recombination in atm mutant mice was increased later during development. In contrast, p53 appears to have a role in suppressing homologous recombination early during development, when p53 is known to spontaneously promote p21 activity. The timing of the increased spontaneous recombination was similar in the Gadd45a- and p53-deficient mice. This temporal resolution suggests that Atm and p53 can act to maintain genomic integrity by different mechanisms in certain in vivo contexts.

Animals↗

Left ventricular remodeling: pathophysiology and treatment.

Left ventricular (LV) remodeling, which can result from myocardial damage or ventricular pressure or volume overload, has genomic, cellular, and interstitial components with associated changes in ventricular size, shape, wall thickness, and function. It is a process that is detectable and measurable clinically, generally progressive, and associated with adverse outcomes. However, it is amenable to intervention, prevention, or reversal. Following myocardial infarction (MI), LV remodeling is particularly likely in patients with transmural or anterior infarction and in those with failed reperfusion or LV failure. Infarct artery patency and neurohormonal blockade are key management considerations for prevention or reversal of LV remodeling. Combination treatment with angiotensin-converting enzyme inhibition and beta-blockade is of proven benefit following MI, improving LV remodeling and long-term outcomes.

Adrenergic beta-Antagonists↗

[Bacteria and their role in allergic diseases].

From the beginning of life, human immune system is affected by interactions with different microorganisms. Immediately after the birth bacteria colonize mucous tissues and namely the gastrointestinal tract, which was antenatally sterile. Bacteria are involved in allergic inflammation by two different ways. They can either initiate the allergic response or they can diminish it. To the negative factors, which can trigger the allergic response belong superantigens, namely the bacterial enterotoxins. Positive factors include mycobacterial antigens, intestinal microflora, pathogen-associated molecular patterns and CpG motives that belong to components of the bacterial genome DNA. The effect of lipopolysaccharide from gram-negative bacteria on the development of allergic inflammation is two faced. Lipopolysaccharide has a protective role when the infection precedes the contact with allergen for a long time. Short period between the infection and allergen exposition leads in a sensitized person to the provocation of allergic disease. These and other factors are important in relation to the so-called hygiene hypothesis where the T regulatory lymphocytes seem to play the key role in the balance between Th1 and Th2 lymphocytes.

Bacteria↗

IS200: an old and still bacterial transposon.

IS200 is a mobile element found in a variety of eubacterial genera, such as Salmonella, Escherichia, Shigella, Vibrio, Enterococcus, Clostridium, Helicobacter, and Actinobacillus. In addition, IS200-like elements are found in archaea. IS200 elements are very small (707-711 bp) and contain a single gene. Cladograms constructed with IS200 DNA sequences suggest that IS200 has not spread among eubacteria by horizontal transfer; thus it may be an ancestral component of the bacterial genome. Self-restraint may have favored this evolutionary endurance; in fact, unlike typical mobile elements, IS200 transposes rarely. Tight repression of transposase synthesis is achieved by a combination of mechanisms: inefficient transcription, protection from impinging transcription by a transcriptional terminator, and repression of translation by a stem-loop mRNA structure. A consequence of IS200 self-restraint is that the number and distribution of IS200 elements remain fairly constant in natural populations of bacteria. This stability makes IS200 a suitable molecular marker for epidemiological and ecological studies, especially when the number of IS200 copies is high. In Salmonella enterica, IS200 fingerprinting is extensively used for strain discrimination.

Archaea↗

A novel repetitive DNA sequence in lemon [Citrus limon (L.) Burm.] and related species Bruna.

