bluuebunny/crossref_metadata_2025 huggingface dataset:
Acupuncture and traditional Chinese veterinary medicine for treatment of a mare with rectal paralysis
Authors: Sleeper M. M. , Fishman K. , MacKay R. J. , Brown M. , Bauck A. G. , Xie H.
Published: November 2016

An 8‐year‐old Appaloosa mare with rectal paralysis due to a cosmetic ethanol ‘tail block’ was treated with traditional Chinese veterinary medicine treatments including acupuncture and herbal medicine. Her rectal and tail tone gradually improved after the treatment. At 4 months after initial presentation, the mare was able to produce faecal piles on a regular basis, and manual evacuations were no longer needed. Significant improvement was within 30 days of beginning treatment. At 8 months, the owner indicated that the mare had normal defaecation, was able to swish the tail from side to side and lift the tail to urinate, and had no evidence of straining to defaecate or colic.
Social policy by numbers. How international organisations construct global policy proposals
Authors: Berten John , Leisering Lutz
Published: November 2016

Considering the socio‐economic and cultural diversity of the world, it is a bold undertaking by international organisations to propose welfare policies designed to apply to all or many countries. We argue that since the 1990s, new instruments of quantification have extended the knowledge base of international organisations, helping them to design and communicate policy proposals with a global scope. We map these numerical instruments in the field of basic income protection, showing that they serve to identify global social problems and to design global models of welfare. Three case studies illustrate the findings. To make sense of the spread of quantification, we draw on world society theory, arguing that the numerical instruments create a global space of observation, comparison and deliberation regarding social reform. We conclude that numerical instruments have facilitated the expansion of global social protection since the 1990s, but have also narrowed social concerns in the process.
Influence of Escherichia coli chaperone DnaK on protein immunogenicity
Authors: Ratanji Kirsty D. , Derrick Jeremy P. , Kimber Ian , Thorpe Robin , Wadhwa Meenu , Dearman Rebecca J.
Published: November 2016

The production of anti‐drug antibodies can impact significantly upon the safety and efficacy of biotherapeutics. It is known that various factors, including aggregation and the presence of process‐related impurities, can modify and augment the immunogenic potential of proteins. The purpose of the investigations reported here was to characterize in mice the influence of aggregation and host cell protein impurities on the immunogenicity of a humanized single‐chain antibody variable fragment (scFv), and mouse albumin. Host cell protein impurities within an scFv preparation purified from Escherichia coli displayed adjuvant‐like activity for responses to the scFv in BALB/c strain mice. The 70 000 MW E. coli chaperone protein DnaK was identified as a key contaminant of scFv by mass spectrometric analysis. Preparations of scFv lacking detectable DnaK were spiked with recombinant E. coli DnaK to mimic the process‐related impurity. Mice were immunized with monomeric and aggregated preparations, with and without 0·1% DnaK by mass. Aggregation alone enhanced IgM and IgG2a antibody responses, but had no significant effect on total IgG or IgG1 responses. The addition of DnaK further enhanced IgG and IgG2a antibody responses, but only in the presence of aggregated protein. DnaK was shown to be associated with the aggregated scFv by Western blot analysis. Experiments with mouse albumin showed an overall increase in immunogenicity with protein aggregation alone, and the presence of DnaK increased the vigour of the IgG2a antibody response further. Collectively these data reveal that DnaK has the potential to modify and enhance immunogenicity when associated with aggregated protein.
Case management effectiveness in reducing hospital use: a systematic review
Authors: Joo J.Y. , Liu M.F.
Published: November 2016

Aim

This systematic review synthesizes recent evidence of the effectiveness of case management in reducing hospital use by individuals with chronic illnesses.

Background

Hospital use by individuals with chronic illnesses accounts for 66% of healthcare costs in the United States. its has been cited as care coordination that can reduce healthcare costs; however, its effectiveness in improving hospital use outcomes is contradictory, and no review has yet synthesized recent studies of case management with respect to hospital use outcomes.

Methods

This systematic review followed the Cochrane processes and was guided by use of PRISMA statements. Five electronic databases were searched to obtain randomized controlled trials published within the last 10 years that evaluated case management hospital use as a primary outcome by individuals with chronic illnesses.

Results

Ten studies published between 2007 and 2015 were retrieved and assessed for risk of methodological bias. All studies used case management as an intervention, focused on transitional care services and reported hospital use, including readmissions and emergency department and hospital visits, as a primary outcome. Analysis of the studies showed that case management greatly reduced hospital readmissions and emergency department visits.

Limitations

Only studies published in English were searched, and retrieved studies tended to report positive results.

Conclusions

There was strong evidence of significant reductions in hospital use with case management as an intervention. However, other results about the efffectiveness of case management remain mixed; more rigorously designed studies with case management interventions are needed.

Implications for nursing and health policy

The complexity and cost of chronic illnesses means that case management should be considered as a tool to improve quality of care and lower healthcare costs.
Association between dermoscopic and reflectance confocal microscopy features of cutaneous melanoma with BRAF mutational status
Authors: Bombonato C. , Ribero S. , Pozzobon F.C. , Puig‐Butille J.A. , Badenas C. , Carrera C. , Malvehy J. , Moscarella E. , Lallas A. , Piana S. , Puig S. , Argenziano G. , Longo C.
Published: November 2016

Background

Melanomas harbouring common genetic mutations might share certain morphological features detectable with dermoscopy and reflectance confocal microscopy. BRAF mutational status is crucial for the management of metastatic melanoma.

