bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spawning site selection and redd gravel characteristics of sea trout Salmo trutta in the lowland streams of Lithuania
Authors: Nika Nerijus , Virbickas Tomas , Kontautas Antanas 
Published: January 2011

Abstract
To date, no characterization of spawning habitats on scientific basis was made for the eastern Baltic salmonid populations. The aim of the present study was to characterize spawning habitat preferences and redd gravel structure of sea trout in lowland streams of western Lithuania. The redd position at the habitat-unit scale, microhabitat hydrological characteristics and the redd gravel structure have been analyzed. The spawning site selection by sea trout was related to the in-stream characteristics, but not to the riparian features. Redds were positioned mainly in the transitional pool-riffle zones, associated with close proximity to potential cover for spawners. At the microhabitat scale, sites with relatively consistent hydrological parameters (mode of water depth 0.25–0.40 m, flow velocity 0.4–0.7 m s−1 and Froude number 0.2–0.4) were selected from a wide range of available sites. Egg incubation conditions, in terms of the redd gravel structure in the spring, were of intermediate quality, while varied widely within particular reaches. According to the results of the present study, it is apparent that sea trout have particular preferences for spawning sites, which should be considered in emerging river-restoration projects.
Blood levels of Polycyclic Aromatic Hydrocarbons in Women with Benign and Malignant Breast Lesions: A case-control study
Authors: Singh Vipul K , Anand M , Rawtani D , Singh Uday P , Patel DK , Mehrotra PK , Mathur N , Siddiqui MKJ 
Published: January 2011

Objective: As part of our program to investigate the possible role of environmental pollutants in the incidence of breast cancer in India, we conducted for the first time a hospital based case-control study where blood polycyclic aromatic hydrocarbons (PAHs) levels were determined in women suffering from benign and malignant breast lesions, and compared with those of disease free controls drawn from similar socioeconomic environment residing in and around New Delhi, India. Material & Methods: Anthracene, phenanthrene, fluoranthene, naphthalene, pyrene, benzo (a) pyrene, benzo (k) fluoranthene and dibenzo (a,h) anthracene were determined by HPLC-FD. Results: Level of total PAHs in control, benign and malignant groups (30 numbers in each) were 142.05 ± 50.84, 185.99 ± 61.97 and 200.74 ± 55.05 μg / L respectively. Mean levels of naphthalene, phenanthrene, pyrene and benzo (k) fluoranthene were higher in both malignant and benign groups than in control but the difference was not statistically significant. Of the total PAHs, 3–ringed compounds were found much higher (89%) in controls than in benign (52%) and malignant groups (54%). However, the percentage sum of 2, 4 and 5-ringed PAHs were much higher in malignant (46%) and benign (48%) groups when compared with those of controls (11%). Conclusion: Results of the present study indicate that higher levels of PAHs (especially non-carcinogenic), though statistically non-significant, were present in cases with benign and malignant breast lesions than in those of controls. Key Words: Polycyclic Aromatic Hydrocarbons; Breast cancer; Benign lesions; HPLC-FD DOI: 10.3126/ajms.v1i2.2924Asian Journal of Medical Sciences 1 (2010) 80-86
In vitro Propagation and Callus Formation of Bacopa monnieri (L.) Penn.
Authors: Showkat Patni , Zaidi Yaseer , Asghar Suhail , Jamaluddin Shamsuddin 
Published: January 2011

An important medicinal herb, namely Bacopa monnieri (L.) Penn. showed best results on MS with 1 mg/l IAA and 1 mg/l IBA for culture initiation, multiple shoot proliferation, bud breakage, shoot length, shoot numbers and cluster formation. For rooting the best result was obtained on MS solidified with 7 g/l of agar along with sugar 20 gm/l for root, shoot ratio and number of roots. The best hardening was achieved in a mixture of soil : soilrite (1 : 1) where the survival rate was 94%. Further, for callus formation the best result was obtained in the leaf explants on MS supplemented with 0.5 mg/l 2, 4-D. HPLC and HPTLC profile of regenerated shoots revealed a phytochemicals profile similar to that of the market samples and mother plants. The presence of bacoside was detected through HPTLC and HPLC. Key words: Bacopa monnieri, Micropropagation, Bacoside D.O.I. 10.3329/ptcb.v20i2.6890 Plant Tissue Cult. & Biotech. 20(2): 119-125, 2010 (December)
Somatic Embryogenesis and Plant Regeneration in Ephedra foliata (Boiss.); a non Coniferous Gymnosperm
Authors: Dhiman Manjul , Sharma Vandana , Moitra Sushma 
Published: January 2011

