bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biological conversion assay using Clostridium phytofermentans to estimate plant feedstock quality
Authors: Lee Scott J , Warnick Thomas A , Pattathil Sivakumar , Alvelo-Maurosa Jesús G , Serapiglia Michelle J , McCormick Heather , Brown Virginia , Young Naomi F , Schnell Danny J , Smart Lawrence B , Hahn Michael G , Pedersen Jeffrey F , Leschine Susan B , Hazen Samuel P 
Published: February 2012

Abstract

Background
There is currently considerable interest in developing renewable sources of energy. One strategy is the biological conversion of plant biomass to liquid transportation fuel. Several technical hurdles impinge upon the economic feasibility of this strategy, including the development of energy crops amenable to facile deconstruction. Reliable assays to characterize feedstock quality are needed to measure the effects of pre-treatment and processing and of the plant and microbial genetic diversity that influence bioconversion efficiency.

Results
We used the anaerobic bacterium Clostridium phytofermentans to develop a robust assay for biomass digestibility and conversion to biofuels. The assay utilizes the ability of the microbe to convert biomass directly into ethanol with little or no pre-treatment. Plant samples were added to an anaerobic minimal medium and inoculated with C. phytofermentans, incubated for 3 days, after which the culture supernatant was analyzed for ethanol concentration. The assay detected significant differences in the supernatant ethanol from wild-type sorghum compared with brown midrib sorghum mutants previously shown to be highly digestible. Compositional analysis of the biomass before and after inoculation suggested that differences in xylan metabolism were partly responsible for the differences in ethanol yields. Additionally, we characterized the natural genetic variation for conversion efficiency in Brachypodium distachyon and shrub willow (Salix spp.).

Conclusion
Our results agree with those from previous studies of lignin mutants using enzymatic saccharification-based approaches. However, the use of C. phytofermentans takes into consideration specific organismal interactions, which will be crucial for simultaneous saccharification fermentation or consolidated bioprocessing. The ability to detect such phenotypic variation facilitates the genetic analysis of mechanisms underlying plant feedstock quality.
PinX1 regulation of telomerase activity and apoptosis in nasopharyngeal carcinoma cells
Authors: Lai Xiao-Fen , Shen Cong-Xiang , Wen Zhong , Qian Yu-Hong , Yu Chao-Sheng , Wang Jun-Qi , Zhong Ping-Neng , Wang Hai-Li 
Published: February 2012

Abstract

Background
Human interacting protein X1 (PinX1) has been identified as a critical telomerase inhibitor and proposed to be a putative tumor suppressor gene. Loss of PinX1 has been found in a large variety of malignancies, however, its function in inhibiting telomerase activity of tumor cells is not well documented. Here we show that PinX1 is essential for down-regulation telomerase activity of nasopharyngeal carcinoma.

Methods
Expression vectors of human PinX1 (pEGFP-C3-PinX1) and its small interfering RNA (PinX1-FAM-siRNA) were constructed and transfected into NPC. Their effects on mRNA of telomerase catalytic subunit (hTERT), telomerase activity, cell proliferation, cell migration, wound healing, cell cycles and apoptosis were examined using semi-quantitative RT-PCR, stretch PCR, MTT assay, Transwell, scratch assay and flow cytometry, respectively.

Results
Transfection of pEGFP-C3-PinX1 and PinX1-FAM-siRNA increased and reduced PinX1 mRNA by 1.6-fold and 70%, respectively. Over-expression of PinX1 decreased hTERT mRNA by 21%, reduced telomerase activity, inhibited cell growth, migration and wound healing ability, arrested cells in G0/G1 phase, and increased apoptotic index. In contrast, down-regulation of PinX1 did not alter the above characteristics.