Repetitive DNA sequences constitute a significant component of most eukaryotic genomes, and the isolation and characterization of such sequences provide an insight into the organization of the genome of interest. Here, we report the isolation and molecular characterization of a novel repetitive DNA sequence from the genome of Citrus limon. Digestion of C. limon DNA with MboI produced a prominent fragment of approximately 600 bp. Southern blotting revealed a ladder composed of DNA fragments that are multimers of the 600 bp Mbo I band. This suggests that MboI isolated a novel satellite, named C. limon satellite DNA 600 (CL600). Methylation analyses using Sau3AI-MboI isoschizomers demonstrated that most cytosine residues in the GATC sites of this element were methylated in C. limon. This sequence was also found in related citrus plants, like grapefruit and orange, and the hardiest close relatives of Citrus, such as kumquat and trifoliate orange.

Base Sequence↗

[Analysis of the primary structure of DNA sequences flanking MDG1].

MDG is a very important component of the Drosophila genome. MDG have many sites of localisation in chromosomes and can change their localisation. Perhaps the process of MDG integration has some specificity. To study this problem we sequenced the flanking region of MDG1 DNA. The analysis of this sequences reveals the following features. 1. The 5'-flanking sequences contain 7 TATA-boxex, 5 of which form a cluster. 2. The 3'-flanking sequences contain TTTAAA block which is similar to TATA-box for alpha- and gamma-casein genes of mammals. 3. The flanking region are rich in repeated sequences, the longest of which TCCTCCT (R) and TTCTTC (R2) are on the 5'-flank and on the 3'-flank respectively, so that the whole structure is: 5'-R1NNR1-MDG1-R2NNR2-3', where N is some nucleotide. 5'-flanking sequences are AT-rich, while the 3'-flank contains 10 consecutive thymidines 4 nucleotides apart from MDG1. The MDG1 and MDG "17.6" share several common repeats in the flanking sequences, the longest of which TACTTACAT is 63 bases upstream MDG1 and 11 bases upstream MDG "17.6". This sequence differs strongly from the consensus enhancer sequence.

Animals↗

Transfer of Drosophila melanogaster transponsable genetic element mdg-4 into plant cells.

The copia-like element mdg-4, as a component of the Drosophila genomic fragment Dm111, was cloned into the vector pIB16. The chimaeric plasmid pIB16 [Dm111] was used to transform tobacco cells as a cointegrate with pTiC58 (Agrobacterium tumefaciens), pTiC58::pIB16 [Dm111]. The growth properties of primary crown-gall tumours were followed, and the DNA of one Nicotiana tabacum transformant was further analysed. The DNA/DNA molecular hybridization of digests of genomic DNA with 32P-labelled pDm111 probe demonstrated full-length insertion of Dm111 into N. tabacum genome. We were not able to detect any common sequence with Dm111 in untransformed tobacco cells.

Animals↗

Tomato yellow leaf curl virus from Sardinia is a whitefly-transmitted monopartite geminivirus.

The genome of an isolate of tomato yellow leaf curl virus from Sardinia, Italy (TYLCV-S), a geminivirus transmitted by the whitefly Bemisia tabaci, has been cloned and sequenced. The single circular DNA molecule comprises 2770 nucleotides. Genome organisation closely resembles that of the DNA A component of the whitefly-transmitted geminiviruses with a bipartite genome. A 1.8 mer of the TYLCV-S genome in a binary vector of Agrobacterium tumefaciens is infectious upon agroinoculation of tomato plants. Typical tomato yellow leaf curl disease symptoms developed about three weeks after inoculation. The disease was transmitted by the natural vector B.tabaci from agroinfected plants to test plants, reproducing in this way the full biological cycle and proving that the genome of TYLCV-S consists of only one circular single-stranded DNA molecule. Contrary to the other whitefly-transmitted geminiviruses described so far, there is no evidence for the existence nor the necessity of a second component (B DNA) in the TYLCV-S genome.

Agrobacterium tumefaciens↗

[A model for clinical study based on genome science--trials in disorders of the immune system and allergies].

