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The purpose of this study was to quantify head motion between isometric erector spinae (ES) contraction strategies, paradigms, and intensities in the development of a neuroimaging protocol for the study of neural activity associated with trunk motor control in individuals with low back pain. Ten healthy participants completed two contraction strategies; (1) a supine upper spine (US) press and (2) a supine lower extremity (LE) press. Each contraction strategy was performed at electromyographic (EMG) contraction intensities of 30, 40, 50, and 60% of an individually determined maximum voluntary contraction (MVC) (±10% range for each respective intensity) with real-time, EMG biofeedback. A cyclic contraction paradigm was performed at 30% of MVC with US and LE contraction strategies. Inertial measurement units (IMUs) quantified head motion to determine the viability of each paradigm for neuroimaging. US vs LE hold contractions induced no differences in head motion. Hold contractions elicited significantly less head motion relative to cyclic contractions. Contraction intensity increased head motion in a linear fashion with 30% MVC having the least head motion and 60% the highest. The LE hold contraction strategy, below 50% MVC, was found to be the most viable trunk motor control neuroimaging paradigm.

Topical imiquimod 5% cream has been investigated as off-label primary or adjuvant treatment for melanoma in situ, lentigo maligna type (LM). Herein, we present the largest known case series of lentigo maligna treated with topical imiquimod, with up to 17 years of follow-up, and include a recurrence-free survival analysis. In this case series, 103 lesions were retrospectively evaluated for treatment response and recurrence following a course of topical imiquimod with or without tazarotene gel 0.1% pretreatment between January 1, 2002 and March 31, 2019, and prospectively followed through November 15, 2019. Over median follow-up of 5.1 years (mean = 6.2 years, S = 5.2 years, range, 0.08ndash;17.1 years), including 29.1% LM withgt;10 years follow-up, we observed a response rate of 97.1% (100/103), with 8 local recurrences (8/100, 8.0%) developing at mean 2.9 years (SD: 2.7 years). Local recurrence was significantly associated with a history of failed excision (P= 0.001),lt;60 applications of imiquimod (P= 0.04) and partial clinical clearance (P= 0.0003). Recurrence-free survival analysis demonstrated significant risk-stratification for low and high-risk groups (P= 0.0001). Long term risk for recurrence showed significant differences among low- and high-risk cases, with low-risk cases demonstrating favorable long-term outcomes, comparable to conventional and staged surgery. Our observed low recurrence in a large case series with long-term follow-up suggests the efficacy of topical 5% imiquimod for LM and emphasizes the need for randomized control trials comparing imiquimod with, or as an adjunct to, surgical treatment. J Drugs Dermatol. 2021;20(3):346-348. doi:10.36849/JDD.5660.

Gastrointestinal lipomas are rare, often colonic tumors. The stomach is an unusual site of involvement of lipomas, accounting for less than 5% of all gastrointestinal lipomas and less than 3% of all benign gastric neoplasms. They are usually asymptomatic, and symptoms develop as the tumor grows. Gastric lipomas can present with massive bleeding from an ulcerating tumor and can be life-threatening if left untreated. We present a case of an ulcerating gastric lipoma that presented as an acute upper gastrointestinal hemorrhage. The patient was treated with Billroth II procedure and final pathology showed an ulcerating submucosal lipoma. The diagnosis of gastric lipoma is often suspected incidentally on imaging, then confirmed via biopsy. Definitive treatment of large lesions typically requires surgery, however, newer endoscopic techniques are being utilized for resection of these benign tumors.

