bluuebunny/crossref_metadata_2025 huggingface dataset:
Neuroprotective Effect of Caffeoylquinic Acids from Artemisia princeps Pampanini against Oxidative Stress‐Induced Toxicity in PC‐12 Cells
Authors: Lee Sang Gil , Lee Hyungjae , Nam Tae Gyu , Eom Seok Hyun , Heo Ho Jin , Lee Chang Yong , Kim Dae‐Ok
Published: February 2011

Abstract:  Phenolics in dry Artemisia princeps Pampanini, an herbal plant traditionally consumed as food ingredients in Korea was extracted, fractionated, and quantified as well as evaluated for its neuroprotection for PC‐12 cells. Whole extract had 5,852 mg gallic acid equivalents/100 g of total phenolics and 6,274 mg and 9,698 mg vitamin C equivalents/100 g of antioxidant capacities assayed by DPPH and ABTS radicals, respectively. The fraction extracted with n‐butanol had the highest levels of total phenolics and antioxidant capacity than the other fractions (n‐hexane, chloroform, ethyl acetate, and water). Using a reversed‐phase HPLC system, caffeoylquinic acid (CQA) and its derivatives such as 3‐CQA, 4‐CQA, 5‐CQA, 1,5‐diCQA, 3,4‐diCQA, 3,5‐diCQA, and 4,5‐diCQA were isolated and quantified. The whole extract and its n‐butanol fraction yielded 3,5‐diCQA with the highest amount, which consisted of approximately 36.8% and 33.5%, respectively. The whole extract, the n‐butanol fraction, and 3,5‐diCQA showed neuroprotective effect on PC‐12 cells under the insult of amyloid ß peptide in a dose‐dependent manner. Treatments of the whole extract and the n‐butanol fraction for PC‐12 cells under oxidative stress increased approximately 1.6 and 2.4 times higher cell viability, compared with the control without treatments. For PC‐12 cells treated with 3,5‐diCQA, intracellular oxidative stress decreased by 51.3% and cell viability increased up to 2.8 times compared to the control with oxidative insult of amyloid ß peptide only. These results indicate that phenolics from A. princeps Pampanini alleviated the oxidative stress and enhanced the viability of PC‐12 cells, suggesting that it may be applied as a dietary antineurodegenerative agent in functional foods.
Biofilms of Listeria monocytogenes Produced at 12 ° C either in Pure Culture or in Co‐Culture with Pseudomonas aeruginosa Showed Reduced Susceptibility to Sanitizers
Authors: Lourenço António , Machado Henrique , Brito Luisa
Published: February 2011

Abstract:  The biofilm‐forming ability of 21 Listeria monocytogenes isolates, previously pulsotyped and corresponding to 16 strains, from different origins was evaluated using the Calgary Biofilm Device®, at 37 °C. Biofilms of 4 selected strains were also produced either on pure cultures or on co‐cultures with Pseudomonas aeruginosa (PAO1), at 12 °C and at 37 °C. For these biofilms, the minimum biofilm eradication concentrations (MBECs) of 4 commercial dairy sanitizers (1 alkyl amine acetate based—T99, 2 chlorine based—T66 and DD, and 1 phosphoric acid based—BP) were determined. Listeria monocytogenes biofilms grown, either at 37 °C or 12 °C, were able to achieve similar cell densities by using different incubation periods (24 h and 7 d, respectively). In co‐culture biofilms, P. aeruginosa was the dominant species, either at 37 °C or at 12 °C, representing 99% of a total biofilm population of 6 to 7 log CFU/peg. Co‐culture biofilms were generally less susceptible than L. monocytogenes pure cultures. More interestingly, the biofilms produced at 12 °C were usually less susceptible to the sanitizers than when produced at 37 °C. Single or co‐culture biofilms of L. monocytogenes and PAO1, particularly produced at 12 °C, retrieved MBEC values for agents T99 and BP that were, at times, above the maximum in‐use recommended concentrations for these agents. The results presented here reinforce the importance of the temperature used for biofilm formation, when susceptibility to sanitizers is being assessed.

Practical Application:  Since most food plants have cold wet growth niches in production and storage areas, susceptibility testing should be performed on biofilms produced at refrigeration temperatures. Moreover, the efficiency of the sanitizers used in food industries should be performed on mixed culture biofilms, since in field conditions these will predominate. The results presented here highlight the importance of the temperature used for biofilm formation, when susceptibility to disinfectants is being assessed, as biofilms produced at lower temperature were less susceptible to sanitizers.
Physical and Antibacterial Properties of Edible Films Formulated with Apple Skin Polyphenols
Authors: Du W.‐X. , Olsen C.W. , Avena‐Bustillos R.J. , Friedman M. , McHugh T.H.
Published: February 2011

Abstract:  Fruit and vegetable skins have polyphenolic compounds, terpenes, and phenols with antimicrobial and antioxidant activity. These flavoring plant essential oil components are generally regarded as safe. Edible films made from fruits or vegetables containing apple skin polyphenols have the potential to be used commercially to protect food against contamination by pathogenic bacteria. The main objective of this study was to evaluate physical properties as well as antimicrobial activities against Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella enterica of apple skin polyphenols at 0% to 10% (w/w) concentrations in apple puree film‐forming solutions formulated into edible films. Commercial apple skin polyphenol powder had a water activity of 0.44 and high total soluble phenolic compounds and antioxidant capacity (995.3 mg chlorogenic acid/100 g and 14.4 mg Trolox/g, respectively). Antimicrobial activities of edible film containing apple skin polyphenols were determined by the overlay method. Apple edible film with apple skin polyphenols was highly effective against L. monocytogenes. The minimum concentration need to inactive L. monocytogenes was 1.5%. However, apple skin polyphenols did not show any antimicrobial effect against E. coli O157:H7 and S. enterica even at 10% level. The presence of apple skin polyphenols reduced water vapor permeability of films. Apple skin polyphenols increased elongation of films and darkened the color of films. The results of the present study show that apple skin polyphenols can be used to prepare apple‐based antimicrobial edible films with good physical properties for food applications by direct contact.
Highly Stable, Edible Cellulose Films Incorporating Chitosan Nanoparticles
Authors: de Moura Márcia R. , Lorevice Marcos V. , Mattoso Luiz H.C. , Zucolotto Valtencir
Published: February 2011

