bluuebunny/crossref_metadata_2025 huggingface dataset:
Establishment of a Kit‐negative cell line of melanocyte precursors from mouse neural crest cells
Authors: Kawa Yoko , Soma Yoshinao , Nakamura Masayuki , Ito Masaru , Kawakami Tamihiro , Baba Takako , Sibahara Kuniko , Ohsumi Kayoko , Ooka Shiho , Watabe Hidenori , Ono Hirotake , Hosaka Eri , Kimura Satoko , Kushimoto Tsuneto , Mizoguchi Masako
Published: May 2005

We previously established a mouse neural crest cell line named NCCmelb4, which is positive for Kit and negative for tyrosinase. NCCmelb4 cells were useful to study the effects of extrinsic factors such as retinoic acids and vitamin D3 on melanocyte differentiation, but in order to study the development of melanocytes from multipotent neural crest cells, cell lines of melanocyte progenitors in earlier developmental stages are needed. In the present study, we established an immortal cell line named NCCmelb4M5 that was derived from NCCmelb4 cells. NCCmelb4M5 cells do not express Kit and are immortal and stable in the absence of Kit ligand. They are positive for melanocyte markers such as tyrosinase‐related protein 1 and DOPAchrome tautomerase and they contain stage I melanosomes. Interestingly, glial fibrillary acidic protein, which is a marker for glial cells, is also positive in NCCmelb4M5 cells, while NCCmelb4 cells are negative for this protein. Immunostaining and a cell ELISA assay revealed that 12‐O‐tetradecanoylphorbol 13‐acetate (TPA) and cholera toxin (CT) induce Kit expression in NCCmelb4M5 cells. Real‐time polymerase chain reaction analysis also demonstrated the induction of Kit mRNA by TPA and CT. Microphthalmia‐associated transcription factor mRNA is simultaneously enhanced by the same treatment. Kit induced by TPA/CT in NCCmelb4M5 cells disappeared after the cells were subcultured and incubated without TPA/CT. These findings show that NCCmelb4M5 cells have the potential to differentiate into Kit‐positive melanocyte precursors and may be useful to study mechanisms of development and differentiation of melanocytes in mouse neural crest cells.
An oxygen transporter hemocyanin can act on the late pathway of melanin synthesis
Authors: Adachi Kohsuke , Wakamatsu Kazumasa , Ito Shosuke , Miyamoto Nari , Kokubo Takeshi , Nishioka Takaaki , Hirata Takashi
Published: May 2005

5,6‐Dihydroxyindole (DHI) and 5,6‐dihydroxyindole‐2‐carboxylic acid (DHICA) are precursors of eumelanin. The effects of crustacean hemolymph proteins on these eumelanin‐related metabolites were investigated. Zymogram analysis indicated that polymers of hemocyanin (Hc) subunits converted DHI into black pigment while no effects were observed using DHICA as a substrate. Spectrum changes for mixtures of purified Hc and DHI showed a profile similar to oxidized DHI by mushroom tyrosinase while Hc had only slight effects on DHICA. Typical inhibitors of tyrosinase and phenoloxidase severely hampered the production of oxidized DHI. Taken together with previous results, these data indicate that Hc plays a crucial role in the conversion of DHI in the hemolymph of crustaceans, which promotes late reactions in the melanin synthetic pathway as well as early reactions (oxidation of tyrosine and DOPA to dopaquinone).
Performance of Galia‐type melons grafted on to Cucurbita rootstock in Monosporascus cannonballus‐infested and non‐infested soils
Authors: COHEN R , BURGER Y , HOREV C , PORAT A , EDELSTEIN M
Published: May 2005

Galia‐type melons grafted on to the Cucurbita rootstock‘TZ 148’and non‐grafted controls were evaluated for vegetative development under greenhouse conditions. In general, the development of grafted and non‐grafted plants was similar within a cultivar. The horticultural and pathological performances of the Galia‐type melons ‘Carrera’, ‘NUN‐5554’, ‘6003’ and ‘Arava’ were evaluated in experiments conducted in non‐infested and Monosporascus‐infested soils. In non‐infested soil, grafted and non‐grafted ‘Carrera’, ‘NUN‐5554’ and ‘Arava’ had the same yields. The yield of grafted ‘6003’ was significantly higher than that of its non‐grafted control. Responses of grafted and non‐grafted Galia‐type melons to Monosporascus cannonballus were evaluated and compared in the spring and autumn growing seasons. Significant differences in disease incidence were found among cultivars, between grafted and non‐grafted plants, and between growing seasons. Disease reduction and the beneficial effect of grafting on yield were more pronounced in the spring. The results indicate that Galia‐type melons can be grafted successfully, but the cultivation of the grafted plants should be adapted to each growing area and season.
Development of species‐specific primers for the ectoparasitic nematode species Xiphinema brevicolle, X. diffusum, X. elongatum, X. ifacolum and X. longicaudatum (Nematoda: Longidoridae) based on ribosomal DNA sequences
Authors: OLIVEIRA CLAUDIO M G , FENTON BRIAN , MALLOCH GAYNOR , BROWN DEREK J F , NEILSON ROY
Published: May 2005

