Using indaziflam for integrated weed management in managed and natural ecosystems

2020 Fall.Includes bibliographical references.Indaziflam is a relatively new herbicide for natural area weed management. It is unique because it inhibits cellulose biosynthesis and it controls annual weeds as the seeds germinate. This soil active herbicide provides the opportunity to control winter annual grasses and annual broadleaf weeds without impacting established perennial grasses and forbs. These characteristics are key to managing weeds, while promoting the growth of native vegetation. Indaziflam was a key component in the development of an integrated weed management plan for Denver International Airport (DEN). DEN supports a diverse set of landscapes, from the Pena Boulevard Transport Corridor to shortgrass prairie, natural areas, and riparian corridors. DEN is faced with several challenges when managing vegetation, with weed invasion being one of the most important. Kochia (Bassia scoparia) and downy brome (Bromus tectorum L.) pose the greatest threats to desirable vegetation and healthy, sustainable ecosystems. Kochia is an invasive broadleaf that is a prolific seed producer and can spread quickly. Downy brome is also a highly invasive winter annual grass that can fill open niches in native plant communities. Current vegetation management at DEN does not adequately control weeds and does not promote the growth of desirable vegetation. Therefore, site-specific research assessing passive and active restoration practices was conducted to develop a landscape management plan to help improve and promote native vegetation. Two research studies were established at DEN, both with remnant native grasses that were also invaded by downy brome and kochia. The objective was to demonstrate passive restoration. We hypothesized that weed control using indaziflam and other post-emergent herbicides would provide 2+ years of control. Downy brome, kochia, and perennial grass cover and biomass were collected in 2019 and 2020 to measure herbicide impacts and plant community responses. Averaged across both sites, downy brome cover, 2 years after treatment (YAT), was reduced to < 2% in all indaziflam plots compared to the control (~75% cover). At both sites, perennial grass biomass increased 5- to 10 – fold once downy brome competition was removed. These invaded sites with remnant grass populations responded positively with timely weed management. Active restoration was employed at two sites that were void of desirable grass species. Perennial grasses were drill seeded and protected from weed competition with adaptive weed management, primarily with selective herbicides. With adequate weed control and supplemental irrigation, crested wheatgrass was the only grass that successfully established (83% stand frequency). This study illustrates the challenges associated with revegetating degraded sites and the necessity of providing adaptive weed management. Furthermore, the information derived from these studies was used to develop management prioritization categories to assist DEN in making strategic decisions for managing weeds and restoring sites across the airport property. The final management plan represents the culmination of the site-specific, research-based recommendations made and will be utilized by DEN land management to improve current practices. This project also demonstrated the utility of using indaziflam in a managed ecosystem. In natural ecosystems invaded by downy brome, indaziflam provides similar opportunities for passive restoration. Downy brome produces large amounts of litter in these ecosystems that act as continuous fine fuel. Prescribed burning is often used as a tool to remove plant litter and provide downy brome control and can be followed by herbicide treatments to extend control; however, combining prescribed burning with indaziflam has not been evaluated. We hypothesized that removing the litter layer using prescribed fire before applying indaziflam alone or combined with post-emergent herbicides would increase herbicide efficacy and extend downy brome control. In September 2017, two downy-brome infested sites were burned. In March 2018, indaziflam was applied alone or in combination with post-emergent herbicides to the burned area as well as non-burned plots. Downy brome cover and the desirable plant community responses were evaluated to determine burning and treatment effects. Downy brome cover was reduced in all herbicide treatments in the burned plots compared to the non-burned plots at both sites 2 years after treatment (YAT) (Site 1 - 6.5% ± 1.2 SE vs. 19.8% ± 2.6; Site 2 - 7% ± 1.5 vs. 15.5% ± 1.7). Desirable plant species cover, richness, and diversity were not negatively impacted by burning or herbicide treatments. Perennial cool-season grass cover responded positively to burning at site 1, while the perennial forb community responded positively to burning at site 2. Plant diversity and species richness also increased at site 2 in the burned plots which was due to the increase in the number of native forb species. This study demonstrates that burning extended downy brome control even at lower indaziflam use rates, without reducing the diversity of the desirable plant community. This research also demonstrates the utility of using indaziflam in natural ecosystems

