Comparative Genomics and Transduction Potential of Enterococcus faecalis Temperate Bacteriophages

To determine the relative importance of temperate bacteriophage in the horizontal gene transfer of fitness and virulence determinants of Enterococcus faecalis, a panel of 47 bacteremia isolates were treated with the inducing agents mitomycin C, norfloxacin, and UV radiation. Thirty-four phages were purified from culture supernatants and discriminated using pulsed-field gel electrophoresis (PFGE) and restriction mapping. From these analyses the genomes of eight representative phages were pyrosequenced, revealing four distinct groups of phages. Three groups of phages, ΦFL1 to 3, were found to be sequence related, with ΦFL1A to C and ΦFL2A and B sharing the greatest identity (87 to 88%), while ΦFL3A and B share 37 to 41% identity with ΦFL1 and 2. ΦFL4A shares 3 to 12% identity with the phages ΦFL1 to 3. The ΦFL3A and B phages possess a high DNA sequence identity with the morphogenesis and lysis modules of Lactococcus lactis subsp. cremoris prophages. Homologs of the Streptococcus mitis platelet binding phage tail proteins, PblA and PblB, are encoded on each sequenced E. faecalis phage. Few other phage genes encoding potential virulence functions were identified, and there was little evidence of carriage of lysogenic conversion genes distal to endolysin, as has been observed with genomes of many temperate phages from the opportunist pathogens Staphylococcus aureus and Streptococcus pyogenes. E. faecalis JH2-2 lysogens were generated using the eight phages, and these were examined for their relative fitness in Galleria mellonella. Several lysogens exhibited different effects upon survival of G. mellonella compared to their isogenic parent. The eight phages were tested for their ability to package host DNA, and three were shown to be very effective for generalized transduction of naive host cells of the laboratory strains OG1RF and JH2-2.Enterococcus faecalis is a member of the natural flora of humans and colonizes the gastrointestinal and vaginal tracts and the oral cavity. In recent years it has emerged as an important opportunistic nosocomial pathogen and is a causative agent of bacteremia, infective endocarditis, and surgical wound and urinary tract infections. The accumulation of acquired antibiotic resistance determinants, in addition to its intrinsic resistance and tenacity, has given rise to the evolution of clinical isolates of E. faecalis that are therapeutically problematic (19). Greater notoriety was afforded to this species following the observed transfer of the conjugative transposon Tn1546 to Staphylococcus aureus, imparting vancomycin resistance (11). Subsequent analysis has revealed that multiple independent E. faecalis-dependent vanA transfers had occurred in the United States prior to 2007 (50). This places enterococci in an important and dynamic position within the health care system, warranting their increased study.The specific determinants that are proposed to contribute to the virulence of E. faecalis are not universally present, and expression of the cognate genes is variable (21, 37). For example, in a recent study of 106 clonally diverse strains of E. faecalis the metallopeptidase gelatinase (GelE) was shown to be expressed in less than 60% of 106 genotypically positive isolates, whereas expression of cytolysin was less frequently observed (expression in ∼25% of isolates, with 30% being genotypically positive) (33). A proposed pathogenicity island identified with E. faecalis V583 (49) is composed of a variable gene set encoding the virulence determinants enterococcal surface protein, cytolysin, and aggregation substance. This highly variable 150-kb mobile element contains many components of unknown function that are hypothesized to facilitate survival and/or transmission in the health care setting (34, 40, 49).Two sequenced and annotated genomes of E. faecalis have been completed and published to date. These are the blood isolate and first-observed vancomycin-resistant strain V583 (40) and the oral isolate OG1RF, used as a common laboratory strain (8). A major difference between these genomes is the presence in V583 of seven regions containing phage-associated sequences. In contrast, OG1RF contains only one phage remnant, which was proposed by McBride et al. (33) to form part of the core genome, a theory supported by the presence in OG1RF of this phage remnant region together with two CRISPR loci. CRISPR sequences provide sequence-specific resistance to bacteriophages via the assembly of phage DNA sequences interspersed as spacers between repeats, in concert with associated cas genes, which collectively operate as an RNA-based gene silencing mechanism (5, 6, 28, 30, 36, 42). This elegant heritable mechanism is proposed to limit horizontal gene transfer of bacteriophage, transposable elements, and conjugative plasmids (9, 10, 32).Within the firmicute division of Gram-positive bacteria, temperate bacteriophages are key vectors for the horizontal transfer of virulence genes. In Staphylococcus aureus, bacteriophages encode and mobilize an impressive array of immune evasion genes (54, 55) and Panton-Valentine leukocidin (43). Several bacteriophage-encoded virulence determinants also contribute to pathogenesis in group A Streptococcus (2, 3, 4).The role of bacteriophages in the virulence of E. faecalis is not clear. Encoded within seven phage-related sequences of strain V583, there are multiple reported homologs of the Streptococcus mitis platelet-binding proteins PblA and PblB (7) and a ferrochelatase (40). In contrast, the absence of mobile genetic elements (MGEs) in strain OG1RF led Bourgogne et al. (8) to speculate that they did not engender virulence in E. faecalis.In this study we determined the morphology and complete genome sequences of eight induced bacteriophages purified from clinical isolates of E. faecalis. We sought to determine the potential carriage of genes that might contribute to the virulence or fitness of this organism and characterize the capacity of these phages to participate in transduction.     

