The complete genome sequence of unculturable obtained through clinical metagenomic next-generation sequencing.

Introduction: Diagnosing poses challenges, and it's unclear if its rare isolation is due to infrequent occurrence or its fastidious nutritional requirements.

Methods: This study analyzes the complete genome sequence of , obtained directly from the pus of a sternum infection in a lung transplant patient using metagenomic sequencing.

Results: Genome analysis revealed limited therapeutic options for the infection, primarily susceptibility to tetracyclines.

Staphylococcal cassette chromosome mec containing a novel mec gene complex, B4.

Objectives: To describe a new subclass of mec class B complex identified in Staphylococcus epidermidis.

Methods: Four S. epidermidis isolates obtained from bloodstream infections in patients at University Medical Center Groningen (UMCG) were analysed by phenotypic antibiotic susceptibility testing and WGS.

Genome-Wide Transcriptional Regulation and Chromosome Structural Arrangement by GalR in .

The regulatory protein, GalR, is known for controlling transcription of genes related to D-galactose metabolism in . Here, using a combination of experimental and bioinformatic approaches, we identify novel GalR binding sites upstream of several genes whose function is not directly related to D-galactose metabolism. Moreover, we do not observe regulation of these genes by GalR under standard growth conditions.

DksA and ppGpp directly regulate transcription of the Escherichia coli flagellar cascade.

The components of the Escherichia coli flagella apparatus are synthesized in a three-level transcriptional cascade activated by the master regulator FlhDC. The cascade co-ordinates the synthesis rates of a large number of gene products with each other and with nutritional conditions. Recent genome-wide studies have reported that flagellar transcription is altered in cells lacking the transcription regulators DksA or ppGpp, but some or all reported effects could be indirect, and some are contradictory.

The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse.

Escherichia coli DH10B was designed for the propagation of large insert DNA library clones. It is used extensively, taking advantage of properties such as high DNA transformation efficiency and maintenance of large plasmids. The strain was constructed by serial genetic recombination steps, but the underlying sequence changes remained unverified.

Transcription profiling of the stringent response in Escherichia coli.

The bacterial stringent response serves as a paradigm for understanding global regulatory processes. It can be triggered by nutrient downshifts or starvation and is characterized by a rapid RelA-dependent increase in the alarmone (p)ppGpp. One hallmark of the response is the switch from maximum-growth-promoting to biosynthesis-related gene expression.

Connecting quantitative regulatory-network models to the genome.

Motivation: An important task in computational biology is to infer, using background knowledge and high-throughput data sources, models of cellular processes such as gene regulation. Nachman et al. have developed an approach to inferring gene-regulatory networks that represents quantitative transcription rates, and simultaneously estimates both the kinetic parameters that govern these rates and the activity levels of unobserved regulators that control them.

SspA is required for acid resistance in stationary phase by downregulation of H-NS in Escherichia coli.

The stringent starvation protein A (SspA) is a RNA polymerase-associated protein and is required for transcriptional activation of bacteriophage P1 late promoters. However, the role of SspA in gene expression in Escherichia coli is essentially unknown. In this work, we show that SspA is essential for cell survival during acid-induced stress.

Global transcriptional programs reveal a carbon source foraging strategy by Escherichia coli.

By exploring global gene expression of Escherichia coli growing on six different carbon sources, we discovered a striking genome transcription pattern: as carbon substrate quality declines, cells systematically increase the number of genes expressed. Gene induction occurs in a hierarchical manner and includes many factors for uptake and metabolism of better but currently unavailable carbon sources. Concomitantly, cells also increase their motility.

Systematic mutagenesis of the Escherichia coli genome.

A high-throughput method has been developed for the systematic mutagenesis of the Escherichia coli genome. The system is based on in vitro transposition of a modified Tn5 element, the Sce-poson, into linear fragments of each open reading frame. The transposon introduces both positive (kanamycin resistance) and negative (I-SceI recognition site) selectable markers for isolation of mutants and subsequent allele replacement, respectively.

TOUSLED kinase activity oscillates during the cell cycle and interacts with chromatin regulators.

The TOUSLED (TSL)-like nuclear protein kinase family is highly conserved in plants and animals. tsl loss of function mutations cause pleiotropic defects in both leaf and flower development, and growth and initiation of floral organ primordia is abnormal, suggesting that basic cellular processes are affected. TSL is more highly expressed in exponentially growing Arabidopsis culture cells than in stationary, nondividing cells.

The F-box-containing protein UFO and AGAMOUS participate in antagonistic pathways governing early petal development in Arabidopsis.

The UNUSUAL FLORAL ORGANS (UFO) gene is required for multiple processes in the developing Arabidopsis flower, including the proper patterning and identity of both petals and stamens. The gene encodes an F-box-containing protein, UFO, which interacts physically and genetically with the Skp1 homolog, ASK1. In this report, we describe four ufo alleles characterized by the absence of petals, which uncover another role for UFO in promoting second whorl development.