bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative phylogeography in a genus of coral reef fishes: biogeographic and genetic concordance in the Caribbean
Authors: TAYLOR MICHAEL S. , HELLBERG MICHAEL E. 
Published: February 2006

AbstractGeographic barriers that limit the movement of individuals between populations may create or maintain phylogenetically discrete lineages. Such barriers are often inferred from geographic surveys of a single mitochondrial marker to identify phylogenetic splits. Mitochondrial DNA, however, has an effective population size one‐fourth that of nuclear DNA, which can facilitate the rapid evolution of monophyletic mtDNA lineages in the absence of geographic barriers. The identification of geographic barriers will thus be more robust if barriers are proposed a priori, and tested with multiple independent genetic markers in multiple species. Here, we tested two proposed marine biogeographic breaks located at the Mona Passage in the Caribbean Sea and at the southern end of Exuma Sound in the Bahamas. We sequenced mitochondrial cytochrome b (400 bp) and nuclear rag1 (573 bp) for nine species and colour forms (183 individuals total) within the teleost genus Elacatinus (Gobiidae) that span the proposed breaks. Our results showed that Mona Passage separated mtcyb and rag1 lineages, with no genetic exchange between populations separated by just 23 km. However, the Central Bahamas barrier was only weakly supported by our data. Importantly, neither barrier coincided with deep genetic splits. This suggests that these two barriers did not initially isolate regional populations, but instead disrupt ongoing gene flow between regions. Our inferred relationships further suggested a division of the Caribbean region into northwestern and southeastern regions, a pattern reflected by some freshwater and terrestrial vertebrates. Our results, coupled with genetic and demographic data from other reef fishes and corals, provide robust support for the Mona Passage as a long‐term biogeographic barrier for Caribbean animals.
Polar assembly of the type IV pilus secretin in Myxococcus xanthus
Authors: Nudleman Eric , Wall Daniel , Kaiser Dale 
Published: February 2006

SummaryThe type IV pilus filament of Myxococcus xanthus penetrates the outer membrane through a gated channel – the PilQ secretin. Assembly of the channel and formation of PilQ multimeric complexes that resist disassembly in heated detergent is correlated with the release of a 50 kDa fragment of PilQ. Tgl lipoprotein is required for PilQ assembly in M. xanthus, because PilQ monomers but no heat and detergent‐resistant complexes are present in a strain from which tgl has been deleted. PilQ protein is often found in single patches at both poles of the cell. Tgl, however, is found in a patch at only one pole that most likely identifies the piliated cell pole. Tgl protein that has been transferred from another cell by contact stimulation leads to secretin assembly in the recipient. Pilus proteins PilQ, PilG, PilM, PilN, PilO and PilP are also required for the donation of Tgl by contact stimulation to a stimulation recipient. We suggest that these proteins are parts of a polar superstructure that holds PilQ monomers in a cluster and ready for Tgl to bring about secretin assembly.
Changes in flagellin glycosylation affect Campylobacter autoagglutination and virulence
Authors: Guerry Patricia , Ewing Cheryl P. , Schirm Michael , Lorenzo Maria , Kelly John , Pattarini Dawn , Majam Gary , Thibault Pierre , Logan Susan 
Published: February 2006

SummaryAnalysis of the complete flagellin glycosylation locus of Campylobacter jejuni strain 81–176 revealed a less complex genomic organization than the corresponding region in the genome strain, C. jejuni NCTC 11168. Twenty‐four of the 45 genes found between Cj1293 and Cj1337 in NCTC 11168 are missing in 81–176. Mutation of six new genes, in addition to three previously reported, resulted in a non‐motile phenotype, consistent with a role in synthesis of pseudaminic acid (PseAc) or transfer of PseAc to flagellin. Mutation of Cj1316c or pseA had been shown to result in loss of the acetamidino form of pseudaminic acid (PseAm). Mutation of a second gene also resulted in loss of PseAm, as well as a minor modification that appears to be PseAm extended with N‐acetyl‐glutamic acid. Previously described mutants in C. jejuni 81–176 and Campylobacter coli VC167 that produced flagella lacking PseAm or PseAc failed to autoagglutinate. This suggests that interactions between modifications on adjacent flagella filaments are required for autoagglutination. Mutants (81–176) defective in autoagglutination showed a modest reduction in adherence and invasion of INT407 cells. However, there was a qualitative difference in binding patterns to INT407 cells using GFP‐labelled 81–176 and mutants lacking PseAm. A mutant lacking PseAm was attenuated in the ferret diarrhoeal disease model.
Inorganic polyphosphate interacts with ribosomes and promotes translation fidelity in vitro and in vivo
Authors: McInerney Peter , Mizutani Taeko , Shiba Toshikazu 
Published: February 2006