Disorders of the immune system, such as allergies, have multi-factorial etiologies that include both genetic and environmental components. The recent advances in genome science have facilitated two strategies for studying the genetic basis of disease: (1) systematic analysis of gene expression profiles and (2) comprehensive analysis of gene variations, such as polymorphisms. Here, we describe a unique research institute, Genox Research Inc., that can relate the clinical profile of a patient to genotyping and molecular profiling. Systematic gene expression analyses using differential display have been performed to explore genes related to allergy, and revealed 93 differentially expressed candidate genes in T-cells. Also, a single nucleotide polymorphism(SNP) analysis project has been designed to mine disease-related and/or drug-response-related genes involved in allergic disorders using biochip technologies. As exemplified above, clinical studies based on these applications of genome science would be of considerable value in clarifying our understanding of multi-gene disorders.

Gene Expression Profiling↗

A posttranslational modification of fimbriae drives pathogenicity in Klebsiella pneumoniae.

Antimicrobial resistance is a severe public health burden. Especially concerning are multidrug resistant (MDR) infections, which restrict treatment options and significantly increase mortality risk. A major cause of MDR infections worldwide is carbapenem-resistant Klebsiella pneumoniae (CRKp). The predominant CRKp sequence type worldwide is ST258. However, the factors underlying ST258's epidemic success are not well defined. Genomic analyses of clinical isolates of CRKp have found that the two-component regulatory system CrrAB is a genomic feature of ST258, suggesting that it may contribute to its global dominance. Despite this, the molecular details underpinning CrrAB's contribution to ST258 Kp biology and pathogenicity are poorly understood. We used RNA-sequencing to identify the regulon of CrrA and found that CrrAB induces the expression of a gene, encoding Crr-regulated fimbriae modifying protein (CfmP), that is essential for pathogenesis driven by this two-component system. We performed mass spectrometry analyses of fimbriae purified from Kp expressing or lacking cfmP and found that CfmP induces a novel oxidation to a histidine residue in the major pilin subunit of fimbriae, FimA. We demonstrate that this oxidation significantly increases host cell adhesion and high bacterial loads within the host. CrrAB also drives high antibiotic resistance in CRKp. Thus, our results place CrrAB at the intersection of pathogenicity and antibiotic resistance supporting its function as an important regulatory system driving the global dominance of ST258.

Klebsiella pneumoniae↗

Whole-genome analysis of Oryza sativa reveals similar architecture of two-component signaling machinery with Arabidopsis.

The two-component system (TCS), which works on the principle of histidine-aspartate phosphorelay signaling, is known to play an important role in diverse physiological processes in lower organisms and has recently emerged as an important signaling system in plants. Employing the tools of bioinformatics, we have characterized TCS signaling candidate genes in the genome of Oryza sativa L. subsp. japonica. We present a complete overview of TCS gene families in O. sativa, including gene structures, conserved motifs, chromosome locations, and phylogeny. Our analysis indicates a total of 51 genes encoding 73 putative TCS proteins. Fourteen genes encode 22 putative histidine kinases with a conserved histidine and other typical histidine kinase signature sequences, five phosphotransfer genes encoding seven phosphotransfer proteins, and 32 response regulator genes encoding 44 proteins. The variations seen between gene and protein numbers are assumed to result from alternative splicing. These putative proteins have high homology with TCS members that have been shown experimentally to participate in several important physiological phenomena in plants, such as ethylene and cytokinin signaling and phytochrome-mediated responses to light. We conclude that the overall architecture of the TCS machinery in O. sativa and Arabidopsis thaliana is similar, and our analysis provides insights into the conservation and divergence of this important signaling machinery in higher plants.

Amino Acid Sequence↗

Carotenoid biosynthesis structural genes in carrot (Daucus carota): isolation, sequence-characterization, single nucleotide polymorphism (SNP) markers and genome mapping.

