With the goal of solving the whole-cell problem with Escherichia coli K-12 as a model cell, highly accurate genomes were determined for two closely related K-12 strains, MG1655 and W3110. Completion of the W3110 genome and comparison with the MG1655 genome revealed differences at 267 sites, including 251 sites with short, mostly single-nucleotide, insertions or deletions (indels) or base substitutions (totaling 358 nucleotides), in addition to 13 sites with an insertion sequence element or defective prophage in only one strain and two sites for the W3110 inversion. Direct DNA sequencing of PCR products for the 251 regions with short indel and base disparities revealed that only eight sites are true differences. The other 243 discrepancies were due to errors in the original MG1655 sequence, including 79 frameshifts, one amino-acid residue deletion, five amino-acid residue insertions, 73 missense, and 17 silent changes within coding regions. Errors in the original MG1655 sequence (o1 per 13 000 bases) were mostly within portions sequenced with out-dated technology based on radioactive chemistry.

Transsphenoidal microsurgery is an effective means of control for patients with adrenocorticotrophic hormone-producing microadenomas. Clinical outcome correlated well with the size of the tumor, as measured on preoperative imaging studies, and with postoperative morning cortisol levels following an overnight dexamethasone suppression test. Postoperative cortisol levels can be used as a useful prognostic indicator of the likelihood of future recurrence following transsphenoidal adenomectomy in CD.

. (2007) Am. J. Physiol. 293, H2680 -H2692). To understand the underlying mechanisms leading to such cardiac defects, the functional domains of mXin␣ and its interacting proteins were investigated. Interaction studies using co-immunoprecipitation, pull-down, and yeast two-hybrid assays revealed that mXin␣ directly interacts with ␤-catenin. The ␤-catenin-binding site on mXin␣ was mapped to amino acids 535-636, which overlaps with the known actin-binding domains composed of the Xin repeats. The overlapping nature of these domains provides insight into the molecular mechanism for mXin␣ localization and function. Purified recombinant glutathione S-transferase-or His-tagged mXin␣ proteins are capable of binding and bundling actin filaments, as determined by co-sedimentation and electron microscopic studies. The binding to actin was saturated at an approximate stoichiometry of nine actin monomers to one mXin␣. A stronger interaction was observed between mXin␣ C-terminal deletion and actin as compared with the interaction between full-length mXin␣ and actin. Furthermore, force expression of green fluorescent protein fused to an mXin␣ C-terminal deletion in cultured cells showed greater stress fiber localization compared with force-expressed GFP-mXin␣. These results suggest a model whereby the C terminus of mXin␣ may prevent the fulllength molecule from binding to actin, until the ␤-catenin-binding domain is occupied by ␤-catenin. The binding of mXin␣ to ␤-catenin at the adherens junction would then facilitate actin binding. In support of this model, we found that the actin binding and bundling activity of mXin␣ was enhanced in the presence of ␤-catenin.The striated muscle-specific Xin genes encode proteins containing several proline-rich regions, a highly conserved sequence homologous to the Myb-A and Myb-B DNA-binding domain, and a region with 15-28 16-amino acid (aa) 4 repeating units (called the Xin repeats) (1-3). In the mouse, two Xin genes, mXin␣ and mXin␤, exist, whereas only one cXin gene is found in the chick. The expression of both cXin and mXin␣ is regulated by the muscle transcription factor, MEF2C, and the homeodomain transcription factor, Nkx2.5 (1, 2). Similarly, the expression of mXin␤ (also termed myomaxin) is also under the control of MEF2A (4). Treatment of chick embryos with cXin antisense oligonucleotides results in abnormal cardiac morphogenesis and a disruption in cardiac looping, suggesting that Xin plays an essential role in cardiac development (2). Embryonic lethality was expected based on this antisense oligonucleotide experiment in chicks; however, viable and fertile mXin␣ knock-out mice were observed. This viability probably results from functional compensation through the up-regulation of mXin␤ at both message and protein levels (5). Consistent with the compensatory role of mXin␤, we have previously shown that mXin␤, like mXin␣ (2, 6), localizes to the intercalated disc of the adult heart (5). Despite this compensation, the adult mXin␣-deficient mouse hearts are hypertrophied and exhibit c...