Vertebral osteomyelitis is usually secondary to hematogenous seeding from direct inoculation during spinal surgery or from adjacent soft tissue infection; the most common organism being Staphylococcus aureus. We present a case of a 31-year-old male who was found to have vertebral osteomyelitis secondary to Lactobacillus species. The patient with a past medical history significant for hepatitis C, intravenous (IV) drug use, and nicotine dependence presented with severe back pain that started one month ago. His pain was located in the middle and lower back, radiating to his abdomen, and both lower extremities. The patient admitted to abusing IV heroin daily and sharing needles with his fiancée. CT of the abdomen and pelvis with contrast revealed marked irregularity of the endplates at the L3-L4 level and mild irregularity of the endplates at the L4-L5 level suggestive of osteomyelitis/discitis with no evidence of a paraspinal fluid collection. Core biopsy of the superior endplate of L4 and adjacent disc material was done and sent for microbiology and pathology review. His bone culture came back positive for Lactobacillus species; however, blood cultures remained negative. Clinical improvement was noted after starting antibiotics, and the patient was discharged on six weeks of oral clindamycin. When thinking of Lactobacillus, a simple probiotic comes to mind, clinicians need to be more vigilant in recognizing its different strains as possible infectious microorganisms. As described in our case, and other cases of bacteremia secondary to Lactobacillus, Lactobacillus should no longer be regarded as merely a contaminant.

Acute acalculous cholecystitis is defined as acute inflammatory disease of the gallbladder without evidence of gallstones or cystic duct obstruction. Imaging studies typically show a distended acalculous gallbladder with thickened walls. Heart failure is well known to cause congestive hepatopathy and can be associated with isolated gallbladder edema which is often difficult to differentiate from acalculous cholecystitis. We present a case of cholecystalgia secondary to isolated gallbladder edema without hepatic congestion in a patient with non-ischemic cardiomyopathy mimicking the presentation of acalculous cholecystitis. A 46-year-old female with a past medical history of recently diagnosed non-ischemic cardiomyopathy during a prior hospitalization. Echocardiogram showed biventricular heart failure with EF of 15 to 20% with severe left and right ventricular dilatation and global hypokinesis. Left heart catherization showed no angiographic evidence of coronary artery disease and right heart catheterization demonstrated pulmonary hypertension secondary to left heart disease. She left against medical advice and was non-compliant with her medications. Approximately one month later, she presented with shortness of breath and orthopnea. On physical examination, jugular venous distention, S3 gallop, diffuse crackles and anasarca were noted. Labs showed BNP of 12,735. Chest CT revealed cardiomegaly and diffuse interstitial edema with bilateral pleural effusions and no signs of pulmonary embolus. Metoprolol and bumetanide were initiated for management of her acutely decompensated congestive heart failure. Several days after admission, she developed severe sharp RUQ pain associated with nausea and vomiting. She was tachypneic, diaphoretic with severe tenderness in the RUQ. Abdominal ultrasound revealed no signs of congestive hepatopathy but revealed a diffuse, edematous thickening of the gallbladder wall without evidence of stones. Hepatobiliary scintigraphy revealed preserved gallbladder function with an EF of 88%. The remainder of her care was focused on optimization of the patient’s congestive heart failure with complete resolution of her symptoms. Acute decompensation of congestive heart failure can result in an increase in pulmonary or systemic venous pressure, which may result in vascular congestion. The vascular distention can lead to isolated distention of the gallbladder wall that can mimic symptoms of acalculous cholecystitis. In such patient’s cholecystectomy or percutaneous cholecystostomy is not warranted. Radiographic evidence and symptoms usually resolve with optimization of congestive heart failure treatment. This case details the under-recognized presentation of secondary cholecystalgia in a patient with acute RUQ pain and underlying congestive heart failure.

Drug induced angioedema can be allergic or non-allergic depending on the specific mediators leading to the reaction. Allergic angioedema is due to histamine release and has a rapid onset including an urticarial rash that responds to antihistamines and glucocorticoids. Non-allergic angioedema is likely due to increases in bradykinin, and has a much slower onset without an urticarial rash; it only resolves with discontinuation of the offending medication. Mirabegron, a beta 3-adrenergic receptor agonist, is widely prescribed medication for urinary urge incontinence and overactive bladder. This case report presents a patient with angioedema following the use of mirabegron for urinary incontinence whose angioedema symptom had been previous misattributed. The history, clinical examination, and diagnostic parameters led to the diagnosis of mirabegron induced angioedema and she was successfully treated with discontinuation of the medication. Though rare, angioedema is a side effect of mirabegron and can be life-threatening. Therefore thorough history taking and a high index of suspicion are crucial to correlate relevant exposure and onset of symptoms and should be considered in all patients on the medication who have a consistent presentation.