Objectives

To correlate the dermoscopic characteristics of primary cutaneous melanomas with BRAF mutational status. Furthermore, a subset of tumours has also been analysed for the presence of possible confocal features that might be linked with BRAF status.

Methods

Retrospectively acquired dermoscopic and confocal images of patients with melanoma in tertiary referral academic centres: Skin Cancer Unit in Reggio Emilia and at the Melanoma Unit in Barcelona. Kruskal–Wallis test, logistic regressions, univariate and multivariate analyses have been performed to find dermoscopic and confocal features significantly correlated with BRAF mutational status.

Results

Dermoscopically, the presence of irregular peripheral streaks and ulceration were positive predictors of BRAF‐mutated melanomas with a statistically significance value, while dotted vessels were more represented in wild‐type melanomas. None of the evaluated reflectance confocal microscopy features were correlated with genetic profiling.

Conclusions

Ulceration and irregular peripheral streaks represent dermoscopic feature indicative for BRAF‐mutated melanoma, while dotted vessels are suggestive for wild‐type melanoma.
Re‐establishment of the genus Monostichodus Vaillant 1886 (Characiformes, Distichodontidae)
Authors: Musschoot T. , Snoeks J.
Published: November 2016

Pellegrin rejected the validity of Monostichodus elongatus, described by Vaillant and type species of the genus Monostichodus, based on the lack of a proper species description, and redescribed Vaillant's specimens as Hemistichodus vaillanti. After review of the relevant articles in the International Code of Zoological Nomenclature, however, no arguments were found to consider M. elongatus as a nomen nudum. This implies that Hemistichodus should be considered as a junior synonym of the genus Monostichodus, which includes three valid species: M. elongatus (with Hemistichodus vaillanti as a junior synonym), M. mesmaekersi and M. lootensi.
Using transient elastography to predict hepatocellular carcinoma recurrence after radiofrequency ablation
Authors: Lee Yu Rim , Park Soo Young , Kim Seung Up , Jang Se Young , Tak Won Young , Kweon Young Oh , Kim Beom Kyung , Park Jun Yong , Kim Do Young , Ahn Sang Hoon , Han Kwang‐Hyub , Hur Keun
Published: November 2016

Background and Aim

Liver stiffness (LS) value determined using transient elastography (TE) can be used to assess the degree of liver fibrosis. The study investigated whether TE can predict the recurrence of hepatocellular carcinoma (HCC) after radiofrequency ablation (RFA).

Methods

This study retrospectively enrolled 228 patients with HCC who received TE and RFA as the first‐line treatment for HCC between 2008 and 2015. Cox regression analysis was used to identify independent predictors of HCC recurrence.

Results

The median age of the study population (170 men and 58 women) was 61 years. During the study period, HCC recurrence and mortality developed in 125 (54.8%) and 37 (16.2%) patients after RFA, respectively. Liver cirrhosis, platelet count, multiple tumors, and LS value were the independent predictors of HCC recurrence. When the study population was stratified into early (< 12 months) and late (≥ 12 months) recurrence groups, LS value was an independent predictor of late recurrence, along with liver cirrhosis and spleen diameter. The risk of late recurrence was higher in patients with LS values of ≥ 13 kPa than in those with LS values of < 13 kPa (adjusted hazard ratio [HR] = 4.507, 95% confidence interval [CI] 2.131–7.724, P < 0.001). Recurrence was the only predictor of overall survival (HR = 18.583, 95% CI 2.424–142.486, P = 0.005).

Conclusions

Findings of this study suggest that LS measurement using TE can be a useful predictor of HCC recurrence after RFA.
Preparing Family Caregivers to Recognize Delirium Symptoms in Older Adults After Elective Hip or Knee Arthroplasty
Authors: Bull Margaret J. , Boaz Lesley , Maadooliat Mehdi , Hagle Mary E. , Gettrust Lynn , Greene Maureen T. , Holmes Sue Baird , Saczynski Jane S.
Published: November 2016

Objectives

To test the feasibility of a telephone‐based intervention that prepares family caregivers to recognize delirium symptoms and how to communicate their observations to healthcare providers.

Design

Mixed‐method, pre–post quasi‐experimental design.

Setting

A Midwest Veterans Affairs Medical Center and a nonprofit health system.

Participants

Forty‐one family caregiver‐older adult dyads provided consent; 34 completed the intervention.

Intervention

Four telephone‐based education modules using vignettes were completed during the 3 weeks before the older adult's hospital admission for elective hip or knee replacement. Each module required 20 to 30 minutes.

Measurements

Interviews were conducted before the intervention and 2 weeks and 2 months after the older adult's hospitalization. A researcher completed the Confusion Assessment Method (CAM) and a family caregiver completed the Family Version of the Confusion Assessment Method (FAM‐CAM) 2 days after surgery to assess the older adults for delirium symptoms.

Results

Family caregivers’ knowledge of delirium symptoms improved significantly from before the intervention to 2 weeks after the intervention and was maintained after the older adult's hospitalization. They also were able to recognize the presence and absence of delirium symptoms in the vignettes included in the intervention and in the older adult after surgery. In 94% of the cases, the family caregiver rating on the FAM‐CAM approximately 2 days after the older adult's surgery agreed with the researcher rating on the CAM. Family caregivers expressed satisfaction with the intervention and stated that the information was helpful.

