Shared synteny (also known as conserved synteny) describes preserved co-localization of genes on chromosomes of different species. During evolution, rearrangements to the genome such as chromosome translocations may separate two loci, resulting in the loss of synteny between them. Conversely, translocations can also join two previously separate pieces of chromosomes together, resulting in a gain of synteny between loci. Stronger-than-expected shared synteny can reflect selection for functional relationships between syntenic genes, such as combinations of alleles that are advantageous when inherited together, or shared regulatory mechanisms.[3]. The term is sometimes also used to describe preservation of the precise order of genes on a chromosome passed down from a common ancestor,[4][5][6][7] although many geneticists reject this use of the term.[8]. The analysis of synteny in the gene order sense has several applications in genomics. Shared synteny is one of the most reliable criteria for ...
Akirin is a nuclear protein that acts in several metazoan pathways regulating development and cell proliferation (Nowak and Baylies 2012). Akirin is present as one copy in invertebrates and has duplicated in the vertebrate ancestor resulting in two homologs (Akirin1 and Akirin2) encoding proteins with ∼70% sequence similarity (Macqueen and Johnston 2009). The two vertebrate proteins have mostly overlapping functions, however in mouse Akirin2 is essential for development while Akirin1 is not (Goto et al. 2007). Conditional knockout of Akirin2 in mouse determined it is involved in development of limb, brain, and muscle tissues (Bosch et al. 2016; 2018; 2019). The first published role for Akirin described its function in the immune system. Depletion of Akirin in Drosophila leads to dysfunction of the innate immune system resulting in sensitivity to bacterial infection (Goto et al. 2007). In mouse, loss of Akirin2 also leads to increased sensitivity to bacterial infection due to defects in B-cell ...
TY - JOUR. T1 - Equine synteny mapping of comparative anchor tagged sequences (CATS) from human Chromosome 5. AU - Caetano, Alexandre R.. AU - Lyons, Leslie A. AU - Laughlin, Thomas F.. AU - OBrien, Stephen J.. AU - Murray, James D.. AU - Bowling, Ann T.. PY - 1999. Y1 - 1999. N2 - Comparative anchor tagged sequences (CATS) from human Chromosome 5 (HSA5) were used as PCR primers to produce molecular markers for synteny mapping in the horse. Primer sets for 21 genes yielded eight horse-specific markers, which were mapped with the UC Davis horse-mouse somatic cell hybrid panel into two synteny groups: UCD14 and UCD21. These data, in conjunction with earlier human chromosome painting studies of the horse karyotype and synteny mapping of horse microsatellite markers physically mapped by FISH, confirm the assignment of UCD21 to ECA21 and suggest that UCD14 is located on ECA14. In addition, our results can be used to substantiate previously published data which indicate that ECA21 contains material ...
The IMD pathway in Drosophila regulates the systemic immune response against Gram‐negative bacteria, and the molecular cascade from the PGRP‐LC receptor down to the activation of the NF‐κB factor Relish has been extensively studied. The Akirin molecule is required for IMD target gene activation by the Relish transcription factor (Goto et al, 2008), and this finding suggests that IMD effector gene transcription might depend on additional factors that remained to be identified. In order to further elucidate NF‐κB‐dependent gene activation, we re‐explore the IMD pathway using Akirin as a starting point. We undertook an unbiased two‐hybrid screen that identified BAP60 as an Akirin transcriptional partner during the innate immune response, confirming the data of the protein‐interaction map of the fly proteome (Giot et al, 2003). Additionally, we show that BAP55, an Actin‐related component of the SWI/SNF Brahma complex (Papoulas et al, 1998; Armstrong et al, 2002), engages Akirin ...