The objective of this study was to develop single‐step PCR species‐specific primers that reliably discriminate four economically important Xiphinema species (X. brevicolle, X. elongatum, X. ifacolum and X. longicaudatum) and X. diffusum that is taxonomically very similar to X. brevicolle. Each species‐specific reverse primer was located in the ITS‐1 rDNA region and was used in combination with a universal forward primer located in the 18S rDNA gene. Primer reliability was confirmed by screening seven and 11 populations, respectively of X. diffusum and X. elongatum. Potential species‐specific primers were also identified for X. brevicolle, X. longicaudatum and X. ifacolum, however too few populations of these species were available to thoroughly assess their reliability. For all species‐specific primers, specificity was demonstrated by the absence of cross‐reactions with 14 non‐target Xiphinema species. Multiplex PCR was effective and reproducible for two (X. longicaudatum and X. ifacolum) or three (X. brevicolle, X. diffusum and X. elongatum) of the target nematode species, thus improving the applicability of the diagnostic primers.
Effects of light, temperature and water stress on germination of Artemisia sphaerocephala
Authors: ZHENG YUANRUN , XIE ZHIXIAO , GAO YONG , JIANG LIANHE , XING XUERONG , SHIMIZU HIDEYUKI , RIMMINGTON GLYN M
Published: May 2005

Artemisia sphaerocephala is widely used for vegetation rehabilitation, but its germination is very low after air seeding of achenes. We explored effects of light, temperature and water stress on germination. Results show that both final percent germination and germination rate were increased by temperature increment, with the highest values occurring at 15: 25°C (night: day) in dark and 20: 30°C under light. Light inhibited germination, especially at lower alternating temperatures (5: 15°C and 10: 20°C). The alternating temperature window for germination was slightly narrower under light than in dark, and germination was slower under light than in dark across the temperature range. Achenes incubated in the dark and at constant temperatures had over 80% germination at 10 to 25°C, with an optimum at 20°C. Under dark and 25μmol m‐2 s‐1 light flux density at 10: 20°C, final percent germination was over 94%, but if the light flux density was increased to 100 and 400 μmol m‐2 s‐1, final percent germination was significantly lower (64% and 38% respectively). However, achenes could keep their germination capacity for a long time (over 50 days) and germinate well after going back to the dark. Germination was also lower under water stress and few achenes germinated at ‐1.4 MPa. This was more pronounced at high and low temperatures. Given these findings and the prevailing climatic characteristics, the most suitable time for air seeding of achenes may be mid‐May.
Production and properties of monoclonal antibodies to Solanum nodiflorum mottle sobemovirus
Authors: JONES A TEIFION , COWAN GRAHAM H , McGAVIN WENDY J , ROBERTS IAN M , TORRANCE LESLEY
Published: May 2005

Black raspberry necrosis virus (BRNV) reaches only very low concentrations in herbaceous plants and is difficult to maintain in culture. However, in a mixed culture with an unrelated virus, Solanum nodiflorum mottle (SNMV), in the genus Sobemovirus, the concentration of BRNV particles increases about 1000‐fold. In attempts to produce monoclonal antibodies (MAbs) to BRNV for diagnostic use, purified virus particles from the mixed virus culture were used as immunogen and the resultant antibodies screened against cultures of SNMV alone, BRNV+SNMV and healthy plant extracts. None of the virus‐specific MAbs obtained in this way was specific to BRNV but six were specific to SNMV. Although the original objective was not achieved, the SNMV MAbs were characterised and used to study serological properties of SNMV and other Sobemoviruses. Characterisation of the six SNMV MAbs showed that four were IgG3, one IgG1 and the other IgG2b. SNMV was detected by all six MAbs in ELISA, by five in Western blotting, by three in agarose gel double diffusion tests, but only one was suitable for trapping virus particles in immuno‐electron microscopy (IEM). In Western blotting using virus in sap extracts of Nicotiana clevelandii, each of the five MAbs detected a single major band of Mc. 31 000 in sap containing SNMV, and additional bands of lower mass attributed to degradation of coat protein. In various serological tests, no cross‐reactions were detected between SNMV and seven other viruses from the genus Sobemovirus. However, in IEM but not in Western blotting, significant cross‐reactions were observed between SNMV and Velvet tobacco mottle virus, another species from the genus Sobemovirus. The significance of these different findings is discussed.
Responses of potato cultivars to the common scab pathogens, Streptomyces scabies and S. turgidiscabies
Authors: HILTUNEN L H , WECKMAN A , YLHÄINEN A , RITA H , RICHTER E , VALKONEN J P T
Published: May 2005

A glasshouse experiment was conducted to study the responses to Streptomyces scabies and S. turgidiscabies in potato cultivars Bellona, Matilda and Sabina (Solanum tuberosum). Potatoes were grown in a peat‐sand mixture inoculated with one of the two strains of either S. scabies or S. turgidiscabies. Logit models were used to analyse the data on disease incidence and severity, whereas the data on emergence and yield were tested by analysis of variance. S. turgidiscabies, a recently described potato pathogen in Finland, possessed a high ability to cause superficial, raised and pitted lesions on all three cultivars tested. Symptoms induced by S. turgidiscabies were similar to those of S. scabies, regardless of the cultivar, which suggests that the two causal organisms of common scab cannot be distinguished based on symptoms. Infection by S. turgidiscabies and S. scabies delayed emergence, had the tendency to decrease the yield, and increased the proportion of small tubers in the yield, regardless of the potato cultivar. Differences in the levels of resistance to common scab were evident between potato cultivars, since cvs. Matilda and Bellona showed higher disease incidence and more severe scab symptoms than cv. Sabina.
Broad‐based resistance to pigeonpea sterility mosaic disease in wild relatives of pigeonpea (Cajanus: Phaseoleae)
Authors: KUMAR P LAVA , LATHA T K S , KULKARNI N K , RAGHAVENDRA N , SAXENA K B , WALIYAR F , RANGASWAMY K T , MUNIYAPPA V , DORISWAMY SABITHA , JONES A TEIFION
Published: May 2005