Conclusion

Delivery of a telephone‐based intervention appears feasible. All family caregivers who began the program completed the four education modules. Future studies evaluating the effectiveness of the educational program should include a control group.
The tetrapyrrole synthesis pathway as a model of horizontal gene transfer in euglenoids
Authors: Lakey Bryan , Triemer Richard
Published: November 2016

The history of euglenoids may have begun as early as ~2 bya. These early phagotrophs ate cyanobacteria, archaea, and eubacteria, and the subsequent appearance of red algae and chromalveolates provided euglenoids with additional food sources. Following the appearance of green algae, euglenoids acquired a chloroplast via a secondary endosymbiotic event with a green algal ancestor. This endosymbiosis also involved a massive transfer of nuclear‐encoded genes from the symbiont nucleus to the host. Expecting these genes to have a green algal origin, this research has shown, through the use of DNA‐sequences and the analysis of phylogenetic relationships, that many housekeeping genes have a red algal/chromalveolate ancestry. This suggested that many other endosymbiotic/horizontal gene transfers, which brought genes from chromalveolates to euglenoids, may have been taking place long before the acquisition of the chloroplast. The investigation of the origin of the enzymes involved in the tetrapyrrole synthesis pathway provided insights into horizontal gene transfer in euglenoids and demonstrated that the euglenoid nuclear genome is a mosaic comprised of genes from the ancestral lineage plus genes transferred endosymbiotically/horizontally from green, red, and chromalveolates lineages.
Genomic and metagenomic technologies to explore the antibiotic resistance mobilome
Authors: Martínez José L. , Coque Teresa M. , Lanza Val F. , de la Cruz Fernando , Baquero Fernando
Published: November 2016

Antibiotic resistance is a relevant problem for human health that requires global approaches to establish a deep understanding of the processes of acquisition, stabilization, and spread of resistance among human bacterial pathogens. Since natural (nonclinical) ecosystems are reservoirs of resistance genes, a health‐integrated study of the epidemiology of antibiotic resistance requires the exploration of such ecosystems with the aim of determining the role they may play in the selection, evolution, and spread of antibiotic resistance genes, involving the so‐called resistance mobilome. High‐throughput sequencing techniques allow an unprecedented opportunity to describe the genetic composition of a given microbiome without the need to subculture the organisms present inside. However, bioinformatic methods for analyzing this bulk of data, mainly with respect to binning each resistance gene with the organism hosting it, are still in their infancy. Here, we discuss how current genomic methodologies can serve to analyze the resistance mobilome and its linkage with different bacterial genomes and metagenomes. In addition, we describe the drawbacks of current methodologies for analyzing the resistance mobilome, mainly in cases of complex microbiotas, and discuss the possibility of implementing novel tools to improve our current metagenomic toolbox.
Immunomodulation by helminths: Similar impact on type 1 and type 2 diabetes?
Authors: Surendar J. , Indulekha K. , Hoerauf A. , Hübner M. P.
Published: November 2016

The incidence of both type 1 (T1D) and type 2 diabetes (T2D) is drastically increasing, and it is predicted that the global prevalence of diabetes will reach almost 600 million cases by 2035. Even though the pathogenesis of both types of diabetes is distinct, the immune system is actively involved in both forms of the disease. Genetic and environmental factors determine the risk to develop T1D. On the other hand, sedentary life style, surplus of food intake and other lifestyle changes contribute to the increase of T2D incidence. Improved sanitation with high‐quality medical treatment is such an environmental factor that has led to a continuous reduction of infectious diseases including helminth infections over the past decades. Recently, a growing body of evidence has implicated a negative association between helminth infections and diabetes in humans as well as animal models. In this review, we discuss studies that have provided evidence for the beneficial impact of helminth infections on T1D and T2D. Possible mechanisms are presented by which helminths prevent T1D onset by mitigating pancreatic inflammation and confer protection against T2D by improving insulin sensitivity, alleviating inflammation, augmenting browning of adipose tissue and improving lipid metabolism and insulin signalling.
Use of the gonadotropin‐releasing hormone (GnRH) stimulation test to monitor gonadal function in intact adult male cats
Authors: Romagnoli S , Baldan A , Righetti C , Fontaine C , Scenna L , Badon T , Stelletta C , Milani C , Cecchetto M , Mollo A
Published: November 2016

Contents

The gonadotropin‐releasing hormone (GnRH) stimulation test is a common procedure used to investigate normality of the pituitary‐gonadal axis in mammals. There is very little information on the technique, its efficacy and side effects in small animals and in particular no information for male cats. In dogs, such test is performed by intravenous (IV) administration. With cats, the number of times the animal needs to be restrained for blood sampling should be the least possible. The purpose of this study was to assess efficacy and side effects of the GnRHstimulation test in tomcats comparing theIVwith the intramuscular (IM) route of administration. A GnRHstimulation test was performed in eight adult tomcats throughIMorIVadministration of 50 μg gonadorelin. The response of the pituitary‐gonadal axis was assessed by measuring serum testosterone on blood samples collected prior to and 1 hr following treatment. When considering each single group of cats, the post‐stimulation serum testosterone values were significantly higher than the pre‐treatment ones (p < .05). When comparing the two groups of cats, basal testosterone concentrations did not differ, and also post‐GnRHtestosterone concentrations did not differ. In conclusion, in the cats of our study, the GnRHstimulation test produced the same results following theIMor theIVroute of administration. Therefore, in tomcats, theIMroute can be considered as effective as theIVone and should be preferred when doing a GnRHtest.
Narrative skills predict peer adjustment across elementary school years
Authors: Davidson Alice J. , Walton Marsha D. , Kansal Bhavna , Cohen Robert
Published: November 2016