SummaryInorganic polyphosphate is a biological macromolecule consisting of multiple phosphates linked by high‐energy bonds. Polyphosphate occurs in cells from all domains of life, and is known to play roles in a diverse collection of cellular functions. Here we examine the relationship between polyphosphate and protein synthesis in Escherichia coli. We report that polyphosphate associates with E. coli ribosomes in vitro. Characterization of this interaction reveals that both long‐chain and short‐chain polyphosphates interact with the ribosome. Intact 70S ribosomes, as well as 50S and 30S subunits, display a specific interaction with polyphosphate that is mediated primarily by contacts with ribosomal proteins. Additionally, we examined functional consequences of a ppk mutation, which severely reduces levels of intracellular polyphosphate. Extracts from ppk mutants contain lower levels of polysomes than wild‐type cells, suggesting a defect in mRNA utilization or the mRNA–ribosome interaction. Ribosomes from wild‐type and ppk mutant cells were isolated, and their activities were compared using a polyU RNA in vitro translation assay. While rates of polyphenylalanine synthesis are similar, use of ribosomes from ppk cells results in a misincorporation rate about five times higher compared with the rate observed when ribosomes from wild‐type cells are used. Mistranslation rates in vivo were measured directly, and ppk mutants displayed higher readthrough frequencies for two different stop codons. Taken together, these results indicate that polyphosphate plays an important role in maintaining optimal translation efficiency in vivo and in vitro.
The Escherichia coli plasma membrane contains two PHB (prohibitin homology) domain protein complexes of opposite orientations
Authors: Chiba Shinobu , Ito Koreaki , Akiyama Yoshinori 
Published: February 2006

SummaryTwo membrane proteases, FtsH and HtpX, are jointly essential for Escherichia coli cell viability, presumably through their abilities to degrade abnormal membrane proteins. To search for additional cellular factors involved in membrane protein quality control, we isolated multicopy suppressors that alleviated the growth defect of the ftsH/htpX dual disruption mutant. One of them was ybbK, which is renamed qmcA, encoding a membrane‐bound prohibitin homology (PHB) domain family protein. Multicopy suppression was also observed with hflK–hflC, encoding another set of PHB domain membrane proteins, which had been known to form a complex (HflKC) and to interact with FtsH. Whereas the ΔftsH sfhC21 (a viability defect suppressor for ΔftsH) strain exhibited temperature sensitivity in the presence of cAMP, additional disruption of both qmcA and hflK–hflC exaggerated the growth defect. Pull‐down and sedimentation experiments showed that QmcA, like HflKC, forms an oligomer and interacts with FtsH. Protease accessibility assays revealed that QmcA, unlike periplasmically exposed HflKC, possesses a cytoplasmically disposed large C‐terminal domain, thus assuming the type I (NOUT‐CIN) orientation. We discuss possible significance of having PHB domains on both sides of the membrane.
Mechanisms of microbially enhanced Fe acquisition in red clover (Trifolium pratense L.)
Authors: JIN CHONG WEI , HE YUN FENG , TANG CAI XIAN , WU PING , ZHENG SHAO JIAN 
Published: February 2006

ABSTRACTSoil microorganisms may play an important role in plant Fe uptake from soils with low Fe bioavailability, but there is little direct experimental evidence to date. We grew red clover, an Fe‐efficient leguminous plant, in a calcareous soil to investigate the role of soil microbial activity in plant Fe uptake. Compared with plants grown in non‐sterlie (NS) grown plants, growth and Fe content of the sterile(s) grown plants was significantly inhibited, but was improved by foliar application of Fe EDTA, indicating that soil microbial activity should play an important role in plant Fe acquisition. When soil solution was incubated with phenolic root exudates from Fe‐deficient red clover, a few microbial species thrived while growth of the rest was inhibited, suggesting that the Fe‐deficient (– Fe) root exudates selectively influenced the rhizosphere's microbial community. Eighty six per cent of the phenolic‐tolerant microbes could produce siderophore [the Fe(III) chelator] under – Fe conditions, and 71% could secrete auxin‐like compounds. Interestingly, the synthetic and microbial auxins (MAs) significantly enhanced the Ferric reduction system, suggesting that MAs, in addition to siderophores, are important to plant Fe uptake. Finally, plant growth and Fe uptake in sterilized soil were significantly increased by rhizobia inoculation. Root Fe–EDTA reductase activity in the – Fe plant was significantly enhanced by rhizobia infection, and the rhizobia could produce auxin but not siderophore under Fe‐limiting conditions, suggesting that the contribution of nodulating rhizobia to plant Fe uptake can be at least partially attributed to stimulation of turbo reductase activity through nodule formation and auxin production in the rhizosphere. Based on these observations, we propose as a model that root exudates from – Fe plants selectively influence the rhizosphere microbial community, and the microbes in turn favour plant Fe acquisition by producing siderophores and auxins.
The potential of nonpathogenic Fusarium oxysporum and other biological control organisms for suppressing fusarium wilt of banana
Authors: Nel B. , Steinberg C. , Labuschagne N. , Viljoen A. 
Published: February 2006