Background: A concerning trend in society today is the development of lifelong diseases, such as hypertension, at an early age. The sequelae of prolonged uncontrolled hypertension are devastating and include the development of vascular disease, kidney disease, and ultimately increased mortality among other things. Though it is thought that today’s children are affected by chronic conditions such as hypertension more frequently than in previous generations, this has not been thoroughly analyzed. This study aimed to evaluate incidence of hypertension, as well as mortality rates in patients with a diagnosis of hypertension in 2 different hospitalized patient populations, children ages 0-12 and adolescents ages 13-18 over the course of a 7-year period from 2005-2012. Methods: An NIS database was queried from 2005-2012. Exclusion criteria included patients greater than >18 years old and patients with secondary causes of hypertension, as this study was looking at essential hypertension only. Analysis was performed via chi square or t test with SAS 9.4, all values were significant when p Results: As per our analysis, the incidence of hypertension in the pediatric populations had a decline in 2006, but since then it has been on the rise while hypertension in the adolescent age group showed a consistent upward trend. Furthermore, our data also revealed that the incidence of hypertension was highest in the Caucasian race in comparison to the other races, with a p-value of < 0.001. Lastly, the likelihood of mortality in hospitalized pediatric populations with a diagnosis of hypertension was 2.03 while in adolescents it was 0.84 with a p value of Discussion: It is thought that the increase in incidence of hypertension in these patient populations could potentially be due to the high sodium, high fat, and low fiber diets of most American citizens. It is well documented that obesity is an epidemic in the youth of America and we believe an analysis of the correlation between hypertension and obesity in these patient populations is warranted, as it is possible that dietary modification in these patients could result in a lower incidence of hypertension, and thus lower mortality and morbidity rates.

Elastofibroma dorsi (ED) is a benign connective tissue tumor that most commonly occurs on the inferior pole of the scapula. It can be found incidentally on radiologic imaging or due to clinical symptoms. Patients may become apprehensive due to it mimicking new malignancy or recurrence of prior malignancy. Treatment is only recommended in symptomatic cases and biopsy is usually unnecessary. We present a case of a 70-year-old female status-post lung cancer resection who was found to have a lump at the inferior pole of her right scapula. She was seen by multiple different specialties and subsequently, a biopsy confirmed her mass to be consistent with ED. Since ED is a benign soft tissue tumor, educating physicians is of utmost importance to avoid pursuing unnecessary diagnosis and to thereby decrease the cost of care to the patient. Therapeutic excision should only be performed in symptomatic patients and observing these lesions in asymptomatic patients would be sufficient.

Sphingosine 1-phosphate (S1P) is a cellular signaling molecule that has been implicated in a variety of diseases including cancer, fibrosis, Alzheimer's, and sickle cell disease. It is formed from the phosphorylation of sphingosine (Sph) by sphingosine kinase (SphK) and SphK exists as two isoforms-"SphK1 and SphK2, which differ with respect to their cellular activity and localization. As the key mediators in the synthesis of S1P, SphKs have attracted attention as viable targets for pharmaceutical inhibition. To validate their potential as therapeutic targets, we aimed to develop potent, selective, and in vivo active inhibitors of SphK. Herein, we describe the design, synthesis and biological evaluation of SphK2 inhibitors. We first describe the development of six SphK2 inhibitors that assess the utility of replacing lipophilic tail groups with heterocyclic rings. These six compounds demonstrate that the lipid binding pocket for SphK2 cannot accommodate compounds with tail groups that are conformationally restricted or positively charged. We then describe the development of aminothiazole-based analogues of an SphK1-selective inhibitor. A library of 37 aryl-substituted aminothiazole tail groups were synthesized, revealing a structure-activity relationship study that examines electronic effects on the aryl-substituted aminothiazoles and the effect of modifying the amino portion of the aminothiazole. These molecules show surprisingly good potency and selectivity for SphK2. In particular, we highlight 3.20dd (SLC4101431), a biphenyl aminothiazole that is the post potent and selective SphK2 inhibitor to date, with an SphK2 Ki of 90 nM and 100-fold selectivity for SphK2. This molecule's in vivo activity will also be discussed. Mitochondrial uncouplers are small molecules that shuttle protons from the inter membrane space to the mitochondrial matrix independent of ATP synthase, which disrupts oxidative phosphorylation and promotes increased nutrient metabolism for homeostasis to be maintained. Consequently, small molecule mitochondrial uncouplers have been pursued as probes for mitochondrial function and as potential therapeutics for the treatment of obesity and type 2 diabetes. Herein, we describe the design, synthesis, and biological evaluation of small molecule mitochondrial uncouplers. We report a library of 52 compounds that have good mitochondrial uncoupling activity over a wide therapeutic range, including 5.16t (SHC4111522) and 5.17i (SHC4091665), which have EC50 values of 0.63 uM and 1.53 uM, respectively, and achieve at least 2-fold increase in oxygen consumption rates relative to basal levels. With these molecules, we demonstrate that pKa and cLogP significantly contribute to uncoupling activity and must be accounted for when developing new generation small molecule mitochondrial uncouplers. Ph. D.