Sterility mosaic disease (SMD), an important biotic constraint on pigeonpea (Cajanus cajan) in the Indian subcontinent, is caused by Pigeonpea sterility mosaic virus (PPSMV) transmitted by the eriophyid mite, Aceria cajani. Distinct PPSMV isolates occur in different geographical regions and broad‐based resistance to all these isolates is scarce in cultivated pigeonpea germplasm. Wild relatives of pigeonpea, which are known to possess resistance to several pests and diseases, were evaluated for broad‐based SMD resistance. One hundred and fifteen wild Cajanus accessions from six species (C. albicans, C. platycarpus, C. cajanifolius, C. lineatus, C. scarabaeoides and C. sericeus) were evaluated against three PPSMV isolates prevailing in peninsular India. Evaluations were done under greenhouse conditions in endemic locations of each isolate through mite‐mediated virus inoculation. Fifteen accessions showed resistance to all three isolates: ICP 15614, 15615, 15626, 15684, 15688, 15700, 15701, 15725, 15734, 15736, 15737, 15740, 15924, 15925 and 15926. Most of the wild accessions did not support mite multiplication. The majority of the accessions resistant to PPSMV following inoculations with viruliferous mites were susceptible by graft inoculation, suggesting that vector resistance is conferring resistance to infection with PPSMV. The 15 accessions identified as being resistant to infection to all three virus isolates tested are cross compatible with pigeonpea by traditional breeding. They are therefore useful for exploitation in breeding programmes to increase both the level of SMD resistance and to diversify its genetic base in the cultivated pigeonpea gene pool.
Long‐term effects of prey‐availability, partnering and temperature on overall egg capsule output of ‘New Zealand flatworms’,Arthurdendyus triangulates
Authors: BAIRD JOHN , FAIRWEATHER IAN , MURCHIE ARCHIE K
Published: May 2005

Arthurdendyus triangulatusis an invasive terrestrial flatworm that preys on earthworms. To assessA. triangulatusegg capsule production, flatworms were maintained in ventilated polypropylene tubs (7.5 L) kept in controlled environment (CE) chambers or outdoors in the ground. Controlled environment chambers were maintained at 8°C or 14°C, flatworms kept singly or paired within tubs and offeredEisenia fetidaaccording to a weight equalling one‐eighth or one‐half of the mean flatworm weight, or left unfed. The tubs were a successful method for keeping flatworms, with some surviving for over one year. The greatest number of egg capsules produced by an individualA. triangulatuswas nine over a 16 week period for a flatworm kept at 14°C and fed at the one‐half regime (0.56 egg capsules flatworm‐1week‐1). Although the effects of treatments varied with CE chambers, there was some evidence from flatworms kept outdoors, that feeding affected egg capsule output, with those flatworms fed at the one‐half regime tending to produce more egg capsules (P= 0.057). Flatworms at the one‐eighth regime or that were unfed produced progressively lighter egg capsules and substantially declined in weight themselves. Nevertheless, even unfed flatworms continued to produce egg capsules for 18 weeks. The lightest egg capsule weighed 8 mg, whilst the heaviest was 180 mg. In the CE chambers at 14°C, there was evidence for two different reproductive/survival strategies. Some flatworms produced cumulatively more egg capsules the longer they survived, whereas others lived longer but produced fewer egg capsules. Flatworms kept without a partner still produced egg capsules up to 35 weeks later. Egg capsules contained a mean of 4.14 (CE chambers) or 4.62 (outdoors) juveniles, with a maximum of 11. Overall, juveniles were 45% of the weight of egg capsules, although larger egg capsules had more juveniles, which comprised a greater proportion of the egg capsule. The conversion of earthworm prey to egg capsule production was estimated at 13%.
Patterns of spread of two non‐persistently aphid‐borne viruses in lupin stands under four different infection scenarios
Authors: JONES R A C
Published: May 2005

Patterns of spread of Bean yellow mosaic virus (necrotic type, BYMV‐N) and Cucumber mosaic virus (CMV) were examined in stands of narrow‐leafed lupin (Lupinus angustifolius) where naturally occurring aphid vectors moved them from external or internal primary virus sources. The lupin stands were: commercial crops near BYMV‐infected clover pasture with or without an intervening non‐host barrier crop; a large rectangular block with BYMV‐N and CMV sources on opposite sides and a narrow, non‐host barrier crop facing the BYMV‐N source; and a plot within which seed‐infected lupin plants acted as internal CMV sources. When BYMV‐N spread into commercial crops in the absence of a non‐host barrier, there was a steep decline in its incidence with distance from the crop edge. However, when a 20 m‐wide perimeter barrier of oats intervened between the two, there was only a shallow decline. When CMV and BYMV‐N spread from opposite directions into a block with a 0.25 m‐wide oat barrier between it and the BYMV‐N source, the BYMV‐N incidence gradient was shallow but in the opposite direction the CMV gradient was steep. When CMV spread from primary sources within a plot, infection was concentrated in large internal patches. Spread of BYMV‐N was more diffuse with more isolated symptomatic plants and small clusters than occurred with CMV, spread of which was more comprehensive, reacting the near monocyclic and polycyclic patterns of spread with BYMV‐N with CMV respectively. Spread of both viruses was greater along than across rows, especially with CMV. With BYMV‐N, three different phased cycles of secondary spread were evident in the individual symptomatic plants within the small clusters that formed away from the edges of lupin stands. These findings help validate inclusion of perimeter non‐host barriers within an integrated disease management strategy for BYMV‐N in lupin.
Molecular genetic analysis of silencing in two lines of Triticum aestivum transformed with the reporter gene construct pAHC25
Authors: HOWARTH JONATHAN R , JACQUET JEAN N , DOHERTY ANGELA , JONES HUW D , CANNELL MARTIN E
Published: May 2005

