bluuebunny/crossref_metadata_2025_split huggingface dataset:
Conservation of a domestic metapopulation structured into related and partly admixed strains
Authors: Ramljak Jelena , Bunevski Gjoko , Bytyqi Hysen , Marković Božidarka , Brka Muhamed , Ivanković Ante , Kume Kristaq , Stojanović Srđan , Nikolov Vasil , Simčič Mojca , Sölkner Johann , Kunz Elisabeth , Rothammer Sophie , Seichter Doris , Grünenfelder Hans‐Peter , Broxham Elli T. , Kugler Waltraud , Medugorac Ivica 
Published: March 2018

AbstractPreservation of genetic diversity is one of the most pressing challenges in the planetary boundaries concept. Within this context, we focused on genetic diversity in a native, unselected and highly admixed domesticated metapopulation. A set of 1,828 individuals from 60 different cattle breeds was analysed using a medium density SNP chip. Among these breeds, 14 Buša strains formed a metapopulation represented by 350 individuals, while the remaining 46 breeds represented the global cattle population. Genetic analyses showed that the scarcely selected and less differentiated Buša metapopulation contributed a substantial proportion (52.6%) of the neutral allelic diversity to this global taurine population. Consequently, there is an urgent need for synchronized maintenance of this highly fragmented domestic metapopulation, which is distributed over several countries without sophisticated infrastructure and highly endangered by continuous replacement crossing as part of the global genetic homogenization process. This study collected and evaluated samples, data and genomewide information and developed genome‐assisted cross‐border conservation concepts. To detect and maintain genetic integrity of the metapopulation strains, we designed and applied a composite test that combines six metrics based on additive genetic relationships, a nearest neighbour graph and the distribution of semiprivate alleles. Each metric provides distinct information components about past admixture events and offers an objective and powerful tool for the detection of admixed outliers. The here developed conservation methods and presented experiences could easily be adapted to comparable conservation programmes of domesticated or other metapopulations bred and kept in captivity or under some other sort of human control.
Rapid divergence of mussel populations despite incomplete barriers to dispersal
Authors: Maas Diede L. , Prost Stefan , Bi Ke , Smith Lydia L. , Armstrong Ellie E. , Aji Ludi P. , Toha Abdul Hamid A. , Gillespie Rosemary G. , Becking Leontine E. 
Published: March 2018

AbstractStriking genetic structure among marine populations at small spatial scales is becoming evident with extensive molecular studies. Such observations suggest isolation at small scales may play an important role in forming patterns of genetic diversity within species. Isolation‐by‐distance, isolation‐by‐environment and historical priority effects are umbrella terms for a suite of processes that underlie genetic structure, but their relative importance at different spatial and temporal scales remains elusive. Here, we use marine lakes in Indonesia to assess genetic structure and assess the relative roles of the processes in shaping genetic differentiation in populations of a bivalve mussel (Brachidontes sp.). Marine lakes are landlocked waterbodies of similar age (6,000–10,000 years), but with heterogeneous environments and varying degrees of connection to the sea. Using a population genomic approach (double‐digest restriction‐site‐associated DNA sequencing), we show strong genetic structuring across populations (range FST: 0.07–0.24) and find limited gene flow through admixture plots. At large spatial scales (>1,400 km), a clear isolation‐by‐distance pattern was detected. At smaller spatial scales (<200 km), this pattern is maintained, but accompanied by an association of genetic divergence with degree of connection. We hypothesize that (incomplete) dispersal barriers can cause initial isolation, allowing priority effects to give the numerical advantage necessary to initiate strong genetic structure. Priority effects may be strengthened by local adaptation, which the data may corroborate by showing a high correlation between mussel genotypes and temperature. Our study indicates an often‐neglected role of (evolution‐mediated) priority effects in shaping population divergence.
Genetic signatures through space, time and multiple disturbances in a ubiquitous brooding coral
Authors: Underwood Jim N. , Richards Zoe T. , Miller Karen J. , Puotinen Marji L. , Gilmour James P. 
Published: March 2018

