bluuebunny/crossref_metadata_2025_split huggingface dataset:
Manipulation of ruminal fermentation and methane production by supplementation of rain tree pod meal containing tannins and saponins in growing dairy steers
Authors: Anantasook N. , Wanapat M. , Cherdthong A. 
Published: January 2013

SummaryFour rumen‐fistulated dairy steers were used in a 2 × 2 factorial arrangement in a 4 × 4 Latin square design. The main factors were two roughage‐to‐concentrate ratios (R:C, 60:40 and 40:60) and two supplementation levels of rain tree pod meal (RPM) [0 or unsupplemented and 60 g/kg of total dry matter (DM) intake]. Chopped 30 g/kg of urea‐treated rice straw was used as a roughage source. All animals received dietary according to respective R:C ratios at 25 g/kg body weight. The RPM contained condensed tannins and crude saponins at 84 and 143 g/kg of DM respectively. It was found that total volatile fatty acids (VFAs) and propionate concentrations were increased (p < 0.01), while acetate concentration, acetate‐to‐propionate ratio, CH4 production and protozoal numbers were decreased (p < 0.01) when steers were supplemented with RPM and 600 g/kg of concentrate. Allantoin excretion was found different by both R:C ratio and supplementation of RPM, with the highest value at R:C of 40:60 with 60 g/kg RPM (123.6 mmol/day) (p < 0.05). Allantoin absorption and microbial crude protein were increased (p < 0.05) with an increasing concentrate ratio. Moreover, efficiency of microbial protein synthesis was increased (p < 0.05) by feeding a higher ratio of concentrate (R:C 40:60) and supplementation of RPM. Based on this study, it is suggested that supplementation of RPM was beneficial for dairy cows fed on high roughage ratio, which could improved rumen fermentation by reducing fermentation gas loss, thus improving VFA profiles and thus enhancing efficiency of microbial protein synthesis.
High‐altitude hypoxia and periodic breathing during sleep: gender‐related differences
Authors: Lombardi Carolina , Meriggi Paolo , Agostoni Piergiuseppe , Faini Andrea , Bilo Grzegorz , Revera Miriam , Caldara Gianluca , Di Rienzo Marco , Castiglioni Paolo , Maurizio Bussotti , Gregorini Francesca , Mancia Giuseppe , Parati Gianfranco ,   The Highcare Investigators
Published: January 2013

SUMMARYHigh‐altitude exposure is characterized by the appearance of periodic breathing during sleep. Only limited evidence is available, however, on the presence of gender‐related differences in this breathing pattern. In 37 healthy subjects, 23 male and 14 female, we performed nocturnal cardio‐respiratory monitoring in the following conditions: (1) sea level; (2) first/second night at an altitude of 3400 m; (3) first/second night at an altitude of 5400 m and after a 10 day sojourn at 5400 m. At sea level, a normal breathing pattern was observed in all subjects throughout the night. At 3400 m the apnea–hypopnea index was 40.3 ± 33.0 in males (central apneas 77.6%, central hypopneas 22.4%) and 2.4 ± 2.8 in females (central apneas 58.2%, central hypopneas 41.8%; P < 0.01). During the first recording at 5400 m, the apnea–hypopnea index was 87.5 ± 35.7 in males (central apneas 60.0%, central hypopneas 40.0%) and 41.1 ± 44.0 in females (central apneas 73.2%, central hypopneas 26.8%; P < 0.01), again with a higher frequency of central events in males as seen at lower altitude. Similar results were observed after 10 days. With increasing altitude, there was also a progressive reduction in respiratory cycle length during central apneas in males (26.9 ± 3.4 s at 3400 m and 22.6 ± 3.7 s at 5400 m). Females, who displayed a significant number of central apneas only at the highest reached altitude, were characterized by longer cycle length than males at similar altitude (30.1 ± 5.8 s at 5400 m). In conclusion, at high altitude, nocturnal periodic breathing affects males more than females. Females started to present a significant number of central sleep apneas only at the highest reached altitude. After 10 days at 5400 m gender differences in the apnea–hypopnea index similar to those observed after acute exposure were still observed, accompanied by differences in respiratory cycle length.
Sustained virologic response after therapy with the HCV protease inhibitor narlaprevir in combination with peginterferon and ribavirin is durable through long‐term follow‐up
Authors: Hotho D. M. , de Bruijne J. , Spaan M. , Treitel M. A. , Boonstra A. , de Knegt R. J. , Janssen H. L. A. , Reesink H. W. 
Published: January 2013