Unpredictable silencing of foreign genes introduced into wheat by particle bombardment transformation has been previously observed. To investigate the cause of this silencing, we selected two independent wheat lines that had been transformed via the particle gun with plasmid pAHC25 containing the genes uidA (GUS) and bar (BASTA herbicide‐resistance) each controlled by the maize ubiquitin promoterintron (Ubil). One of these lines (WT2) had shown progressive reductions in transgenic phenotype in successive generations until GUS activity and herbicide‐resistance were undetectable in all progeny of the T3 generation tested. A second line, (WT1) exhibited the expected levels of GUS expression and herbicide‐resistance up to the T3 generation except for the loss of transgenic phenotype in a single T1 segregant. Transgene stability, silencing and integration locus was investigated in three generations in both lines. The silencing observed in the WT2 line was found to be acting at the transcription level for both the uidA and bar genes. Analysis of transgene promoter methylation in selected T1, T2 and T3 individuals revealed a positive link between methylation status and gene silencing. The silenced T1 individual from line WT1 was also linked to promoter methylation and insertion locus rearrangement. Fluorescence in situ hybridisation (FISH) revealed highly divergent transgene insertion loci for WT1 and WT2. WT1 was detected close to the telomere whereas the WT2 insertion was located in the region of the centromere. The effect of these findings on transgene silencing and stability are discussed.
The evolution of oligotrophy: implications for the breeding of crop plants for low input agricultural systems
Authors: RAVEN J A , ANDREWS M , QUIGG A
Published: May 2005

Oligotrophy, the obligate or facultative capacity to live in low‐nutrient habitats, has played a major role in the evolution of photosynthetic organisms.

Energy/carbon deficiency: evolution of photosynthesis about 3.5 Gyr (billion years) ago, then use of H2O as electron donor, and accumulation of O2 from about 2.3 Gyr ago.

Deficiency in combined N: evolution of biological N2 fixation about 2.0‐2.3 Gyr ago.

Deficiency in soluble relative to particulate organic C: evolution of phagotrophy in eukaryotes, opening the way to endosymbiotic origin of photosynthesis in eukaryotes.

Deficiency of P and Fe resulting from oxygenation: evolution of mechanisms increasing access to P and Fe.

Deficiency of H2O for land plants gaining C from the atmosphere: evolution of homoiohydry following origin of significant land flora from 0.5 Gyr ago.

Deficiency of CO2 resulting from increased weathering by land plants: evolution of large leaves.

Increased competition for resources among land plants: evolution of mechanisms economizing in use of soil‐derived resources, and increasing ability to acquire resources.

Economising on resource use in photosynthetic organisms is subject to a number of constraints. There are very limited possibilities for reducing the use of N in proteins with a given catalytic function, but greater possibilities using substitution of an analogous protein with that function. The same applies to Fe. Possibilities for economising on the use of P are very limited if the growth rate is to be maintained: the marine cyanobacterium Prochlorococcus is a good example of restricted P requirement. H2O use can be constrained by C4 and, especially, CAM photosynthesis.

A possible role of the study of oligotrophy in the context of sustainable, low‐input agriculture includes modified agricultural practice to minimise losses of resources. Information on oligotrophy and its evolution can also be used to inform the alteration of crop plants by genetic modification related to resource acquisition (e.g. associative, or nodule‐based, symbiotic diazotrophy) and the economy of resource use (e.g. partial or complete conversion of a C3 crop to a C4 crop which could economise in the use of N and/or H2O). The attempts to convert C3 to C4 plants have not thus far been fully successful, and the advantages of conversion to C4 are being increasingly offset by the effect of increasing atmospheric CO2 on C3 plants. However, more success has been achieved with selection of the most appropriate diazotrophic symbionts for crop plants in particular environments.
Amplified fragment length polymorphism among Rhynchosporium secalis isolates collected from a single barley field in Syria
Authors: KIROS‐MELES A , UDUPA S , ABANG M M , ABU‐BLAN H , BAUM M , CECCARELLI S , YAHYAOUI A H
Published: May 2005

AFLP markers were used to measure the amount and distribution of genetic variation among Rhynchosporium secalis isolates on a microgeographical scale in Syria. Forty isolates hierarchically sampled from a single barley field were assayed for AFLP variation using primer combinations not previously tested in populations of the pathogen from Syria. In contrast to a previous study, which showed high clonality within field populations of R. secalis in Syria, the present study revealed a much higher level of genetic diversity, stressing the important roles that sampling strategies and the choice of primers/primer combinations play in the evaluation of genetic variation in R. secalis populations at a microgeographical scale. A high level of genetic variation was found to occur on a fine scale throughout the pathogen population examined, with 40 different haplotypes being identified among the 40 isolates sampled. Data were consistent with the hypothesis that the primary inoculum originated from a genetically diverse founding population, which may have consisted of ascospores of an as yet undescribed teleomorph and/or asexual spores of a highly mutable local population.
Structural Basis of Energy Transduction in the Transport Cycle of MsbA
Authors: Dong Jinhui , Yang Guangyong , Mchaourab Hassane S.
Published: May 2005