The importance of peer adjustment in middle childhood coincides with developing social cognitive and discursive skills that include the ability to make personal narrative accounts. Authoring personal stories promotes attention to the sequence of events, the causal connections between events, the moral significance of what has happened, and the motives that drive human action: these skills may be critical for the establishment and maintenance of satisfying peer relationships during elementary school. This study extended previous research by considering whether narrative skills in written stories about peer interactions predicted peer adjustment. As part of an ongoing longitudinal study, 92 children wrote narratives about peer experiences and completed surveys on measures of peer adjustment for two school years. Cross‐lagged panel models indicated that chronological and thematic coherence and reports of moral concerns in narratives in the first year of the study contributed to lower peer disliking in the subsequent academic year. Reports of motives in Year 1 narratives contributed to lower levels of loneliness and peer victimization in Year 2. Writing personal narratives that are coherent and attentive to moral concerns and motives may be especially beneficial for children who have difficulty connecting with peers. We discuss implications for classroom practices.
Daily links between school problems and youth perceptions of interactions with parents: A diary study of school‐to‐home spillover
Authors: Bai Sunhye , Reynolds Bridget M. , Robles Theodore F. , Repetti Rena L.
Published: November 2016

This study examined how academic and peer problems at school are linked to family interactions at home on the same day, using eight consecutive weeks of daily diary data collected from early adolescents (60% female; M age = 11.28, SD = 1.50), mothers and fathers in 47 families. On days when children reported more academic problems at school, they, but not their parents, reported less warmth and more conflict with mothers, and more conflict and less time spent around fathers. These effects were partially explained by same‐day child reports of higher negative mood. Peer problems were less consistently associated with parent‐child interactions over and above the effects of academic problems that day. A one‐time measure of parent‐child relationship quality moderated several daily associations, such that the same‐day link between school problems and child‐report of family interactions was stronger among children who were closer to their parents.
The responses of soil, litter and root carbon stocks to the conversion of forest regrowth to crop and tree production systems used by smallholder farmers in eastern Amazonia
Authors: Lemos E. C. M. , Vasconcelos S. S. , Santiago W. R. , de Oliveira Junior M. C. M. , de A. Souza C. M.
Published: November 2016

The impact of substituting forests for smallholder agricultural production systems on soil carbon (C) stocks is not well understood in Brazilian Amazonia. Most surveys of soil C stocks are restricted to the top 30 cm of soil and do not include measurements of litter and root stocks. Here, we quantify the stocks of C in soil (0–100 cm depth), aboveground litter and coarse roots of traditional (slash‐and‐burn) and alternative (Schizolobium amazonicum‐planted forest and silvopastoral system) smallholder agricultural systems, which were compared with a reference area (forest regrowth) in the eastern Amazonia. The soil C stocks in the 0–100 cm layer were larger in the forest regrowth treatment (156.8 ± 15.5 Mg/ha) than in the other treatments (S. amazonicum = 85.3 ± 6.5, silvopastoral = 108.0 ± 4.4 Mg/ha) but did not differ from the soil C stock in the slash‐and‐burn treatment (127.2 ± 6.1 Mg/ha). The soil C stocks at the 0–30 cm layer, which represented 33–50% of the total C of the 0–100 cm layer, did not differ among the treatments. The litter C stocks were ranked in the following order: silvopastoral > forest regrowth > S. amazonicum > slash‐and‐burn. The forest regrowth treatment had a greater coarse root C stock (0.84 ± 0.10 Mg/ha) than the other treatments (silvopastoral = 0.28 ± 0.03, S. amazonicum = 0.18 ± 0.03, slash‐and‐burn = 0.27 ± 0.04 Mg/ha). Soil, litter and root C stocks were negatively impacted by the conversion of forest regrowth to cultivation systems.
Plasma is a strategic resource
Authors: Strengers Paul F.W. , Klein Harvey G.
Published: November 2016

Plasma‐derived medicinal products (PDMPs) such as immunoglobulins and clotting factors are listed by the World Health Organization as essential medicines. These and other PDMPs are crucial for the prophylaxis and treatment of patients with bleeding disorders, immune deficiencies, autoimmune and inflammatory diseases, and a variety of congenital deficiency disorders. While changes in clinical practice in developed countries have reduced the need for red blood cell transfusions thereby significantly reducing the collection volumes of whole blood and recovered plasma suitable for fractionation, the need for PDMPs worldwide continues to increase. The majority of plasma supplies for the manufacture of PDMPs is met by the US commercial plasma industry. However, geographic imbalance in the collection of plasma raises concerns that local disruptions of plasma supplies could result in regional and global shortages of essential PDMPs. Plasma, which fits the definition of a strategic resource, that is, “an economically important raw material which is subject to a higher risk of supply interruption,” should be considered a strategic resource comparable to energy and drinking water. Plasma collections should be increased outside the United States, including in low‐ and middle‐income countries. The need for capacity building in these countries is an essential part to strengthen quality plasma collection. This will require changes in national and regional policies. We advocate the need for the restoration of an equitable balance of the international plasma supply to reduce the risk of supply shortages worldwide. Strategic independence of plasma should be endorsed on a global level.
Pattern-generation and pattern-transfer for single-digit nano devices
Authors: Rangelow Ivo W. , Ahmad Ahmad , Ivanov Tzvetan , Kaestner Marcus , Krivoshapkina Yana , Angelov Tihomir , Lenk Steve , Lenk Claudia , Ishchuk Valentyn , Hofmann Martin , Nechepurenko Diana , Atanasov Ivaylo , Volland Burkhard , Guliyev Elshad , Durrani Zahid , Jones Mervyn , Wang Chen , Liu Dixi , Reum Alexander , Holz Mathias , Nikolov Nikolay , Majstrzyk Wojciech , Gotszalk Teodor , Staaks Daniel , Dallorto Stefano , Olynick Deirdre L.
Published: November 2016