SummaryAchievement of a sustained virologic response (SVR) after peginterferon (PEG‐IFN) and ribavirin (RBV) treatment is considered to be a marker for the cure of chronic hepatitis C virus (HCV) infection. Long‐term follow‐up of patients with SVR after treatment with a direct acting antiviral has not yet been described. We used a randomized placebo‐controlled, double‐blind, two‐period phase 1b trial that was conducted in 40 HCV genotype 1 (treatment‐naïve and treatment‐experienced)‐infected patients. Nineteen patients achieved SVR after treatment with the HCV protease inhibitor narlaprevir followed by PEG‐IFN/RBV. In these patients, HCV‐RNA tests were scheduled at 3, 6, 12 and 24 months after end of treatment. Patients were followed for a median of 27 months (range 15–32) after end of treatment with a median number of follow‐up visits of 4 (range 3–8). All patients remained HCV‐RNA negative over time. SVR achieved following narlaprevir and PEG‐IFN/RBV‐therapy was durable up to 32 months after the end of treatment.
Coupling ordination techniques and GAM to spatially predict vegetation assemblages along a climatic gradient in an ENSO‐affected region of extremely high climate variability
Authors: Muenchow Jannes , Feilhauer Hannes , Bräuning Achim , Rodríguez Eric F. , Bayer Fabian , Rodríguez Rodolfo A. , von Wehrden Henrik 
Published: January 2013

AbstractQuestionsEl Niño Southern Oscillation (ENSO) is a strong driver of climatic and ecosystem variability in coastal NW Peru. La Niña amplifies the already dry local conditions, and led to depleted ecosystems in 2011. However, the 2012 La Niña event triggered rainfall far above the average. (1) Did plant species diversity, primary productivity and vegetation assemblages change along a climatic gradient between two climatologically different La Niña years; (2) Is there a difference in explanatory power of environmental predictors between the 2 yr; and (iii) is it possible to predict the observed vegetation patterns spatially?LocationTransect along a climatic gradient in the Sechura Desert of Piura, NW Peru (corresponds to the terrestrial part of the El Niño region 1 + 2) – a region of extremely high climatic variability.MethodsWe visited 50 30 m × 30 m randomly sampled plots in 2011 and 2012. A Procrustes analysis of two non‐metric multidimensional scaling (NMDS) ordinations provided information on the temporal change of species assemblages. Variation partitioning revealed the differences in explanatory power of the predictors. We employed a generalized additive model (GAM) to fit the scores of the first ordination axis with a floristic gradient map as a result.ResultsGenerally, higher rainfall resulted in a positive feedback when considering biodiversity, productivity and vegetation assemblages. The floristic gradient map resulting from the GAM displayed the spatial distribution of the three main assemblages along the climatic gradient. Edaphic variables added no independent portion to the explanation of the vegetation assemblages, but explained in conjunction with topography and NDVI a considerable amount of the variance.ConclusionsStrong Atlantic easterly winds crossing the Andes can boost plant growth even during a La Niña situation. This underscores the need for a deeper understanding of ENSO‐related climate variability of ENSO. Combining vegetation maps with accurate predictions of such climatic anomalies would aid the effective execution of conservation and recovery strategies. Additionally, coupling an unconstrained ordination with a GAM appears to be a promising tool for vegetation mapping, especially in the presence of a non‐linear gradient.
Coexistence between the southern river otter and the alien invasive North American mink in marine habitats of southern Chile
Authors: Medina‐Vogel G. , Barros M. , Organ J. F. , Bonesi L. 
Published: January 2013