We used site-directed spin-labeling and electron paramagnetic resonance spectroscopy to characterize the conformational motion that couples energy expenditure to substrate translocation in the multidrug transporter MsbA. In liposomes, ligand-free MsbA samples conformations that depart from the crystal structures, including looser packing and water penetration along the periplasmic side. Adenosine triphosphate (ATP) binding closes the substrate chamber to the cytoplasm while increasing hydration at the periplasmic side, consistent with an alternating access model. Accentuated by ATP hydrolysis, the changes in the chamber dielectric environment and its geometry provide the likely driving force for flipping amphipathic substrates and a potential exit pathway. These results establish the structural dynamic basis of the power stroke in multidrug-resistant ATP-binding cassette (MDR ABC) transporters.
The Structure of a pH-Sensing Mycobacterial Adenylyl Cyclase Holoenzyme
Authors: Tews Ivo , Findeisen Felix , Sinning Irmgard , Schultz Anita , Schultz Joachim E. , Linder Jürgen U.
Published: May 2005

Class III adenylyl cyclases contain catalytic and regulatory domains, yet structural insight into their interactions is missing. We show that the mycobacterial adenylyl cyclase Rv1264 is rendered a pH sensor by its N-terminal domain. In the structure of the inhibited state, catalytic and regulatory domains share a large interface involving catalytic residues. In the structure of the active state, the two catalytic domains rotate by 55° to form two catalytic sites at their interface. Two α helices serve as molecular switches. Mutagenesis is consistent with a regulatory role of the structural transition, and we suggest that the transition is regulated by pH.
Structure of the ABC Transporter MsbA in Complex with ADP·Vanadate and Lipopolysaccharide
Authors: Reyes Christopher L. , Chang Geoffrey
Published: May 2005

Select members of the adenosine triphosphate (ATP)-binding cassette (ABC) transporter family couple ATP binding and hydrolysis to substrate efflux and confer multidrug resistance. We have determined the x-ray structure of MsbA in complex with magnesium, adenosine diphosphate, and inorganic vanadate (Mg·ADP·V
i
) and the rough-chemotype lipopolysaccharide, Ra LPS. The structure supports a model involving a rigid-body torque of the two transmembrane domains during ATP hydrolysis and suggests a mechanism by which the nucleotide-binding domain communicates with the transmembrane domain. We propose a lipid “flip-flop” mechanism in which the sugar groups are sequestered in the chamber while the hydrophobic tails are dragged through the lipid bilayer.
Freedom and Rules: The Acquisition and Reprogramming of a Bird's Learned Song
Authors: Gardner Timothy J. , Naef Felix , Nottebohm Fernando
Published: May 2005

Canary song is hierarchically structured: Short stereotyped syllables are repeated to form phrases, which in turn are arranged to form songs. This structure occurs even in the songs of young isolates, which suggests that innate rules govern canary song development. However, juveniles that had never heard normal song imitated abnormal synthetic songs with great accuracy, even when the tutor songs lacked phrasing. As the birds matured, imitated songs were reprogrammed to form typical canary phrasing. Thus, imitation and innate song constraints are separate processes that can be segregated in time: freedom in youth, rules in adulthood.
Two Chemically Distinct Pools of Organic Nitrogen Accumulate in the Ocean
Authors: Aluwihare Lihini I. , Repeta Daniel J. , Pantoja Silvio , Johnson Carl G.
Published: May 2005

The chemical dynamics of marine dissolved organic nitrogen (DON), a reservoir featuring surface accumulations even in areas where nitrogen limits productivity, have yet to be resolved. We exploited differences in the acid lability of amide bonds within high-molecular-weight (HMW) DON to show that vertical DON profiles result in part from the presence of two chemically distinct pools of amide. Half of HMWDON in surface waters is present as
N
-acetyl amino polysaccharides. In contrast, nearly all deep-sea HMWDON, and therefore, most HMWDON, is present in amides that resist both chemical hydrolysis and biological degradation.
Titan's Magnetic Field Signature During the First Cassini Encounter
Authors: Backes Heiko , Neubauer Fritz M. , Dougherty Michele K. , Achilleos Nicholas , André Nicolas , Arridge Christopher S. , Bertucci Cesar , Jones Geraint H. , Khurana Krishan K. , Russell Christopher T. , Wennmacher Alexandre
Published: May 2005

The magnetic field signature obtained by Cassini during its first close encounter with Titan on 26 October 2004 is presented and explained in terms of an advanced model. Titan was inside the saturnian magnetosphere. A magnetic field minimum before closest approach marked Cassini's entry into the magnetic ionopause layer. Cassini then left the northern and entered the southern magnetic tail lobe. The magnetic field before and after the encounter was approximately constant for ∼20 Titan radii, but the field orientation changed exactly at the location of Titan's orbit. No evidence of an internal magnetic field at Titan was detected.
Cassini Measurements of Cold Plasma in the Ionosphere of Titan
Authors: Wahlund J.-E. , Boström R. , Gustafsson G. , Gurnett D. A. , Kurth W. S. , Pedersen A. , Averkamp T. F. , Hospodarsky G. B. , Persoon A. M. , Canu P. , Neubauer F. M. , Dougherty M. K. , Eriksson A. I. , Morooka M. W. , Gill R. , André M. , Eliasson L. , Müller-Wodarg I.
Published: May 2005