Single-electron devices operating at room temperature require sub-5 nm quantum dots having tunnel junctions of comparable dimensions. Further development in nanoelectronics depends on the capability to generate mesoscopic structures and interfacing these with complementary metal–oxide–semiconductor devices in a single system. The authors employ a combination of two novel methods of fabricating room temperature silicon single-electron transistors (SETs), Fowler–Nordheim scanning probe lithography (F-N SPL) with active cantilevers and cryogenic reactive ion etching followed by pattern-dependent oxidation. The F-N SPL employs a low energy electron exposure of 5–10 nm thick high-resolution molecular resist (Calixarene) resulting in single nanodigit lithographic performance [Rangelow et al., Proc. SPIE 7637, 76370V (2010)]. The followed step of pattern transfer into silicon becomes very challenging because of the extremely low resist thickness, which limits the etching depth. The authors developed a computer simulation code to simulate the reactive ion etching at cryogenic temperatures (−120 °C). In this article, the authors present the alliance of all these technologies used for the manufacturing of SETs capable to operate at room temperatures.
Genome Sequences of Eight Prophages Isolated from Lactococcus lactis Dairy Strains
Authors: Oliveira Joana , Mahony Jennifer , Lugli Gabriele Andrea , Hanemaaijer Laurens , Kouwen Thijs , Ventura Marco , van Sinderen Douwe
Published: November 2016

P335 group phages represent the most divergent phage group infecting dairy
Lactococcus lactis
strains and have significant implications for the dairy processing industry. Here, we report the complete genome sequences of eight lactococcal prophages chemically induced from industrial lactococcal strains that propagate lytically on one of two laboratory strains.
Complete Genome Sequences of Group III
Campylobacter
Bacteriophages PC5 and PC14
Authors: Janež Nika , Peterka Matjaž , Accetto Tomaž
Published: November 2016

Here, we present the whole-genome sequences of bacteriophages PC5 and PC14 specific for
Campylobacter jejuni
, a leading cause of gastroenteritis in developed countries. Their genomes are syntenic to those of group III
Campylobacter
bacteriophages and share more than 90% identity at the nucleotide level with members of this group.
Draft Genome Sequence of Microcystis aeruginosa NIES-98, a Non-Microcystin-Producing Cyanobacterium from Lake Kasumigaura, Japan
Authors: Yamaguchi Haruyo , Suzuki Shigekatsu , Sano Tomoharu , Tanabe Yuuhiko , Nakajima Nobuyoshi , Kawachi Masanobu
Published: November 2016

Microcystis aeruginosa
is a well-known bloom-forming cyanobacterium. We newly sequenced the whole genome of
M. aeruginosa
NIES-98, which is a non-microcystin-producing strain isolated from Lake Kasumigaura, Japan. The genome contains approximately 5.0 Mbp, with an average G+C content of 42.41% and 5,140 predicted protein-coding genes.
Complete Genome Sequence of Leptospira alstonii Serovar Room22 Strain GWTS #1
Authors: Nally Jarlath E. , Bayles Darrell O. , Hurley Daniel , Fanning Séamus , McMahon Barry J. , Arent Zbigniew
Published: November 2016

We report here the complete genome sequence of
Leptospira alstonii
serovar Room22 strain GWTS #1. This is the first isolate of
L. alstonii
to be cultured from a mammal and in western Europe, and it represents a new serovar of pathogenic leptospires.
Draft Genome Sequence of the Type Strain Desulfuribacillus alkaliarsenatis AHT28, an Obligately Anaerobic, Sulfidogenic Bacterium Isolated from Russian Soda Lake Sediments
Authors: Abin Christopher A. , Hollibaugh James T.
Published: November 2016

Desulfuribacillus alkaliarsenatis
AHT28
T
is an obligately anaerobic, sulfur- and arsenate-reducing haloalkaliphile that was isolated from Russian soda lake sediments. Here, we present the 3.1-Mb draft genome sequence for this strain, consisting of 36 contigs with a G+C content of 37.5% and 2,978 protein-coding sequences.
Draft Genome Sequences of Two Ralstonia pickettii Strains with Different Aminoglycoside Resistance Phenotypes
Authors: Vaz-Moreira Ivone , Tamames Javier , Martínez José Luis , Manaia Célia M.
Published: November 2016

The genomes of two
Ralstonia pickettii
strains (H2Cu2 and H2Cu5), isolated from hospital effluent in a selective medium containing CuSO
4,
were sequenced. They presented MICs of >256 and 6 µg/ml for the aminoglycoside gentamicin, respectively. The 5.2-Mb draft genomes have 40 contigs for strain H2Cu2 and 113 for H2Cu5.
Genome Sequence of Bellavista Virus, a Novel Orthobunyavirus Isolated from a Pool of Mosquitoes Captured near Iquitos, Peru
Authors: Hang Jun , Yang Yu , Kuschner Robert A. , Evangelista Julio , Astete Helvio , Halsey Eric S. , Kochel Tadeusz J. , Forshey Brett M.
Published: November 2016