Comparison of the genome sequences of three Pseudomonas fluorescens strains reveals a heterogeneity reminiscent of a species complex rather than a single species, Background Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. Results Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. Conclusions P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.

Sulfobacillus acidophilus Norris et al. 1996 is a member of the genus Sulfobacillus which comprises five species of the order Clostridiales. Sulfobacillus species are of interest for comparison to other sulfur and iron oxidizers and also have biomining applications. This is the first completed genome sequence of a type strain of the genus Sulfobacillus, and the second published genome of a member of the species S. acidophilus. The genome, which consists of one chromosome and one plasmid with a total size of 3,557,831 bp harbors 3,626 protein-coding and 69 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Chromohalobacter salexigens is one of nine currently known species of the genus Chromohalobacter in the family Halomonadaceae. It is the most halotolerant of the so-called 'moderately halophilic bacteria' currently known and, due to its strong euryhaline phenotype, it is an established model organism for prokaryotic osmoadaptation. C. salexigens strain 1H11(T) and Halomonas elongata are the first and the second members of the family Halomonadaceae with a completely sequenced genome. The 3,696,649 bp long chromosome with a total of 3,319 protein-coding and 93 RNA genes was sequenced as part of the DOE Joint Genome Institute Program DOEM 2004.

Isosphaera pallida (ex Woronichin 1927) Giovannoni et al. 1995 is the type species of the genus Isosphaera. The species is of interest because it was the first heterotrophic bacterium known to be phototactic, and it occupies an isolated phylogenetic position within the Planctomycetaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the genus Isosphaera and the third of a member of the family Planctomycetaceae. The 5,472,964 bp long chromosome and the 56,340 bp long plasmid with a total of 3,763 protein-coding and 60 RNA genes are part of the Genomic Encyclopedia of Bacteria and Archaea project.

Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the euryarchaeal class Archaeoglobi, which is currently represented by the single family Archaeoglobaceae, containing six validly named species and two strains ascribed to the genus 'Geoglobus' which is taxonomically challenged as the corresponding type species has no validly published name. All members were isolated from marine hydrothermal habitats and are obligate anaerobes. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the second completed genome sequence of a member of the class Archaeoglobi. The 1,563,423 bp genome with its 1,858 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Chitinophaga pinensis Sangkhobol and Skerman 1981 is the type strain of the species which is the type species of the rapidly growing genus Chitinophaga in the sphingobacterial family 'Chitinophagaceae'. Members of the genus Chitinophaga vary in shape between filaments and spherical bodies without the production of a fruiting body, produce myxospores, and are of special interest for their ability to degrade chitin. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family 'Chitinophagaceae', and the 9,127,347 bp long single replicon genome with its 7,397 protein-coding and 95 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Haloterrigena turkmenica (Zvyagintseva and Tarasov 1987) Ventosa et al. 1999, comb. nov. is the type species of the genus Haloterrigena in the euryarchaeal family Halobacteriaceae. It is of phylogenetic interest because of the yet unclear position of the genera Haloterrigena and Natrinema within the Halobacteriaceae, which created some taxonomic problems historically. H. turkmenica, was isolated from sulfate saline soil in Turkmenistan, is a relatively fast growing, chemoorganotrophic, carotenoid-containing, extreme halophile, requiring at least 2 M NaCl for growth. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Haloterrigena, but the eighth genome sequence from a member of the family Halobacteriaceae. The 5,440,782 bp genome (including six plasmids) with its 5,287 protein-coding and 63 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a human-pathogenic organism that has been isolated from a large variety of human tissues. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long genome with its 4,944 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Veillonella parvula (Veillon and Zuber 1898) Prévot 1933 is the type species of the genus Veillonella in the family Veillonellaceae within the order Clostridiales. The species V. parvula is of interest because it is frequently isolated from dental plaque in the human oral cavity and can cause opportunistic infections. The species is strictly anaerobic and grows as small cocci which usually occur in pairs. Veillonellae are characterized by their unusual metabolism which is centered on the activity of the enzyme methylmalonyl-CoA decarboxylase. Strain Te3(T), the type strain of the species, was isolated from the human intestinal tract. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the large clostridial family Veillonellaceae, and the 2,132,142 bp long single replicon genome with its 1,859 protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Rhodothermus marinus Alfredsson et al. 1995 is the type species of the genus and is of phylogenetic interest because the Rhodothermaceae represent the deepest lineage in the phylum Bacteroidetes. R. marinus R-10(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated from marine hot springs off the coast of Iceland. Strain R-10(T) is strictly aerobic and requires slightly halophilic conditions for growth. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Rhodothermus, and only the second sequence from members of the family Rhodothermaceae. The 3,386,737 bp genome (including a 125 kb plasmid) with its 2914 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Thermanaerovibrio acidaminovorans (Guangsheng et al. 1997) Baena et al. 1999 is the type species of the genus Thermanaerovibrio and is of phylogenetic interest because of the very isolated location of the novel phylum Synergistetes. T. acidaminovorans Su883(T) is a Gram-negative, motile, non-spore-forming bacterium isolated from an anaerobic reactor of a sugar refinery in The Netherlands. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from a member of the phylum Synergistetes. The 1,848,474 bp long single replicon genome with its 1765 protein-coding and 60 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Desulfotomaculum acetoxidans Widdel and Pfennig 1977 was one of the first sulfate-reducing bacteria known to grow with acetate as sole energy and carbon source. It is able to oxidize substrates completely to carbon dioxide with sulfate as the electron acceptor, which is reduced to hydrogen sulfide. All available data about this species are based on strain 5575(T), isolated from piggery waste in Germany. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a Desulfotomaculum species with validly published name. The 4,545,624 bp long single replicon genome with its 4370 protein-coding and 100 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Eggerthella lenta (Eggerth 1935) Wade et al. 1999, emended Würdemann et al. 2009 is the type species of the genus Eggerthella, which belongs to the actinobacterial family Coriobacteriaceae. E. lenta is a Gram-positive, non-motile, non-sporulating pathogenic bacterium that can cause severe bacteremia. The strain described in this study has been isolated from a rectal tumor in 1935. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Eggerthella, and the 3,632,260 bp long single replicon genome with its 3123 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Leptotrichia buccalis (Robin 1853) Trevisan 1879 is the type species of the genus, and is of phylogenetic interest because of its isolated location in the sparsely populated and neither taxonomically nor genomically adequately accessed family 'Leptotrichiaceae' within the phylum 'Fusobacteria'. Species of Leptotrichia are large, fusiform, non-motile, non-sporulating rods, which often populate the human oral flora. L. buccalis is anaerobic to aerotolerant, and saccharolytic. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of the order 'Fusobacteriales' and no more than the second sequence from the phylum 'Fusobacteria'. The 2,465,610 bp long single replicon genome with its 2306 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Vibrio cholerae , the causative agent of cholera, is a bacterium autochthonous to the aquatic environment, and a serious public health threat. V. cholerae serogroup O1 is responsible for the previous two cholera pandemics, in which classical and El Tor biotypes were dominant in the sixth and the current seventh pandemics, respectively. Cholera researchers continually face newly emerging and reemerging pathogenic clones carrying diverse combinations of phenotypic and genotypic properties, which significantly hampered control of the disease. To elucidate evolutionary mechanisms governing genetic diversity of pandemic V. cholerae , we compared the genome sequences of 23 V. cholerae strains isolated from a variety of sources over the past 98 years. The genome-based phylogeny revealed 12 distinct V. cholerae lineages, of which one comprises both O1 classical and El Tor biotypes. All seventh pandemic clones share nearly identical gene content. Using analogy to influenza virology, we define the transition from sixth to seventh pandemic strains as a “shift” between pathogenic clones belonging to the same O1 serogroup, but from significantly different phyletic lineages. In contrast, transition among clones during the present pandemic period is characterized as a “drift” between clones, differentiated mainly by varying composition of laterally transferred genomic islands, resulting in emergence of variants, exemplified by V. cholerae O139 and V. cholerae O1 El Tor hybrid clones. Based on the comparative genomics it is concluded that V. cholerae undergoes extensive genetic recombination via lateral gene transfer, and, therefore, genome assortment, not serogroup, should be used to define pathogenic V. cholerae clones.