The Cassini Radio and Plasma Wave Science (RPWS) Langmuir probe (LP) sensor observed the cold plasma environment around Titan during the first two flybys. The data show that conditions in Saturn's magnetosphere affect the structure and dynamics deep in the ionosphere of Titan. The maximum measured ionospheric electron number density reached 3800 per cubic centimeter near closest approach, and a complex chemistry was indicated. The electron temperature profiles are consistent with electron heat conduction from the hotter Titan wake. The ionospheric escape flux was estimated to be 10
25
ions per second.
Cassini Radar Views the Surface of Titan
Authors: Elachi C. , Wall S. , Allison M. , Anderson Y. , Boehmer R. , Callahan P. , Encrenaz P. , Flamini E. , Franceschetti G. , Gim Y. , Hamilton G. , Hensley S. , Janssen M. , Johnson W. , Kelleher K. , Kirk R. , Lopes R. , Lorenz R. , Lunine J. , Muhleman D. , Ostro S. , Paganelli F. , Picardi G. , Posa F. , Roth L. , Seu R. , Shaffer S. , Soderblom L. , Stiles B. , Stofan E. , Vetrella S. , West R. , Wood C. , Wye L. , Zebker H.
Published: May 2005

The Cassini Titan Radar Mapper imaged about 1% of Titan's surface at a resolution of â¼0.5 kilometer, and larger areas of the globe in lower resolution modes. The images reveal a complex surface, with areas of low relief and a variety of geologic features suggestive of dome-like volcanic constructs, flows, and sinuous channels. The surface appears to be young, with few impact craters. Scattering and dielectric properties are consistent with porous ice or organics. Dark patches in the radar images show high brightness temperatures and high emissivity and are consistent with frozen hydrocarbons.
Reconstructing the Origin of Andaman Islanders
Authors: Thangaraj Kumarasamy , Chaubey Gyaneshwer , Kivisild Toomas , Reddy Alla G. , Singh Vijay Kumar , Rasalkar Avinash A. , Singh Lalji
Published: May 2005

The origin of the Andaman "Negrito" and Nicobar "Mongoloid" populations has been ambiguous. Our analyses of complete mitochondrial DNA sequences from Onges and Great Andaman populations revealed two deeply branching clades that share their most recent common ancestor in founder haplogroup M, with lineages spread among India, Africa, East Asia, New Guinea, and Australia. This distribution suggests that these two clades have likely survived in genetic isolation since the initial settlement of the islands during an out-of-Africa migration by anatomically modern humans. In contrast, Nicobarese sequences illustrate a close genetic relationship with populations from Southeast Asia.
Implementation of the Semiclassical Quantum Fourier Transform in a Scalable System
Authors: Chiaverini J. , Britton J. , Leibfried D. , Knill E. , Barrett M. D. , Blakestad R. B. , Itano W. M. , Jost J. D. , Langer C. , Ozeri R. , Schaetz T. , Wineland D. J.
Published: May 2005

We report the implementation of the semiclassical quantum Fourier transform in a system of three beryllium ion qubits (two-level quantum systems) confined in a segmented multizone trap. The quantum Fourier transform is the crucial final step in Shor's algorithm, and it acts on a register of qubits to determine the periodicity of the quantum state's amplitudes. Because only probability amplitudes are required for this task, a more efficient semiclassical version can be used, for which only single-qubit operations conditioned on measurement outcomes are required. We apply the transform to several input states of different periodicities; the results enable the location of peaks corresponding to the original periods. This demonstration incorporates the key elements of a scalable ion-trap architecture, suggesting the future capability of applying the quantum Fourier transform to a large number of qubits as required for a useful quantum factoring algorithm.
Titan's Atmospheric Temperatures, Winds, and Composition
Authors: Flasar F. M. , Achterberg R. K. , Conrath B. J. , Gierasch P. J. , Kunde V. G. , Nixon C. A. , Bjoraker G. L. , Jennings D. E. , Romani P. N. , Simon-Miller A. A. , Bézard B. , Coustenis A. , Irwin P. G. J. , Teanby N. A. , Brasunas J. , Pearl J. C. , Segura M. E. , Carlson R. C. , Mamoutkine A. , Schinder P. J. , Barucci A. , Courtin R. , Fouchet T. , Gautier D. , Lellouch E. , Marten A. , Prangé R. , Vinatier S. , Strobel D. F. , Calcutt S. B. , Read P. L. , Taylor F. W. , Bowles N. , Samuelson R. E. , Orton G. S. , Spilker L. J. , Owen T. C. , Spencer J. R. , Showalter M. R. , Ferrari C. , Abbas M. M. , Raulin F. , Edgington S. , Ade P. , Wishnow E. H.
Published: May 2005

Temperatures obtained from early Cassini infrared observations of Titan show a stratopause at an altitude of 310 kilometers (and 186 kelvin at 15°S). Stratospheric temperatures are coldest in the winter northern hemisphere, with zonal winds reaching 160 meters per second. The concentrations of several stratospheric organic compounds are enhanced at mid- and high northern latitudes, and the strong zonal winds may inhibit mixing between these latitudes and the rest of Titan. Above the south pole, temperatures in the stratosphere are 4 to 5 kelvin cooler than at the equator. The stratospheric mole fractions of methane and carbon monoxide are (1.6 ± 0.5) × 10
-2
and (4.5 ± 1.5) × 10
-5
, respectively.
The Cassini UVIS Stellar Probe of the Titan Atmosphere
Authors: Shemansky Donald E. , Stewart A. Ian F. , West Robert A. , Esposito Larry W. , Hallett Janet T. , Liu Xianming
Published: May 2005