Abstract:  The need for biodegradable polymers for packaging has fostered the development of novel, biodegradable polymeric materials from natural sources, as an alternative to reduce amount of waste and environmental impacts. The present investigation involves the synthesis of chitosan nanoparticles–carboxymethylcellulose films, in view of their increasing areas of application in packaging industry. The entire process consists of 2‐steps including chitosan nanoparticles preparation and their incorporation in carboxymethylcellulose films. Uniform and stable particles were obtained with 3 different chitosan concentrations. The morphology of chitosan nanoparticles was tested by transmission electron microscopy, revealing the nanoparticles size in the range of 80 to 110 nm. The developed film chitosan nanoparticles–carboxymethylcellulose films were characterized by Fourier transform infrared spectroscopy (FT‐IR), thermogravimetric analysis, solubility tests, and mechanical analysis. Improvement of thermal and mechanical properties were observed in films containing nanoparticles, with the best results occurring upon addition of nanoparticles with 110 nm size in carboxymethylcellulose films.

Practical Application:  Carboxymethylcellulose films containing chitosan nanoparticles synthesized and characterized in this article could be a potential material for food and beverage packaging applications products due to the increase mechanical properties and high stability. The potential application of the nanocomposites prepared would be in packaging industry to extend the shelf life of products.
Parental acceptance of restraint methods used for children with intellectual disabilities during dental care
Authors: Oliveira Ana Cristina Borges , Paiva Saul Martins , Pordeus Isabela Almeida
Published: February 2011

This study evaluated 209 Brazilian parents' acceptance of the use of restraint during dental care for their children with intellectual disabilities. Participants were interviewed end they also watched a video on physical restraint techniques, sedation, and general anesthesia. There was a statistically significant relationship for 22.9% of the parents. The odds ratio revealed that participants were more likely to accept physical restraints for their child when parents were over the age of 35 and from an underprivileged economic class and when the children had previously experienced physical restraints. Dental healthcare professionals should consider the individual needs of each patient and consult with the child's family if there is a need to use restraints.
LACTIC ACIDOSIS AFTER CONCOMITANT TREATMENT WITH METFORMIN AND TENOFOVIR IN A PATIENT WITH HIV INFECTION
Authors: Aperis Georgios , Paliouras Christos , Zervos Angelos , Arvanitis Antonios , Alivanis Polichronis
Published: February 2011

We present an uncommon case of lactic acidosis after concomitant administration of Metformin and Tenofovir. This is a 74‐year‐old man with a history of diabetes mellitus receiving treatment with metformin. He had coronary artery disease and HIV infection treated with emtricitabine, tenofovir and recently started on efavirenz. He presented with zoster‐like abdominal pain, tachypnoea, nausea and vomiting. On clinical examination, the patient was afebrile, hypotensive and tachycardic, he was markedly dehydrated and oliguric. The abdomen was soft, tender on palpation, not distended without rebound tenderness. The arterial blood gases revealed marked lactic acidosis and the laboratory tests on admission showed acute renal failure. The patient received nine treatments of slow continuous veno‐venous hemofiltration (CVVHF). Despite the prolonged period of anuria, urine output progressively improved after 25 days and serum biochemical parameters of renal function returned to normal within 40 days. Health professionals must be aware of this uncommon effect in patients on antiretroviral treatment. Prompt initiation of CVVHF resulted in resolution of both lactic acidosis and renal failure.
TOTAL DOSE INFUSION OF INTRAVENOUS IRON IN PATIENTS WITH CHRONIC KIDNEY DISEASE RECEIVING HAEMODIALYSIS
Authors: Fenwick Sean , Peebles George
Published: February 2011

A regimen of a single high dose iron administration was initially adopted for patients commencing haemodialysis (HD) treatment. Iron stores are established and iron metabolism and erythropoiesis stabilise allowing haematinic parameters to be more confidently assessed for use in anaemia management decisions. High doses of IV iron delay the need for subsequent iron supplementation. A high‐dose, low‐frequency iron infusion regimen for all HD patients was adopted. The outcomes of administering this dosage regimen are reported as observational retrospective analysis using patient record data in 2009.

Patients received three [median; semi‐interquartile range (SIQR) 0.5] high‐dose iron infusions during the year. The median infusion dose was 1100 mg iron (SIQR 0.0) and the median amount of iron received during the year by each patient was 3200 mg (SIQR 750). The median haemoglobin (Hb) level prior to infusion was 108 g/l and post infusion 114 g/l; ZHb = 2.656, p = 0.008). Ferritin levels increased from a median of 376 μg/l preinfusion to 690 μg/l postinfusion; Zferritin =–4.796, p < 0.001.