Summary This paper describes the genome sequence of M. thermoacetica (f. Clostridium thermoaceticum), which is the model acetogenic bacterium that has been widely used for elucidating the WoodLjungdahl pathway of CO and CO2 fixation. This pathway, which is also known as the reductive acetyl-CoA pathway, allows acetogenic (often called homoacetogenic) bacteria to convert glucose stoichiometrically into three mol of acetate and to grow autotrophically using H2 and CO as electron donors and CO2 as an electron acceptor. Methanogenic archaea use this pathway in reverse to grow by converting acetate into methane and CO2. Acetogenic bacteria also couple the Wood-Ljungdahl pathway to a variety of other pathways to allow the metabolism of a wide variety of carbon sources and electron donors (sugars, carboxylic acids, alcohols, and aromatic compounds) and electron acceptors (CO2, nitrate, nitrite, thiosulfate, dimethylsulfoxide, and aromatic carboxyl groups). The genome consists of a single circular 2628784 bp chromosome encoding 2615 open reading frames, which includes 2523 predicted protein-encoding genes. Of these, 1834 genes (70.13%) have been assigned tentative functions, 665 (25.43%) matched genes of unknown function, and the remaining 24 (0.92%) had no database match. Two thousand three hundred eighty-four (91.17%) of the ORFs in the M. thermoacetica genome can be grouped in ortholog clusters. This first genome sequence of an acetogenic bacterium provides important information related to how acetogens engage their extreme metabolic diversity by switching among different carbon substrates and electron donors/acceptors and how they conserve energy by anaerobic respiration. Our genome analysis indicates that the key genetic trait for homoacetogenesis is the core acs gene cluster of the Wood-Ljungdahl pathway.

The chassis is the cellular host used as a recipient of engineered biological systems in synthetic biology. They are required to propagate the genetic information and to express the genes encoded in it. Despite being an essential element for the appropriate function of genetic circuits, the chassis is rarely considered in their design phase. Consequently, the circuits are transferred to model organisms commonly used in the laboratory, such as Escherichia coli, that may be suboptimal for a required function. In this review, we discuss some of the properties desirable in a versatile chassis and summarize some examples of alternative hosts for synthetic biology amenable for engineering. These properties include a suitable life style, a robust cell wall, good knowledge of its regulatory network as well as of the interplay of the host components with the exogenous circuits, and the possibility of developing whole-cell models and tuneable metabolic fluxes that could allow a better distribution of cellular resources (metabolites, ATP, nucleotides, amino acids, transcriptional and translational machinery). We highlight Pseudomonas putida, widely used in many different biotechnological applications as a prominent organism for synthetic biology due to its metabolic diversity, robustness and ease of manipulation.

Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode proteins involved in the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered: vir -related genes encoding a type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft Roseobacter genomes include those for carbon monoxide oxidation, dimethylsulfoniopropionate demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation.