The Cassini Ultraviolet Imaging Spectrometer (UVIS) observed the extinction of photons from two stars by the atmosphere of Titan during the Titan flyby. Six species were identified and measured: methane, acetylene, ethylene, ethane, diacetylene, and hydrogen cyanide. The observations cover altitudes from 450 to 1600 kilometers above the surface. A mesopause is inferred from extraction of the temperature structure of methane, located at 615 km with a temperature minimum of 114 kelvin. The asymptotic kinetic temperature at the top of the atmosphere determined from this experiment is 151 kelvin. The higher order hydrocarbons and hydrogen cyanide peak sharply in abundance and are undetectable below altitudes ranging from 750 to 600 km, leaving methane as the only identifiable carbonaceous molecule in this experiment below 600 km.
Intensive Titan Exploration Begins
Authors: Mahaffy Paul R.
Published: May 2005

The Cassini Orbiter spacecraft first skimmed through the tenuous upper atmosphere of Titan on 26 October 2004. This moon of Saturn is unique in our solar system, with a dense nitrogen atmosphere that is cold enough in places to rain methane, the feedstock for the atmospheric chemistry that produces hydrocarbons, nitrile compounds, and Titan's orange haze. The data returned from this flyby supply new information on the magnetic field and plasma environment around Titan, expose new facets of the dynamics and chemistry of Titan's atmosphere, and provide the first glimpses of what appears to be a complex, fluid-processed, geologically young Titan surface.
On the Origin of Leprosy
Authors: Monot Marc , Honoré Nadine , Garnier Thierry , Araoz Romulo , Coppée Jean-Yves , Lacroix Céline , Sow Samba , Spencer John S. , Truman Richard W. , Williams Diana L. , Gelber Robert , Virmond Marcos , Flageul Béatrice , Cho Sang-Nae , Ji Baohong , Paniz-Mondolfi Alberto , Convit Jacinto , Young Saroj , Fine Paul E. , Rasolofo Voahangy , Brennan Patrick J. , Cole Stewart T.
Published: May 2005

Leprosy, a chronic human disease with potentially debilitating neurological consequences, results from infection with
Mycobacterium leprae
. This unculturable pathogen has undergone extensive reductive evolution, with half of its genome now occupied by pseudogenes. Using comparative genomics, we demonstrated that all extant cases of leprosy are attributable to a single clone whose dissemination worldwide can be retraced from analysis of very rare single-nucleotide polymorphisms. The disease seems to have originated in Eastern Africa or the Near East and spread with successive human migrations. Europeans or North Africans introduced leprosy into West Africa and the Americas within the past 500 years.
Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription
Authors: Lewinski M. K. , Bisgrove D. , Shinn P. , Chen H. , Hoffmann C. , Hannenhalli S. , Verdin E. , Berry C. C. , Ecker J. R. , Bushman F. D.
Published: May 2005

We have investigated regulatory sequences in noncoding human DNA that are associated with repression of an integrated human immunodeficiency virus type 1 (HIV-1) promoter. HIV-1 integration results in the formation of precise and homogeneous junctions between viral and host DNA, but integration takes place at many locations. Thus, the variation in HIV-1 gene expression at different integration sites reports the activity of regulatory sequences at nearby chromosomal positions. Negative regulation of HIV transcription is of particular interest because of its association with maintaining HIV in a latent state in cells from infected patients. To identify chromosomal regulators of HIV transcription, we infected Jurkat T cells with an HIV-based vector transducing green fluorescent protein (GFP) and separated cells into populations containing well-expressed (GFP-positive) or poorly expressed (GFP-negative) proviruses. We then determined the chromosomal locations of the two classes by sequencing 971 junctions between viral and cellular DNA. Possible effects of endogenous cellular transcription were characterized by transcriptional profiling. Low-level GFP expression correlated with integration in (i) gene deserts, (ii) centromeric heterochromatin, and (iii) very highly expressed cellular genes. These data provide a genome-wide picture of chromosomal features that repress transcription and suggest models for transcriptional latency in cells from HIV-infected patients.
Selective Replication of Coronavirus Genomes That Express Nucleocapsid Protein
Authors: Schelle Barbara , Karl Nadja , Ludewig Burkhard , Siddell Stuart G. , Thiel Volker
Published: May 2005

The coronavirus nucleocapsid (N) protein is a structural protein that forms a ribonucleoprotein complex with genomic RNA. In addition to its structural role, it has been described as an RNA-binding protein that might be involved in coronavirus RNA synthesis. Here, we report a reverse genetic approach to elucidate the role of N in coronavirus replication and transcription. We found that human coronavirus 229E (HCoV-229E) vector RNAs that lack the N gene were greatly impaired in their ability to replicate, whereas the transcription of subgenomic mRNA from these vectors was easily detectable. In contrast, vector RNAs encoding a functional N protein were able to carry out both replication and transcription. Furthermore, modification of the transcription signal required for the synthesis of N protein mRNAs in the HCoV-229E genome resulted in the selective replication of genomes that are able to express the N protein. This genetic evidence leads us to conclude that at least one coronavirus structural protein, the N protein, is involved in coronavirus replication.
Long-Range RNA-RNA Interactions Circularize the Dengue Virus Genome
Authors: Alvarez Diego E. , Lodeiro María F. , Ludueña Silvio J. , Pietrasanta Lía I. , Gamarnik Andrea V.
Published: May 2005