The median time between infusions was 125 days (approximately four months). The 51 patients (76%) who received three or less infusions within the study period received 2537 mg (mean) of iron. These findings indicate that both Hb and ferritin levels can be adequately managed using a high‐dose, low‐frequency regimen of IV iron in patients undergoing HD.
PREVENTION OF INFECTION IN PATIENTS WITH CHRONIC KIDNEY DISEASE PART II: HEALTHCARE‐ASSOCIATED INFECTIONS
Authors: Redmond Avril , Donlon Sheila , Boyle Gerard , McCann Margaret , Einarsdottir Hildur
Published: February 2011

This second article, in a three‐part CE series on the preventions of infection in patients with chronic kidney disease, focuses on healthcare‐associated infections and blood borne viruses that are prevalent within the haemodialysis environment. It also informs the reader of the relevant infection and prevention precaution guidelines and their application within a haemodialysis setting.
Idiopathic solitary cutaneous xanthoma in a dog
Authors: Banajee Kaikhushroo H. , Orandle Marlene S. , Ratterree William , Bauer Rudy W. , Gaunt Stephen D.
Published: February 2011

Abstract: A 6‐year‐old female spayed Boxer mix dog was presented with multiple cutaneous masses, one of which was determined to be a xanthoma. Fine‐needle aspirates of this mass revealed large round cells that were consistent with macrophages. These macrophages had lightly basophilic cytoplasm that was filled with many clear circular spaces that varied in size. The nuclei of these cells displayed mild anisokaryosis with condensed chromatin and lacked prominent nucleoli. The cytologic interpretation was lipid‐laden histiocytic inflammation most consistent with a cutaneous xanthoma, which was confirmed histologically. Mild hypertriglyceridemia and persistent moderate hypercholesterolemia were present. After ruling out other causes of hyperlipidemia, we concluded that the dog likely had idiopathic hyperlipidemia with secondary xanthoma formation.
Cytologic patterns of lymphadenopathy in canine monocytic ehrlichiosis
Authors: Mylonakis Mathios E. , Borjesson Dori L. , Leontides Leonidas , Siarkou Victoria I. , Theodorou Konstantina , Koutinas Alexander F.
Published: February 2011

Background: Recognition of different cytologic patterns in lymph nodes (LNs) from dogs with canine monocytic ehrlichiosis (CME) and noninfectious causes of lymphoid reactivity may have diagnostic utility.

Objectives: The aims of the present study were to compare cytologic patterns in LNs of dogs with different phases of CME, to investigate the association of cytologic pattern and presence of Ehrlichia spp. morulae, and to compare patterns of lymphoid reactivity between dogs with CME and those with noninfectious causes of lymphoid hyperplasia.

Methods: Cytologic preparations of LNs from 35 dogs with nonmyelosuppressive CME (group A), 16 dogs with myelosuppressive CME (group B), 26 dogs with noninfectious diseases (group C), and 15 healthy dogs (group D) were evaluated. Percentages of lymphocyte types, plasma cells, macrophages, neutrophils, and eosinophils were determined. Samples from dogs in groups A and B were evaluated for the presence of morulae.

Results: Cytologic abnormalities in LNs were recorded in 54% of dogs in group A, 88% in group B, 39% in group C, and 0% in group D and were more frequent (P=.02) in dogs with myelosuppressive CME than those with nonmyelosuppressive CME. Plasma cell hyperplasia was more frequent in CME than in noninfectious diseases (P=.03). An association between the presence of cytologic abnormalities and morulae in group A dogs was not found.

Conclusions: Dogs with myelosuppressive CME have more lymphoid cytologic abnormalities than dogs with nonmyelosuppressive CME. LN plasmacytosis is the major pattern of lymphadenopathy in dogs with CME and is found more frequently in dogs with CME than in dogs with noninfectious causes of lymphadenopathy.
Serum α‐1‐acid glycoprotein concentrations in 26 dogs with pyometra
Authors: Hagman Ragnvi
Published: February 2011

Background:The acute phase protein, α‐1‐acid glycoprotein (AGP), has been proposed to have a role in immunomodulation and to be a nonspecific antimicrobial agent. We suggest that AGP may be increased in dogs with pyometra and possibly to a greater extent in dogs also manifesting signs of systemic inflammatory response syndrome (SIRS).

Objectives:Our objectives were to evaluate serum AGP concentrations in dogs diagnosed with pyometra compared with clinically healthy female dogs and to determine if AGP concentrations were correlated with severity of disease.

Methods:Twenty‐six dogs with pyometra and 18 clinically healthy intact female dogs were included in this prospective study. A diagnosis of pyometra was verified by histopathologic examination after ovariohysterectomy in the pyometra group. A commercially available single radial immunodiffusion test was used for AGP analysis. Clinical findings, laboratory variables, and hospitalization times were compared.

Results:Mean AGP concentration in dogs with pyometra (1943 ± 913 mg/L, mean ± SD), was significantly higher (P<.001) than in healthy dogs (495 ± 204 mg/L). Mean AGP concentration in dogs in the pyometra group with (n=18) or without (n=8) SIRS did not differ. Animals with a prolonged hospital stay had higher AGP concentrations.

Conclusions:Pyometra was associated with increased serum concentrations of the acute phase protein AGP. AGP concentrations were associated with severity of disease as measured by duration of hospitalization. As AGP binds basic drugs, further studies of its pharmacokinetic and pharmacodynamic propreties in cases of pyometra may be of clinical interest.
Paraneoplastic leukocytosis in a dog with a renal carcinoma
Authors: Petterino Claudio , Luzio Elisabetta , Baracchini Luca , Ferrari Angelo , Ratto Alessandra
Published: February 2011