Embryos from mature seeds of Ephedra foliata were excised and used as explant after longitudinal splitting. Half embryos were cultured in vitro to assess their morphogenic potential. When 2 - 10 µM 2,4-D with 2 - 10 µM Kn was used in MS with 10% coconut milk callus, roots and somatic embryos were induced. Lower concentration of 2 and 5 µM 2,4-D with 2 to 15 µM Kn gave best responses in terms of percentage of cultures showing somatic embryos. greater degree of callusing was obtained in a combination of 8 - 10 µM 2,4-D with Kn, but frequency of somatic embryos was low. Substituting BAP for Kn in the medium containing 2,4-D showed almost the same response as that in 2,4-D and Kn. The percentage of cultures showing root formation was low as compared to Kn combinations. Somatic embryos developed, but with a lesser frequency. When different concentrations of NAA were added with Kn, only rooting and callusing occurred. On this medium, there was a total absence of somatic embryos. When somatic embryos were transferred to a hormone free medium, they grew within 10 - 15 days. The fully grown somatic embryos then germinated and developed into plantlets. Chromosomal count confirmed retention of ploidy level. Plantlets from somatic embryos were transferred to pots containing sterilized mixture of coarse sand and garden soil in equal proportions. They survived well and formed new nodes and internodes after nearly one month. Key words: Ephedra, Somatic embryogenesis, Micropropagation, Ephedrine D.O.I. 10.3329/ptcb.v20i2.6893 Plant Tissue Cult. & Biotech. 20(2): 133-143, 2010 (December)
Agrobacterium-mediated Genetic Transformation for Local Cultivars of Potato (Solanum tuberosum L.) Using Marker Genes
Authors: Borna Rita Sarah , Hoque M. I. , Sarker R. H. 
Published: January 2011

Genetic transformation using nodal and internodal segments from three economically important potato (Solanum tuberosum L.) varieties namely, Diamant, Cardinal and Granola was conducted using an Agrobacterium tumefaciens strain LBA4404 harbouring binary plasmid pBI12 containing the GUS and nptII genes. Node and internodal segments were used for direct regeneration as well as regeneration with the intervention of callus. best responses were obtained for direct regeneration of shoots when the explants were cultured on MS supplemented with 4.0 mg/l BAP +1.0 mg/l IAA, 1.5 mg/l BAP + 0.5 mg/l IAA and 5.0 mg/l BAP +1.0 mg/l IAA in Diamant, Cardinal and Granola, respectively. In Diamant spontaneous in vitro microtuberization was obtained from these proliferated shoots. Further culturing of these in vitro grown green microtubers regenerated a large number of shoots on MS containing 4.0 mg/l BAP +1.0 mg/l IAA. By combining the best treatments, this protocol yielded an average transformation rate of 87% of treared explants. Stable expression of GUS gene was visualized in the various parts of transformed shoots through histochemical assay. Genomic DNA was isolated from transformed shoots and stable integration of the GUS and nptII genes was confirmed by PCR analysis. Key words: Potato, in vitro regeneration, transformation D.O.I. 10.3329/ptcb.v20i2.6894 Plant Tissue Cult. & Biotech. 20(2): 145-155, 2010 (December)
Tuberous Roots an Ideal System for High Frequency In vitro Regeneration in Plumbago rosea L.
Authors: Jose Binoy , Satheeshkumar K. 
Published: January 2011

Tuberous root explants of Plumbago rosea L. cultured in MS containing 3.5 mg/l BAP showed high frequency of shoot bud regeneration (62.33 ± 0.66; 0.26 ± 0.07 cm) within eight weeks. Subculture of shoot clumps (22.17 ± 0.90 shoots; 0.26 ± 0.07 cm) from the initial clump exhibited extensive rate of shoot multiplication (123.4 ± 1.029 shoots, 0.22 ± 0.01 cm) per each clump and produced a total of 369 shoots in 3.5 mg/l BAP in six weeks. Within two weeks of culture in basal liquid medium, shoot elongation (6.16 ± 0.14 cm) occurred and after three weeks in MS solid medium supplemented with 0.1 mg/l IAA, rooting (14.7 ± 1.2) initiated on the shoots. Ninety six per cent of the rooted plants were established under the shade nethouse with regular watering. Key words: Plumbago rosea, tuberous root, multiple shoots, High frequency D.O.I. 10.3329/ptcb.v20i2.6915 Plant Tissue Cult. & Biotech. 20(2): 203-209, 2010 (December)
READS - A Resource for Plant Non-coding Regulatory Sequence Analysis
Authors: Shahid Saima , Elias Sabrina M. , Biswas Sudip , Seraj Zeba I. 
Published: January 2011