Simultaneous amplicon sequencing to explore co- occurrence patterns of bacterial, archaeal and eukaryotic microorganisms in rumen microbial communities

Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats

Nutrient-based diet modifications impact on the gut microbiome of the Javan slow loris (Nycticebus javanicus)

Environment and diet are key factors which shape the microbiome of organisms. There is also a disparity between captive and wild animals of the same species, presumably because of the change in diet. Being able to reverse the microbiome to the wild type is thus particularly important for the reintroduction efforts of Critically Endangered animals. The Javan slow loris (Nycticebus javanicus) is a suitable model, being kept in the thousands within rescue centres throughout Southeast Asia. With next-generation sequencing, we show how a naturalistic diet impacts the gut microbiome of captive slow lorises (Primates: Nycticebus). A comparison of the microbiome of wild animals with captive animals that had been fed a standard captive or improved diet reveals strong microbiome differences between wild and captive animals; however, diet changes failed to alter the microbiome of captive populations significantly. Bifidobacterium was the most abundant genus in wild animals (46.7%) while Bacteroides (11.6%) and Prevotella (18.9%) were the most abundant in captive animals fed the captive and improved diets, respectively. Correlation analyses of nutrients with microbial taxa suggest important implications in using nutrition to suppress potential pathogens, with soluble fibre and water-soluble carbohydrates both being associated with opposing microbiome profiles. The improved diet significantly increased microbe diversity, which exemplifies the importance of high fibre diets; however, wild individuals had lower diversity, which contradicts recent studies. Detection of methanogens appeared to be dependent on diet and whether the animals were living in captivity or in the wild. This study highlights the potential of nutrition in modulating the microbiome of animals prior to release. Unexpectedly, the results were not as significant as has been suggested in recent studies

The Ty1 integrase protein can exploit the classical nuclear protein import machinery for entry into the nucleus

Like its retroviral relatives, the long terminal repeat retrotransposon Ty1 in the yeast Saccharomyces cerevisiae must traverse a permanently intact nuclear membrane for successful transposition and replication. For retrotransposition to occur, at least a subset of Ty1 proteins, including the Ty1 integrase, must enter the nucleus. Nuclear localization of integrase is dependent upon a C-terminal nuclear targeting sequence. However, the nuclear import machinery that recognizes this nuclear targeting signal has not been defined. We investigated the mechanism by which Ty1 integrase gains access to nuclear DNA as a model for how other retroelements, including retroviruses like HIV, may utilize cellular nuclear transport machinery to import their essential nuclear proteins. We show that Ty1 retrotransposition is significantly impaired in yeast mutants that alter the classical nuclear protein import pathway, including the Ran-GTPase, and the dimeric import receptor, importin-α/β. Although Ty1 proteins are made and processed in these mutant cells, our studies reveal that an integrase reporter is not properly targeted to the nucleus in cells carrying mutations in the classical nuclear import machinery. Furthermore, we demonstrate that integrase coimmunoprecipitates with the importin-α transport receptor and directly binds to importin-α. Taken together, these data suggest Ty1 integrase can employ the classical nuclear protein transport machinery to enter the nucleus

A comprehensive 1000 Genomes-based genome-wide association meta-analysis of coronary artery disease

Existing knowledge of genetic variants affecting risk of coronary artery disease (CAD) is largely based on genome-wide association studies (GWAS) analysis of common SNPs. Leveraging phased haplotypes from the 1000 Genomes Project, we report a GWAS meta-analysis of 185 thousand CAD cases and controls, interrogating 6.7 million common (MAF>0.05) as well as 2.7 million low frequency (0.005<MAF<0.05) variants. In addition to confirmation of most known CAD loci, we identified 10 novel loci, eight additive and two recessive, that contain candidate genes that newly implicate biological processes in vessel walls. We observed intra-locus allelic heterogeneity but little evidence of low frequency variants with larger effects and no evidence of synthetic association. Our analysis provides a comprehensive survey of the fine genetic architecture of CAD showing that genetic susceptibility to this common disease is largely determined by common SNPs of small effect siz