Abstract:A 7‐year‐old male German Shepherd dog in poor body condition had a 3‐month history of intermittent hematuria. Nonregenerative anemia, mild leukocytosis, marked hypoalbuminemia, and hematuria were observed. Subsequently, marked neutrophilia and moderate monocytosis were noted; anemia, hypoalbuminemia, and hematuria persisted; and the dog developed disseminated intravascular coagulation. Ultrasonographic examination of the abdomen revealed the presence of an enlarged and irregularly shaped right kidney with a large area of cavitation, and a nephrectomy was performed 30 days after initial examination. Cytologic examination of fine‐needle aspirates and imprints of the right kidney revealed a neoplastic cell population suggestive of renal carcinoma. The histopathologic diagnosis was chromophobic cystic‐papillary renal carcinoma. The tumor cells expressed granulocytic/macrophage‐colony–stimulating factor (GM‐CSF), detected by immunohistochemical staining, and elaboration of GM‐CSF by the tumor may have mediated the leukocytosis in this dog. Following excision of the tumor, neutrophil and monocyte counts were only mildly increased. The dog died 135 days after initial presentation, and a necropsy was not permitted. Paraneoplastic neutrophilic leukocytosis is an uncommon finding and may be caused by elaboration of CSF by neoplastic cells.
Flow Boiling of R134a in Circular Microtubes—Part II: Study of Critical Heat Flux Condition
Authors: Basu Saptarshi , Ndao Sidy , Michna Gregory J. , Peles Yoav , Jensen Michael K.
Published: February 2011

A detailed experimental study was carried out on the critical heat flux (CHF) condition for flow boiling of R134a in single circular microtubes. The test sections had inner diameters (ID) of 0.50 mm, 0.96 mm, and 1.60 mm. Experiments were conducted over a large range of mass flux, inlet subcooling, saturation pressure, and vapor quality. CHF occurred under saturated conditions at high qualities and increased with increasing mass fluxes, tube diameters, and inlet subcoolings. CHF generally, but not always, decreases with increasing saturation pressures and vapor qualities. The experimental data were mapped to the flow pattern maps developed by Hasan [2005, “Two-Phase Flow Regime Transitions in Microchannels: A Comparative Experimental Study,” Nanoscale Microscale Thermophys. Eng., 9, pp. 165–182] and Revellin and Thome [2007, “A New Type of Diabatic Flow Pattern Map for Boiling Heat Transfer in Microchannels,” J. Micromech. Microeng., 17, pp. 788–796]. Based on these maps, CHF mainly occurred in the annular flow regime in the larger tubes. The flow pattern for the 0.50 mm ID tube was not conclusively identified. Four correlations—the Bowring correlation, the Katto-Ohno correlation, the Thome correlation, and the Zhang correlation—were used to predict the experimental data. The correlations predicted the correct experimental trend, but the mean absolute error (MAE) was high (>15%) A new correlation was developed to fit the experimental data with a MAE of 10%.
Analysis of the Ideality Factor of a-Si:H Solar Cells
Authors: Al Tarabsheh A. , Etier I.
Published: February 2011

This paper analyzes the ideality factor of amorphous silicon (a-Si:H) solar cells as a function of both the thickness of the intrinsic layer and the applied voltage to the cells. The ideality factor in this work is extracted from the current/voltage characteristic that is calculated by solving the continuity and transport equations and taking into account the contributions of diffusion and drift currents for minority and majority carriers and, especially, the nonequality of mobilities and lifetimes of electrons and holes in a-Si:H solar cells.
Development and Performance of a Controllable Autoloading Needle-Free Jet Injector
Authors: Hemond Brian D. , Taberner Andrew , Hogan Cathy , Crane Bryan , Hunter Ian W.
Published: February 2011

A jet injector platform technology that provides improved performance over existing jet injectors through the use of a controllable linear Lorentz-force actuator and software-based control system has been developed. Injectors designed on this platform are capable of delivering injections using arbitrary pressure pulse shaping. Pulse shaping has been shown to allow a wide degree of control over the depth to which the injection is delivered. A software-based injector control system improves repeatability and allows for automatic reloading of the injector, a task that would be difficult to implement using existing jet injector platforms. A design for a prototype autoloading controllable jet injector (cJI) based on this platform is detailed. The injection capability of this cJI was evaluated both in-vitro and in-vivo using a tissue analog, excised porcine tissue, and ovine tissue. An analysis of the cJI’s performance indicates that this design is capable of delivering a controllable volume of fluid to a controllable depth based entirely on the parameter’s input into the control software.
Multicomponent Molten Salt Mixtures Based on Nitrate/Nitrite Anions
Authors: Cordaro Joseph G. , Rubin Nicholas C. , Bradshaw Robert W.
Published: February 2011

Molten salts are a promising medium for thermal energy transfer and storage. They have a very low vapor pressure and most are unreactive in air. Over the past 3 decades, Sandia National Laboratories has investigated a variety of molten salt mixtures of alkali nitrates and, most recently, quaternary mixtures of sodium, calcium, lithium, and potassium nitrate salts. This effort led to the discovery of mixtures with liquidus temperatures below 100°C. We have now extended this work to the mixed nitrate/nitrite anion system and found compositions with liquidus temperatures below 80°C. In this paper, we present experimental results exploring the lithium, sodium, and potassium compositional space with a 1:1 molar mixture of nitrate/nitrite. From our work, we have identified a five-component system with a liquidus temperature near 70°C. Physical properties of these salts, such as viscosity and density, are reported as well as thermal stability in air. Such a molten salt mixture, with a low liquidus temperature, has the potential to make parabolic trough collectors economically competitive with traditional power generation schemes.
Two-Dimensional Nanosheets Produced by Liquid Exfoliation of Layered Materials
Authors: Coleman Jonathan N. , Lotya Mustafa , O’Neill Arlene , Bergin Shane D. , King Paul J. , Khan Umar , Young Karen , Gaucher Alexandre , De Sukanta , Smith Ronan J. , Shvets Igor V. , Arora Sunil K. , Stanton George , Kim Hye-Young , Lee Kangho , Kim Gyu Tae , Duesberg Georg S. , Hallam Toby , Boland John J. , Wang Jing Jing , Donegan John F. , Grunlan Jaime C. , Moriarty Gregory , Shmeliov Aleksey , Nicholls Rebecca J. , Perkins James M. , Grieveson Eleanor M. , Theuwissen Koenraad , McComb David W. , Nellist Peter D. , Nicolosi Valeria
Published: February 2011