AbstractThe interaction between native and introduced predators can be an important determinant of the success of introduced species and of the magnitude of their effects. In Europe, it has been shown that the American mink Neovison vison can be affected by native competitors; however, such evidence has not been found in South America. We studied the southern river otter Lontra provocax and the American mink at five marine sites, where they coexisted, and at one freshwater site, where only mink were present, in southern Chile. We used the signs of both species to study their habitat use and diet, and radio tracking to study their activity patterns. The results indicated that otters and minks tended to use different habitats in marine environments, the otter favouring littoral areas that are rocky and steep while the mink favours areas of gravel with a gently sloping intertidal zone. These differences were also reflected in their diets. At one of the coastal sites where the diet of the two species was similar, the activity pattern of minks was mostly diurnal, which is unusual. While differential habitat use may be the way through which the American mink is able to coexist with the southern river otter in coastal habitats of southern Chile, it is possible that otters are having an effect on individual minks by affecting their activity patterns, although more observations are needed to confirm this hypothesis.
Clinal variation in colony breeding structure and level of inbreeding in the subterranean termitesReticulitermes flavipesandR. grassei
Authors: Vargo Edward L. , Leniaud Laurianne , Swoboda Lois E. , Diamond Sarah E. , Weiser Michael D. , Miller Dini M. , Bagnères Anne‐Geneviève 
Published: January 2013

AbstractSocial insects exhibit remarkable variation in their colony breeding structures, both within and among species. Ecological factors are believed to be important in shaping reproductive traits of social insect colonies, yet there is little information linking specific environmental variables with differences in breeding structure. Subterranean termites (Rhinotermitidae) show exceptional variation in colony breeding structure, differing in the number of reproductives and degree of inbreeding; colonies can be simple families headed by a single pair of monogamous reproductives (king and queen) or they can be extended families headed by multiple inbreeding neotenic reproductives (wingless individuals). Using microsatellite markers, we characterized colony breeding structure and levels of inbreeding in populations over large parts of the range of the subterranean termitesReticulitermes flavipesin theUSAandR. grasseiin Europe. Combining these new data with previous results on populations of both species, we found that latitude had a strong effect on the proportion of extended‐family colonies inR. flavipesand on levels of inbreeding in both species. We examined the effect of several environmental variables that vary latitudinally; while the degree of inbreeding was greatest in cool, moist habitats in both species, seasonality affected the species differently. Inbreeding inR. flavipeswas most strongly associated with climatic variables (mean annual temperature and seasonality), whereas nonclimatic variables, including the availability of wood substrate and soil composition, were important predictors of inbreeding inR. grassei. These results are the first showing that termite breeding structure is shaped by local environmental factors and that species can vary in their responses to these factors.
Molecular patterns of introgression in a classic hybrid zone between theAustralian tree frogs,Litoria ewingiiandL. paraewingi: evidence of a tension zone
Authors: Smith Katie L. , Hale Joshua M. , Kearney Michael R. , Austin Jeremy J. , Melville Jane 
Published: January 2013

AbstractHybrid zones provide a rare opportunity to explore the processes involved in reproductive isolation and speciation. The southern hybrid zone between the southeastern Australian tree frogsLitoria ewingiiandL. paraewingihas been comprehensively studied over the last 40 years, primarily using reproductive compatibility experiments and male advertisement calls. We used mitochondrialDNA(mtDNA) and eight nuclear microsatellite markers to characterize this hybrid zone along a historically studied transect and to test various dispersal‐dependent and dispersal‐independent hybrid zone models. The species are genetically distinct and the level of hybridization within the contact zone is low, with the majority of admixed individuals representing later‐generation hybrids. Based on previous experimental genetic compatibility studies, we predicted that hybrids withL. paraewingimtDNAwould be more frequent than hybrids withL. ewingiimtDNA. Surprisingly, a greater proportion of the identified hybrids hadL. ewingiimtDNA. Geographical cline analyses showed a sharp transition in allele frequencies across the transect, and both the mtDNAand microsatellite data showed concordant cline centres, but were best supported by a model that allowed width to vary. Overall, theL. ewingii–L. paraewingihybrid zone is best characterized as a tension zone, due to the narrow cline width, concordant genetic clines and low levels of hybridization.
The molecular basis of invasiveness: differences in gene expression of native and introduced common ragweed (Ambrosia artemisiifolia) in stressful and benign environments
Authors: Hodgins Kathryn A. , Lai Zhao , Nurkowski Kristin , Huang Jie , Rieseberg Loren H. 
Published: January 2013