A novel orthobunyavirus, Bellavista virus, was isolated from
Culex (Melanoconion) portesi
mosquitoes in the Bellavista neighborhood of Iquitos, Peru, in 2009. The assembled segment L, M, and S sequences of strain PRD0552 are 6,950, 4,469, and 1,256 bases in length, respectively, comprising complete protein-coding sequences and partial terminal untranslated sequences.
Draft Genome Sequence of Mycobacterium bovis Strain D-10-02315 Isolated from Wild Boar
Authors: Branger Maxime , Hauer Amandine , Michelet Lorraine , Karoui Claudine , Cochard Thierry , De Cruz Krystel , Henault Sylvie , Boschiroli María Laura , Biet Franck
Published: November 2016

Mycobacterium bovis
is the etiologic agent of bovine tuberculosis, a chronic infectious disease, affecting livestock, wild animals, and sometimes humans. We report the draft genome sequence of a
Mycobacterium bovis
strain isolated from wild boar of spoligotype SB0120 (or BCG-like) also present in wildlife-livestock multi-host systems.
Complete Genome Sequence of a Colistin Resistance Gene (
mcr-1
)-Bearing Isolate of Escherichia coli from the United States
Authors: Meinersmann Richard J. , Ladely Scott R. , Bono James L. , Plumblee Jodie R. , Hall M. Carolina , Genzlinger Linda L. , Cook Kimberly L.
Published: November 2016

Transmissible colistin resistance conferred by the
mcr-1
gene-bearing IncI2 plasmid has been recently reported in
Escherichia coli
in the United States. We report here the completed genome sequence of a second
E. coli
strain isolated from swine in the United States that carried the
mcr-1
gene on an IncI2-type plasmid.
Complete Genome Sequence of Aggregatibacter actinomycetemcomitans Strain IDH781
Authors: May Anthony C. , Ehrlich Rachel L. , Balashov Sergey , Ehrlich Garth D. , Shanmugam Mayilvahanan , Fine Daniel H. , Ramasubbu Narayanan , Mell Joshua Chang , Cugini Carla
Published: November 2016

We report here the complete genomic sequence and methylome of
Aggregatibacter actinomycetemcomitans
strain IDH781. This rough strain is used extensively as a model organism to characterize localized aggressive periodontitis pathogenesis, the basic biology and oral cavity colonization of
A. actinomycetemcomitans
, and its interactions with other members of the oral microbiome.
Isolation, characterization, and inactivation of the APA1 gene encoding yeast diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase
Authors: Plateau P , Fromant M , Schmitter J M , Buhler J M , Blanquet S
Published: November 2016

The gene encoding diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A) phosphorylase from yeast was isolated from a lambda gt11 library. The DNA sequence of the coding region was determined, and more than 90% of the deduced amino acid sequence was confirmed by peptide sequencing. The Ap4A phosphorylase gene (APA1) is unique in the yeast genome. Disruption experiments with this gene, first, supported the conclusion that, in vivo, Ap4A phosphorylase catabolizes the Ap4N nucleotides (where N is A, C, G, or U) and second, revealed the occurrence of a second Ap4A phosphorylase activity in yeast cells. Finally, evidence is provided that the APA1 gene product is responsible for most of the ADP sulfurylase activity in yeast extracts.
Transcription from the P1 promoters of Micromonospora echinospora in the absence of native upstream DNA sequences
Authors: Baum E Z , Buttner M J , Lin L S , Rothstein D M
Published: November 2016

We demonstrated previously that the 0.4-kilobase DNA fragment from Micromonospora echinospora contains multiple tandem promoters, P1a, P1b, P1c, and P2, which are also functional when cloned into Streptomyces lividans. We now show by in vitro transcription with Streptomyces RNA polymerase that each of these promoters is an authentic initiation site, rather than a processing site for transcripts which initiate further upstream. The DNA sequence requirements for the closely spaced promoters P1a, P1b, and P1c, which are coordinately induced during stationary phase in M. echinospora, were examined by deletional analysis in S. lividans. The P1a and P1b promoters were functional despite deletion of native sequences 5 and 17 base pairs upstream of each initiation site, respectively. Thus, P1a and P1b had greatly reduced upstream DNA sequence requirements compared with typical procaryotic promoters. In contrast, transcription from promoter P1c was significantly decreased when native sequences 34 base pairs upstream were replaced.
New mre genes mreC and mreD, responsible for formation of the rod shape of Escherichia coli cells
Authors: Wachi M , Doi M , Okada Y , Matsuhashi M
Published: November 2016

New shape-determining genes in the mre cluster at 71 min on the Escherichia coli chromosome map, named mreC and mreD, were identified by complementation experiments using delta mre-678 mutant cells, which have a 5-kilobase-pair deletion encompassing the mre region, and by DNA sequencing. The delta mre-678 mutant cells required three genes, the previously reported mreB gene and the two new genes, to restore the normal rod shape of the cells and normal sensitivity of growth to mecillinam. The mreC gene is preceded by the mreB gene and by a 65-base-pair spacing sequence containing a palindrome sequence and a possible Shine-Dalgarno sequence. The deduced amino acid sequence of the MreC protein consists of 367 amino acid residues with a molecular weight of 39,530. The initiation codon of the mreD gene overlaps the termination codon of the mreC gene by one nucleotide residue. The deduced amino acid sequence of the MreD protein consists of 162 amino acid residues with a molecular weight of 18,755. In vitro, the coding frames of mreC and mreD produced proteins with Mrs of 40,000 and 15,000, respectively, as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
Nucleotide transport in Rhodobacter capsulatus
Authors: Carmeli C , Lifshitz Y
Published: November 2016