Layered transition metal dichalcogenides, such as tungsten disulfide, are exfoliated into atomically thin flakes.
Ultralong-Range Polaron-Induced Quenching of Excitons in Isolated Conjugated Polymers
Authors: Bolinger Joshua C. , Traub Matthew C. , Adachi Takuji , Barbara Paul F.
Published: February 2011

Visualization of the fluorescence of a single–conducting-polymer chain provides insight into energy-relaxation mechanisms.
Better Science Needed for Restoration in the Gulf of Mexico
Authors: Bjorndal Karen A. , Bowen Brian W. , Chaloupka Milani , Crowder Larry B. , Heppell Selina S. , Jones Cynthia M. , Lutcavage Molly E. , Policansky David , Solow Andrew R. , Witherington Blair E.
Published: February 2011

In the wake of the BP oil spill, U.S. agencies need research plans to collect data that will aid in managing and assessing marine species and ecosystems.
The 2010 Amazon Drought
Authors: Lewis Simon L. , Brando Paulo M. , Phillips Oliver L. , van der Heijden Geertje M. F. , Nepstad Daniel
Published: February 2011

Amazonia experienced lower rainfall and higher calculated carbon emissions from tree deaths than in the 2005 drought.
Linked by Migrating Waterfowl
Seeking Refuge
Birds and Landscapes of the Pacific Flyway

by Robert M. Wilson

University of Washington Press, Seattle, 2010. 281 pp. $35, £23.99. ISBN 9780295990026. Weyerhaeuser Environmental Books.
Authors: Davis Frederick R.
Published: February 2011

Focusing on the western United States, Wilson describes efforts over the past century to meet the needs of migrant ducks and geese in landscapes transformed by human demands for agriculture and water.
The Human Genome at 10: Successes and Challenges
Authors: Venter J. Craig
Published: February 2011

We have come a long way in genomics; however, for genome sequencing to reach its full potential we still have a long way to go.
What Defines Us?
Authors: Cole-Turner Ronald
Published: February 2011

The Human Genome Project undermines cherished ideas about human uniqueness. But it also hints at a new vision of humanity.
Lessons from Genomics
Authors: Alberts Bruce
Published: February 2011

In February 2001,
Nature
and
Science
provided the first detailed look at the human genome: a string of some 3 billion nucleotides whose unique sequence forms the genetic blueprint for each individual. This momentous occasion made headlines around the world. Now that a decade has elapsed, where has this achievement led us and where are we going with other such ambitious endeavors? Throughout this month in
Science
, the News and Commentary sections will present viewpoints and analyses of the effects of the genomics revolution on science and society (see
http://scim.ag/genome10
). Many lessons can be derived from the Human Genome Project that should be helpful in guiding other large science projects through their inevitable challenges.
*
With Reforms Under Way, International Centers Ask: Where Is the Money?
Authors: Normile Dennis
Published: February 2011

Scientists and administrators involved in the Consultative Group on International Agricultural Research say reforms aimed at reinvigorating research efforts and boosting financial support are bearing fruit, but they are also wondering what has happened to the promised money.
NIH Report Urges Greater Emphasis on Training for All Graduate Students
Authors: Mervis Jeffrey
Published: February 2011

A new report by the flagship training institute at the U.S. National Institutes of Health attempts to redefine the goals of graduate and postdoctoral training and prods biomedical scientists to become better mentors.
The Human Genome (Patent) Project
Authors: Kean Sam
Published: February 2011

A decade of research has scientists asking if patent priorities are misaligned.
Discovery and Phylogenetic Analysis of Novel Members of Class b Enterotoxigenic Escherichia coli Adhesive Fimbriae
Authors: Nada Rania A. , Shaheen Hind I. , Khalil Sami B. , Mansour Adel , El-Sayed Nasr , Touni Iman , Weiner Matthew , Armstrong Adam W. , Klena John D.
Published: February 2011

Enterotoxigenic
Escherichia coli
(ETEC) is recognized to be a common cause of acute watery diarrhea in children from developing countries. Colonization factors (CFAs) have been identified predominantly in ETEC isolates secreting heat-stable enterotoxin (ST) or cosecreting ST with a heat-labile toxin (LT). We hypothesized that LT-only-secreting ETEC produces unique colonization factors not previously described in ST and LTST-secreting ETEC. A set of degenerate primers based on nucleotide sequence similarities between the major structural genes of CS20 (
csnA
), CS18 (
fotA
), CS12 (
cswA
), and porcine antigen 987 (
fasA
) was developed and used to screen a collection of 266 LT-secreting ETEC isolates in which no known CFA was detected. PCR-amplified products of different molecular masses were obtained from 49 (18.4%) isolates. Nucleotide sequence analysis of the PCR amplicons followed by GenBank nucleotide BLASTn analysis revealed five novel DNA sequences; translated amino acid BLASTx analysis confirmed sequence similarity to class 1b major structural proteins encoded by
csnA
,
fotA
, and
fasA
. Strains expressing the novel CFAs were phylotyped and analyzed using multilocus sequence typing (MLST; Achtman scheme), and the types detected were compared to those of a collection of archived global
E. coli
strains. In conclusion, application of the degenerate primer sets to ETEC isolates from surveillance studies increased the total number of ETEC isolates with detectable CFAs by almost 20%. Additionally, MLST analysis suggests that for many CFAs, there may be a requirement for certain genetic backgrounds to acquire and maintain plasmids carrying genes encoding CFAs.
Evaluation of Four Commercial Rapid Immunochromatographic Assays for Detection of Cryptosporidium Antigens in Stool Samples: a Blind Multicenter Trial
Authors: Agnamey Patrice , Sarfati Claudine , Pinel Claudine , Rabodoniriina Meja , Kapel Nathalie , Dutoit Emmanuel , Garnaud Cécile , Diouf Momar , Garin Jean-François , Totet Anne , Derouin F. ,   for the ANOFEL Cryptosporidium National Network
Published: February 2011