Understanding the genetic component of scoliosis in humans has relied on the assumption that spine development is conserved across species. Since evolutionary conserved genes tend to lie within synteny blocks (HSBs) and genes which are not conserved lie within evolutionary breakpoint regions (EBRs), HSB analysis may be used to determine if spine development is conserved across species. We hypothesized that vertebral patterning genes are conserved in amniotes and their location is within stable or
To help understand mechanisms of vertebrate genome evolution, we have compared zebrafish and tetrapod gene maps. It has been suggested that translocations are fixed more frequently than inversions in mammals. Gene maps showed that blocks of conserved syntenies between zebrafish and humans were large, but gene orders were frequently inverted and transposed. This shows that intrachromosomal rearrangements have been fixed more frequently than translocations. Duplicated chromosome segments suggest that a genome duplication occurred in ray-fin phylogeny, and comparative studies suggest that this event happened deep in the ancestry of teleost fish. Consideration of duplicate chromosome segments shows that at least 20% of duplicated gene pairs may be retained from this event. Despite genome duplication, zebrafish and humans have about the same number of chromosomes, and zebrafish chromosomes are mosaically orthologous to several human chromosomes. Is this because of an excess of chromosome fissions in ...
Comparing strains within the same microbial species has proven effective in the identification of genes and genomic regions responsible for virulence, as well as in the diagnosis and treatment of infe
Human AKIRIN1 full-length ORF (1 a.a. - 192 a.a.) recombinant protein with GST-tag at N-terminal. (H00079647-P01) - Products - Abnova
From the greek on the same string, it is used in genetics to refer to the phenomenon that genes in one organism can be in the same order as those in a...
Recent advances in comparative genomics have considerably improved our knowledge of the evolution of mammalian karyotype architecture. One of the breakthroughs was the preferential localization of evolutionary breakpoints in regions enriched in repetitive sequences (segmental duplications, telomeres and centromeres). In this context, we investigated the contribution of ribosomal genes to genome reshuffling since they are generally located in pericentromeric or subtelomeric regions, and form repeat clusters on different chromosomes. The target model was the genus Mus which exhibits a high rate of karyotypic change, a large fraction of which involves centromeres. The chromosomal distribution of rDNA clusters was determined by in situ hybridization of mouse probes in 19 species. Using a molecular-based reference tree, the phylogenetic distribution of clusters within the genus was reconstructed, and the temporal association between rDNA clusters, breakpoints and centromeres was tested by maximum likelihood
Akirin is a recently discovered nuclear factor that plays an important role in innate immune responses. Beyond its role in innate immune responses, Akirin has recently been shown to play an important role in skeletal myogenesis. In this article, we will briefly review the structure and tissue distribution of Akirin and discuss recent advances in our understanding of its role and signal pathway in skeletal myogenesis.
Abstract Background It is difficult to accurately interpret chromosomal correspondences such as true orthology and paralogy due to significant divergence of genomes from a common ancestor. Analyses are particularly problematic among lineages that have repeatedly experienced whole genome duplication (WGD) events. To compare multiple "subgenomes" derived from genome duplications, we need to relax the traditional requirements of "one-to-one" syntenic matchings of genomic regions in order to reflect "one-to-many" or more generally "many-to-many" matchings. However this relaxation may result in the identification of synteny blocks that are derived from ancient shared WGDs that are not of interest. For many downstream analyses, we need to eliminate weak, low scoring alignments from pairwise genome comparisons. Our goal is to objectively select subset of synteny blocks whose total scores are maximized while respecting the duplication history of the genomes in comparison. We call this "quota-based" ...
They say you cant teach an old dog new tricks, but it turns out you can use new epigenomic tricks to tell you how old a dog is. The heuristic that to get a dogs age in human years, you multiply by seven is a little simplistic, and due for an update using epigenomic insights. The lab of Trey Ideker at the University of California, San Diego wanted to define epigenetic aging in dogs and compare it to known DNA methylation changes in humans with age.. Existing tools for the dog genome were not suitable for the task however. RRBS and WGBS cover a large number of CpGs, but they dont always get the exact same CpG sites at low read depth. The authors wanted to be able to make evolutionary comparisons of high-quality dog methylomes with other mammals. They wanted to identify CpGs in dogs that are syntenic with CpGs on human Illumina arrays, creating a high quality panel of dog methylomes with substantial coverage of CpGs noted in prior human studies. They developed a method called Synteny Bisulfite ...