Characterization of apparently balanced chromosomal rearrangements from the developmental genome anatomy project

Apparently balanced chromosomal rearrangements in individuals with major congenital anomalies represent natural experiments of gene disruption and dysregulation. These individuals can be studied to identify novel genes critical in human development and to annotate further the function of known genes. Identification and characterization of these genes is the goal of the Developmental Genome Anatomy Project (DGAP). DGAP is a multidisciplinary effort that leverages the recent advances resulting from the Human Genome Project to increase our understanding of birth defects and the process of human development. Clinically significant phenotypes of individuals enrolled in DGAP are varied and, in most cases, involve multiple organ systems. Study of these individuals' chromosomal rearrangements has resulted in the mapping of 77 breakpoints from 40 chromosomal rearrangements by FISH with BACs and fosmids, array CGH, Southern-blot hybridization, MLPA, RT-PCR, and suppression PCR. Eighteen chromosomal breakpoints have been cloned and sequenced. Unsuspected genomic imbalances and cryptic rearrangements were detected, but less frequently than has been reported previously. Chromosomal rearrangements, both balanced and unbalanced, in individuals with multiple congenital anomalies continue to be a valuable resource for gene discovery and annotation.     

Adventitious Shoot Regeneration and Micropropagation in Calendula officinalis L.

Hypocotyl, cotyledon and cotyledonary node explants of Calendula officinalis L were cultured on Murashige and Skoog (MS) media supplemented with various concentrations of thidiazuron (TDZ), kinetin (KIN), -naphthaleneacetic acid (NAA) and indole-3-butyric acid (IBA) to induce adventitious shoot regeneration and micropropagation. The highest frequency of adventitious shoot regeneration was achieved from hypocotyl and cotyledon explants on MS media supplemented with 0.75 mg dm^–3 TDZ and either 0.25 or 0.50 mg dm^–3 IBA. Efficient in vitro clonal propagation was also induced from cotyledonary nodes on a range of media supplemented with 0.75 mg dm^–3 TDZ and 0.05 mg dm^–3 NAA or 2 mg dm^–3 KIN and 1 mg dm^–3 NAA. Regenerated shoots were excised and rooted in MS medium supplemented with 1 mg dm^–3 NAA. The rooted plantlets were finally transferred to pots.     

Insurance Status Is Associated with Treatment Allocation and Outcomes after Subarachnoid Hemorrhage

Objective

Subarachnoid hemorrhage (SAH) is a particularly devastating type of stroke which is responsible for one third of all stroke-related years of potential life lost before age 65. Surgical treatment has been shown to decrease both morbidity and mortality after subarachnoid hemorrhage. We hypothesized that payer status other than private insurance is associated with lower allocation to surgical treatment for patients with SAH and worse outcomes.

Design

We examined the association between insurance type and surgical treatment allocation and outcomes for patients with SAH while adjusting for a wide range of patient and hospital factors. We analyzed the Nationwide Inpatient Sample hospital discharge database using survey procedures to produce weighted estimates representative of the United States population.

Patients

We studied 21047 discharges, representing a weighted estimate of 102595 patients age 18 and above with a discharge diagnosis of SAH between 2003 and 2008.

