Academic literature on the topic 'Taxon-Specific-Biomarker'

Phytophthora cinnamomi is a devastating pathogen causing root and crown rot and dieback diseases of nearly 5000 plant species. Accurate and rapid detection of P. cinnamomi plays a fundamental role within the current disease prevention and management programs. In this study, a novel effector gene PHYCI_587572 was found as unique to P. cinnamomi based on a comparative genomic analysis of 12 Phytophthora species. Its avirulence homolog protein 87 (Avh87) is characterized by the Arg-Xaa-Leu-Arg (RxLR) motif. Avh87 suppressed the pro-apoptotic protein BAX- and elicitin protein INF1-mediated cell death of Nicotiana benthamiana. Furthermore, a recombinase polymerase amplification-lateral flow dipstick detection assay targeting this P. cinnamomi-specific biomarker was developed. While successfully detected 19 P. cinnamomi isolates of a global distribution, this assay lacked detection of 37 other oomycete and fungal species, including P. parvispora, a sister taxon of P. cinnamomi. In addition, it detected P. cinnamomi from artificially inoculated leaves of Cedrus deodara. Moreover, the RPA-LFD assay was found to be more sensitive than a conventional PCR assay, by detecting as low as 2 pg of genomic DNA in a 50-µL reaction. It detected P. cinnamomi in 13 infested soil samples, while the detection rate was 46.2% using PCR. Results in this study indicated that PHYCI_587572 is a unique biomarker for detecting P. cinnamomi. Although PHYCI_587572 was identified as an effector gene based on the RxLR motif of Avh87 and the avirulence activity on Nicotiana, its exact genetic background and biological function on the natural hosts of P. cinnamomi warrant further investigations.

To help resolve current controversies surrounding the fundamental question of synchrony between end-Permian mass extinction on land and in the sea, we examined the marine Permian–Triassic reference section at Meishan (southeastern China) for land-derived molecular degradation products of pentacyclic triterpenoids with oleanane carbon skeletons, diagnostic for the Permian plant genus Gigantopteris. We identified a continuous quantitative record of mono-aromatic des-A-oleanane, which abruptly ends in the main marine extinction interval just below the Permian-Triassic boundary. This taxon-specific molecular biomarker, therefore, reveals in unmatched detail the timing and tempo of the demise of one of the most distinctive Permian plants and provides evidence of synchronous extinction among continental and marine organisms. Parallel reduction in the relative abundance of lignin phenols confirms that aridity-driven extinction was not restricted to Gigantopteris but likely affected the entire wetland flora of the equatorial South China microcontinent.

AbstractFatty acid (FA) content and composition of zooplankton in Puget Sound, Washington (USA) was studied to investigate the nutritional quality of diverse zooplankton prey for juvenile salmon (Oncorhynchus spp.) in terms of their essential fatty acid (EFA) content. The study focus was on eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and arachidonic acid (ARA) as these are key FA needed to maintain growth and development of juvenile fish. The different zooplankton taxa varied in their FA composition. Much of the variation in FA composition was driven by 18:1ω9 (a biomarker of carnivory), ARA, DHA, and FA characteristic of diatoms, which are linked to zooplankton diet sources. Gammarid and hyperiid amphipods contained the highest amount of EFA, particularly the gammarid amphipod Cyphocaris challengeri, while shrimp and copepods had much lower EFA content. Crab larvae, which are important prey for juvenile salmon in Puget Sound, had intermediate EPA + DHA content and the lowest DHA/EPA ratio, and were rich in diatom biomarkers. Temporal and spatial trends in zooplankton lipids were less apparent than the taxonomic differences, although the EFA content increased from spring to summer in Cancridae zoeae and the amphipod C. challengeri. These results on taxon-specific EFA content provide baseline information on the nutritional quality of zooplankton that can be applied in food web models. Combining zooplankton fatty acid data (quality) with taxon-specific zooplankton biomass data (quantity) enables development of new, sensitive indicators of juvenile fish production to help assess recent declines in salmon production in the Pacific Northwest and predict future adult returns.