A bacterial artificial chromosome (BAC) library was made from P. triticina race 1, BBBD and probed with Pt homologs of genes encoding two predicted Pgt secreted effectors and a DNA marker mapping to a region of avirulence. Three BACs, 103 Kb, 112 Kb, and 166 Kb, were sequenced, assembled, and open reading frames were identified. Orthologous genes were identified in Pgt and local conservation of gene order (microsynteny) was observed. Pairwise protein identities ranged from 26 to 99%. One Pt BAC, containing a RAD18 ortholog, shares syntenic regions with two Pgt scaffolds, which could represent both haplotypes of Pgt. Gene sequence is diverged between the species as well as within the two haplotypes. In all three BAC clones, gene order is locally conserved, however, gene shuffling has occurred relative to Pgt. These regions are further diverged by differing insertion loci of LTR-retrotransposon, Gypsy, Copia, Mutator, and Harbinger mobile elements. Uncharacterized Pt open reading frames were also ...
abstract = {Transcription of inflammatory genes in innate immune cells is coordinately regulated by transcription factors, including NF-κB, and chromatin modifiers. However, it remains unclear how microbial sensing initiates chromatin remodeling. Here, we show that Akirin2, an evolutionarily conserved nuclear protein, bridges NF-κB and the chromatin remodeling SWI/SNF complex by interacting with BRG1-Associated Factor 60 (BAF60) proteins as well as IκB-ζ, which forms a complex with the NF-κB p50 subunit. These interactions are essential for Toll-like receptor-, RIG-I-, and Listeria-mediated expression of proinflammatory genes including Il6 and Il12b in macrophages. Consistently, effective clearance of Listeria infection required Akirin2. Furthermore, Akirin2 and IκB-ζ recruitment to the Il6 promoter depend upon the presence of IκB-ζ and Akirin2, respectively, for regulation of chromatin remodeling. BAF60 proteins were also essential for the induction of Il6 in response to LPS ...
Use Bio-Rads PrimePCR assays, controls, templates for your target gene. Every primer pair is optimized, experimentally validated, and performance guaranteed.
Structural homology in the Solanaceae: analysis of genomic regions in support of synteny studies in tomato, potato and pepper: We have analysed the structural h
Protein Of Unknown Function; SPS22 Has A Paralog, SPS2, That Arose From The Whole Genome Duplication; Redundant With Sps2p For The Organization Of The Beta-glucan Layer Of The Spore Wall
Ortholog metrics are calculated for some groups of species, and these are used to classify a "high confidence" set of orthologs. The methodology uses two orthogonal sources of information, gene order conservation (GOC) and whole genome alignments (WGA).. The "GOC score" metric for a pair of orthologs measures whether the two genes up- and downstream of each gene in the ortholog pair are also orthologous, and allows for inversions and gene insertions. The "WGA coverage" metric determines the extent to which the orthologous regions have been aligned by pairwise LASTz alignments, primarily based on exonic coverage, with a small contribution from intronic coverage. Both metrics have a value between 0 and 100.. There is only an expectation for gene order conservation between species that are evolutionarily close; thus the GOC score is only calculated within Diptera, Chelicerata, and Hemiptera. Similarly, pairwise WGAs, and thus the related metric, are only available for a subset of fairly ...
Abstract Using single-copy conserved ortholog set (COSII) and simple sequence repeat (SSR) markers, we have constructed two genetic maps for diploid Nicotiana species, N. tomentosi..
My own research interests which map onto these targets are flowering time, leaf senescence and how plant chemistry affects the conversion efficiency of energy crops. Research tools that have or are being developed include bacterial artificial chromosome (BAC) libraries, genetic, trait and physical maps, the establishment of forward mutation populations, the exploitation of syntenic relationships to associate genotype to phenotype, and the development of high throughput virtual phenotyping methods including the use of infrared spectroscopy for cell wall chemistry.. ...
My own research interests which map onto these targets are flowering time, leaf senescence and how plant chemistry affects the conversion efficiency of energy crops. Research tools that have or are being developed include bacterial artificial chromosome (BAC) libraries, genetic, trait and physical maps, the establishment of forward mutation populations, the exploitation of syntenic relationships to associate genotype to phenotype, and the development of high throughput virtual phenotyping methods including the use of infrared spectroscopy for cell wall chemistry.. ...