Conclusions
PinX1 may play important roles in NPC proliferation, migration and apoptosis and has application potential in tumor-targeted gene therapy.
The clinical use of biomarkers as prognostic factors in Ewing sarcoma
Authors: van Maldegem Annmeik M , Hogendoorn Pancras CW , Hassan Andrew B 
Published: February 2012

Abstract
Ewing Sarcoma is the second most common primary bone sarcoma with 900 new diagnoses per year in Europe (EU27). It has a poor survival rate in the face of metastatic disease, with no more than 10% survival of the 35% who develop recurrence. Despite the remaining majority having localised disease, approximately 30% still relapse and die despite salvage therapies. Prognostic factors may identify patients at higher risk that might require differential therapeutic interventions. Aside from phenotypic features, quantitative biomarkers based on biological measurements may help identify tumours that are more aggressive. We audited the research which has been done to identify prognostic biomarkers for Ewing sarcoma in the past 15 years. We identified 86 articles were identified using defined search criteria. A total of 11,625 patients were reported, although this number reflects reanalysis of several cohorts. For phenotypic markers, independent reports suggest that tumour size > 8 cm and the presence of metastasis appeared strong predictors of negative outcome. Good histological response (necrosis > 90%) after treatment appeared a significant predictor for a positive outcome. However, data proposing biological biomarkers for practical clinical use remain un-validated with only one secondary report published. Our recommendation is that we can stratify patients according to their stage and using the phenotypic features of metastases, tumour size and histological response. For biological biomarkers, we suggest a number of validating studies including markers for 9p21 locus, heat shock proteins, telomerase related markers, interleukins, tumour necrosis factors, VEGF pathway, lymphocyte count, and a number of other markers including Ki-67.
Histone deacetylase inhibitors enhance expression of NKG2D ligands in Ewing sarcoma and sensitize for natural killer cell-mediated cytolysis
Authors: Berghuis Dagmar , Schilham Marco W , Vos Hanneke I , Santos Susy J , Kloess Stephan , Buddingh' Emilie P , Egeler R Maarten , Hogendoorn Pancras CW , Lankester Arjan C 
Published: February 2012

Abstract

Background
Ewing sarcoma patients have a poor prognosis despite multimodal therapy. Integration of combination immunotherapeutic strategies into first-/second-line regimens represents promising treatment options, particularly for patients with intrinsic or acquired resistance to conventional therapies. We evaluated the susceptibility of Ewing sarcoma to natural killer cell-based combination immunotherapy, by assessing the capacity of histone deacetylase inhibitors to improve immune recognition and sensitize for natural killer cell cytotoxicity.

Methods
Using flow cytometry, ELISA and immunohistochemistry, expression of natural killer cell receptor ligands was assessed in chemotherapy-sensitive/-resistant Ewing sarcoma cell lines, plasma and tumours. Natural killer cell cytotoxicity was evaluated in Chromium release assays. Using ATM/ATR inhibitor caffeine, the contribution of the DNA damage response pathway to histone deacetylase inhibitor-induced ligand expression was assessed.

Results
Despite comparable expression of natural killer cell receptor ligands, chemotherapy-resistant Ewing sarcoma exhibited reduced susceptibility to resting natural killer cells. Interleukin-15-activation of natural killer cells overcame this reduced sensitivity. Histone deacetylase inhibitor-pretreatment induced NKG2D-ligand expression in an ATM/ATR-dependent manner and sensitized for NKG2D-dependent cytotoxicity (2/4 cell lines). NKG2D-ligands were expressed in vivo, regardless of chemotherapy-response and disease stage. Soluble NKG2D-ligand plasma concentrations did not differ between patients and controls.

Conclusion
Our data provide a rationale for combination immunotherapy involving immune effector and target cell manipulation in first-/second-line treatment regimens for Ewing sarcoma.
Clustering of HIV-1 Subtypes Based on gp120 V3 Loop electrostatic properties
Authors: López de Victoria Aliana , Kieslich Chris A , Rizos Apostolos K , Krambovitis Elias , Morikis Dimitrios 
Published: February 2012