The aim of this study was to evaluate the ability of nonpathogenic F. oxysporum and Trichoderma isolates from suppressive soils in South Africa to suppress fusarium wilt of banana in the glasshouse. Several biological control agents and commercial biological control products were included in the study. The isolates were first screened in vitro on potato dextrose agar. In glasshouse evaluations, the fungal and bacterial isolates were established on banana roots before they were replanted in pathogen‐infested soil, while the commercial biocontrol agents were applied as directed by the supplier. Banana plantlets were evaluated for disease development after 7 weeks. In vitro tests showed none of the nonpathogenic isolates suppressed Fusarium oxysporum f.sp. cubense (Foc), while slight suppression was observed with the two Trichoderma isolates. Results of the glasshouse evaluations revealed that two of the nonpathogenic F. oxysporum isolates, CAV 255 and CAV 241, reduced fusarium wilt incidence by 87·4 and 75·0%, respectively. The known biological control agent Fo47 did not suppress Foc significantly. Pseudomonas fluorescens strain WCS 417, known for its ability to suppress other fusarium wilt diseases (WCS 417), reduced disease incidence by 87·4%. These isolates should be further evaluated for potential application in the field, independently and in combination.
Sequence stratigraphy of a Late Devonian ramp‐situated reef system in the Western Canada Sedimentary Basin: dynamic responses to sea‐level change and regressive reef development
Authors: MACNEIL ALEX J. , JONES BRIAN 
Published: February 2006

AbstractThe Alexandra Formation, located in the Northwest Territories of Canada, is formed of a Late Devonian (Frasnian) reef system that developed on a gently sloping, epicontinental ramp in the Western Canada Sedimentary Basin. High‐resolution sequence stratigraphic analysis of its deposits delineates two reef complexes that are separated by a Type I sequence boundary. The second reef complex developed on the outer ramp, basinward of the first, after sea‐level fell ≈17 m. Stratigraphic complexity of the second reef complex was a result of its initiation during forced regression, and its development through an entire cycle of sea‐level rise followed by sea‐level fall. Its highstand systems tract was not characterized by high rates of carbonate production or sediment shedding. Rather, these features took place as sea‐level fell, after its highstand systems tract. The sequence stratigraphic framework of this regressive reef system highlights a number of depositional parameters that differ from high‐relief, shelf‐situated reef systems with steep, narrow margins. These have implications for understanding the controls on the development of ramp‐situated reef systems, and the nature of reef systems with gently sloping profiles. This study demonstrates that the development of stromatoporoid reef systems may be far more complex than generally realized, and that high‐resolution sequence stratigraphy may provide the tools for better understanding of complex, often enigmatic, aspects of these systems.
Sedimentology and stratigraphy of a transgressive, muddy gravel beach: Waterside Beach, Bay of Fundy, Canada
Authors: DASHTGARD SHAHIN E. , GINGRAS MURRAY K. , BUTLER KARL E. 
Published: February 2006