Protein Of Unknown Function; Deletion Mutant Shows Strong Genetic Interaction With Cdc28-as1 Mutant In The Presence Of 1-NM-PP1; DCV1 Has A Paralog, YOL019W, That Arose From The Whole Genome Duplication
New research conducted by the University of Nebraska-Lincolns James Schnable will use corn to test the idea that the emergence of specialized body parts occurs through whole genome duplication.
Background: Phosphodiesterase 6 (PDE6) is a protein complex that hydrolyses cGMP and acts as the effector of the vertebrate phototransduction cascade. The PDE6 holoenzyme consists of catalytic and inhibitory subunits belonging to two unrelated gene families. Rods and cones express distinct genes from both families: PDE6A and PDE6B code for the catalytic and PDE6G the inhibitory subunits in rods while PDE6C codes for the catalytic and PDE6H the inhibitory subunits in cones. We performed phylogenetic and comparative synteny analyses for both gene families in genomes from a broad range of animals. Furthermore, gene expression was investigated in zebrafish. Results: We found that both gene families expanded from one to three members in the two rounds of genome doubling (2R) that occurred at the base of vertebrate evolution. The PDE6 inhibitory subunit gene family appears to be unique to vertebrates and expanded further after the teleost-specific genome doubling (3R). We also describe a new family ...
Comparative Genomics: Gene and Genome Duplication. What are the molecular, phenotypic, and taxonomic outcomes of gene and whole genome duplication? We use two gene families, opsins and olfactory receptors, as models to answer these questions. Most of the opsin research involves fishes including guppies, the four-eyed fish, sticklebacks, various flatfish and zebrafish. The research on olfactory receptors (ORs) involves cnidarians, sea urchins and amphioxus. Recently weve added gene duplication and cancer evolution, and gene colinearity (conserved synteny) to our research repertoire. I also co-supervise graduate students who study tube worm population genetics and protein-protein interaction networks.. ...
In this study, we applied a phylogenetic footprinting approach to identify CNSs in 10 dicot species. This approach uses both alignment-based and alignment-free techniques and combines different gene orthology prediction methods that do not rely on synteny information. In this manner, it circumvents the step of whole-genome alignment, which is difficult owing to the frequent nature of polyploidy and genome rearrangements in plant genomes. As such, our approach is well suited to incorporate more distantly related species, including many-to-many gene orthology relationships. A set of high-quality comparator species was selected for each query species, ensuring that a saturated substitution rate in the absence of selection was present. Across all experiments, 1,032,291 CNSs were detected for 243,187 genes. A strong correlation was detected between the number of CNSs and the total number of genes present in a genome, whereas no strong correlation could be detected between the total number of CNSs and ...
This page provides quick access to the Comparative mapping functions available in the Map Viewer. Currently, comparative maps are calculated using HomoloGene orthology predictions. Once the gene pairs have been established, blocks of conserved syteny can be established using the positions of each gene object in their respective builds. Data used to calculate the Gene Table View is available from our FTP site.. ...
nearly causes my machine to run out of memory (16G), takes a couple of days to run, and results in a blast output of 5.1G and 84 million rows--thats 84 million blast hits with an e-value below 0.001! By definition, that output is dominated by the repetitive elements. Repetitive elements are interesting, but in the case were we want to look at synteny, we have to wade through that 5.1G of stuff to find the very small chunk of data we need. This adds time to run the sequence comparison, time to parse, time to plot, time to analyze, and data to store, etc ...
«Collinearity» In geometry, collinearity is a property of a set of points, specifically, the property of lying on a single line. A set of points with this property is ...
Hey guys! I really need help with this problem and I have no one else to ask as everyone is gone for the day....I was hoping someone could help me out and expla
BOMBYX mori, the domesticated silkworm, is one of the most genetically well-studied insects, with 246 mutations that have been sorted into 27 linkage groups (LGs) (Banno et al. 2005). Genome projects and related work are underway using B. mori as a model organism for Lepidoptera, the most serious group of agricultural pests (for recent review, see Goldsmith et al. 2004). Large-scale sequencing projects of expressed sequence tags (ESTs) (Mita et al. 2003; Cheng et al. 2004) and whole-genome shotgun (WGS) sequences (Mita et al. 2004; Xia et al. 2004) have been performed, and our knowledge of silkworm genes and genome sequence has dramatically increased. However, basic genome research on this insect is still far behind compared with other model organisms such as Drosophila melanogaster, and assignment of fundamental information such as genome sequences, ESTs, BAC contigs, mutant phenotypes, and chromosomal locations on detailed linkage maps is an urgent priority.. Two preliminary molecular linkage ...