AbstractAlthough the evolutionary and ecological processes that contribute to plant invasion have been the focus of much research, investigation into the molecular basis of invasion is just beginning. Common ragweed (Ambrosia artemisiifolia) is an annual weed native to North America and has been introduced to Europe where it has become invasive. Using a custom‐designed NimbleGen oligoarray, we examined differences in gene expression between five native and six introduced populations of common ragweed in three different environments (control, light stress and nutrient stress), as well as two different time points. We identified candidate genes that may contribute to invasiveness in common ragweed based on differences in expression between native and introduced populations from Europe. Specifically, we found 180 genes where range explained a significant proportion of the variation in gene expression and a further 103 genes with a significant range by treatment interaction. Several of these genes are potentially involved in the metabolism of secondary compounds, stress response and the detoxification of xenobiotics. Previously, we found more rapid growth and greater reproductive success in introduced populations, particularly in benign and competitive (light stress) environments, and many of these candidate genes potentially underlie these growth differences. We also found expression differences among populations within each range, reflecting either local adaptation or neutral processes, although no associations with climate or latitude were identified. These data provide a first step in identifying genes that are involved with introduction success in an aggressive annual weed.
Fine‐grained adaptive divergence in an amphibian: genetic basis of phenotypic divergence and the role of nonrandom gene flow in restricting effective migration among wetlands
Authors: Richter‐Boix Alex , Quintela María , Kierczak Marcin , Franch Marc , Laurila Anssi 
Published: January 2013

AbstractAdaptive ecological differentiation among sympatric populations is promoted by environmental heterogeneity, strong local selection and restricted gene flow. High gene flow, on the other hand, is expected to homogenize genetic variation among populations and therefore prevent local adaptation. Understanding how local adaptation can persist at the spatial scale at which gene flow occurs has remained an elusive goal, especially for wild vertebrate populations. Here, we explore the roles of natural selection and nonrandom gene flow (isolation by breeding time and habitat choice) in restricting effective migration among local populations and promoting generalized genetic barriers to neutral gene flow. We examined these processes in a network of 17 breeding ponds of the moor frog Rana arvalis, by combining environmental field data, a common garden experiment and data on variation in neutral microsatellite loci and in a thyroid hormone receptor (TRβ) gene putatively under selection. We illustrate the connection between genotype, phenotype and habitat variation and demonstrate that the strong differences in larval life history traits observed in the common garden experiment can result from adaptation to local pond characteristics. Remarkably, we found that haplotype variation in the TRβ gene contributes to variation in larval development time and growth rate, indicating that polymorphism in the TRβ gene is linked with the phenotypic variation among the environments. Genetic distance in neutral markers was correlated with differences in breeding time and environmental differences among the ponds, but not with geographical distance. These results demonstrate that while our study area did not exceed the scale of gene flow, ecological barriers constrained gene flow among contrasting habitats. Our results highlight the roles of strong selection and nonrandom gene flow created by phenological variation and, possibly, habitat preferences, which together maintain genetic and phenotypic divergence at a fine‐grained spatial scale.
Detecting selection along environmental gradients: analysis of eight methods and their effectiveness for outbreeding and selfing populations
Authors: De Mita Stéphane , Thuillet Anne‐Céline , Gay Laurène , Ahmadi Nourollah , Manel Stéphanie , Ronfort Joëlle , Vigouroux Yves 
Published: January 2013