AbstractThe predominance of self‐recruitment in many reef‐building corals has fundamental and complex consequences for their genetic diversity, population persistence and responses to climate change. Knowledge of genetic structure over local scales needs to be placed within a broad spatial context, and also integrated with genetic monitoring through time to disentangle these consequences. Here, we examined patterns of genetic diversity over multiple spatio‐temporal scales across tropical Australia in the ubiquitous brooding coral, Seriatopora hystrix. We also analysed complimentary environmental and demographic data to elucidate the seascape drivers of these patterns. Large genetic differences were detected between the east vs. west coasts of Australia. In northwest Australia, geographic differentiation dominated genetic structure over multiple scales. However, three sympatric lineages were detected at the largest offshore reef system (Scott Reef). Similar to the differences observed among putative species in eastern Australia, these lineages were associated with different levels of wave exposure. Local genetic structure within the Scott Reef system was relatively stable over 10 years, but temporal differences were observed that reflected small but important genetic changes over a few generations during recovery after severe bleaching. These results highlight the importance of self‐recruitment together with occasional longer distance connectivity for the persistence of a metapopulation across spatially and temporally variable environments. Our multidimensional research provides a foundation for further long‐term genetic monitoring to inform conservation strategies and highlights that sampling scales, ecological effects and cryptic diversity are important considerations to develop realistic understanding of the evolutionary resilience of corals.
Scale and direction of adaptive introgression between black cottonwood (Populus trichocarpa) and balsam poplar (P. balsamifera)
Authors: Suarez‐Gonzalez Adriana , Hefer Charles A. , Lexer Christian , Cronk Quentin C. B. , Douglas Carl J. 
Published: March 2018

AbstractIntrogression can introduce novel genetic variation at a faster rate than mutation alone and result in adaptive introgression when adaptive alleles are maintained in the recipient genome over time by natural selection. A previous study from our group demonstrated adaptive introgression fromPopulus balsamiferaintoP. trichocarpain a target genomic region. Here we expand our local ancestry analysis to the whole genome of both parents to provide a comprehensive view of introgression patterns and to identify additional candidate regions for adaptive introgression genomewide.Populus trichocarpais a large, fast‐growing tree of mild coastal regions of the Pacific Northwest, whereasP. balsamiferais a smaller stature tree of continental and boreal regions with intense winter cold. The species hybridize where they are parapatric. We detected asymmetric patterns of introgression across the whole genome of these two poplar species adapted to contrasting environments, with stronger introgression fromP. balsamiferatoP. trichocarpathan vice versa. AdmixedP. trichocarpaindividuals contained more genomic regions with unusually high levels of introgression (19 regions) and also the largest introgressed genome fragment (1.02 Mb) compared with admixedP. balsamifera(nine regions). Our analysis also revealed numerous candidate regions for adaptive introgression with strong signals of selection, notably related to disease resistance, and enriched for genes that may play crucial roles in survival and adaptation. Furthermore, we detected a potential overrepresentation of subtelomeric regions inP. balsamiferaintrogressed intoP. trichocarpaand possible protection of sex‐determining regions from interspecific gene flow.
Mitonuclear discordance in wolf spiders: Genomic evidence for species integrity and introgression
Authors: Ivanov Vladislav , Lee Kyung Min , Mutanen Marko 
Published: March 2018

AbstractSystematists and taxonomists have benefited greatly from the emergence of molecular methods. Species identification has become straightforward through DNA barcoding and the rapid build‐up of massive DNA barcode reference libraries. In animals, mitonuclear discordance can significantly complicate the process of species identification and delimitation. The causes of mitonuclear discordance are either biological (e.g., introgression, incomplete lineage sorting, horizontal gene transfer androgenesis) or induced by operational factors (e.g., human error with specimen misidentification or incorrect species delimitation). Moreover, endosymbionts may play an important role in promoting fixation of mitochondrial genomes. Here, we study the mitonuclear discordance of wolf spiders species (Lycosidae) (independent cases from Alopecosa aculeata and Pardosa pullata groups) that share identical COI DNA barcodes. We approached the case utilizing double‐digest restriction site‐associated DNA sequencing (ddRADseq) to obtain and analyse genomic‐scale data. Our results suggest that the observed cases of mitonuclear discordance are not due to operational reasons but result from biological processes. Further analysis indicated introgression and that incomplete lineage sorting is unlikely to have been responsible for the observed discrepancy. Additional survey of endosymbionts provided ideas on further research and their role in shaping mitochondrial DNA distribution patterns. Thus, ddRADseq grants an efficient way to study the taxonomy of problematic groups with insight into underlying evolutionary processes.
Gene expression profiles of glucose toxicity‐exposed islet microvascular endothelial cells
Authors: Liu Mingming , Lu Wenbao , Hou Qunxing , Wang Bing , Sheng Youming , Wu Qingbin , Li Bingwei , Liu Xueting , Zhang Xiaoyan , Li Ailing , Zhang Honggang , Xiu Ruijuan 
Published: March 2018