Identification and analysis of regulatory sequences that control gene expression can be greatly facilitated by database-assisted bioinformatic approaches. READS (Regulatory Element Analysis DatabaSe) has been created as a web-accessible freely available database of plant non-coding regulatory sequences. It currently contains more than 300 known and putative promoters of constitutive as well as stress inducible genes belonging to diverse plants. The database has been manually curated with promoters collected mainly from scientific publications, thereafter cross-referenced with other resources (NCBI database, PubMed, PubMed Central). A user-friendly interface has been provided to allow easy access and analysis of data using different query options. A blast utility has also been provided, allowing users to search against all entries in the database. For each promoter, certain features such as expression data, GC content, core elements etc., were provided to assist in characterization of the regulatory sequences. To our knowledge, READS is the first plant promoter database that allows retrieval of sequences based on expression pattern. Thus the database can be utilized as a useful resource for identification of important putative regulatory cis-elements in promoters by analysis of upstream regions of hundreds of co-regulated or co-expressed genes. Such knowledge can also be of use for identifying minimal or stress inducible promoters for effective transgene expression. We aim to provide the most up-to-date collection of promoters of well-characterized stress inducible and constitutively expressed genes from many plant species. Hence, this resource will be updated regularly to incorporate new sequences. READs is available at http://www.pbtlabdu.net/READS/. Key words: Promoter database, stress inducible, constitutive, gene expression, cis-element D.O.I. 10.3329/ptcb.v20i2.6916 Plant Tissue Cult. & Biotech. 20(2): 211-223, 2010 (December)
Frequency of HEV contamination in sewerage waters in Pakistan
Authors: Ahmad Tahir , Waheed Yasir , Tahir Sadia , Safi Sher Zaman , Fatima Kaneez , Afzal Muhammad Sohail , Farooqi Zia-ur-Rehman , Qadri Ishtiaq 
Published: January 2011

Introduction: Enteric viruses, including Hepatitis E virus (HEV), are able to persist under environmental conditions and may cause public health problems by contaminating natural and drinking water resources. Routine procedures for monitoring viruses in water samples have not been established for the water microbiology screening panel. Methodology: Eighty-six raw sewerage samples were collected from the different regions of Islamabad and Rawalpindi, the twin cities of Pakistan. Samples were concentrated for HEV, using a polyethylene glycol-based method followed by viral RNA extraction using a commercial kit-based method. Reverse transcription polymerase chain reaction (RT-PCR) with HEV specific primers was used for the detection of HEV. Results: The present investigation focused on 86 raw sewerage water samples taken from different locations of drainage outlets of Islamabad and Rawalpindi. After careful experimentation, 35 samples were found to be RT-PCR positive. Nineteen (44.7%) out of 47 samples from Rawalpindi city were HEV positive while 16 (41.02%) out of 39 samples from Islamabad were HEV positive. All positive samples were found in the highly congested areas. Conclusions: The high detection rate of HEV in this study shows that HEV circulates at a relatively high frequency in the sewerage waters in Pakistan. This study is the first report on detection of HEV from sewerage waste water from Pakistan and suggests that HEV might be a potent indicator of viral pollution in environmental specimens.
Plasmid-mediated quinolone resistance in expanded spectrum beta lactamase producing enterobacteriaceae in Morocco
Authors: Bouchakour Mohammed , Zerouali Khalid , Gros Claude Jean David Perrier , Amarouch Hamid , El Mdaghri Naima , Courvalin Patrice , Timinouni Mohammed 
Published: January 2011