Abstract Background Neutropenic fever (NF) occurs in >70% of hematopoietic cell transplantation (HCT) recipients, without a documented etiology in most cases. Antibiotics used to prevent and treat NF disrupt the gut microbiota; these disruptions predict higher post-transplant mortality. We hypothesized that specific features in the gut microbial community may mediate the risk of NF. Methods We searched a large gut microbiota database in allogeneic HCT recipients (12,546 stool samples, 1,278 patients) to find pairs with (cases) vs. without (controls) NF on the same day relative to transplantation and with a stool sample on the previous day. 179 such pairs were matched in the underlying disease and graft source. Several other important clinical variables were similar between the groups. Results The gut microbiota of cases on the day before NF had a lower abundance of Blautia than their matched controls on the same day post-transplant, suggesting a protective role for Blautia. Microbiota network analysis did not find any differences in community structure between the groups, suggesting a single-taxon effect. To identify putative mechanisms, we searched a gut microbiome and serum metabolome database of acute leukemia patients receiving chemotherapy and identified 139 serum samples collected within 24 hours after a stool sample from the same patient. Greater Blautia abundances predicted higher levels of next-day citrulline, a biomarker of total enterocyte mass. Conclusions These findings support a model where Blautia protects against NF by improving intestinal health. Therapeutic restoration of Blautia may help prevent NF, thus reducing antibiotic exposures and transplant-related mortality.

Abstract Background Diarrhea is a major cause of morbidity and mortality in young calves, resulting in considerable economic loss for dairy farms. To determine if some gut microbes might have resistance to dysbiotic process with calf diarrhea by dictating the microbial co-occurrence patterns from birth to post-weaning, we examined the dynamic development of the gut microbiota and diarrhea status using two animal trials, with the first trial having 14 Holstein dairy calves whose fecal samples were collected 18 times over 78 d from birth to 15 d post-weaning and the second trial having 43 Holstein dairy calves whose fecal samples were collected daily from 8 to 18 days of age corresponding to the first diarrhea peak of trial 1. Results Metataxonomic analysis of the fecal microbiota showed that the development of gut microbiota had three age periods with birth and weaning as the separatrices. Two diarrhea peaks were observed during the transition of the three age periods. Fusobacteriaceae was identified as a diarrhea-associated taxon both in the early stage and during weaning, and Clostridium_sensu_stricto_1 was another increased genus among diarrheic calves in the early stage. In the neonatal calves, Prevotella_2 (ASV4 and ASV26), Prevotella_9 (ASV43), and Alloprevotella (ASV14) were negatively associated with Clostridium_sensu_stricto_1 (ASV48), the keystone taxa of the diarrhea-phase module. During weaning, unclassified Muribaculaceae (ASV28 and ASV44), UBA1819 (ASV151), Barnesiella (ASV497), and Ruminococcaceae_UCG-005 (ASV254) were identified being associated with non-diarrheic status, and they aggregated in the non-diarrhea module of co-occurrence patterns wherein unclassified Muribaculaceae (ASV28) and Barnesiella (ASV497) had a direct negative relationship with the members of the diarrhea module. Conclusions Taken together, our results suggest that the dynamic successions of calf gut microbiota and the interactions among some bacteria could influence calf diarrhea, and some species of Prevotella might be the core microbiota in both neonatal and weaning calves, while species of Muribaculaceae might be the core microbiota in weaning calves for preventing calf diarrhea. Some ASVs affiliated with Prevotella_2 (ASV4 and ASV26), Prevotella_9 (ASV43), Alloprevotella (AVS14), unclassified Muribaculaceae (ASV28 and ASV44), UBA1819 (ASV151), Ruminococcaceae_UCG-005 (ASV254), and Barnesiella (ASV497) might be proper probiotics for preventing calf diarrhea whereas Clostridium_sensu_stricto_1 (ASV48) might be the biomarker for diarrhea risk in specific commercial farms.