Adapterama I: Universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru &amp; iNext)

Glenn, Travis C.; Nilsen, Roger; Sanders, Jon G.; Bayona‐Vásquez, Natalia J.; Finger, John W.; Pierson, Todd W.; Bentley, Kerin E.; Hoffberg, Sandra L.; Louha, Swarnali; León, Francisco J. García‐De; Río-Portilla, Miguel A. Del; Reed, Kurt D.; Anderson, Jennifer L.; Meece, Jennifer K.; Aggrey, Samuel E.; Rekaya, Romdhane; Alabady, Magdy S.; Bélanger, Myriam; Winker, Kevin; Faircloth, Brant C.

doi:10.1101/049114

Cited by 123 publications

(138 citation statements)

References 45 publications

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“…The locus-specific primers (forward: 16S_341_F, and reverse: 16S_785_R) were used to target the V3-V4 region of 16S rRNA (Table 2). The Read 1 and Read 2 sequencing primers were Illumina-specific iTru_R1_5′_fusion and iTru_R2_5′_fusion In addition, a total of 20 internal tags ranging from 5 nucleotides (NTs) to 8 NTs long were used; 8 of them were the forward fusion primers and 12 the reverse fusion primers (Table 2) (19). Following the preparation of Taggi-matrix library, the PCR mix (Kapa Biosystems, Inc., Boston, MA) was added, together with forward fusion primers (including the Read 1 sequencing primer, Read 1 tag and forward locus-specific primer) and reverse fusion primers (including the Read 2 sequencing primer, Read 2 tag and reverse locus-specific primer).…”

Section: Methodsmentioning

confidence: 99%

Genistein prevention of hyperglycemia and improvement of glucose tolerance in adult non-obese diabetic mice are associated with alterations of gut microbiome and immune homeostasis

Huang¹,

Xu²,

Lefever³

et al. 2017

Toxicology and Applied Pharmacology

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Although studies have linked soy phytoestrogen 4,7,4-trihydroxyisoflavone genistein (GEN) to reduced type 1 diabetes (T1D) risk, the mechanism of dietary GEN on T1D remains unknown. In our studies, adult non-obese diabetic (NOD) mouse model was employed to investigate the effects of GEN exposure on blood glucose level (BGL), glucose tolerance, gut microbiome, and immune responses. Adult male and female NOD mice were fed with either soy-based or casein-based diet, and received GEN at 20 mg/kg body weight by gavage daily. The BGL and immune responses (represented by serum antibodies, cytokines and chemokines, and histopathology) were monitored, while the fecal gut microbiome was sequenced for 16S ribosomal RNA to reveal any alterations in gut microbial communities. A significantly reduced BGL was found in NOD males fed with soy-based diet on day 98 after initial dosing and an improved glucose tolerance was observed on both diets. In addition, an anti-inflammatory response (suggested by reduced IgG2b and cytokine/chemokine levels, and alterations in the microbial taxonomy) was accompanied by an altered β-diversity in gut microbial species. Among the NOD females exposed to GEN, a later onset of T1D was observed. However, the profiles of gut microbiome, antibodies and cytokines/chemokines were all indicative of pro-inflammation This study demonstrated an association among GEN exposure, gut microbiome alteration, and immune homeostasis in NOD males. Although the mechanisms underlying the protective effects of GEN in NOD mice need to be explored further, the current study suggested a GEN-induced sex-specific effect in inflammatory status and gut microbiome.

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Section: Methodsmentioning

confidence: 99%

Genistein prevention of hyperglycemia and improvement of glucose tolerance in adult non-obese diabetic mice are associated with alterations of gut microbiome and immune homeostasis

Huang¹,

Xu²,

Lefever³

et al. 2017

Toxicology and Applied Pharmacology

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“…We sheared 10-138 ng input DNA to a target size of approximately 600 bp by sonication using a Diagenode BioRuptor (Diagenode Inc., Denville, NJ, USA), and this product served as input for a modified genomic DNA library preparation protocol (Kapa Hyper Prep Library Kit, Kapa Biosystems) that included SPRI bead cleanup using an AMPure substitute [37] and custom dual-indexing barcodes [38]. For UCE enrichment, we pooled 8-10 libraries together at equimolar concentrations and adjusted pool concentrations to 147 ng ml 21 .…”

Section: Materials and Methods (A) Taxon Samplingmentioning

confidence: 99%

The acacia ants revisited: convergent evolution and biogeographic context in an iconic ant/plant mutualism

Ward

Branstetter

2017

Proc. R. Soc. B.