Introduction: Although independently acquired, plasmid-mediated quinolone resistance appears to be linked with extended-spectrum or AmpC-type beta-lactamases. Since no data are available in African countries, the prevalence of qnr genes at the University Hospital Ibn Rochd, Casablanca, Morocco, was investigated. Methodology: Between October 2006 and March 2007, the following 39 randomly selected non-duplicate Enterobacteriaceae producing an extended-spectrum beta-lactamase (ESBL), representing 20% of ESBL strains with respect to species and ward origin, were collected: Escherichia coli (n = 16); Klebsiella spp (n = 14); Enterobacter cloacae (n = 8); Proteus mirabilis (n = 1). Antibiotic susceptibility testing was performed according to CLSI guidelines. ESBL detection was performed by the double disc diffusion test. A multiplex PCR was conducted to detect qnrA, qnrB and qnrS genes that were confirmed by sequencing of the PCR product. Results: The estimated overall prevalence of qnr reached 36% (n = 14; qnrA, 10.25%; qnrB, 23.07%; qnrS, 2.56%). Genes were identified in E. coli, Klebsiella and Enterobacter with a respective prevalence of 18.7%, 50% and 62.5%. The qnr genes were detected in nine wards and qnrA1, qnrB1-B2-B4 and qnrS1 variants were identified. Three genes were identified among nalidixic acid susceptible strains (n = 6); three of those were also susceptible to ciprofloxacin. Among nalidixic acid and ciprofloxacin resistant strains, all strains had qnrB. Conclusions: This study highlights the high prevalence of qnr genes among ESBL strains in the Ibn Rochd CHU, Casablanca. Moreover, qnr were present in quinolone-susceptible strains which could lead to in vivo selection of ciprofloxacin-resistant strains.
Fidelity of Bats to Forest Sites Revealed From Mist-Netting Recaptures
Authors: Perry Roger W. 
Published: January 2011

Abstract
Although site fidelity to permanent roost structures by bats is generally known, long-term fidelity to areas such as foraging or drinking sites is unknown. Furthermore, mist-net recaptures of bats over multiple years are rarely reported. Extensive mist-net surveys were conducted over the course of 8 y in the Ouachita National Forest of central Arkansas, United States to investigate long-term site fidelity and recapture rates of individually marked forest bats. Among eight species that were captured, five species were recaptured over spans ≥1 y, including eastern red bats Lasiurus borealis, Seminole bats L. seminolus, evening bats Nycticeius humeralis, tri-colored bats Lasiurus borealis, and northern long-eared bats Myotis septentrionalis. Some individuals were recaptured multiple times over multiple years, and the maximum span over which an individual was recaptured was 1 y for Seminole bats, 2 y for tri-colored bats, 3 y for evening bats, 4 y for eastern red bats, and 5 y for northern long-eared bats. These results indicate long-term site fidelity by multiple bat species to particular forest sites, primarily pools along small intermittent streams. Proximity to these sites should be considered when conducting management activities.
A Novel and Divergent Role of Granzyme A and B in Resistance to Helminth Infection
Authors: Hartmann Wiebke , Marsland Benjamin J. , Otto Benjamin , Urny Jens , Fleischer Bernhard , Korten Simone 
Published: January 2011

Abstract
Granzyme (gzm) A and B, proteases of NK cells and T killer cells, mediate cell death, but also cleave extracellular matrices, inactivate intracellular pathogens, and induce cytokines. Moreover, macrophages, Th2 cells, regulatory T cells, mast cells, and B cells can express gzms. We recently reported gzm induction in human filarial infection. In this study, we show that in rodent filarial infection with Litomosoides sigmodontis, worm loads were significantly reduced in gzmA×B and gzmB knockout mice during the whole course of infection, but enhanced only early in gzmA knockout compared with wild-type mice. GzmA/B deficiency was associated with a defense-promoting Th2 cytokine and Ab shift, enhanced early inflammatory gene expression, and a trend of reduced alternatively activated macrophage induction, whereas gzmA deficiency was linked with reduced inflammation and a trend toward increased alternatively activated macrophages. This suggests a novel and divergent role for gzms in helminth infection, with gzmA contributing to resistance and gzmB promoting susceptibility.
The Evolution and Regulation of the Mucosal Immune Complexity in the Basal Chordate Amphioxus
Authors: Huang Shengfeng , Wang Xin , Yan Qingyu , Guo Lei , Yuan Shaochun , Huang Guangrui , Huang Huiqing , Li Jun , Dong Meiling , Chen Shangwu , Xu Anlong 
Published: January 2011