AbstractObjectiveIslet microcirculation is mainly composed by IMECs. The aim of the study was to investigate the differences in gene expression profiles of IMECs upon glucose toxicity exposure and insulin treatment.MethodsIMECs were treated with 5.6 mmol L−1 glucose, 35 mmol L−1 glucose, and 35 mmol L−1 glucose plus 10−8 mol L−1 insulin, respectively. Gene expression profiles were determined by microarray and verified by qPCR. GO terms and KEGG analysis were performed to assess the potential roles of differentially expressed genes. The interaction and expression tendency of differentially expressed genes were analyzed by Path‐Net algorithm.ResultsCompared with glucose toxicity‐exposed IMECs, 1574 mRNAs in control group and 2870 mRNAs in insulin‐treated IMECs were identified with differential expression, respectively. GO and KEGG pathway analysis revealed that these genes conferred roles in regulation of apoptosis, proliferation, migration, adhesion, and metabolic process etc. Additionally, MAPK signaling pathway and apoptosis were the dominant nodes in Path‐Net. IMECs survival and function pathways were significantly changed, and the expression tendency of genes from euglycemia and glucose toxicity exposure to insulin treatment was revealed and enriched in 7 patterns.ConclusionsOur study provides a microcirculatory framework for gene expression profiles of glucose toxicity‐exposed IMECs.
RbpA and σB association regulates polyphosphate levels to modulate mycobacterial isoniazid‐tolerance
Authors: Wang Zhongwei , Cumming Bridgette M. , Mao Chunyou , Zhu Yan , Lu Pei , Steyn Adrie J.C. , Chen Shiyun , Hu Yangbo 
Published: March 2018

SummaryTo facilitate survival under drug stresses, a small population of Mycobacterium tuberculosis can tolerate bactericidal concentrations of drugs without genetic mutations. These drug‐tolerant mycobacteria can be induced by environmental stresses and contribute to recalcitrant infections. However, mechanisms underlying the development of drug‐tolerant mycobacteria remain obscure. Herein, we characterized a regulatory pathway which is important for the tolerance to isoniazid (INH) in Mycobacterium smegmatis. We found that the RNA polymerase binding protein RbpA associates with the stress response sigma factor σB, to activate the transcription of ppk1, the gene encoding polyphosphate kinase. Subsequently, intracellular levels of inorganic polyphosphate increase to promote INH‐tolerant mycobacteria. Interestingly, σB and ppk1 expression varied proportionately in mycobacterial populations and positively correlated with tolerance to INH in individual mycobacteria. Moreover, sigB and ppk1 transcription are both induced upon nutrient depletion, a condition that stimulates the formation of INH‐tolerant mycobacteria. Over‐expression of ppk1 in rbpA knockdown or sigB deleted strains successfully restored the number of INH‐tolerant mycobacteria under both normal growth and nutrient starved conditions. These data suggest that RbpA and σB regulate ppk1 expression to control drug tolerance both during the logarithmic growth phase and under the nutrition starved conditions.
Stable isotope analysis of fecal material provides insight into the diet of fin whales
Authors: Arregui Marina , Borrell Asunción , Víkingsson Gisli , Ólafsdóttir Droplaug , Aguilar Alex 
Published: March 2018

AbstractIn cetaceans, stable isotope analysis of tissues overcomes some of the potential biases encountered in studies of diet based on stomach content or fecal analysis. However, stable isotope ratios of tissues are only indicative of long‐term feeding and may be misleading when recent shifts in prey consumption have occurred. Stable isotope ratios of feces stand as a potential alternative source for resolving short‐term diet, but may be biased by digestive enzymes and bacteria. We investigate whether fecal stable isotope ratios of freshly dead fin whales are consistent with those of the main food found in their stomachs (krill) and with those of other potential prey. Results show that stable isotope ratios of krill remain unaltered after their transit along the digestive tract and, therefore, values in feces are reliable indicators of this prey consumption. In addition, the low isotope ratios of feces that visually appeared to contain only fish remains revealed a substantial contribution of krill in the digested food. This demonstrates that macroscopic gross fecal analysis may be misleading because less digestible components, like fish bones, may be overrepresented. We conclude that stable isotope ratios of feces contribute significant information to other techniques for short‐term diet reconstruction.
Xanthomonas arboricola pv. pruni, causal agent of bacterial spot of stone fruits and almond: its genomic and phenotypic characteristics in the X. arboricola species context
Authors: Garita‐Cambronero Jerson , Palacio‐Bielsa Ana , Cubero Jaime 
Published: March 2018