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Phylogenetic and biogeographic analyses can enhance our understanding of multispecies interactions by placing the origin and evolution of such interactions in a temporal and geographical context. We use a phylogenomic approach—ultraconserved element sequence capture—to investigate the evolutionary history of an iconic multispecies mutualism: Neotropical acacia ants ( Pseudomyrmex ferrugineus group) and their associated Vachellia hostplants. In this system, the ants receive shelter and food from the host plant, and they aggressively defend the plant against herbivores and competing plants. We confirm the existence of two separate lineages of obligate acacia ants that convergently occupied Vachellia and evolved plant-protecting behaviour, from timid ancestors inhabiting dead twigs in rainforest. The more diverse of the two clades is inferred to have arisen in the Late Miocene in northern Mesoamerica, and subsequently expanded its range throughout much of Central America. The other lineage is estimated to have originated in southern Mesoamerica about 3 Myr later, apparently piggy-backing on the pre-existing mutualism. Initiation of the Pseudomyrmex / Vachellia interaction involved a shift in the ants from closed to open habitats, into an environment with more intense plant herbivory. Comparative studies of the two lineages of mutualists should provide insight into the essential features binding this mutualism.

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“…New microsatellites were developed by sequencing randomly sheared DNA from wild-caught voucher specimen MRT04 (Supplementary Table S1), using the iTru library protocol and a 600 cycle MiSeq v3 sequencing kit (Glenn et al, 2016;Schmidt et al, 2016). Sequences containing microsatellite motifs with uninterrupted length of > = 15 were extracted from merged paired-end reads using the QDD pipeline version 3.1 (Meglécz et al, 2014).…”

Section: Molecular Methodsmentioning

confidence: 99%

Conservation genetics of the Mary River turtle (Elusor macrurus) in natural and captive populations

Schmidt

Espinoza²,

Connell³

et al. 2017

Aquatic Conservation

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1. Many thousands of Mary River turtle eggs were harvested for the pet trade in the 1960s and 1970s before it was recognized as a new species in a unique genus. Pet turtles and their descendants still survive in captive collections. Elusor macrurus is now an endangered species after suffering dramatic population declines along the single Australian river that constitutes its entire range. 2. A conservation genetic assessment was conducted to evaluate population subdivision within the remaining wild population of the Mary River turtle; to compare diversity of the wild population with a captive sample derived from the pet trade; and to establish a baseline estimate of effective population size (N e ) to assist with future monitoring and recovery. 3. Microsatellite analysis indicated panmixia throughout most of the Mary River catchment with the exception of one downstream tributary -Tinana Creek (pop. Specific F ST = 0.154). Subdivision between Tinana Creek and Mary River is a feature common to multiple co-distributed freshwater taxa including the threatened Australian lungfish and Mary River cod. Microsatellite diversity of the wild adult population was low (average H S = 0.554) and not significantly different from that of a sample of captive turtles from the pet tradeindicating genetic diversity may be well represented in captive stocks. Mitochondrial DNA diversity was extremely limited, with only two haplotypes found in the wild and a single shared haplotype in captive turtles.4. Estimates of N e applicable to the entire species in the wild were~136 and~158 using two independent methods. A reasonable management objective should be retention of N e levels >100 during recovery of the species. Additional recommendations include that Mary River turtles be listed as Critically Endangered, and that a recovery plan be developed that considers 'headstarting'using captive bred stocks to supplement the wild population.

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Adapterama I: Universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

Cited by 123 publications

References 45 publications

Genistein prevention of hyperglycemia and improvement of glucose tolerance in adult non-obese diabetic mice are associated with alterations of gut microbiome and immune homeostasis

Genistein prevention of hyperglycemia and improvement of glucose tolerance in adult non-obese diabetic mice are associated with alterations of gut microbiome and immune homeostasis

The acacia ants revisited: convergent evolution and biogeographic context in an iconic ant/plant mutualism

Conservation genetics of the Mary River turtle (Elusor macrurus) in natural and captive populations

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