AbstractBackgroundThe V3 loop of the glycoprotein gp120 of HIV-1 plays an important role in viral entry into cells by utilizing as coreceptor CCR5 or CXCR4, and is implicated in the phenotypic tropisms of HIV viruses. It has been hypothesized that the interaction between the V3 loop and CCR5 or CXCR4 is mediated by electrostatics. We have performed hierarchical clustering analysis of the spatial distributions of electrostatic potentials and charges of V3 loop structures containing consensus sequences of HIV-1 subtypes.ResultsAlthough the majority of consensus sequences have a net charge of +3, the spatial distribution of their electrostatic potentials and charges may be a discriminating factor for binding and infectivity. This is demonstrated by the formation of several small subclusters, within major clusters, which indicates common origin but distinct spatial details of electrostatic properties. Some of this information may be present, in a coarse manner, in clustering of sequences, but the spatial details are largely lost. We show the effect of ionic strength on clustering of electrostatic potentials, information that is not present in clustering of charges or sequences. We also make correlations between clustering of electrostatic potentials and net charge, coreceptor selectivity, global prevalence, and geographic distribution. Finally, we interpret coreceptor selectivity based on the N6X7T8|S8X9sequence glycosylation motif, the specific positive charge location according to the 11/24/25 rule, and the overall charge and electrostatic potential distribution.ConclusionsWe propose that in addition to the sequence and the net charge of the V3 loop of each subtype, the spatial distributions of electrostatic potentials and charges may also be important factors for receptor recognition and binding and subsequent viral entry into cells. This implies that the overall electrostatic potential is responsible for long-range recognition of the V3 loop with coreceptors CCR5/CXCR4, whereas the charge distribution contributes to the specific short-range interactions responsible for the formation of the bound complex. We also propose a scheme for coreceptor selectivity based on the sequence glycosylation motif, the 11/24/25 rule, and net charge.
Advances in on-sea-ice seismic reflection methods using an air gun: McMurdo Sound, Antarctica
Authors: Sunwall David A. , Speece Marvin A. , Pekar Stephen F. 
Published: February 2012

During the austral spring of 2008, 48 km of multichannel seismic reflection data were collected on a sea-ice platform east of New Harbor, Southern McMurdo Sound, Antarctica. These seismic data were collected to support the Antarctic Geological Drilling Program whose goal is to recover sedimentary rock cores from the continental margin of Antarctica and to better understand the climatic, cryospheric, and tectonic history of Antarctica. A Generator-Injector air gun, deployed through holes drilled in the sea ice, was used for a seismic source, and reflected energy was recorded on a snow streamer consisting of 60 gimbaled geophones. The Offshore New Harbor seismic system has increased the rate of data acquisition by 53% compared to previous Antarctic air-gun/snow-streamer seismic systems. In addition to conventional on-sea-ice seismic data processing, new processing steps were used to correct problems associated with the use of a Generator-Injector air gun in a sea-ice environment. Source timing errors, caused by miscommunications between the Generator-Injector air gun and air-gun controller, were corrected. Newly discovered bubble-plume static errors and bubble-plume wavelet distortions degraded seismic data quality and are attributed to bubble plumes created by the Generator-Injector air-gun blast. Our investigation shows that these bubble plumes were preserved for at least 40 hours beneath the sea ice and created isolated low-velocity zones. Using finite-element methods, we reproduced static errors and wavelet distortions by incorporating the effects of bubble plumes into the finite-element model. The results of finite-element modeling confirmed our hypothesis that bubble-plume static errors and bubble-plume wavelet distortions were caused by near-surface low-velocity features. Therefore, we incorporated new processing steps which remove bubble-plume effects and improve the quality of final seismic sections.
Potassium Channel Mutant KCNJ5 T158A Expression in HAC-15 Cells Increases Aldosterone Synthesis
Authors: Oki Kenji , Plonczynski Maria W. , Luis Lam Milay , Gomez-Sanchez Elise P. , Gomez-Sanchez Celso E. 
Published: February 2012