SummaryBackgroundXanthomonas arboricola pv. pruni (Xap) causes bacterial spot of stone fruits and almond, an important disease that may reduce the yield and vigour of the trees, as well as the marketability of affected fruits. Xap lies within the Xanthomonas genus, which has been intensively studied because of its strain specialization and host range complexity. Here, we summarize the recent advances in our understanding of the complexities of Xap, including studies of the molecular features that result after comparative phenotypic and genomic analyses, in order to obtain a clearer overview of the bacterial behaviour and infection mechanism in the context of the X. arboricola species.Taxonomic statusBacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadaceae; Genus Xanthomonas; Species X. arboricola; Pathovar pruni.Host range and symptomsXap infects most Prunus species, including apricot, peach, nectarine, plum and almond, and occasionally cherry. Symptoms are found on leaves, fruits, twigs and branches or trunks. In severe infections, defoliation and fruit dropping may occur.DistributionBacterial spot of stone fruits and almond is worldwide in distribution, with Xap being isolated in Africa, North and South America, Asia, Europe and Oceania. It is a common disease in geographical areas in which stone fruits and almonds are grown. Xap is listed as a quarantine organism in several areas of the world.GenomeThe genomes of six isolates from Xap have been publicly released. The genome consists of a single chromosome of around 5 000 000 bp with 65 mol% GC content and an extrachromosomal plasmid element of around 41 000 bp with 62 mol% GC content. Genomic comparative studies in X. arboricola have allowed the identification of putative virulence components associated with the infection process of bacterial spot of stone fruits and almond.Disease controlManagement of bacterial spot of stone fruits and almond is based on an integrated approach that comprises essential measures to avoid Xap introduction in a production zone, as well as the use of tolerant or resistant plant material and chemical treatments, mainly based on copper compounds. Management programmes also include the use of appropriate cultivation practices when the disease is already established. Finally, for the effective control of the disease, appropriate detection and characterization methods are needed for use in symptomatic or asymptomatic samples as a first approach for pathogen exclusion.Useful websiteshttps://gd.eppo.int/taxon/XANTPR; http://www.cost.eu/COST_Actions/ca/CA16107; http://www.xanthomonas.org
Activation of PhoBR under phosphate‐rich conditions reduces the virulence of Xanthomonas oryzae pv. oryzae
Authors: Zheng Dehong , Xue Bingbing , Shao Yanan , Yu Haoquan , Yao Xiaoyan , Ruan Lifang 
Published: March 2018

SummaryThe two‐component signal transduction system PhoBR regulates the adaptation to phosphate limitation and the virulence of many animal bacterial pathogens. However, PhoBR in phytopathogens has rarely been investigated. In this study, we found that PhoBR in Xanthomonas oryzae pv. oryzae (Xoo), the pathogen of rice bacterial leaf blight, also regulates the adaptation to phosphate starvation. Unexpectedly, rice leaves infected by the phoBR‐deleted mutant and wild‐type PXO99A showed similar lesions, indicating that PhoBR is unnecessary for the virulence of Xoo. phoBR was found to be silenced during host infection, whereas artificially constitutive PhoBR expression attenuated virulence on host rice and growth in phosphate‐rich media. RNA‐sequencing (RNA‐seq) was then performed to investigate the global effect caused by constitutive PhoBR activation. RNA‐seq and further experiments revealed that the PhoBR regulon in Xoo comprised a wide range of genes. Nutrient transport and metabolism readjustments that resulted from PhoBR regulon activation may be responsible for growth attenuation. Our findings suggest that growth reduction regulated by PhoBR is a fitness cost of adaptation to phosphate starvation. PhoBR in Xoo is activated under phosphate‐limited conditions, which could exist in epiphytic and saprophytic surviving phases, and is strictly repressed within phosphate‐rich host plants to minimize fitness costs.
Wheat streak mosaic virus: a century old virus with rising importance worldwide
Authors: Singh Khushwant , Wegulo Stephen N. , Skoracka Anna , Kundu Jiban Kumar 
Published: March 2018