Certain types of gene families, such as those encoding most families of transcription factors, maintain their chromosomal syntenic positions throughout angiosperm evolutionary time. Other nonsyntenic gene families are prone to deletion, tandem duplication, and transposition. Here, we describe the chromosomal positional history of all genes in Arabidopsis thaliana throughout the rosid superorder. We introduce a public database where researchers can look up the positional history of their favorite A. thaliana gene or gene family. Finally, we show that specific gene families transposed at specific points in evolutionary time, particularly after whole-genome duplication events in the Brassicales, and suggest that genes in mobile gene families are under different selection pressure than syntenic genes. ...
Transcriptional regulation of inflammatory gene expression has been at the forefront of studies of innate immunity and is coordinately regulated by transcription factors, including NF-κB, and chromatin modifiers. The growing evidence for involvement of chromatin in the regulation of gene expression in innate immune cells, has uncovered an evolutionarily conserved role of microbial sensing and chromatin remodeling. Toll-like receptors and RIG-I-like receptors trigger these signaling pathways leading to transcriptional expression of a set of genes involved in inflammation. Tightly regulated control of this gene expression is a paramount, and often foremost, goal of most biological endeavors. In this review, we will discuss the recent progress about the molecular mechanisms governing control of pro-inflammatory gene expression by an evolutionarily conserved novel nuclear protein Akirin2 in macrophages and its emergence as an essential link between NF-κB and chromatin remodelers for transcriptional
The Rosaceae contains many economically valuable crop genera, including Malus (apple), Fragaria (strawberry), and Prunus (stone fruit). There has been increasing interest in the development of linkage
Comparative genomics allow hypotheses about the content of the genome of ancestral species and for many major branching points on the tree of life, hypothetical ancestral genomes can be reconstructed
Brent has updated Gobes visualization to use translucent wedges for connecting regions of sequence similarity, and a host of other improvements.=== [[Image:Gobe-new-vis.png,thumb,center,600px,New translucent wedges for linking regions of sequence similarity. Results can be recreated [http://tinyurl.com/lywu23 here].]] [[Image:gobe-new.png,thumb,400px,New visualization of gobe]] [[Image:gobe-old.png,thumb,400px,Old visualization of gobe]] Gobe is the name for the interface for GEvo that allows users interact with sequence alignments from multiple genomic regions. Gobe is written in Flash and requires the latest version of Adobes [http://www.adobe.com/products/flashplayer/ Flash Player] to work. Gobe allows uses to select regions of sequence similarity and will draw lines connecting those regions in order to identify and characterize patterns of genome evolution such as synteny, inversions, duplications, transpositions, insertions, and deletions. Gobe can be downloaded ...
Oliver, R.E., Tinker, N.A., Lazo, G.R., Chao, S., Jellen, E.N., Carson, M.L., Rines, H.W., Obert, D.E., Lutz, J.D., Shackelford, I., Korol, A., Wight, C.P., Gardner, K.M., Hattori, J., Beattie, A.D., Bjørnstad, A., Bonman, J.M., Jannink, J.-L., Sorrells, M.E., Brown Guedira, G.L., Mitchell Fetch, J.W., Harrison, S.A., Howarth, C.J., Ibrahim, A.A., Kolb, F.L., McMullen, M.S., Murphy, J.P., Ohm, H.W., Rossnagel, B.G., Yan, W., Miclaus, K.J., Hiller, J., Maughan, P.J., Redman Hultz, R.R., Anderson, J.M., Islamovic, E., and Jackson, E.W. (2013). SNP discovery and chromosome anchoring provide the first physically-anchored hexaploid oat map and reveal synteny with model species., PLoS ONE, 8(3, Article No.e58068). doi : 10.1371/journal.pone. ...