AbstractSediments exposed at low tide on the transgressive, hypertidal (>6 m tidal range) Waterside Beach, New Brunswick, Canada permit the scrutiny of sedimentary structures and textures that develop at water depths equivalent to the upper and lower shoreface. Waterside Beach sediments are grouped into eleven sedimentologically distinct deposits that represent three depositional environments: (1) sandy foreshore and shoreface; (2) tidal‐creek braid‐plain and delta; and, (3) wave‐formed gravel and sand bars, and associated deposits. The sandy foreshore and shoreface depositional environment encompasses the backshore; moderately dipping beachface; and a shallowly seaward‐dipping terrace of sandy middle and lower intertidal, and muddy sub‐tidal sediments. Intertidal sediments reworked and deposited by tidal creeks comprise the tidal‐creek braid plain and delta. Wave‐formed sand and gravel bars and associated deposits include: sediment sourced from low‐amplitude, unstable sand bars; gravel deposited from large (up to 5·5 m high, 800 m long), landward‐migrating gravel bars; and zones of mud deposition developed on the landward side of the gravel bars. The relationship between the gravel bars and mud deposits, and between mud‐laden sea water and beach gravels provides mechanisms for the deposition of mud beds, and muddy clast‐ and matrix‐supported conglomerates in ancient conglomeratic successions. Idealized sections are presented as analogues for ancient conglomerates deposited in transgressive systems. Where tidal creeks do not influence sedimentation on the beach, the preserved sequence consists of a gravel lag overlain by increasingly finer‐grained shoreface sediments. Conversely, where tidal creeks debouch onto the beach, erosion of the underlying salt marsh results in deposition of a thicker, more complex beach succession. The thickness of this package is controlled by tidal range, sedimentation rate, and rate of transgression. The tidal‐creek influenced succession comprises repeated sequences of: a thin mud bed overlain by muddy conglomerate, sandy conglomerate, a coarse lag, and capped by trough cross‐bedded sand and gravel.
Long‐term study of Japanese encephalitis virus infection in Anopheles subpictus in Cuddalore district, Tamil Nadu, South India
Authors: Thenmozhi V. , Rajendran R. , Ayanar K. , Manavalan R. , Tyagi B. K. 
Published: February 2006

SummaryObjective  To investigate the role of Anopheles subpictus Grassi as a vector of Japanese encephalitis virus (JEV) transmission in Cuddalore, an area of Tamil Nadu endemic for the disease.Method  We collected 98 pools (4900 specimens) of wild adult male An. subpictus mosquitoes outdoors during dusk hours and screened them for JEV antigen by antigen‐capture Enzyme Linked Immunosorbent Assay. Additionally, over a period of 1 year, we tested 166 pools (8300 specimens) of wild adult female An. subpictus mosquitoes collected indoors for JEV.Results  Four pools of male An. subpictus tested positive. This indicates possible natural transovarial transmission of the virus through An. subpictus. Nineteen female pools were positive with a minimum infection rate of 2.3. From January through March the maximum infection rate was highest: 5.0 compared with 1.7 between April and September and 2.1 from October to December, although the difference was not statistically significant. From the 19 positive female pools, four isolates were confirmed as JEV by insect bioassay.Conclusion  The role of An. subpictus as a secondary vector in JEV transmission in Cuddalore, Tamil Nadu lends support to the hypothesis of periodic epidemics in the region.
Cutaneous phaeohyphomycosis caused by an Itraconazole and Amphoterecin B resistant strain ofVeronaeae botryosa
Authors: Chen Yu‐Ting , Lin Hao‐Chiung , Huang Chieh‐Chen , Lo Yuan‐Hsin 
Published: February 2006

Background Although the dematiaceous fungusVeronaea botryosais rarely encountered clinically, it can be pathogenic.Methods A patient with a history of diabetes mellitus, coronary artery disease, and Cushing's syndrome had recurrent multifocal, crusted, brownish‐red noduloplaques on the right forearm, left upper limb, and right knee. A skin biopsy was obtained for histopathology and fungal cultures.Results The histopathology showed brownish hyphae and yeast‐like cells scattered in granulomatous infiltrates. Slide cultures revealed erect and straight conidiophores with two‐celled cylindrical conidia, which have round tops and truncated bases. The fungus was identified asVeronaea botryosa. The disease slowly progressed despite a 6‐month itraconazole regimen (200 mg daily). Subsequent use of Amphoterecin B produced only mild clinical improvements. Susceptibility tests showed resistance to both agents.Conclusions Cutaneous phaeohyphomycosis caused byV. botryosais extremely rare. Antifungal susceptibility tests are important for choosing the appropriate drug and predicting the clinical outcome.
Histoid leprosy – unusual presentation
Authors: Nair S. Pradeep , Moorthy K. Prasanna , Suprakasan Sukumaran , Jayapalan Sabeena , Mini Gomathy 
Published: February 2006

