bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pre‐culturing human adipose tissue mesenchymal stem cells under hypoxia increases their adipogenic and osteogenic differentiation potentials
Authors: Valorani M. G. , Montelatici E. , Germani A. , Biddle A. , D'Alessandro D. , Strollo R. , Patrizi M. P. , Lazzari L. , Nye E. , Otto W. R. , Pozzilli P. , Alison M. R. 
Published: April 2012

AbstractObjectivesHypoxia is an important factor in many aspects of stem‐cell biology including their viability, proliferation, differentiation and migration. We evaluated whether low oxygen level (2%) affected human adipose tissue mesenchymal stem‐cell (hAT‐MSC) phenotype, population growth, viability, apoptosis, necrosis and their adipogenic and osteogenic differentiation potential.Materials and methodshAT‐MSCs from four human donors were cultured in growth medium under either normoxic or hypoxic conditions for 7 days and were then transferred to normoxic conditions to study their differentiation potential.ResultsHypoxia enhanced hAT‐MSC expansion and viability, whereas expression of mesenchymal markers such as CD90, CD73 and endothelial progenitor cell marker CD34, remained unchanged. We also found that pre‐culturing hAT‐MSCs under hypoxia resulted in their enhanced ability to differentiate into adipocytes and osteocytes.ConclusionsThis protocol could be useful for maximizing hAT‐MSC potential to differentiate in vitro into the adipogenic and osteogenic lineages, for use in plastic and reconstructive surgery, and in tissue engineering strategies.
Subthreshold desensitization of human basophils re‐capitulates the loss of Syk and FcεRI expression characterized by other methods of desensitization
Authors: MacGlashan D. 
Published: April 2012

AbstractBackgroundClinical desensitization of patients to drugs involves progressive exposure to escalating doses of drug over a period of 24 h. In prior studies, this method was re‐capitulated in vitro to also demonstrate loss of mast cell or basophil responsiveness. However, most signalling studies of human basophils have identified changes in signalling by using other methods of inducing cellular desensitization.ObjectiveThis study examined two well‐described endpoints of basophil desensitization, loss of syk or FcεRI expression, under conditions of subthreshold desensitization.MethodsThe loss of FcεRI and syk was examined in human basophils.ResultsIt was shown that both loss of syk and FcεRI/IgE occurred during an escalating series of stimulation (anti‐IgE Ab) and that expression loss occurred despite the presence of little histamine release. If basophils were first cultured for 3 days in 10 ng/mL IL‐3, the concentration‐dependence of histamine release shifted to 100‐fold lower concentrations of stimulus. However, loss of syk did not show any change in its EC50 while loss of FcεRI also shifted 100‐fold. From the perspective of early signal element activation, the marked shift in the EC50 for histamine release was not accompanied by similar shifts in the EC50s for several signalling elements. The EC50s for phospho‐Src, phospho‐SHIP1, phospho‐Syk, or phospho‐Cbl did not change while the EC50s for phospho‐Erk and the cytosolic calcium response did shift 100‐fold.ConclusionsThese studies show that under normal conditions, subthreshold desensitization leads to loss of two critical signalling molecules (FcεRI and syk) but under at least one condition, treatment with IL‐3, it is possible to markedly blunt the loss of syk, but not FcεRI, while executing a proper subthreshold titration. These data also suggest that IL‐3 modifies only the sensitivity of signalling elements that are downstream of syk activation.
GH levels and insulin sensitivity are differently associated with biomarkers of cardiovascular disease in active acromegaly
Authors: Boero L. , Manavela M. , Meroño T. , Maidana P. , Gómez Rosso L. , Brites F. 
Published: April 2012