Primary aldosteronism is the most common cause of secondary hypertension, most frequently due to an aldosterone-producing adenoma or idiopathic hyperaldosteronism. Somatic mutations of the potassium channel KCNJ5 in the region of the selectivity filter have been found in a significant number of aldosterone-producing adenomas. There are also familial forms of primary aldosteronism, one of which, familial hyperaldosteronism type 3 which to date has been found in one family who presented with a severe abnormality in aldosterone and 18-oxocortisol production and hypertrophy and hyperplasia of the transitional zone of the adrenal cortex. In familial hyperaldosteronism type 3, there is a genomic mutation causing a T158A change of amino acids within the selectivity filter region of the KCNJ5 gene.
We are reporting our studies demonstrating that lentiviral-mediated expression of a gene carrying the T158A mutation of the KCNJ5 in the HAC15 adrenal cortical carcinoma cell line causes a 5.3-fold increase in aldosterone secretion in unstimulated HAC15-KCNJ5 cells and that forskolin-stimulated aldosterone secretion was greater than that of angiotensin II. Expression of the mutated KCNJ5 gene decreases plasma membrane polarization, allowing sodium and calcium influx into the cells. The calcium channel antagonist nifedipine and the calmodulin inhibitor W-7 variably inhibited the effect. Overexpression of the mutated KCNJ5 channel resulted in a modest decrease in HAC15 cell proliferation.
These studies demonstrate that the T158A mutation of the KCNJ5 gene produces a marked stimulation in aldosterone biosynthesis that is dependent on membrane depolarization and sodium and calcium influx into the HAC15 adrenal cortical carcinoma cells.
Stable isotope tracer reveals that viviparous snakes transport amino acids to offspring during gestation
Authors: Van Dyke James U. , Beaupre Steven J. 
Published: February 2012

SUMMARY
Viviparity and placentation have evolved from oviparity over 100 times in squamate reptiles (lizards and snakes). The independent origins of placentation have resulted in a variety of placental morphologies in different taxa, ranging from simple apposition of fetal and maternal tissues to endotheliochorial implantation that is homoplasious with mammalian placentation. Because the eggs of oviparous squamates transport gases and water from the environment and calcium from the eggshell, the placentae of viviparous squamates are thought to have initially evolved to accomplish these functions from within the maternal oviduct. Species with complex placentae have also been shown to rely substantially, or even primarily, on placental transport of organic nutrients for embryonic nutrition. However, it is unclear whether species with only simple placentae are also capable of transporting organic nutrients to offspring. Among viviparous squamates, all of the snakes that have been studied thus far have been shown to have simple placentae. However, most studies of snake placentation are limited to a single lineage, the North American Natricinae. We tested the abilities of four species of viviparous snakes – Agkistrodon contortrix (Viperidae), Boa constrictor (Boidae), Nerodia sipedon (Colubridae: Natricinae) and Thamnophis sirtalis (Colubridae: Natricinae) – to transport diet-derived amino acids to offspring during gestation. We fed [15N]leucine to pregnant snakes, and compared offspring 15N content with that of unlabeled controls. Labeled females allocated significantly more 15N to offspring than did controls, but 15N allocation did not differ among species. Our results indicate that viviparous snakes are capable of transporting diet-derived amino acids to their offspring during gestation, possibly via placentation.
In the face of hypoxia: myoglobin increases in response to hypoxic conditions and lipid supplementation in cultured Weddell seal skeletal muscle cells
Authors: De Miranda Michael A. , Schlater Amber E. , Green Todd L. , Kanatous Shane B. 
Published: February 2012