We examined the breeding system, reproductive output and pollination ecology of Abronia ammophila Greene, a rare and highly restricted endemic of Yellowstone National Park, Wyoming, USA. Floral morphology permits the automatic deposition of self-pollen on the stigma of individual flowers, and male and female reproductive functions temporally overlap. In controlled hand-pollination treatments, we found no significant difference among pollination treatments (unmanipulated, self-pollinated or cross-pollination). The species maintains a long reproductive season with high reproductive output (natural seed set ranged from 59 to 84%). Our results, along with pollinator observations, suggest that A. ammophila exhibits a mixed-mating system: the species can produce seed without pollinators (via either autogamy or agamospermy), but is also visited by an array of pollinating insects that included moths, butterflies and bumblebees. However, noctuid moths were the most abundant pollinators. In contrast, other Abronia species are obligate outcrossers. The mixed-mating system of A. ammophila may have evolved as a consequence of ecological pressures such as scarcity of mates or pollinators.

Summary 1 Niche pre-emption and competitive exclusion is unsatisfactory as a sole explanation for the apparent paradox of a large number of monophyletic taxa in the Macaronesian island flora. 2 Undetected hybridizations have been proposed as an additional plausible explanation. In addition, hybrid swarm theory predicts that hybridizations between invading species would promote adaptive radiation. 3 We suggest that branching processes and coalescence offer yet another plausible explanation allowing for multiple colonizations of closely related taxa, which, because of their later local extinction or hybridization, would lead to apparent monophyly in the molecular record. 4 The cause of such widespread radiation of a few taxa has not been explained, but may involve intermediate conditions of disturbance or productivity. This proposition has, to date, only been tested in a microbial model system, but it offers a reasonable explanation for the patterns observed in the Macaronesian flora, and perhaps in other island floras worldwide.

Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria. Strain DS-1(T) is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that catalyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first completed genome sequence of the genus Parvibaculum, and the first genome sequence of a representative of the family Rhodobiaceae.

Thermodesulfatator indicus Moussard et al. 2004 is a member of the Thermodesulfobacteriaceae, a family in the phylum Thermodesulfobacteria that is currently poorly characterized at the genome level. Members of this phylum are of interest because they represent a distinct, deep-branching, Gram-negative lineage. T. indicus is an anaerobic, thermophilic, chemolithoautotrophic sulfate reducer isolated from a deep-sea hydrothermal vent. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 2,322,224 bp long chromosome with its 2,233 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Tolumonas auensis Fischer-Romero et al. 1996 is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability to produce toluene from phenylalanine and other phenyl precursors, as well as phenol from tyrosine. This is of interest because toluene is normally considered to be a tracer of anthropogenic pollution in lakes, but T. auensis represents a biogenic source of toluene. Other than Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4(T) is the only other member in the family Aeromonadaceae with a completely sequenced type-strain genome. The 3,471,292 bp chromosome with a total of 3,288 protein-coding and 116 RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI 2008.

Kangiella koreensis (Yoon et al. 2004) is the type species of the genus and is of phylogenetic interest because of the very isolated location of the genus Kangiella in the gammaproteobacterial order Oceanospirillales. K. koreensis SW-125(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated from tidal flat sediments at Daepo Beach, Yellow Sea, Korea. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the genus Kangiella and only the fourth genome from the order Oceanospirillales. This 2,852,073 bp long single replicon genome with its 2647 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Sulfurospirillum deleyianum Schumacher et al. 1993 is the type species of the genus Sulfurospirillum. S. deleyianum is a model organism for studying sulfur reduction and dissimilatory nitrate reduction as an energy source for growth. Also, it is a prominent model organism for studying the structural and functional characteristics of cytochrome c nitrite reductase. Here, we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the genus Sulfurospirillum. The 2,306,351 bp long genome with its 2,291 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Methanohalophilus mahiiis the type species of the genusMethanohalophilus, which currently comprises three distinct species with validly published names.Mhp. mahiirepresents moderately halophilic methanogenic archaea with a strictly methylotrophic metabolism. The type strain SLPTwas isolated from hypersaline sediments collected from the southern arm of Great Salt Lake, Utah. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,012,424 bp genome is a single replicon with 2032 protein-coding and 63 RNA genes and part of theGenomic Encyclopedia of Bacteria and Archaeaproject. A comparison of the reconstructed energy metabolism in the halophilic speciesMhp. mahiiwith other representatives of theMethanosarcinaceaereveals some interesting differences to freshwater species.