AbstractThanks to genome‐scale diversity data, present‐day studies can provide a detailed view of how natural and cultivated species adapt to their environment and particularly to environmental gradients. However, due to their sensitivity, up‐to‐date studies might be more sensitive to undocumented demographic effects such as the pattern of migration and the reproduction regime. In this study, we provide guidelines for the use of popular or recently developed statistical methods to detect footprints of selection. We simulated 100 populations along a selective gradient and explored different migration models, sampling schemes and rates of self‐fertilization. We investigated the power and robustness of eight methods to detect loci potentially under selection: three designed to detect genotype–environment correlations and five designed to detect adaptive differentiation (based on FST or similar measures). We show that genotype–environment correlation methods have substantially more power to detect selection than differentiation‐based methods but that they generally suffer from high rates of false positives. This effect is exacerbated whenever allele frequencies are correlated, either between populations or within populations. Our results suggest that, when the underlying genetic structure of the data is unknown, a number of robust methods are preferable. Moreover, in the simulated scenario we used, sampling many populations led to better results than sampling many individuals per population. Finally, care should be taken when using methods to identify genotype–environment correlations without correcting for allele frequency autocorrelation because of the risk of spurious signals due to allele frequency correlations between populations.
Molecular signatures of lineage‐specific adaptive evolution in a unique sea basin: the example of an anadromous goby Leucopsarion petersii
Authors: Kokita Tomoyuki , Takahashi Sayaka , Kumada Hiroki 
Published: January 2013

AbstractClimate changes on various time scales often shape genetic novelty and adaptive variation in many biotas. We explored molecular signatures of directional selection in populations of the ice goby Leucopsarion petersii inhabiting a unique sea basin, the Sea of Japan, where a wide variety of environments existed in the Pleistocene in relation to shifts in sea level by repeated glaciations. This species consisted of two historically allopatric lineages, the Japan Sea (JS) and Pacific Ocean (PO) lineages, and these have lived under contrasting marine environments that are expected to have imposed different selection regimes caused by past climatic and current oceanographic factors. We applied a limited genome‐scan approach using seven candidate genes for phenotypic differences between two lineages in combination with 100 anonymous microsatellite loci. Neuropeptide Y (NPY) gene, which is an important regulator of food intake and potent orexigenic agent, and three anonymous microsatellites were identified as robust outliers, that is, candidate loci potentially under directional selection, by multiple divergence‐ and diversity‐based outlier tests in comparisons focused on multiple populations of the JS vs. PO lineages. For these outlier loci, populations of the JS lineage had putative signals of selective sweeps. Additionally, real‐time quantitative PCR analysis using fish reared in a common environment showed a higher expression level for NPY gene in the JS lineage. Thus, this study succeeded in identifying candidate genomic regions under selection across populations of the JS lineage and provided evidence for lineage‐specific adaptive evolution in this unique sea basin.
Changes in Psp protein binding partners, localization and behaviour upon activation of the Yersinia enterocolitica phage shock protein response
Authors: Yamaguchi Saori , Reid Dylan A. , Rothenberg Eli , Darwin Andrew J. 
Published: January 2013

SummaryPspA, ‐B and ‐C regulate the bacterial phage shock protein stress response by controlling the PspF transcription factor. Here, we have developed complementary approaches to study the behaviour of these proteins at their endogenous levels in Yersinia enterocolitica. First, we observed GFP‐tagged versions with an approach that resolves individual protein complexes in live cells. This revealed that PspA, ‐B and ‐C share common behaviours, including a striking contrast before and after induction. In uninduced cells, PspA, ‐B and ‐C were highly mobile and widely distributed. However, induction reduced mobility and the proteins became more organized. Combining mCherry‐ and GFP‐tagged proteins also revealed that PspA colocalizes with PspB and PspC into large stationary foci, often located close to the pole of induced cells. In addition, co‐immunoprecipitation assays provided the first direct evidence supporting the model that PspA switches binding partners from PspF to PspBC upon induction. Together, these data suggest that PspA, ‐B and ‐C do not stably interact and are highly mobile before induction, perhaps sampling the status of the membrane and each other. However, an inducing signal promotes PspABC complex formation and their relocation to discrete parts of the membrane, which might then be important for mitigating envelope stress.