Cytoplasmic membrane vesicles isolated from the gram-negative photosynthetic bacterium Rhodobacter capsulatus catalyzed the transport of nucleotides. No transport occurred in the intact bacteria unless they were pretreated with EDTA. The transport rate was measured by incorporation of radioactive phosphate into externally added ADP or by incorporation of nonradioactive phosphate into added labeled ADP. The catalytic activities which utilized the added ADP were photosynthetic ATP synthesis, Pi-ADP exchange, and adenylate kinase. These activities were shown to occur on the cytoplasmic side of the internal membrane. The products were found in the outer medium. The rate of nucleotide transport across the membranes was comparable to the rate of photophosphorylation. These results indicated that nucleotides can be transported across the cytoplasmic membrane but not across the outer membrane of the native R. capsulatus cell. Therefore, by analogy to the mitochondrial ATP-ADP translocator, the exchange might function as an energy transfer system to the periplasm of these bacteria.
Point mutations in a conserved region (TonB box) of Escherichia coli outer membrane protein BtuB affect vitamin B12 transport
Authors: Gudmundsdottir A , Bell P E , Lundrigan M D , Bradbeer C , Kadner R J
Published: November 2016

Uptake of cobalamins and iron chelates in Escherichia coli K-12 is dependent on specific outer membrane transport proteins and the energy-coupling function provided by the TonB protein. The btuB product is the outer membrane receptor for cobalamins, bacteriophage BF23, and the E colicins. A short sequence near the amino terminus of mature BtuB, previously called the TonB box, is conserved in all tonB-dependent receptors and colicins and is the site of the btuB451 mutation (Leu-8----Pro), which prevents energy-coupled cobalamin uptake. This phenotype is partially suppressed by certain mutations in tonB. To examine the role of individual amino acids in the TonB box of BtuB, more than 30 amino acid substitutions in residues 6 to 13 were generated by doped oligonucleotide-directed mutagenesis. Many of the mutations affecting each amino acid did not impair transport activity, although some substitutions reduced cobalamin uptake and the Leu-8----Pro and Val-10----Gly alleles were completely inactive. To test whether the btuB451 mutation affects only cobalamin transport, a hybrid gene was constructed which encodes the signal sequence and first 39 residues of BtuB fused to the bulk of the ferrienterobactin receptor FepA (residues 26 to 723). This hybrid protein conferred all FepA functions but no BtuB functions. The presence of the btuB451 mutation in this fusion gene eliminated all of its tonB-coupled reactions, showing that the TonB box of FepA could be replaced by that from BtuB. These results suggest that the TonB-box region of BtuB is involved in active transport in a manner dependent not on the identity of specific side chains but on the local secondary structure.
Erythromycin-induced ribosome stall in the ermA leader: a barricade to 5'-to-3' nucleolytic cleavage of the ermA transcript
Authors: Sandler P , Weisblum B
Published: November 2016

The Staphylococcus aureus ermA gene, whose product confers resistance to the macrolide-lincosamide-streptogramin B family of antibiotics, is induced at the level of translation by nanomolar concentrations of erythromycin. Erythromycin also specifically stabilizes ermA transcripts, and the induced stabilization requires in-phase translation of at least one of two small leader peptides in the 5' leader region of the transcript. Erythromycin-induced mRNA stabilization was tested in three constructions in which the ermA transcript was elongated by making insertions at the ermA transcription start. Whereas mRNA downstream of the leader peptide is stabilized by erythromycin, mRNA upstream is not. In the presence of erythromycin, specific mRNA decay intermediates in both the extended ermA genes and the wild-type ermA gene were detected by both Northern blotting and S1 nuclease mapping. The 5' ends of the intermediates map to the sequences that encode each of the two ermA leader peptides, suggesting that the intermediates are produced by stalled erythromycin-bound ribosomes acting as barricades to degradation by 5'-to-3' RNases. In addition, whereas erythromycin was found previously to stabilize ermA transcripts only physically, an ermC-cat-86 hybrid transcript was stabilized both physically and functionally by erythromycin.
Natural relationships among sulfate-reducing eubacteria
Authors: Devereux R , Delaney M , Widdel F , Stahl D A
Published: November 2016

Phylogenetic relationships among 20 nonsporeforming and two endospore-forming species of sulfate-reducing eubacteria were inferred from comparative 16S rRNA sequencing. All genera of mesophilic sulfate-reducing eubacteria except the new genus Desulfomicrobium and the gliding Desulfonema species were included. The sporeforming species Desulfotomaculum ruminis and Desulfotomaculum orientis were found to be gram-positive organisms sharing 83% 16S rRNA sequence similarity, indicating that this genus is diverse. The gram-negative nonsporeforming species could be divided into seven natural groups: group 1, Desulfovibrio desulfuricans and other species of this genus that do not degrade fatty acids (this group also included "Desulfomonas" pigra); group 2, the fatty acid-degrading "Desulfovibrio" sapovorans; group 3, Desulfobulbus species; group 4, Desulfobacter species; group 5, Desulfobacterium species and "Desulfococcus" niacini; group 6, Desulfococcus multivorans and Desulfosarcina variabilis; and group 7, the fatty acid-oxidizing "Desulfovibrio" baarsii. (The quotation marks are used to indicate the need for taxonomic revision.) Groups 1 to 3 are incomplete oxidizers that form acetate as an end product; groups 4 to 7 are complete oxidizers. The data were consistent with and refined relationships previously inferred by oligonucleotide catalogs of 16S rRNA. Although the determined relationships are generally consistent with the existing classification based on physiology and other characteristics, the need for some taxonomic revision is indicated.
Hydrolysis of bis(5'-nucleosidyl) polyphosphates by Escherichia coli 5'-nucleotidase
Authors: Ruiz A , Hurtado C , Meireles Ribeiro J , Sillero A , Günther Sillero M A
Published: November 2016