SummaryContextAcromegaly is characterized by GH excess and insulin resistance. It is not known which of these disorders is responsible for the increased atherogenic risk in these patients.ObjectiveTo analyse the associations of GH and homoeostasis model assessment (HOMA) with biomarkers of cardiovascular disease and to compare the above‐mentioned variables between patients with active acromegaly and controls.Design and settingThis open cross‐sectional study was conducted at a University Hospital.PatientsTwenty‐two outpatients were compared with sex‐ and age‐matched control subjects.Main outcomesIncluded clinical features, hormonal status, markers of insulin resistance, lipoprotein profile and biomarkers of cardiovascular disease.ResultsPatients presented higher triglyceride (median [IQR]) (1·2[1·1–1·6] vs 0·9[0·6–1·1] mm, P < 0·05), low‐density lipoprotein‐cholesterol (LDL‐C) (mean ± SD) (3·5 ± 0·9 vs 3·0 ± 0·7mm, P < 0·05), apoB (0·98 ± 0·23 vs 0·77 ± 0·22 g/l, P < 0·05), free fatty acid (0·69 ± 0·2 vs 0·54 ± 0·2 mM, P < 0·05), oxidized‐LDL (120 ± 22 vs 85 ± 19 U/l, P < 0·05) and endothelin‐1 (0·90 ± 0·23 vs 0·72 ± 0·17 ng/l, P < 0·05) levels, increased cholesteryl ester transfer protein (CETP) activity (179 ± 27 vs 138 ± 30%/ml/h, P < 0·01) and lower C reactive protein (CRP) (0·25[0·1–0·9] vs 0·85[0·4–1·4] mg/l; P < 0·05) levels than control subjects. Vascular cell adhesion molecule (VCAM‐1) concentration was not different. By multiple linear regression analyses, HOMA explained the variability of triglycerides (25%), high‐density lipoprotein‐cholesterol (HDL‐C) (30%) and CETP activity (28%), while GH independently predicted LDL‐C (18%), oxidized‐LDL (40%) and endothelin‐1 levels (19%).ConclusionsIn patients with active acromegaly, GH excess contributes to the development of insulin resistance, and the interaction between both disturbances would be responsible for the appearance of atherogenic pro‐oxidative and pro‐inflammatory factors. Insulin resistance would be preferably associated with an atherogenic lipoprotein profile and to high CETP activity, while high GH levels would independently predict the increase in LDL‐C, ox‐LDL and endothelin‐1.
Climate oscillations and species interactions: large‐scale congruence but regional differences in the phylogeographic structures of an alpine plant and its monophagous insect
Authors: Borer Matthias , Arrigo Nils , Buerki Sven , Naisbit Russell E. , Alvarez Nadir 
Published: April 2012

AbstractAim  To predict the fate of alpine interactions involving specialized species, using a monophagous beetle and its host plant as a case study.Location  The Alps.Methods  We investigated genetic structuring of the herbivorous beetle Oreina gloriosa and its specific host‐plant Peucedanum ostruthium. We used genome fingerprinting (in the insect and the plant) and sequence data (in the insect) to compare the distribution of the main gene pools in the two associated species and to estimate divergence time in the insect, a proxy for the temporal origin of the interaction. We quantified the similarity in spatial genetic structures by performing a Procrustes analysis, a tool from shape theory. Finally, we simulated recolonization of an empty space analogous to the deglaciated Alps just after ice retreat by two lineages from two species showing unbalanced dependence, to examine how timing of the recolonization process, as well as dispersal capacities of associated species, could explain the observed pattern.Results  Contrasting with expectations based on their asymmetrical dependence, patterns in the beetle and plant were congruent at a large scale. Exceptions occurred at a regional scale in areas of admixture, matching known suture zones in Alpine plants. Simulations using a lattice‐based model suggested these empirical patterns arose during or soon after recolonization, long after the estimated origin of the interaction c. 0.5 million years ago.Main conclusions  Species‐specific interactions are scarce in alpine habitats because glacial cycles have limited the opportunities for co‐evolution. Their fate, however, remains uncertain under climate change. Here we show that whereas most dispersal routes are paralleled at a large scale, regional incongruence implies that the destinies of the species might differ under changing climate. This may be a consequence of the host dependence of the beetle, which locally limits the establishment of dispersing insects.
Evolutionary history of Scinax treefrogs on land‐bridge islands in south‐eastern Brazil
Authors: Bell Rayna C. , Brasileiro Cinthia A. , Haddad Célio F. B. , Zamudio Kelly R. 
Published: April 2012