A 39‐year‐old man presented with a chronic nonhealing toe ulcer and multiple skin‐colored papules on the back, arms, and knees. From an initial small erosion, the toe lesion ulcerated over a 1.5‐year period, while the papules progressed over a 6‐month period, first appearing on the back and then spreading to the arms and knees. The past medical and family history were noncontributory. Pertinent findings included the aforementioned well‐defined, asymmetric, shiny papules (Fig. 1). There were multiple, discrete, erythematous, pedunculated, tumor‐like masses of various sizes over the right thigh (Fig. 2) and a well‐defined 4 cm × 3 cm ulcer on the second toe of the left foot, the floor of which was covered by necrotic slough.Skin‐colored papules of histoid leprosy on the backimagePedunculated tumor‐like masses on the left thighimageThere was distal loss of sensation to temperature, touch, and pain. The greater auricular, ulnar, radial cutaneous and common peroneal nerves were thickened bilaterally, but nontender. A clinical diagnosis of histoid leprosy was made. The differential diagnosis for the tumor‐like thigh masses included dermatofibroma, neurofibroma, and Kaposi's sarcoma.The hemogram, liver/renal function tests, chest X‐ray, and abdominal ultrasound were normal. Human immunodeficiency virus enzyme‐linked immunosorbent assay (HIV ELISA) was negative. The ear lobe smear (ELS) for acid‐fast bacilli showed a bacterial index (BI) of 6+[> 1000 organisms/oil immersion field (oif)] and a morphological index (MI) of 50%. The skin‐colored papules on the back and the pedunculated masses showed a BI of 5+ (100–1000 organisms/oif) and an MI of 50%. The normal skin showed a BI of 4+ (10–100 organisms/oif) and an MI of 5%. Biopsy of the papules and pedunculated tumors showed a well‐circumscribed area of the dermis packed with many acid‐fast organisms and foamy macrophages, consistent with histoid leprosy (Fig. 3). Fite–Faraco stain demonstrated cells packed with lepra bacilli.Skin biopsy showing foamy macrophages packed with many acid‐fast organisms (Fite stain; ×400)imageA final diagnosis of lepromatous leprosy, histoid variant, was made. Dapsone, clofazimine, rifampicin, and, later, ofloxacin were started.
Naproxen‐induced lichen planus: report of 55 cases
Authors: Güneš Ali Tahsin , Fetil Emel , İlknur Turna , Birgin Bahar , Özkan Şebnem 
Published: February 2006

AbstractBackground  Clinical and histopathological differential diagnosis is usually impossible in drug‐induced lichen planus (LP) and idiopathic LP. Naproxen is a nonsteroidal anti‐inflammatory drug, which is widely used for its analgesic, antipyretic and anti‐inflammatory effects. To the best of our knowledge, two case reports on naproxen‐induced LP have been reported.Methods  Fifty‐five patients with LP, and a history of naproxen intake before their eruption, were investigated.Results  Twenty‐five patients (45.5%) had a history of naproxen intake prior to their eruption without any other medication. Twelve patients (21.8%) had a history of simultaneous use of naproxen with other drugs that were reported as inducers of LP. Eighteen patients (32.7%) had given a history of using naproxen together with drugs that had not been previously reported as inducers of LP. Moreover, in 42 patients, eruptive‐type LP development after naproxen intake, is an interesting observation. New lesions were not observed after the cessation of naproxen intake in any of the patients.Conclusion  Naproxen might be accepted as an important inducer for LP, especially for the eruptive form.
Current modalities and new advances in the treatment of basal cell carcinoma
Authors: Ceilley Roger I. , Del Rosso James Q. 
Published: February 2006

AbstractBasal cell carcinoma (BCC) is one of the most common cancers. Surgical extirpation is currently the standard of care for BCC, which is associated with several advantages and disadvantages. Procedures such as surgical excision used to treat superficial BCC (sBCC) and nodular BCC (nBCC) may have high 5‐year recurrence rates if tumors are not completely excised. Curettage with electrodesiccation is a common method for treating primary BCC. However, multiple cycles are recommended and the procedure can have unsatisfactory cosmetic results (e.g. scarring and hypopigmentation). Mohs micrographic surgery has a low rate of disease recurrence but is a specialized procedure usually limited to specific indications (e.g. high‐risk tumors). Cryosurgery and photodynamic therapy require multiple cycles and are associated with variable cosmetic outcomes and recurrence rates. As with any procedure, potential risks and patient quality‐of‐life issues need to be considered. In addition, substantial patient and healthcare provider inconvenience limit the practical utility of some modalities. Pharmacologic interventions provide another treatment option as adjunctive or monotherapy. Investigations of imiquimod, a novel immune response modifier, have indicated that this topical, noninvasive agent is safe and well tolerated and may be efficacious in the treatment of BCC. This review will highlight the role of standard treatment modalities and introduce new advances in the treatment of BCC.