Common Variants at 10 Genomic Loci Influence Hemoglobin A(1C) Levels via Glycemic and Nonglycemic Pathways

OBJECTIVE-Glycated hemoglobin (HbA(1c)), used to monitor and diagnose diabetes, is influenced by average glycemia over a 2- to 3-month period. Genetic factors affecting expression, turnover, and abnormal glycation of hemoglobin could also be associated with increased levels of HbA(1c). We aimed to identify such genetic factors and investigate the extent to which they influence diabetes classification based on HbA(1c) levels.RESEARCH DESIGN AND METHODS-We studied associations with HbA(1c) in up to 46,368 nondiabetic adults of European descent from 23 genome-wide association studies (GWAS) and 8 cohorts with de novo genotyped single nucleotide polymorphisms (SNPs). We combined studies using inverse-variance meta-analysis and tested mediation by glycemia using conditional analyses. We estimated the global effect of HbA(1c) loci using a multilocus risk score, and used net reclassification to estimate genetic effects on diabetes screening.RESULTS-Ten loci reached genome-wide significant association with HbA(1c), including six new loci near FN3K (lead SNP/P value, rs1046896/P = 1.6 x 10(-26)), HFE (rs1800562/P = 2.6 x 10(-20)), TMPRSS6 (rs855791/P = 2.7 x 10(-14)), ANK1 (rs4737009/P = 6.1 x 10(-12)), SPTA1 (rs2779116/P = 2.8 x 10(-9)) and ATP11A/TUBGCP3 (rs7998202/P = 5.2 x 10(-9)), and four known HbA(1c) loci: HK1 (rs16926246/P = 3.1 x 10(-54)), MTNR1B (rs1387153/P = 4.0 X 10(-11)), GCK (rs1799884/P = 1.5 x 10(-20)) and G6PC2/ABCB11 (rs552976/P = 8.2 x 10(-18)). We show that associations with HbA(1c) are partly a function of hyperglycemia associated with 3 of the 10 loci (GCK, G6PC2 and MTNR1B). The seven nonglycemic loci accounted for a 0.19 (%HbA(1c)) difference between the extreme 10% tails of the risk score, and would reclassify similar to 2% of a general white population screened for diabetes with HbA(1c).CONCLUSIONS-GWAS identified 10 genetic loci reproducibly associated with HbA(1c). Six are novel and seven map to loci where rarer variants cause hereditary anemias and iron storage disorders. Common variants at these loci likely influence HbA(1c) levels via erythrocyte biology, and confer a small but detectable reclassification of diabetes diagnosis by HbA(1c) Diabetes 59: 3229-3239, 201

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes

Occipital nerve block is effective in craniofacial neuralgias but not in idiopathic persistent facial pain

Occipital nerve block (ONB) has been used in several primary headache syndromes with good results. Information on its effects in facial pain is sparse. In this chart review, the efficacy of ONB using lidocaine and dexamethasone was evaluated in 20 patients with craniofacial pain syndromes comprising 8 patients with trigeminal neuralgia, 6 with trigeminal neuropathic pain, 5 with persistent idiopathic facial pain and 1 with occipital neuralgia. Response was defined as an at least 50% reduction of original pain. Mean response rate was 55% with greatest efficacy in trigeminal (75%) and occipital neuralgia (100%) and less efficacy in trigeminal neuropathic pain (50%) and persistent idiopathic facial pain (20%). The effects lasted for an average of 27 days with sustained benefits for 69, 77 and 107 days in three patients. Side effects were reported in 50%, albeit transient and mild in nature. ONBs are effective in trigeminal pain involving the second and third branch and seem to be most effective in craniofacial neuralgias. They should be considered in facial pain before more invasive approaches, such as thermocoagulation or vascular decompression, are performed, given that side effects are mild and the procedure is minimally invasive