Measurements

Multivariable logistic and generalized linear regression analyses were used to assess for any associations between insurance status and surgery allocation and outcomes.

Main Results

Despite the benefits of surgery 66% of SAH patients did not undergo surgical treatment to prevent rebleeding. Mortality was more than twice as likely for patients with no surgical treatment compared to those who received surgery. Medicare patients were significantly less likely to receive surgical treatment.

Conclusions

Nearly two thirds of patients with SAH don''t receive operative care, and Medicare patients were significantly less likely to receive surgical treatment than other patients. Bias against the elderly and those with chronic illness and disability may play a part in these findings. A system of regionalized care for patients presenting with SAH may reduce disparities and improve appropriate allocation to surgical care and deserves prospective study.     

山黧豆属作物在土耳其的栽培与利用状况北大核心CSCD

众所周知,山黧豆起源于巴尔干半岛并传播到世界各地。在土耳其,山黧豆属作物有73个分类群(约1/3为地方特有种),在全国各地均有分布种植,但主要集中在黑海中部、东南部和安纳托利亚东部地区。该文介绍了山黧豆属作物在土耳其全国的分布和在局部地区的食用、观赏等资源利用和保存情况。通常,不同国家人民会因为文化差异形成不同的饮食习惯,但山黧豆大多被用于制作汤、面包或其他咸点。山黧豆的栽培技术则因地制宜,土耳其在边缘土地上进行旱作种植,中国和印度部分地区多采用轮作种植方法等。作为一种极“小众”的作物,山黧豆研究工作的从业人员极少,而且缺乏大型联合研究项目。因此,需要联合化学、表型和分子分析等方法,以保护世界各地包括土耳其在内的地方种质资源,尤其是培育适合土耳其、中国等世界各国的食饲兼用型低β-ODAP品种。总之,选育低β-ODAP或不含β-ODAP的山黧豆品种将有助于丰富人类在食用、饲用和观赏等方面的物种资源利用。     

In vitro culture and biochemical and antioxidant potential of the critically endangered medicinal plant Atropa acuminata Royle ex Lindl of Kashmir Himalaya

In Vitro Cellular & Developmental Biology - Plant - Atropa acuminata Royle is a critically endangered annual herb growing in Kashmir Himalaya and is used as a source of medicine for many...     

Diazoxide preconditioning of endothelial progenitor cells from streptozotocin-induced type 1 diabetic rats improves their ability to repair diabetic cardiomyopathy

Molecular and Cellular Biochemistry - Type 1 diabetes mellitus (DM) is a strong risk factor for the development of diabetic cardiomyopathy (DCM) which is the leading cause of morbidity and...     

Forces and Straw Cutting Performance of Double Disc Furrow Opener in No-Till Paddy Soil

Conservation tillage is an energy efficient and low cost tillage system to improve soil environment compared with conventional tillage systems. However, the rice residue management becomes an “impossible to achieve” task due to high soil moisture content at harvest time and the thickness of rice straw. Disc type furrow openers are used for both seed drilling as well as straw cutting during no tillage sowing. A study was conducted to evaluate the draft requirement and straw cutting performances of different sized furrow openers in no-till paddy soil conditions. Double disc furrow opener was tested on an in-field traction bench for three working depths, i.e. 30, 60 and 90 mm, and three forwarding speeds, i.e. 0.1, 0.2 and 0.3 m/s. The draft and vertical forces on the disc were recorded with load cells. These sensors were connected to a data acquisition system developed with hardware and software. The results revealed that the size of the furrow opener, operating depth and the forwarding speed had significant effects (P<0.05) on the horizontal and vertical forces, and the straw cutting performance. Mean values of the draft were 648.9, 737.2 and 784.6 N for the opener with diameters of 330, 450 and 600 mm respectively, and the vertical forces for similar openers were 904.7, 1553.9 and 1620.4 N, respectively. Furthermore, the mean straw cutting efficiencies for the double disc opener with diameters of 330, 450 and 600 mm were 39.36, 78.47 and 65.46%, respectively. The opener with 450 mm diameter provided higher straw cutting efficiency as compared to 600 mm diameter disc, while lowest straw cutting efficiency was observed with 330 mm diameter disc. The 450 mm diameter opener provided the highest straw cutting efficiency (88.6%) at 90 mm working depth and expressed optimum performance compared with other furrow openers.