AbstractAim  We investigated how Pleistocene refugia and recent (c. 12,000 years ago) sea level incursions shaped genetic differentiation in mainland and island populations of the Scinax perpusillus treefrog group.Location  Brazilian Atlantic Forest, São Paulo state, south‐eastern Brazil.Methods  Using mitochondrial and microsatellite loci, we examined population structure and genetic diversity in three species from the S. perpusillus group, sampled from three land‐bridge islands and five mainland populations, in order to understand the roles of Pleistocene forest fragmentation and sea level incursions on genetic differentiation. We calculated metrics of relatedness and genetic diversity to assess whether island populations exhibit signatures of genetic drift and isolation. Two of the three island populations in this study have previously been described as new species based on a combination of distinct morphological and behavioural characters, thus we used the molecular datasets to determine whether phenotypic change is consistent with genetic differentiation.Results  Our analyses recovered three distinct lineages or demes composed of northern mainland São Paulo populations, southern mainland São Paulo populations, and one divergent island population. The two remaining island populations clustered with samples from adjacent mainland populations. Estimates of allelic richness were significantly lower, and estimates of relatedness were significantly higher, in island populations relative to their mainland counterparts.Main conclusions  Fine‐scale genetic structure across mainland populations indicates the possible existence of local refugia within São Paulo state, underscoring the small geographic scale at which populations diverge in this species‐rich region of the Atlantic Coastal Forest. Variation in genetic signatures across the three islands indicates that the populations experienced different demographic processes after marine incursions fragmented the distribution of the S. perpusillus group. Genetic signatures of inbreeding and drift in some island populations indicate that small population sizes, coupled with strong ecological selection, may be important evolutionary forces driving speciation on land‐bridge islands.
Computerized detection and segmentation of mitochondria on electron microscope images
Authors: MUMCUOGLU E.U. , HASSANPOUR R. , TASEL S.F. , PERKINS G. , MARTONE M.E. , GURCAN M.N. 
Published: April 2012

SummaryMitochondrial function plays an important role in the regulation of cellular life and death, including disease states. Disturbance in mitochondrial function and distribution can be accompanied by significant morphological alterations. Electron microscopy tomography (EMT) is a powerful technique to study the 3D structure of mitochondria, but the automatic detection and segmentation of mitochondria in EMT volumes has been challenging due to the presence of subcellular structures and imaging artifacts. Therefore, the interpretation, measurement and analysis of mitochondrial distribution and features have been time consuming, and development of specialized software tools is very important for high‐throughput analyses needed to expedite the myriad studies on cellular events. Typically, mitochondrial EMT volumes are segmented manually using special software tools. Automatic contour extraction on large images with multiple mitochondria and many other subcellular structures is still an unaddressed problem. The purpose of this work is to develop computer algorithms to detect and segment both fully and partially seen mitochondria on electron microscopy images. The detection method relies on mitochondria's approximately elliptical shape and double membrane boundary. Initial detection results are first refined using active contours. Then, our seed point selection method automatically selects reliable seed points along the contour, and segmentation is finalized by automatically incorporating a live‐wire graph search algorithm between these seed points. In our evaluations on four images containing multiple mitochondria, 52 ellipses are detected among which 42 are true and 10 are false detections. After false ellipses are eliminated manually, 14 out of 15 fully seen mitochondria and 4 out of 7 partially seen mitochondria are successfully detected. When compared with the segmentation of a trained reader, 91% Dice similarity coefficient was achieved with an average 4.9 nm boundary error.
Triangulating the genetic basis of adaptation to multifarious selection
Authors: PFRENDER M. E. 
Published: April 2012