c Eubacterium limosum KIST612 is one of the few acetogens that can produce butyrate from carbon monoxide. We have used a genome-guided analysis to delineate the path of butyrate formation, the enzymes involved, and the potential coupling to ATP synthesis. Oxidation of CO is catalyzed by the acetyl-coenzyme A (CoA) synthase/CO dehydrogenase and coupled to the reduction of ferredoxin. Oxidation of reduced ferredoxin is catalyzed by the Rnf complex and Na ؉ dependent. Consistent with the finding of a Na ؉ -dependent Rnf complex is the presence of a conserved Na ؉ -binding motif in the c subunit of the ATP synthase. Butyrate formation is from acetyl-CoA via acetoacetyl-CoA, hydroxybutyryl-CoA, crotonyl-CoA, and butyryl-CoA and is consistent with the finding of a gene cluster that encodes the enzymes for this pathway. The activity of the butyryl-CoA dehydrogenase was demonstrated. Reduction of crotonyl-CoA to butyryl-CoA with NADH as the reductant was coupled to reduction of ferredoxin. We postulate that the butyryl-CoA dehydrogenase uses flavin-based electron bifurcation to reduce ferredoxin, which is consistent with the finding of etfA and etfB genes next to it. The overall ATP yield was calculated and is significantly higher than the one obtained with H 2 ؉ CO 2 . The energetic benefit may be one reason that butyrate is formed only from CO but not from H 2 ؉ CO 2 .A cetogenic bacteria are a phylogenetically diverse group of strictly anaerobic bacteria able to reduce two molecules of CO 2 to acetate by the Wood-Ljungdahl pathway (WLP) (1-4). Electrons may derive from molecular hydrogen (autotrophic growth), from carbon monoxide, or from organic donors (heterotrophic growth) such as hexoses, pentoses, formate, lactate, alcohols, or methyl group donors (1). Not only does the WLP provide the cell with organic material for biomass formation, but it is also coupled to energy conservation for ATP supply by a chemiosmotic mechanism (2, 5). Every acetogen examined to date uses reduced ferredoxin (Fd) as the electron donor for an ion-translocating membrane protein complex, and acetogens can have either an Fd:NAD ϩ oxidoreductase (Rnf) or an Fd:H ϩ oxidoreductase (Ech) complex for generation of an ion motive force (5). In both cases, the ion gradient can be either an H ϩ or an Na ϩ gradient. The electrochemical ion gradient thus established is then used by a membrane bound, H ϩ -or Na ϩ -translocating F 1 F o ATP synthase (2).Acetate production from CO 2 proceeds via formate that is converted to formyl-tetrahydrofolate (THF) in an ATP-consuming reaction (6). Water is split off from formyl-THF to yield methenyl-THF, which is reduced via methylene-THF to methyl-THF. The latter is condensed with CO (derived from another molecule of CO 2 ) and coenzyme A (CoA) to acetyl-CoA, which is the starting molecule for biosynthetic reactions (4,7,8). Acetyl-CoA is also the precursor of the end product, acetate, that is produced by the enzymes acetyltransferase and acetate kinase. ATP production in the acetate kinase reaction is of special...

X-linked congenital generalized hypertrichosis (CGH), an extremely rare condition characterized by universal overgrowth of terminal hair, was first mapped to chromosome Xq24-q27.1 in a Mexican family. However, the underlying genetic defect remains unknown. We ascertained a large Chinese family with an X-linked congenital hypertrichosis syndrome combining CGH, scoliosis, and spina bifida and mapped the disease locus to a 5.6 Mb critical region within the interval defined by the previously reported Mexican family. Through the combination of a high-resolution copy-number variation (CNV) scan and targeted genomic sequencing, we identified an interchromosomal insertion at Xq27.1 of a 125,577 bp intragenic fragment of COL23A1 on 5q35.3, with one X breakpoint within and the other very close to a human-specific short palindromic sequence located 82 kb downstream of SOX3. In the Mexican family, we found an interchromosomal insertion at the same Xq27.1 site of a 300,036 bp genomic fragment on 4q31.2, encompassing PRMT10 and TMEM184C and involving parts of ARHGAP10 and EDNRA. Notably, both of the two X breakpoints were within the short palindrome. The two palindrome-mediated insertions fully segregate with the CGH phenotype in each of the families, and the CNV gains of the respective autosomal genomic segments are not present in the public database and were not found in 1274 control individuals. Analysis of control individuals revealed deletions ranging from 173 bp to 9104 bp at the site of the insertions with no phenotypic consequence. Taken together, our results strongly support the pathogenicity of the identified insertions and establish X-linked congenital hypertrichosis syndrome as a genomic disorder.