In a multicenter study, potassium dichromate-preserved stools from patients infected with
Cryptosporidium parvum
(
n
= 20),
C. hominis
(
n
= 20), and other
Cryptosporidium
species (
n
= 10) and 60 controls were examined using four immunochromatographic assays. Assay sensitivity ranged between 50.1% and 86.7% for
C. parvum
and C.
hominis
but was <35% for other species.
Imipenem Disc for Detection of KPC Carbapenemase-Producing Enterobacteriaceae in Clinical Practice
Authors: Benenson Shmuel , Temper Violeta , Cohen Matan J. , Schwartz Carmela , Hidalgo-Grass Carlos , Block Colin
Published: February 2011

The global spread of class A-carbapenemase-producing
Enterobacteriaceae
has made the development of a simple test a desirable goal. A disc diffusion test using imipenem was 100% sensitive and 96% specific in identifying carbapenemase-producing organisms, potentially reducing or eliminating the need for the relatively labor-intensive modified Hodge test.
Performance of the Abbott RealTime HIV-1 Viral Load Assay Is Not Impacted by Integrase Inhibitor Resistance-Associated Mutations
Authors: Young Thomas P. , Cloherty Gavin , Fransen Signe , Napolitano Laura , Swanson Priscilla , Herman Christine , Parkin Neil T. , Hackett John
Published: February 2011

The Abbott RealTime HIV-1 viral load assay uses primers and probes targeted to integrase, which is also the target of integrase inhibitors such as raltegravir. Viral loads of 42 raltegravir-susceptible and 40 raltegravir-resistant specimens were determined using RealTime HIV-1 and Roche Monitor (v1.5). The differences in viral load measurements between assays were comparable in the two groups, demonstrating that the RealTime HIV-1 assay can tolerate raltegravir-selected mutations.
Use of the Accessory Genome for Characterization and Typing of Acinetobacter baumannii
Authors: Turton Jane F. , Baddal Buket , Perry Claire
Published: February 2011

Outbreak strains of
Acinetobacter baumannii
are highly clonal, and cross-infection investigations can be difficult. We sought targets based on AbaR resistance islands and on other genes found in some, but not all, sequenced isolates of
A. baumannii
among a set of clinical isolates (
n
= 70) that included multiple representatives of a number of pulsed-field gel electrophoresis (PFGE)-defined types. These included representatives that varied in their profiles at two variable-number tandem repeat (VNTR) loci, which can provide discrimination within a PFGE cluster. Detection, or not, of each element sought provided some degree of discrimination among the set, with the presence or absence of genes coding for a phage terminase (ACICU_02185), a sialic acid synthase (ACICU_00080), a polysaccharide biosynthesis protein (AB57_0094),
aphA1
,
bla
TEM
, and integron-associated orfX (Kyoto Encyclopedia of Genes and Genomes [KEGG] no. K03830) proving the most helpful in discriminating between closely related isolates in our panel. The results support VNTR data in describing distinct populations of highly similar isolates. Such analysis, in combination with other typing methods, can inform epidemiological investigations and provide additional characterization of isolates. Most genotypes carrying
bla
OXA-23-like
were PCR positive for a
yeeA-bla
OXA-23
fragment found in an AbaR4-type island, suggesting that this is widespread.
Combining Culture Techniques for Bartonella: the Best of Both Worlds
Authors: Lynch Tarah , Iverson Jennifer , Kosoy Michael
Published: February 2011

In this study we compared some common
Bartonella
culturing methodologies using four diverse species causing human illnesses. Based on a review of the literature, we focused on three major inconsistencies between protocols: base medium, cell coculture, and temperature. Our data showed that
Bartonella tamiae
demonstrated temperature-dependent growth limitations between common culturing conditions only 2°C apart. Additionally, growth of
B. quintana
was significantly enhanced by the presence of mammalian cell coculture under mammalian cell culture conditions; however, when the medium was modified to incorporate insect cell culture-based medium, coculturing with mammalian cells was no longer needed. In this study, we were able to overcome these temperature- and cell-dependent limitations and accommodate all of the strains tested by combining mammalian cell culture-based medium with insect cell culture-based medium.
The Tegument Protein UL71 of Human Cytomegalovirus Is Involved in Late Envelopment and Affects Multivesicular Bodies
Authors: Schauflinger Martin , Fischer Daniela , Schreiber Andreas , Chevillotte Meike , Walther Paul , Mertens Thomas , von Einem Jens
Published: February 2011