Abstract
Both amphioxus and the sea urchin encode a complex innate immune gene repertoire in their genomes, but the composition and mechanisms of their innate immune systems, as well as the fundamental differences between two systems, remain largely unexplored. In this study, we dissect the mucosal immune complexity of amphioxus into different evolutionary-functional modes and regulatory patterns by integrating information from phylogenetic inferences, genome-wide digital expression profiles, time course expression dynamics, and functional analyses. With these rich data, we reconstruct several major immune subsystems in amphioxus and analyze their regulation during mucosal infection. These include the TNF/IL-1R network, TLR and NLR networks, complement system, apoptosis network, oxidative pathways, and other effector genes (e.g., peptidoglycan recognition proteins, Gram-negative binding proteins, and chitin-binding proteins). We show that beneath the superficial similarity to that of the sea urchin, the amphioxus innate system, despite preserving critical invertebrate components, is more similar to that of the vertebrates in terms of composition, expression regulation, and functional strategies. For example, major effectors in amphioxus gut mucous tissue are the well-developed complement and oxidative-burst systems, and the signaling network in amphioxus seems to emphasize signal transduction/modulation more than initiation. In conclusion, we suggest that the innate immune systems of amphioxus and the sea urchin are strategically different, possibly representing two successful cases among many expanded immune systems that arose at the age of the Cambrian explosion. We further suggest that the vertebrate innate immune system should be derived from one of these expanded systems, most likely from the same one that was shared by amphioxus.
Visualizing the Role of Cbl-b in Control of Islet-Reactive CD4 T Cells and Susceptibility to Type 1 Diabetes
Authors: Hoyne Gerard F. , Flening Eleanor , Yabas Mehmet , Teh Charis , Altin John A. , Randall Katrina , Thien Christine B. F. , Langdon Wallace Y. , Goodnow Christopher C. 
Published: January 2011

Abstract
The E3 ubiquitin ligase Cbl-b regulates T cell activation thresholds and has been associated with protecting against type 1 diabetes, but its in vivo role in the process of self-tolerance has not been examined at the level of potentially autoaggressive CD4+ T cells. In this study, we visualize the consequences of Cbl-b deficiency on self-tolerance to lysozyme Ag expressed in transgenic mice under control of the insulin promoter (insHEL). By tracing the fate of pancreatic islet-reactive CD4+ T cells in prediabetic 3A9-TCR × insHEL double-transgenic mice, we find that Cbl-b deficiency contrasts with AIRE or IL-2 deficiency, because it does not affect thymic negative selection of islet-reactive CD4+ cells or the numbers of islet-specific CD4+ or CD4+Foxp3+ T cells in the periphery, although it decreased differentiation of inducible regulatory T cells from TGF-β–treated 3A9-TCR cells in vitro. When removed from regulatory T cells and placed in culture, Cblb-deficient islet-reactive CD4+ cells reveal a capacity to proliferate to HEL Ag that is repressed in wild-type cells. This latent failure of T cell anergy is, nevertheless, controlled in vivo in prediabetic mice so that islet-reactive CD4+ cells in the spleen and the pancreatic lymph node of Cblb-deficient mice show no evidence of increased activation or proliferation in situ. Cblb deficiency subsequently precipitated diabetes in most TCR:insHEL animals by 15 wk of age. These results reveal a role for peripheral T cell anergy in organ-specific self-tolerance and illuminate the interplay between Cblb-dependent anergy and other mechanisms for preventing organ-specific autoimmunity.
The IL1RN Promoter rs4251961 Correlates with IL-1 Receptor Antagonist Concentrations in Human Infection and Is Differentially Regulated by GATA-1
Authors: Carrol Enitan D. , Payton Antony , Payne Deborah , Miyajima Fabio , Chaponda Mas , Mankhambo Limangeni A. , Banda Daniel L. , Molyneux Elizabeth M. , Cox Helen , Jacobson Greg , Carr Daniel F. , Molyneux Malcolm E. , Stewart James P. , Quinn John P. , Hart C. Anthony , Ollier William E. 
Published: January 2011

Abstract
IL-1R antagonist (IL-1Ra) is required for adequate host defense in invasive pneumococcal disease (IPD). The minor allele of an IL1RN gene (C/T) promoter polymorphism (rs4251961) has been shown to be associated with decreased IL-1Ra production in healthy adults. We genotyped 299 children with IPD, and examined 19 IL1RN haplotype-tagging single-nucleotide polymorphisms. Human embryonic kidney HEK293(T) cells were transfected with the promoter reporter plasmid pGL3p containing either allelic variant C (pGL3pCC) or T (pGL3pTT) with or without cotransfection with an expression construct overexpressing the globin transcription factor GATA-1. Plasma IL-1Ra concentrations were significantly higher in nonsurvivors compared with survivors (p &lt; 0.0005), and the C allele of rs4251961 was associated with a significant increase in plasma IL-1Ra concentrations (p = 0.01) during the acute illness of IPD. These findings were validated in a cohort of 276 treatment-naive HIV-infected adults, with borderline significance (p = 0.058). Functional analyses demonstrated that the activity of the promoter constructs containing the T allele increased ~6-fold as compared with basal activity, and that containing the C allele by ~9-fold (p &lt; 0.001) in the presence of GATA-1. Our findings suggest that the IL-1Ra single-nucleotide polymorphism rs4251961 plays a key role in the pathophysiology of IPD and in other human infections.