Carotenoid pigments are important components of the human diet and carrots are the main dietary sources of the vitamin A precursors alpha- and beta-carotene. Carotenoids play essential biological roles in plants and the genes coding for the carotenoid pathway enzymes are evolutionarily conserved, but little information exists about these genes for carrot. In this study, we utilized published carrot sequences as well as heterologous PCR approaches with primers derived from sequence information of other plant species to isolate 24 putative genes coding for carotenoid biosynthesis enzymes in carrot. Twenty-two of these genes were placed on the carrot genetic linkage map developed from a cross between orange-rooted and white-rooted carrot. The carotenoid genes were distributed in eight of the nine linkage groups in the carrot genome recommending their use for merging maps. Two genes co-localized with a genomic region spanning one of the most significant quantitative trait loci (QTL) for carotenoid accumulation. Carotenoid biosynthesis cDNAs linked to root color mutations and to QTL for carotenoid accumulation may suggest a functional role for them as candidate genes. RACE PCR and reverse transcriptase PCR were used to amplify the full-length transcript for twenty expressed carotenoid biosynthesis genes and sequences were submitted to GenBank. The cloning and sequence information of these genes is useful for PCR-based expression studies and may point toward transgenic approaches to manipulate carotenoid content in carrot.

Base Sequence↗

The genome of Neisseria gonorrhoeae retains the remnants of a two-component regulatory system that once controlled piliation.

An intact activator-binding site upstream of the sigma(54) promoter of the pilin-encoding pilE gene of Neisseria gonorrhoeae suggests gonococci produce a protein capable of binding this sequence. We cloned a chimeric gene, rsp, that has sequence similarity to both the pilS and pilR genes of Pseudomonas aeruginosa encoding a two-component regulatory system that controls piliation. This gene is transcribed in N. gonorrhoeae and indirect evidence suggests that Rsp binds to the activator-binding site of the pilE gene. Despite this, mutation of rsp has no effect on piliation in N. gonorrhoeae, suggesting that the remnants of this regulatory system have persisted in the genome, despite the loss of its original function.

Bacterial Proteins↗

Structural components of influenza C virions.

The genome RNA species of influenza type C virions were analyzed by polyacrylamide gel electrophoresis. The pattern obtained was found to resemble those of other influenza viruses. Six RNA species were resolved, with estimated sizes ranging from 0.37 X 10(6) to 1.25 X 10(6) daltons. The internal ribonucleoproteins of influenza C virions were found to sediment heterogeneously in glycerol velocity gradients as demonstrated previously with influenza A/WSN virus. The ribonucleoproteins possessed diameters of 12 to 15 nm, with lengths ranging from 30 to 100 nm. Of the three major virion polypeptides (molecular weights, 88,000, 66,000, and 26,000), only the largest is glycosylated. Similar polypeptide species were present in influenza C virions of five different strains. All three major proteins of influenza C virions possess electrophoretic mobilities distinguishable from those of the major polypeptides of influenza A/WSN. The 66,000-dalton protein is associated with the ribonucleoprotein components. Two additional glycosylated polypeptides, with estimated molecular weights of 65,000 and 30,000, were detected in virions grown in embryonated eggs, but not in virus particles obtained from chicken embryo fibroblasts.

Glycoproteins↗

Multiple components in restriction enzyme digests of mammalian (insectivore), avian and reptilian genomic DNA hybridize with murine immunoglobulin VH probes.

High molecular weight genomic DNAs isolated from an insectivore, Tupaia, and a representative reptilian, Caiman, and avian, Gallus, were digested with restriction endonucleases transferred to nitrocellulose and hybridized with nick-translated probes of murine VH genes. The derivations of the probes designated S107V (1) and mu 107V (2,3) have been described previously. Under conditions of reduced stringency, multiple hybridizing components were observed with Tupaia and Caiman; only mu mu 107V exhibited significant hybridization with the separated fragments of Gallus DNA. The nick-translated S107V probe was digested with Fnu4H1 and subinserts corresponding to the 5' and 3' regions both detected multiple hybridizing components in Tupaia and Caiman DNA. A 5' probe lacking the leader sequence identified the same components as the intact 5' probe, suggesting that VH coding regions distant as the reptilians may possess multiple genetic components which exhibit significant homology with murine immunoglobulin in VH regions.