SummaryWheat streak mosaic virus (WSMV) causes wheat streak mosaic, a disease of cereals and grasses that threatens wheat production worldwide. It is a monopartite, positive‐sense, single‐stranded RNA virus and the type member of the genus Tritimovirus in the family Potyviridae. The only known vector is the wheat curl mite (WCM, Aceria tosichella), recently identified as a species complex of biotypes differing in virus transmission. Low rates of seed transmission have been reported. Infected plants are stunted and have a yellow mosaic of parallel discontinuous streaks on the leaves. In the autumn, WCMs move from WSMV‐infected volunteer wheat and other grass hosts to newly emerged wheat and transmit the virus which survives the winter within the plant, and the mites survive as eggs, larvae, nymphs or adults in the crown and leaf sheaths. In the spring/summer, the mites move from the maturing wheat crop to volunteer wheat and other grass hosts and transmit WSMV, and onto newly emerged wheat in the fall to which they transmit the virus, completing the disease cycle. WSMV detection is by enzyme‐linked immunosorbent assay (ELISA), reverse transcription‐polymerase chain reaction (RT‐PCR) or quantitative RT‐PCR (RT‐qPCR). Three types of WSMV are recognized: A (Mexico), B (Europe, Russia, Asia) and D (USA, Argentina, Brazil, Australia, Turkey, Canada). Resistance genes Wsm1, Wsm2 and Wsm3 have been identified. The most effective, Wsm2, has been introduced into several wheat cultivars. Mitigation of losses caused by WSMV will require enhanced knowledge of the biology of WCM biotypes and WSMV, new or improved virus detection techniques, the development of resistance through traditional and molecular breeding, and the adaptation of cultural management tactics to account for climate change.
Candida utilis fungaemia following endoscopic intervention on ureteral stent in a kidney transplant recipient: Case report and a review of the literature
Authors: Gaisne Raphaël , Jeddi Fakhri , Morio Florent , Le Clerc Quentin‐Côme , Hourmant Maryvonne , Blancho Gilles , Giral Magali , Cantarovich Diego , Dantal Jacques , Ville Simon 
Published: March 2018

SummaryInfection due to species other than Candida albicans is increasing among solid organ transplant recipients. Candida utilis, commonly used in the food industry, is considered as a low‐virulence yeast. We report the first case of C. utilis fungaemia involving a solid organ transplant recipient. The infection was triggered by the withdrawal of a ureteral stent and was successfully treated with intravenous micafungin. We also propose a review of all reported cases of infection caused by C. utilis.
Molecular detection of fungi of public health importance in wild animals from Southern Brazil
Authors: Losnak Debora O. , Rocha Francielle R. , Almeida Barbara S. , Batista Keila Z. S. , Althoff Sérgio L. , Haupt Josiane , Ruiz Luciana S. , Anversa Laís , Lucheis Simone B. , Paiz Laís M. , Donalisio Maria Rita , Richini Pereira Virginia B. 
Published: March 2018

SummarySome animals have an important relationship with fungal infections, and searching for pathogens in animal samples may be an opportunity for eco‐epidemiological research. Since studies involving wildlife are generally restricted, using samples from road kills is an alternative. The aim of this study was to verify whether pathogenic fungi of public health importance occur in wildlife road kills from Santa Catarina State, Brazil. Organ samples (n = 1063) from 297 animals were analysed according to Polymerase Chain Reaction (PCR) using universal primers to detect fungi in general and, subsequently, using primers specific to Paracoccidioides brasiliensis, Histoplasma capsulatum and Cryptococcus spp. There were 102 samples positive for fungal species. Eight samples were positive for P. brasiliensis, three samples were positive for Cryptococcus spp. and one sample had coinfection by these two fungi. No sample was positive for Histoplasma spp. according to the molecular detection. Genetic sequencing allowed the identification of Fungal sp. in 89 samples, Cryptococcus neoformans in two samples and Aspergillus penicillioides in three samples. This study shows the importance of wild animals in the epidemiology of fungal infections and assists in the mapping of pathogen occurrence in a region that was not previously evaluated.