v1.2.014963.t1(symbB.v1.2.014963.t1) v1.2.023547.t1(symbB.v1.2.023547.t1) v1.2.027690.t1(symbB.v1.2.027690.t1) v1.2.027690.t2(symbB.v1.2.027690.t2) v1.2.027690.t3(symbB.v1.2.027690.t3) v1.2.032089.t1(symbB.v1.2.032089.t1) v1.2.032880.t1(symbB.v1.2.032880.t1 ...
v1.2.007921.t2(symbB.v1.2.007921.t2) v1.2.007922.t1(symbB.v1.2.007922.t1) v1.2.007922.t2(symbB.v1.2.007922.t2) v1.2.007922.t3(symbB.v1.2.007922.t3) v1.2.016339.t1(symbB.v1.2.016339.t1 ...
Despite the recent massive progress in production of vertebrate genome sequence data and large-scale efforts to completely annotate the human genome, we still have scant knowledge of the principles that built genomes in evolution, of genome architecture and its functional organization. This work uses bioinformatics and zebrafish transgenesis to explain a mechanism for the maintenance of long-range conserved synteny across vertebrate genomes and to analyze the arrangement of underlying gene regulation systems. Large mammal-teleost conserved chromosomal segments contain highly conserved non-coding elements (HCNEs), their target genes, as well as phylogenetically and functionally unrelated "bystander" genes. Target genes are developmental and transcriptional regulatory genes with complex, temporally and spatially regulated expression patterns. Bystander genes are not specifically under the control of the regulatory elements that drive the target genes and are usually expressed in different, less ...
ABSTRACT = { Whole genome duplication (WGD) can provide material for evolutionary innovation. Family Salmonidae is ideal for studying the effects ofWGD as the ancestral salmonid underwentWGD relatively recently, ~65Ma, then rediploidized and diversified. Extensive synteny between homologous chromosome arms occurs in extant salmonids, but each species has both conserved and unique chromosomearmfusionsandfissions. Assemblyof large,outbred eukaryoticgenomescanbedifficult, but structural rearrangements within such taxa can be investigated using linkage maps. RAD sequencing provides unprecedented ability to generate high-density linkage maps for nonmodel species, but can result in low numbers of homologous markers between species due to phylogenetic distance or differences in library preparation. Here,we generate a high-density linkagemap (3,826 markers) for the Salvelinus genera (Brook Charr S. fontinalis), and then identify corresponding chromosome arms among the other available salmonid ...
Seven times in On the Origin of Species, Darwin invoked the concept that "nature does not make leaps. Over 50 years after Darwins treatise was published, and now 100 years ago, an article published in the first year of the fledgling journal GENETICS discussed a situation in which nature does in fact make leaps-the origin of novel morphologies after a jump in genomic content by genome duplication (Tupper and Bartlett 1916). Genome duplication appears to have shaped vertebrate evolution in two rounds before the divergence of fish and mammalian lineages (Holland et al. 1994; Dehal and Boore 2005). It was previously known that gene families are often larger in teleosts than in mammals, but it was unclear if this condition arose due to excess preservation of tandem duplicates or to an additional genome duplication event, as suggested by S. Ohno (Ohno 1970). To resolve this question, we used genetic mapping to find the genomic locations of duplicated gene pairs in zebrafish. We found that gene pairs ...
Based on the Ks values of orthologous genes, the divergence of T. parvula and T. salsuginea from Arabidopsis can be placed at approximately 12 million years ago, and the Thellungiella species separated approximately 8 million years ago. The observed genome structures, inversions, and breaks in the colinearity are consistent with the time of divergence.. An obvious difference with respect to Arabidopsis and a specific feature of the Thellungiella species identified genome sequences around the SOS1 gene, one of the well-established salt tolerance determinants (Shi et al., 2000). Irrespective of extensive synteny of the ORFs and the conservation of gene structures for SOS1 between Arabidopsis and T. parvula, colinearity falls apart starting upstream of the first exon in SOS1 (Fig. 3). A hypothesis based on the analysis of SOS1 expression in T. salsuginea (Oh et al., 2009) suggested different expression strength or, possibly, transcript stability. This is further supported in T. parvula by the ...