Alligators and Crocodiles↗

The sequence of the reovirus serotype 3 L3 genome segment which encodes the major core protein lambda 1.

We present the sequence of reovirus serotype 3 (strain Dearing) genome segment L3 which encodes protein lambda 1, one of the two major components of the core shell. The genome segment is 3896 nucleotides long, with 5'- and 3'-noncoding regions of 13 and 181 nucleotides, respectively. Protein lambda 1 is 1233 amino acids long. It is a slightly acidic protein, with a predicted alpha-helix and beta-sheet content of 23.6 and 28.3%, respectively. Its rather low predicted alpha-helix contact is consistent with its being a structural protein. The 123 amino acid long region at its amino terminus is very hydrophilic and contains three alpha-helical regions, one being 26 amino acids long. Protein lambda 1 contains two functional motifs. The first is a nucleotide binding site -TKGKSSG- starting at residue 8, the other is a "zinc finger" motif centered around amino acid residue 194. This suggests that protein lambda 1 functions during the transcription of either dsRNA into plus strands or of plus strands into minus strands, or during both. It displays no significant sequence similarity to any protein sequence in the GenBank data base.

Amino Acid Sequence↗

Plant histidine kinases: an emerging picture of two-component signal transduction in hormone and environmental responses.

In the Arabidopsis thaliana genome, 11 genes encode bacterial-type two-component histidine kinases. Genetic and biochemical analyses indicate that five two-component histidine kinase-like proteins (ETR1, ETR2, EIN4, ERS1, and ERS2) function as ethylene receptors. A hybrid histidine kinase, CRE1 (also known as AHK4), acts as a cytokinin receptor, and a set of response regulators may be involved in cytokinin signal transduction. In addition to CRE1, histidine kinases CKI1 and CKI2 are likely to play important roles in cytokinin signaling. A database search of the entire Arabidopsis genome sequence has identified two additional homologs of CRE1. Arabidopsis seems to employ a hybrid histidine kinase, ATHK1, as an osmosensor. Plants widely use two-component systems in the detection of, and signal transduction by, the growth regulators ethylene and cytokinin, as well as in their responses to environmental stimuli.

Arabidopsis↗

SPC: a SPectral Component approach leveraging Identity-by-Descent graphs to address recent population structure in genomic analysis.

Population structure is a well-known confounder in statistical genetics, particularly in genome-wide association studies (GWAS), where it can lead to inflated test statistics and spurious associations. Traditional methods, such as principal components (PCs), commonly used to adjust for population structure, are limited in capturing fine-scale, non-linear patterns that arise from recent demographic events - patterns that are crucial for understanding rare variant effects. To address this challenge, we propose a novel method called SPectral Components (SPCs), which leverages identity-by-descent (IBD) graphs to capture and transform local, non-linear fine-scale population structure into continuous representations that can be seamlessly integrated into genetic analysis pipelines. Using both simulated datasets and empirical data from the UK Biobank (N ≈ 420,000), we demonstrate that SPCs outperform PCs in adjusting for fine-scale population structure. In simulations, SPCs explained over 90% of the fine-scale population structure with fewer components, while PCs captured less than 5%. In the UK Biobank, SPCs reduced the inflation of p-values in the GWAS of an environmental-driven phenotype by 12% compared to PCs, while maintaining a similar performance to PCs in height, a highly heritable phenotype. Additionally, SPCs improved rare variant association analyses, reducing genomic inflation (e.g., from 7.6 to 1.2 in one analysis), and provided more accurate heritability estimates. Spatial autocorrelation analysis further confirmed the ability of SPCs to account for environmental effects, reducing Moran's I for both environmental and heritable phenotypes more effectively than PCs. Overall, our findings demonstrate that SPCs provide a robust, scalable adjustment for recent population structure, offering a powerful alternative or complement to PCs in large-scale biobank studies.

GWAS↗