SUMMARY
A key cellular adaptation to diving in Weddell seals is enhanced myoglobin concentrations in their skeletal muscles, which serve to store oxygen to sustain a lipid-based aerobic metabolism. The aim of this study was to determine whether seal muscle cells are inherently adapted to possess the unique skeletal muscle adaptations to diving seen in the whole animal. We hypothesized that the seal skeletal muscle cells would have enhanced concentrations of myoglobin de novo that would be greater than those from a C2C12 skeletal muscle cell line and reflect the concentrations of myoglobin observed in previous studies. In addition we hypothesized that the seal cells would respond to environmental hypoxia similarly to the C2C12 cells in that citrate synthase activity and myoglobin would remain the same or decrease under hypoxia and lactate dehydrogenase activity would increase under hypoxia as previously reported. We further hypothesized that β-hydroxyacyl CoA dehydrogenase activity would increase in response to the increasing amounts of lipid supplemented to the culture medium. Our results show that myoglobin significantly increases in response to environmental hypoxia and lipids in the Weddell seal cells, while appearing similar metabolically to the C2C12 cells. The results of this study suggest the regulation of myoglobin expression is fundamentally different in Weddell seal skeletal muscle cells when compared with a terrestrial mammalian cell line in that hypoxia and lipids initially prime the skeletal muscles for enhanced myoglobin expression. However, the cells need a secondary stimulus to further increase myoglobin to levels seen in the whole animal.
The accessory role of the diaphragmaticus muscle in lung ventilation in the estuarine crocodile Crocodylus porosus
Authors: Munns Suzanne L. , Owerkowicz Tomasz , Andrewartha Sarah J. , Frappell Peter B. 
Published: February 2012

SUMMARY
Crocodilians use a combination of three muscular mechanisms to effect lung ventilation: the intercostal muscles producing thoracic movement, the abdominal muscles producing pelvic rotation and gastralial translation, and the diaphragmaticus muscle producing visceral displacement. Earlier studies suggested that the diaphragmaticus is a primary muscle of inspiration in crocodilians, but direct measurements of the diaphragmatic contribution to lung ventilation and gas exchange have not been made to date. In this study, ventilation, metabolic rate and arterial blood gases were measured from juvenile estuarine crocodiles under three conditions: (i) while resting at 30°C and 20°C; (ii) while breathing hypercapnic gases; and (iii) during immediate recovery from treadmill exercise. The relative contribution of the diaphragmaticus was then determined by obtaining measurements before and after transection of the muscle. The diaphragmaticus was found to make only a limited contribution to lung ventilation while crocodiles were resting at 30°C and 20°C, and during increased respiratory drive induced by hypercapnic gas. However, the diaphragmaticus muscle was found to play a significant role in facilitating a higher rate of inspiratory airflow in response to exercise. Transection of the diaphragmaticus decreased the exercise-induced increase in the rate of inspiration (with no compensatory increases in the duration of inspiration), thus compromising the exercise-induced increases in tidal volume and minute ventilation. These results suggest that, in C. porosus, costal ventilation alone is able to support metabolic demands at rest, and the diaphragmaticus is largely an accessory muscle used at times of elevated metabolic demand.
Net superoxide levels: steeper increase with activity in cooler female and hotter male lizards
Authors: Ballen Cissy , Healey Mo , Wilson Mark , Tobler Michael , Wapstra Erik , Olsson Mats 
Published: February 2012

SUMMARY
Ectotherms increase their body temperature in response to ambient heat, thereby elevating their metabolic rate. An often inferred consequence of this is an overall upregulation of gene expression and energetic expenditure, and a concomitant increased production of reactive oxygen species (e.g. superoxide) and, perhaps, a shortened lifespan. However, recent work shows that this may be a superficial interpretation. For example, sometimes a reduced temperature may in fact trigger up-regulation of gene expression. We studied temperature and associated activity effects in male and female Australian painted dragon lizards (Ctenophorus pictus) by allowing the lizards to bask for 4 h versus 12 h, and scoring their associated activity (inactive versus active basking and foraging). As predicted, long-basking lizards (hereafter ‘hot’) showed heightened activity in both sexes, with a more pronounced effect in females. We then tested for sex-specific effects of basking treatment and activity levels on the increase in net levels of superoxide. In males, short-baskers (hereafter ‘cold’) had significantly more rapidly decreasing levels of superoxide per unit increasing activity than hot males. In females, however, superoxide levels increased faster with increasing activity in the cold than in the hot basking treatment, and females earlier in the ovarian cycle had lower superoxide levels than females closer to ovulation. In short, males and females differ in how their levels of reactive oxygen species change with temperature-triggered activity.