A simple, accurate, sensitive and robust assay that can rapidly and specifically measure the death of target cells would have applications in many areas of biomedicine and particularly for the development of novel cellular- and immune-therapeutics. In this study, we describe a novel cytotoxicity assay, termed the Matador assay, which takes advantage of the extreme brightness, stability and glow-like characteristics of recently discovered novel marine luciferases and their engineered derivatives. The assay involves expression of a luciferase of interest in target cells in a manner so that it is preferentially retained within the healthy cells but is either released from dead and dying cells or whose activity can be preferentially measured in dead and dying cells. We demonstrate that this assay is highly sensitive, specific, rapid, and can be performed in a single-step manner without the need for any expensive equipment. We further validate this assay by demonstrating its ability to detect cytotoxicity induced by several cellular and immune-therapeutic agents including antibodies, natural killer cells, chimeric antigen receptor expressing T cells and a bispecific T cell engager.

Congenital diaphragmatic hernia (CDH) is a common life-threatening birth defect. Recessive mutations in the FRAS1-related extracellular matrix 1 (FREM1) gene have been shown to cause bifid nose with or without anorectal and renal anomalies (BNAR) syndrome and Manitoba oculotrichoanal (MOTA) syndrome, but have not been previously implicated in the development of CDH. We have identified a female child with an isolated left-sided posterolateral CDH covered by a membranous sac who had no features suggestive of BNAR or MOTA syndromes. This child carries a maternally-inherited ~86 kb FREM1 deletion that affects the expression of FREM1's full-length transcripts and a paternally-inherited splice site mutation that causes activation of a cryptic splice site, leading to a shift in the reading frame and premature termination of all forms of the FREM1 protein. This suggests that recessive FREM1 mutations can cause isolated CDH in humans. Further evidence for the role of FREM1 in the development of CDH comes from an N-ethyl-N-nitrosourea -derived mouse strain, eyes2, which has a homozygous truncating mutation in Frem1. Frem1(eyes2) mice have eye defects, renal agenesis and develop retrosternal diaphragmatic hernias which are covered by a membranous sac. We confirmed that Frem1 is expressed in the anterior portion of the developing diaphragm and found that Frem1(eyes2) embryos had decreased levels of cell proliferation in their developing diaphragms when compared to wild-type embryos. We conclude that FREM1 plays a critical role in the development of the diaphragm and that FREM1 deficiency can cause CDH in both humans and mice.

An Escherichia coli strain, ECOR28, was found to have insertions of an identical sequence (1,279 bp in length) at 10 loci in its genome. This insertion sequence (named IS621) has one large open reading frame encoding a putative protein that is 326 amino acids in length. A computer-aided homology search using the DNA sequence as the query revealed that IS621 was homologous to the piv genes, encoding pilin gene invertase (PIV). A homology search using the amino acid sequence of the putative protein encoded by IS621 as the query revealed that the protein also has partial homology to transposases encoded by the IS110/IS492 family elements, which were known to have partial homology to PIV. This indicates that IS621 belongs to the IS110/IS492 family but is most closely related to the piv genes. In fact, a phylogenetic tree constructed on the basis of amino acid sequences of PIV proteins and transposases revealed that IS621 belongs to the piv gene group, which is distinct from the IS110/IS492 family elements, which form several groups. PIV proteins and transposases encoded by the IS110/IS492 family elements, including IS621, have four acidic amino acid residues, which are conserved at positions in their N-terminal regions. These residues may constitute a tetrad D-E(or D)-D-D motif as the catalytic center. Interestingly, IS621 was inserted at specific sites within repetitive extragenic palindromic (REP) sequences at 10 loci in the ECOR28 genome. IS621 may not recognize the entire REP sequence in transposition, but it recognizes a 15-bp sequence conserved in the REP sequences around the target site. There are several elements belonging to the IS110/IS492 family that also transpose to specific sites in the repeated sequences, as does IS621. IS621 does not have terminal inverted repeats like most of the IS110/IS492 family elements. The terminal sequences of IS621 have homology with the 26-bp inverted repeat sequences of pilin gene inversion sites that are recognized and used for inversion of pilin genes by PIV. This suggests that IS621 initiates transposition through recognition of their terminal regions and cleavage at the ends by a mechanism similar to that used for PIV to promote inversion at the pilin gene inversion sites.