Morphogenesis of human cytomegalovirus (HCMV) is still only partially understood. We have characterized the role of HCMV tegument protein pUL71 in viral replication and morphogenesis. By using a rabbit antibody raised against the C terminus of pUL71, we could detect the protein in infected cells, as well as in virions showing a molecular mass of approximately 48 kDa. The expression of pUL71, detected as early as 48 h postinfection, was not blocked by the antiviral drug foscarnet, indicating an early expression. The role of pUL71 during virus replication was investigated by construction and analysis of a UL71 stop mutant (TBstop71). The mutant could be reconstituted on noncomplementing cells proving that pUL71 is nonessential for virus replication in human fibroblasts. However, the inhibition of pUL71 expression resulted in a severe growth defect, as reflected by an up to 16-fold reduced extracellular virus yield after a high-multiplicity infection and a small-plaque phenotype. Ultrastructural analysis of cells infected with TBstop71 virus revealed an increased number of nonenveloped nucleocapsids in the cytoplasm, many of them at different stages of envelopment, indicating that final envelopment of nucleocapsids in the cytoplasm was affected. In addition, enlarged multivesicular bodies (MVBs) were found in close proximity to the viral assembly compartment, suggesting that pUL71 affects MVBs during virus infection. The observation of numerous TBstop71 virus particles attached to MVB membranes and budding processes into MVBs indicated that these membranes can be used for final envelopment of HCMV.
Novel Mutations in a Tissue Culture-Adapted Hepatitis C Virus Strain Improve Infectious-Virus Stability and Markedly Enhance Infection Kinetics
Authors: Pokrovskii Maria V. , Bush Caroline O. , Beran Rudolf K. F. , Robinson Margaret F. , Cheng Guofeng , Tirunagari Neeraj , Fenaux Martijn , Greenstein Andrew E. , Zhong Weidong , Delaney William E. , Paulson Matthew S.
Published: February 2011

Hepatitis C virus (HCV) establishes persistent infections and leads to chronic liver disease. It only recently became possible to study the entire HCV life cycle due to the ability of a unique cloned patient isolate (JFH-1) to produce infectious particles in tissue culture. However, despite efficient RNA replication, yields of infectious virus particles remain modest. This presents a challenge for large-scale tissue culture efforts, such as inhibitor screening. Starting with a J6/JFH-1 chimeric virus, we used serial passaging to generate a virus with substantially enhanced infectivity and faster infection kinetics compared to the parental stock. The selected virus clone possessed seven novel amino acid mutations. We analyzed the contribution of individual mutations and identified three specific mutations, core K78E, NS2 W879R, and NS4B V1761L, which were necessary and sufficient for the adapted phenotype. These three mutations conferred a 100-fold increase in specific infectivity compared to the parental J6/JFH-1 virus, and media collected from cells infected with the adapted virus yielded infectious titers as high as 1 × 10
8
50% tissue culture infective doses (TCID
50
)/ml. Further analyses indicated that the adapted virus has longer infectious stability at 37°C than the wild type. Given that the adapted phenotype resulted from a combination of mutations in structural and nonstructural proteins, these data suggest that the improved viral titers are likely due to differences in virus particle assembly that result in significantly improved infectious particle stability. This adapted virus will facilitate further studies of the HCV life cycle, virus structure, and high-throughput drug screening.
Basic Residues in the Foamy Virus Gag Protein
Authors: Matthes Daniel , Wiktorowicz Tatiana , Zahn Juliane , Bodem Jochen , Stanke Nicole , Lindemann Dirk , Rethwilm Axel
Published: February 2011

Foamy virus (FV) capsid proteins have few lysines. Basic residues are almost exclusively represented by arginines indicating positive selective pressure. To analyze the possible functions of this peculiarity, we mutated an infectious molecular clone of the prototypic FV (PFV) to harbor lysines in the Gag protein at arginine-specifying positions and analyzed various aspects of the FV replication cycle. The majority of mutants replicated equally as well in permanent cell cultures as the original wild-type (wt) virus and were genetically stable ingagupon 10 cell-free passages. With respect to the features of late reverse transcription, nucleic acid content, and infectiousness of the virion DNA genome, the majority of mutants behaved like the wt. Several mutants of PFV were ubiquitinated in Gag but unable to generate virus-like particles (VLPs) or to undergo pseudotyping by a heterologous envelope. Using primary cells, however, a replicative disadvantage of the majority of mutants was disclosed. This disadvantage was enhanced upon interferon (IFN) treatment. We found no evidence that the lysine-bearinggagmutants showed more restriction than the wt virus by tetherin (CD317) or Trim5α. A single lysine in PFV Gag was found to be nonessential for transient replication in permanent cell culture if replaced by an arginine residue. Upon replication in primary cells, even without IFN treatment, this mutant was severely impaired, indicating the importance of specifying at least this lysine residue in PFV Gag. The paucity of lysines in FV Gag proteins may be a consequence of preventing proteasomal Gag degradation.
Genome Sequence of Ostreococcus tauri Virus OtV-2 Throws Light on the Role of Picoeukaryote Niche Separation in the Ocean
Authors: Weynberg Karen D. , Allen Michael J. , Gilg Ilana C. , Scanlan David J. , Wilson William H.
Published: February 2011

Ostreococcus tauri
, a unicellular marine green alga, is the smallest known free-living eukaryote and is ubiquitous in the surface oceans. The ecological success of this organism has been attributed to distinct low- and high-light-adapted ecotypes existing in different niches at a range of depths in the ocean. Viruses have already been characterized that infect the high-light-adapted strains.
Ostreococcus tauri
virus (OtV) isolate OtV-2 is a large double-stranded DNA algal virus that infects a low-light-adapted strain of
O. tauri
and was assigned to the algal virus family
Phycodnaviridae
, genus
Prasinovirus
. Our working hypothesis for this study was that different viruses infecting high- versus low-light-adapted
O. tauri
strains would provide clues to propagation strategies that would give them selective advantages within their particular light niche. Sequence analysis of the 184,409-bp linear OtV-2 genome revealed a range of core functional genes exclusive to this low-light genotype and included a variety of unexpected genes, such as those encoding an RNA polymerase sigma factor, at least four DNA methyltransferases, a cytochrome

b
5

, and a high-affinity phosphate transporter. It is clear that OtV-2 has acquired a range of potentially functional genes from its host, other eukaryotes, and even bacteria over evolutionary time. Such piecemeal accretion of genes is a trademark of large double-stranded DNA viruses that has allowed them to adapt their propagation strategies to keep up with host niche separation in the sunlit layers of the oceanic environment.
Exploring the Fitness Landscape of an RNA Virus by Using a Universal Barcode Microarray
Authors: Lauring Adam S. , Andino Raul
Published: February 2011