Secondary and tertiary RNA structures present in viral RNA genomes play essential regulatory roles during translation, RNA replication, and assembly of new viral particles. In the case of flaviviruses, RNA-RNA interactions between the 5′ and 3′ ends of the genome have been proposed to be required for RNA replication. We found that two RNA elements present at the ends of the dengue virus genome interact in vitro with high affinity. Visualization of individual molecules by atomic force microscopy reveled that physical interaction between these RNA elements results in cyclization of the viral RNA. Using RNA binding assays, we found that the putative cyclization sequences, known as 5′ and 3′ CS, present in all mosquito-borne flaviviruses, were necessary but not sufficient for RNA-RNA interaction. Additional sequences present at the 5′ and 3′ untranslated regions of the viral RNA were also required for RNA-RNA complex formation. We named these sequences 5′ and 3′ UAR (upstream AUG region). In order to investigate the functional role of 5′-3′ UAR complementarity, these sequences were mutated either separately, to destroy base pairing, or simultaneously, to restore complementarity in the context of full-length dengue virus RNA. Nonviable viruses were recovered after transfection of dengue virus RNA carrying mutations either at the 5′ or 3′ UAR, while the RNA containing the compensatory mutations was able to replicate. Since sequence complementarity between the ends of the genome is required for dengue virus viability, we propose that cyclization of the RNA is a required conformation for viral replication.
The Open Reading Frame 3 Gene of Hepatitis E Virus Contains a
cis
-Reactive Element and Encodes a Protein Required for Infection of Macaques
Authors: Graff Judith , Nguyen Hanh , Yu Claro , Elkins William R. , St. Claire Marisa , Purcell Robert H. , Emerson Suzanne U.
Published: May 2005

An infectious cDNA clone of hepatitis E virus was mutated in order to prevent synthesis of either open reading frame 2 (ORF2) protein or ORF3 protein. HuH-7 cells transfected with an ORF2-null mutant produced ORF3, and those transfected with an ORF3-null mutant produced ORF2. Silent mutations introduced into a highly conserved nucleotide sequence in the ORF3 coding region eliminated the synthesis of both ORF2 and ORF3 proteins, suggesting that it comprised a
cis
-reactive element. A mutant that was not able to produce ORF3 protein did not produce a detectable infection in rhesus macaques. However, a mutant that encoded an ORF3 protein lacking a phosphorylation site reported to be critical for function was able to replicate its genome in cell culture and to induce viremia and seroconversion in rhesus monkeys, suggesting that phosphorylation of ORF3 protein was not necessary for genome replication or for production of infectious virions.
Interaction with CD4 and Antibodies to CD4-Induced Epitopes of the Envelope gp120 from a Microglial Cell-Adapted Human Immunodeficiency Virus Type 1 Isolate
Authors: Martín-García Julio , Cocklin Simon , Chaiken Irwin M. , González-Scarano Francisco
Published: May 2005

We previously showed that the envelope glycoprotein from an in vitro microglia-adapted human immunodeficiency virus type 1 isolate (HIV-1Bori-15) is able to use lower levels of CD4 for infection and demonstrates greater exposure of the CD4-induced epitope recognized by the 17b monoclonal antibody than the envelope of its parental, peripheral isolate (HIV-1Bori). We investigated whether these phenotypic changes were related to a different interaction of their soluble monomeric gp120 proteins with CD4 or 17b. Equilibrium binding analyses showed no difference between Bori and Bori-15 gp120s. However, kinetic analysis of surface plasmon resonance-based, real-time binding experiments showed that while both proteins have similar association rates, Bori-15 gp120 has a statistically significant, 3-fold-lower dissociation rate from immobilized CD4 than Bori and a statistically significant, 14-fold-lower dissociation rate from 17b than Bori in the absence of soluble CD4. In addition, using the sensitivity to inhibition by anti-CD4 antibodies as a surrogate for CD4:trimeric envelope interaction, we found that Bori-15 envelope-pseudotyped viruses were significantly less sensitive than Bori pseudotypes, with four- to sixfold-higher 50% inhibitory concentration values for the three anti-CD4 antibodies tested. These differences, though small, suggest that adaptation to microglia correlates with the generation of a gp120 that forms a more stable interaction with CD4. Nonetheless, the observation of limited binding changes leaves open the possibility that HIV-1 adaptation to microglia and HIV-associated dementia may be related not only to diminished CD4 dependence but also to changes in other molecular factors involved in the infection process.
Role of the E1
∧
E4 Protein in the Differentiation-Dependent Life Cycle of Human Papillomavirus Type 31
Authors: Wilson Regina , Fehrmann Frauke , Laimins Laimonis A.
Published: May 2005

The most highly expressed protein in the productive life cycle of human papillomaviruses (HPVs) is E1
∧
E4, but its function is not well understood. To investigate the role of E1
∧
E4, we undertook a genetic analysis in the context of the complete HPV type 31 (HPV31) genome. A mutant HPV31 genome (E4M9) was constructed that contained a stop codon in the E4 open reading frame at amino acid 9 and was silent in the overlapping E2 coding sequence. Wild-type and mutant genomes were transfected into normal human foreskin keratinocytes (HFKs) and selected for drug resistance, and pooled cultures were examined for effects of E1
∧
E4 on viral functions. Southern blot analyses of transfected HFKs demonstrated that cells carrying the E4M9 mutant genomes were maintained as episomes at copy numbers similar to those in keratinocytes transfected with wild-type HPV31. Both sets of cells grew at similar rates, exhibited comparable extensions of life spans, and had equivalent levels of early transcripts. Following suspension of the cells in a semisolid medium, differentiation-dependent genome amplification and late gene expression were significantly decreased in cells maintaining the E4M9 mutant genome compared to those with wild-type HPV31. One explanation for these effects could be a reduction in the number of cells harboring mutant genomes that enter S phase upon differentiation. An analysis of cells containing E4M9 mutant genomes in organotypic raft cultures indicated a reduction in bromodeoxyuridine incorporation in differentiated suprabasal cells compared to that seen in wild-type rafts. Our results indicate that the HPV31 E1
∧
E4 protein plays a significant role in promoting HPV genome amplification and S phase maintenance during differentiation.