The development of RFLP linkage maps in hexaploid and diploid oat allows us to study genetic relationships of these species at the DNA level. In this repor
Die Universität zu Köln ist eine Exzellenzuniversität mit dem klassischen Fächerspektrum einer Volluniversität. Als eine der größen Hochschulen Europas arbeitet sie in Forschung und Lehre auch international auf höchstem Niveau.
The genus Bartonella contains Gram-negative arthropod-borne bacteria that are found in many small animal reservoirs and are capable of causing human disease. Bacteria utilize a general stress response system to combat stresses from their surrounding environments. In α-proteobacteria, the general stress response system uses an alternate σ factor as the main regulator and incorporates it with a two-component system into a unique system. Our study identifies the general stress response system in the α-proteobacterium, Bartonella henselae, where the gene synteny is conserved and both the PhyR and alternate σ factor have similar sequence and domain structures with other α-proteobacteria. Furthermore, we showed that the general stress response genes are up-regulated under conditions that mimic the cat flea vector. We also showed that both RpoE and PhyR positively regulate this system and that RpoE also affects transcription of genes encoding heme-binding proteins and the BadA adhesin. Finally, we also
Supplemental file 1 - Yellow colony color coupled with unique colony morphology makes it easy to distinguish the BT-001 strain from other microorganisms in the environment (Fig. S1); alignment of seven homologs of small acid-soluble spore proteins of B. thuringiensis BMB171 along with SspA and SspB of B. subtilis 168 (Fig. S2); synteny analyses of sspA and sspB neighboring genes (Fig. S3); viability of spores of BMB171 and BT-005 strains at 4°C and 37°C during long-term storage (Fig. S4); plasmids used in gene knockout/insertion and antibiotic resistance marker removal (Fig. S5); plasmids used in gene knockout and transposon mutagenesis (Fig. S6); plasmids used in insertion of sporulation-dependent spo0A knockout circuit (Fig. S7); loxP insertion sites at the spo0A locus (Fig. S8); design of two loci for Cre recombinase expression (Fig. S9); spo0A knockout colonies can be clearly distinguished from the wild-type colonies on a DSM agar plate after a 24-h incubation at 30°C (Fig. S10); ...
STAT1 mediates response to interferons and regulates immunity, cell proliferation, apoptosis, and sensitivity of Fanconi Anemia cells to apoptosis after interferon signaling; the roles of STAT1 in embryos, however, are not understood. To explore embryonic functions of STAT1, we investigated stat1b, an unstudied zebrafish co-ortholog of human STAT1. Zebrafish stat1a encodes all five domains of the human STAT1-alpha splice form but, like the human STAT1-beta splice variant, stat1b lacks a complete transactivation domain; thus, two unlinked zebrafish paralogs encode protein forms translated from two splice variants of a single human gene, as expected by sub functionalization after genome duplication. Phylogenetic and conserved synteny studies showed that stat1b and stat1a arose as duplicates in the teleost genome duplication (TGD) and clarified the evolutionary origin of STAT1, STAT2, STAT3, STAT4, STAT5A, STAT5B and STAT6 by tandem and genome duplication. RT-PCR revealed maternal expression of ...
TY - JOUR. T1 - Conserved syntenic clusters of protein coding genes are missing in birds. AU - Lovell, Peter V.. AU - Wirthlin, Morgan. AU - Wilhelm, Larry. AU - Minx, Patrick. AU - Lazar, Nathan H.. AU - Carbone, Lucia. AU - Warren, Wesley C.. AU - Mello, Claudio V.. PY - 2014. Y1 - 2014. N2 - BACKGROUND: Birds are one of the most highly successful and diverse groups of vertebrates, having evolved a number of distinct characteristics, including feathers and wings, a sturdy lightweight skeleton and unique respiratory and urinary/excretion systems. However, the genetic basis of these traits is poorly understood.RESULTS: Using comparative genomics based on extensive searches of 60 avian genomes, we have found that birds lack approximately 274 protein coding genes that are present in the genomes of most vertebrate lineages and are for the most part organized in conserved syntenic clusters in non-avian sauropsids and in humans. These genes are located in regions associated with chromosomal ...