Understanding how natural populations adapt to their local environments is a major research theme for ecological genomics. This endeavour begins by sleuthing for shared genetic similarities among unrelated natural populations sharing adaptive traits to documented selective pressures. When the selective pressures have low dimensionality, and the genetic response is localized to a few genes of major effect, this detective work is relatively straightforward. However, in the real world, populations face a complex mixture of selective pressures and many adaptive responses are the result of changes in quantitative traits that have a polygenic genetic basis. This complex relationship between environment and adaptation presents a significant challenge. How can we begin to identify drivers of adaptation in natural settings? In this issue of Molecular Ecology, Orsini et al. (2012) take advantage of the biological attributes of the freshwater microcrustacean Daphnia (Fig. 1) to disentangle multidimensional selection’s signature on the genome of populations that have repeatedly evolved adaptive responses to isolated selective pressures including predation, parasitism and anthropogenic changes in land use. Orsini et al. (2012) leverage a powerful combination of spatially structured populations in a geographic mosaic of environmental stressors, the historical archive of past genotypes preserved in lake‐bottom sediments and selection experiments to identify sets of candidate genomic regions associated with adaptation in response to these three environmental stressors. This study provides a template for future investigation in ecological genomics, combining multiple experimental approaches with the genomic investigation of a well‐studied ecological model species. Adult Daphnia magna carrying a resting egg in the brood pouch. The water flea Daphnia is a renowned ecological model system and rapidly developing as an ecological and environmental genomics model species. Photo credit Joachim Mergeay.image
Mitogenome sequencing reveals shallow evolutionary histories and recent divergence time between morphologically and ecologically distinct European whitefish (Coregonus spp.)
Authors: JACOBSEN MAGNUS W. , HANSEN MICHAEL M. , ORLANDO LUDOVIC , BEKKEVOLD DORTE , BERNATCHEZ LOUIS , WILLERSLEV ESKE , GILBERT M. THOMAS P. 
Published: April 2012

AbstractThe advent of second‐generation sequencing has made it possible to quickly and economically generate whole mitochondrial genome (mitogenome) sequences. To date, mitogenome studies of nonmodel organisms have demonstrated increased power for resolving interspecies relationships. We explored an alternate use of such data to recover relationships and population history of closely related lineages with a shallow evolutionary history. Using a GS‐FLX platform, we sequenced 106 mitogenomes from the Coregonus lavaretus (Europe) and Coregonus clupeaformis (North America) species complexes to investigate the evolutionary history of the endangered Danish North Sea houting (NSH) and other closely related Danish and Baltic European lake whitefish (ELW). Two well‐supported clades were found within both ELW and NSH, probably reflecting historical introgression via Baltic migrants. Although ELW and NSH are not reciprocally monophyletic, they share no haplotypes, suggesting recent, but strong, reproductive isolation. The divergence time between NSH and the geographically closest ELW population was estimated using IMa, assuming isolation with migration and a new mutation rate estimate chosen to avoid time‐dependency effects. The estimate of c. 2700 bp was remarkably similar to results obtained using microsatellite markers. Within North American C. clupeaformis, the divergence time between the two lineages (Atlantic and Acadian) was estimated as between 20 000 and 60 000 bp. Under the assumption that NSH and ELW colonized Denmark following the last glacial maximum, Bayesian Serial SimCoal analysis showed consistency with a scenario of long‐term stability, resulting from a rapid initial sixfold population expansion. The findings illustrate the utility of mitogenome data for resolving recent intraspecific divergence events and provide evidence for recent reproductive isolation of the phenotypically divergent NSH.
Regulation of proline metabolism in mycobacteria and its role in carbon metabolism under hypoxia
Authors: Berney Michael , Weimar Marion R. , Heikal Adam , Cook Gregory M. 
Published: April 2012

SummaryGenes with a role in proline metabolism are strongly expressed when mycobacterial cells are exposed to nutrient starvation and hypoxia. Here we show that proline metabolism in mycobacteria is mediated by the monofunctional enzymes Δ1‐pyrroline‐5‐carboxylate dehydrogenase (PruA) and proline dehydrogenase (PruB). Proline metabolism was controlled by a unique membrane‐associated DNA‐binding protein PruC. Under hypoxia, addition of proline led to higher biomass production than in the absence of proline despite excess carbon and nitrogen. To identify the mechanism responsible for this enhanced growth, microarray analysis of wild‐type Mycobacterium smegmatis versus pruC mutant was performed. Expression of the DNA repair machinery and glyoxalases was increased in the pruC mutant. Glyoxalases are proposed to degrade methylglyoxal, a toxic metabolite produced by various bacteria due to an imbalance in intermediary metabolism, suggesting the pruC mutant was under methylglyoxal stress. Consistent with this notion, pruB and pruC mutants were hypersensitive to methylglyoxal. Δ1‐pyrroline‐5‐carboxylate is reported to react with methylglyoxal to form non‐toxic 2‐acetyl‐1‐pyrroline, thus providing a link between proline metabolism and methylglyoxal detoxification. In support of this mechanism, we show that proline metabolism protects mycobacterial cells from methylglyoxal toxicity and that functional proline dehydrogenase, but not Δ1‐pyrroline‐5‐carboxylate dehydrogenase, is essential for this protective effect.
Indoleamine 2,3‐dioxygenase Expression and Functional Activity in Dendritic Cells Exposed to Cholera Toxin
Authors: Slavica L. , Nurkkala‐Karlsson M. , Karlson T. , Ingelsten M. , Nyström J. , Eriksson K. 
Published: April 2012