Two enzymatic activities that split diadenosine triphosphate have been reported in Escherichia coli: a specific Mg-dependent bis(5'-adenosyl) triphosphatase (EC 3.6.1.29) and the bis(5'-adenosyl) tetraphosphatase (EC 3.6.1.41). In addition to the activities of these two enzymes, a different enzyme activity that hydrolyzes dinucleoside polyphosphates is described. After purification and study of its molecular and kinetic properties, we concluded that it corresponded to the 5'-nucleotidase (EC 3.1.3.5) that has been described in E. coli. The enzyme was purified from sonic extracts and osmotic shock fluid. From sonic extracts, two isoforms were isolated by chromatography on ion-exchange Mono Q columns; they had a molecular mass of about 100 kilodaltons (kDa). From the osmotic shock fluid, a unique form of 52 kDa was recovered. Mild heating transformed the 100-kDa isoform to a 52-kDa form, with an increase in activity of about threefold. The existence of a 5'-nucleotidase inhibitor described previously, which associates with the enzyme and is not liberated in the osmotic shock fluid, may have been responsible for these results. The kinetic properties and substrate specificities of both forms (52 and 100 kDa) were almost identical. The enzyme, which is known to hydrolyze AMP and uridine-(5')-diphospho-(1)-alpha-D-glucose, but not adenosine-(5')-diphospho-(1)-alpha-D-glucose, was also able to split adenosine-(5')-diphospho-(5)-beta-D-ribose, ribose-5-phosphate, and dinucleoside polyphosphates [diadenosine 5',5'''-P1,P2-diphosphate,diadenosine 5',5'''-P1,P3-triphosphate, diadenosine 5',5'''-P1,P4-tetraphosphate, and bis(5'-guanosyl) triphosphate]. The effects of divalent cations and pH on the rate of the reaction with different substrates were studied.
Structure of a Ruminococcus albus endo-1,4-beta-glucanase gene
Authors: Ohmiya K , Kajino T , Kato A , Shimizu S
Published: November 2016

A chromosomal DNA fragment encoding an endo-1,4-beta-glucanase I (Eg I) gene from Ruminococcus albus cloned and expressed in Escherichia coli with pUC18 was fully sequenced by the dideoxy-chain termination method. The sequence contained a consensus promoter sequence and a structural amino acid sequence. The initial 43 amino acids of the protein were deduced to be a signal sequence, since they are missing in the mature protein (Eg I). High homology was found when the amino acid sequence of the Eg I was compared with that of endoglucanase E from Clostridium thermocellum. Codon usage of the gene was not biased. These results suggested that the properties of the Eg I gene from R. albus was specified from the known beta-glucanase genes of the other organisms.
Isolation and characterization of a Saccharomyces cerevisiae mutant with impaired glutamate synthase activity
Authors: Folch J L , Antaramián A , Rodríguez L , Bravo A , Brunner A , González A
Published: November 2016

A mutant of Saccharomyces cerevisiae that lacks glutamate synthase (GOGAT) activity has been isolated. This mutant was obtained after chemical mutagenesis of a NADP-glutamate dehydrogenase-less mutant strain. The gdh gus mutant is a glutamate auxotroph. The genetic analysis of the gus mutant showed that the GOGAT-less phenotype is due to the presence of two loosely linked mutations. Evidence is presented which suggests the possibility that S. cerevisiae has two GOGAT activities, designated GOGAT A and GOGAT B. These activities can be distinguished by their pH optima and by their regulation by glutamate. Furthermore, one of the mutations responsible for the GOGAT-less phenotype affected GOGAT A activity, while the other mutation affected GOGAT B activity.
Cloning of 1,2-dichloroethane degradation genes of Xanthobacter autotrophicus GJ10 and expression and sequencing of the dhlA gene
Authors: Janssen D B , Pries F , van der Ploeg J , Kazemier B , Terpstra P , Witholt B
Published: November 2016

A gene bank from the chlorinated hydrocarbon-degrading bacterium Xanthobacter autotrophicus GJ10 was prepared in the broad-host-range cosmid vector pLAFR1. By using mutants impaired in dichloroethane utilization and strains lacking dehalogenase activities, several genes involved in 1,2-dichloroethane metabolism were isolated. The haloalkane dehalogenase gene dhlA was subcloned, and it was efficiently expressed from its own constitutive promoter in strains of a Pseudomonas sp., Escherichia coli, and a Xanthobacter sp. at levels up to 30% of the total soluble cellular protein. A 3-kilobase-pair BamHI DNA fragment on which the dhlA gene is localized was sequenced. The haloalkane dehalogenase gene was identified by the known N-terminal amino acid sequence of its product and found to encode a 310-amino-acid protein of molecular weight 35,143. Upstream of the dehalogenase gene, a good ribosome-binding site and two consensus E. coli promoter sequences were present.
Location of sites of transposon Tn916 insertion in the Mycoplasma mycoides genome
Authors: Whitley J C , Finch L R
Published: November 2016

The genome of Mycoplasma mycoides subsp. mycoides GC1176-2 was cleaved into six large fragments by the endonuclease KpnI which also cleaved the transposon Tn916 once. This has allowed genomic mapping of insertion sites for 50 transformants of GC1176-2 containing Tn916. Almost all of the mapped sites were clearly separate. The transformants provide a bank of genomes each with a KpnI site at a different position to facilitate mapping of gene loci.