Studies of viral pathogenesis have relied heavily on analyses of specific clones and their genetic determinants of virulence. It is sometimes difficult to apply this reductionist approach to the study of RNA viruses, which by virtue of their very high mutation rates, exist as a complex mixture of mutants. While quasispecies theory has provided an intellectual framework for exploring the relationship between the viral population structure and phenotype, experimental studies have been limited by the relatively poor resolution of traditional sequencing-based approaches. We have addressed this problem by developing a molecular barcoding strategy in which viral subpopulations are tagged with unique 20-nucleotide sequences. The behavior of these subpopulations can be monitored using a universal barcode microarray. We demonstrate the performance of our barcode microarray platform using poliovirus, a model RNA virus. Using this platform, we explored the fitness landscape occupied by an artificial quasispecies consisting of 48 randomly mutagenized clones. We were able to rapidly derive precise fitness measurements for a majority of these clones and identified a neutral space surrounding the wild type. The experimental paradigm presented here is readily adaptable to other viral systems and can potentially be used to track thousands of variants in a cost-effective manner.
Characterization of the Candiru Antigenic Complex (Bunyaviridae: Phlebovirus), a Highly Diverse and Reassorting Group of Viruses Affecting Humans in Tropical America
Authors: Palacios Gustavo , Tesh Robert , Travassos da Rosa Amelia , Savji Nazir , Sze Wilson , Jain Komal , Serge Robert , Guzman Hilda , Guevara Carolina , Nunes Marcio R. T. , Nunes-Neto Joaquim P. , Kochel Tadeusz , Hutchison Stephen , Vasconcelos Pedro F. C. , Lipkin W. Ian
Published: February 2011

The genus
Phlebovirus
of the family
Bunyaviridae
consists of approximately 70 named viruses, currently assigned to nine serocomplexes (species) based on antigenic similarities. Sixteen other named viruses that show little serologic relationship to the nine recognized groups are also classified as tentative species in the genus. In an effort to develop a more precise classification system for phleboviruses, we are attempting to sequence most of the named viruses in the genus with the goal of clarifying their phylogenetic relationships. In this report, we describe the serologic and phylogenetic relationships of 13 viruses that were found to be members of the Candiru serocomplex; 6 of them cause disease in humans. Analysis of full genome sequences revealed branching inconsistencies that suggest five reassortment events, all involving the M segment, and thus appear to be natural reassortants. This high rate of reassortment illustrates the inaccuracy of a classification system based solely on antigenic relationships.
Epithelial Cells Lining Salivary Gland Ducts Are Early Target Cells of Severe Acute Respiratory Syndrome Coronavirus Infection in the Upper Respiratory Tracts of Rhesus Macaques
Authors: Liu Li , Wei Qiang , Alvarez Xavier , Wang Haibo , Du Yanhua , Zhu Hua , Jiang Hong , Zhou Jingying , Lam Pokman , Zhang Linqi , Lackner Andrew , Qin Chuan , Chen Zhiwei
Published: February 2011

The shedding of severe acute respiratory syndrome coronavirus (SARS-CoV) into saliva droplets plays a critical role in viral transmission. The source of high viral loads in saliva, however, remains elusive. Here we investigate the early target cells of infection in the entire array of respiratory tissues in Chinese macaques after intranasal inoculations with a single-cycle pseudotyped virus and a pathogenic SARS-CoV. We found that angiotensin-converting enzyme 2-positive (ACE2+) cells were widely distributed in the upper respiratory tract, and ACE2+epithelial cells lining salivary gland ducts were the early target cells productively infected. Our findings also have implications for SARS-CoV early diagnosis and prevention.
Human Immunodeficiency Virus Type 1 and Related Primate Lentiviruses Engage Clathrin through Gag-Pol or Gag
Authors: Popov Sergei , Strack Bettina , Sanchez-Merino Victor , Popova Elena , Rosin Heike , Göttlinger Heinrich G.
Published: February 2011

The Gag-Pol polyprotein of human immunodeficiency virus type 1 (HIV-1) is not required for efficient viral particle production. However, premature termination codons in
pol
, particularly in the integrase (IN)-coding region, can markedly impair HIV-1 particle formation, apparently due to the premature activation of the viral protease (PR). We now report that the IN domain of Gag-Pol is required for the incorporation of clathrin into HIV-1 virions. Significantly, PR-dependent effects of point mutations in IN on particle production correlated strictly with their effects on clathrin incorporation. A possible interpretation of these findings is that certain IN mutations impair particle production in a PR-dependent manner by promoting Gag-Pol dimerization, which also occludes a binding site for clathrin. Consistently with this model, the reverse transcriptase (RT) inhibitor efavirenz, which is thought to promote Gag-Pol dimerization, inhibited the incorporation of clathrin into HIV-1 virions. Clathrin-depleted cells produced normal amounts of HIV-1 virions; however, their infectivity was reduced. We also observed that HIV-2 and the simian immunodeficiency virus SIVmac interact with clathrin through one or two copies of a peptide motif in the p6 domain of Gag that resembles the clathrin box of cellular adaptor proteins. Furthermore, the substitution of the hydrophobic residues in the single clathrin box motif of SIVmac caused a replication defect in primary cells. Taken together, our results indicate that primate lentiviruses from two different subgroups functionally interact with clathrin during assembly.