AbstractIndoleamine 2,3‐dioxygenase (IDO), a tryptophan‐metabolizing enzyme expressed by dendritic cells (DC), has the potential to inhibit T cell responses and to promote tolerance. In contrast, cholera toxin (CT), the enterotoxin produced by Vibrio cholerae, promotes T cell responses, partly through its ability to induce DC maturation and promote antigen presentation. We hypothesized that the adjuvant activity of CT is associated with a lack of induction of IDO in DC. To test this hypothesis, monocyte‐derived DC were pulsed with CT, and the IDO mRNA expression, IDO functional activity and cytokine production were measured as well as the ability of DC to induce T cell responses in vitro. Cholera toxin exposure induced enhanced levels of IDO mRNA in DC but no functional IDO protein activity. Cholera toxin pulsing however primed DC for CD40L‐induced IDO protein activity. CD40L stimulation of CT‐pulsed DC induced a modest IL‐12p40 production, but not IL‐12p70 or IL‐23 secretion. Furthermore, CT‐pulsed DC induced strong allogeneic and autologous T cell responses in vitro, which were not affected by the IDO‐specific inhibitor 1‐methyl tryptophan. Our results show that CT per se does not induce the expression of functional IDO protein, although it primes DC for CD40L‐mediated IDO production and IL‐12p40 secretion. Furthermore, CT‐treated DC were equally powerful in their T cell stimulatory capacity as cytokine‐matured DC.
Steroid‐free living donor liver transplantation for HCV – a multicenter prospective cohort study in Japan
Authors: Marubashi Shigeru , Umeshita Koji , Asahara Toshimasa , Fujiwara Kenji , Haga Hironori , Hashimoto Takashi , Hatakeyama Katsuyoshi , Ichida Takafumi , Kanematsu Takashi , Kitajima Masaki , Kiyosawa Kendo , Makuuchi Masatoshi , Miyagawa Shinichi , Satomi Susumu , Soejima Yuji , Takada Yasutsugu , Tanaka Noriaki , Teraoka Satoshi , Monden Morito 
Published: April 2012

AbstractThis prospective, non‐randomized, multicenter cohort study analyzed the safety and efficacy of a steroid‐free immunosuppressive (IS) protocol for hepatitis C virus (HCV)‐positive living donor liver transplant (LDLT) recipients in Japan. Of 68 patients enrolled from 13 transplant centers, 56 fulfilled the inclusion/exclusion criteria; 27 were assigned the steroid‐free IS protocol (Fr group) and 29 the traditional steroid‐containing IS protocol (St group). Serum HCV RNA levels increased over time and were higher in the St group until postoperative day 90 (POD 14, p = 0.013). Preemptive anti‐HCV therapy was started in a higher percentage of recipients (59.3%) in the Fr group than in the St group (31.0%, p = 0.031), mainly due to early HCV recurrence. The incidence of HCV recurrence at one yr was lower in the Fr group (22.2%) than in the St group (41.4%; p = 0.066). The incidence of acute cellular rejection was similar between groups. New onset diabetes after transplant, cytomegalovirus infection, and renal dysfunction were significantly less frequent in the Fr group than in the St group (p = 0.022, p < 0.0001, p = 0.012, respectively). The steroid‐free IS protocol safely reduced postoperative morbidity and effectively suppressed both the HCV viral load in the early post‐transplant period and HCV recurrence in HCV‐positive LDLT recipients.