A multi-omic survey of black cottonwood tissues highlights coordinated transcriptomic and metabolomic mechanisms for plant adaptation to phosphorus deficiency.

Introduction: Phosphorus (P) deficiency in plants creates a variety of metabolic perturbations that decrease photosynthesis and growth. Phosphorus deficiency is especially challenging for the production of bioenergy feedstock plantation species, such as poplars ( spp.), where fertilization may not be practically or economically feasible.

Clinical evaluation of a Borrelia modified two-tiered testing (MTTT) shows increased early sensitivity for Borrelia burgdorferi but not other endemic Borrelia species in a high incidence region for Lyme disease in Wisconsin.

A modified two-tiered testing algorithm (MTTT; ZEUS Scientific) for Borrelia burgdorferi was recently FDA-cleared. We evaluated the MTTT algorithm to confirm Lyme disease and compared the findings in parallel with those obtained using standard two-tiered testing (STTT). Medical records from patients who submitted sera for laboratory confirmation of Lyme-like disease were reviewed.

Dynamics of organic matter molecular composition under aerobic decomposition and their response to the nitrogen addition in grassland soils.

Grassland soils store a substantial proportion of the global soil carbon (C) stock. The transformation of C in grassland soils with respect to chemical composition and persistence strongly regulate the predicted terrestrial-atmosphere C flux in global C biogeochemical cycling models. In addition, increasing atmospheric nitrogen (N) deposition alters C chemistry in grassland soils.

Detection of IFN-γ Secretion in Blood Samples Collected Before and After Treatment of Varying Stages of Lyme Disease.

Background: QuantiFERON enzyme-linked immunosorbent assay (ELISA; Qiagen) with Borrelia burgdorferi peptide antigens was previously shown to reliably detect interferon-γ (IFN-γ) in blood samples from adult patients with early Lyme disease and the response disappeared rapidly after treatment. We evaluated the response before and after appropriate antibiotic therapy in adolescent and adult subjects with more diverse stages of the illness.

Methods: Blood was obtained from patients with clinician-identified Lyme disease with constitutional complaints, erythema migrans, nerve palsy, cardiac abnormality, or arthritis before (n = 68) and 6 weeks (n = 46) and 6 months (n = 45) after therapy.

Strong mineralogic control of soil organic matter composition in response to nutrient addition across diverse grassland sites.

Soil organic matter (SOM) dynamics are central to soil biogeochemistry and fertility. The retention of SOM is governed initially by interactions with minerals, which mediate the sorption of chemically diverse organic matter (OM) molecules via distinct surface areas and chemical functional group availabilities. Unifying principles of mineral-OM interactions remain elusive because of the multi-layered nature of biochemical-mineral interactions that contribute to soil aggregate formation and the heterogeneous nature of soils among ecosystems.

Detection of antibodies to decorin-binding protein A (DbpA) and DbpB after infection of dogs with by tick challenge.

We characterized the antibody response to decorin-binding protein A (DbpA) or DbpB from immune serum samples collected from 27 dogs infected with by ticks. Immunoglobulin M (IgM) antibodies to DbpA or DbpB were rarely detected, but high levels of IgG antibodies to DbpA were detected in 16 of 27 of the immune sera collected 1 mo after infection, 20 of 25 of the sera collected after 2 mo, and each of the 23, 17, or 11 serum samples evaluated after 3, 4, or 5 mo, respectively. In addition, IgG antibodies to DbpB were detected in 22 of 27 ( = 0.

The total microbiome functions in bacteria and fungi.

Unveiling the relationship between phylogeny and function of the microbiome is crucial to determine its contribution to ecosystem functioning. However, while there is a considerable amount of information on microbial phylogenetic diversity, our understanding of its relationship to functional diversity is still scarce. Here we predicted the total microbiome functions of bacteria and fungi on Earth using the total known functions from level 3 of KEGG Orthology by modelling the increase of functions with increasing diversity of bacteria or fungi.

Evaluation of a Novel Multiplex High-Definition PCR Assay for Detection of Tick-Borne Pathogens in Whole-Blood Specimens.

The prevalence of tick-borne infections has been steadily increasing in both number and geographic distribution in the United States and abroad. This increase, in conjunction with the continued recognition of novel pathogens transmitted by ticks, has made accurate diagnosis of these infections challenging. Mainstay serologic tests are insensitive during the acute phase of infection and are often cross-reactive with similar pathogenic and nonpathogenic organisms.

Determining the Reliability of Measuring Mercury Cycling Gene Abundance with Correlations with Mercury and Methylmercury Concentrations.

Methylmercury (MeHg) is a bioaccumulative toxic contaminant in many ecosystems, but factors governing its production are poorly understood. Recent work has shown that the anaerobic microbial conversion of mercury (Hg) to MeHg requires the Hg-methylation genes and that these genes can be used as biomarkers in PCR-based estimators of Hg-methylator abundance. In an effort to determine reliable methods for assessing abundance and diversity and linking them to MeHg concentrations, multiple approaches were compared including metagenomic shotgun sequencing, 16S rRNA gene pyrosequencing and cloning/sequencing gene products.

Identification of metabolite and protein explanatory variables governing microbiome establishment and re-establishment within a cellulose-degrading anaerobic bioreactor.

Proteins, metabolites, and 16S rRNA measurements were used to examine the community structure and functional relationships within a cellulose degrading anaerobic bioreactor. The bioreactor was seeded with bovine rumen fluid and operated with a 4 day hydraulic retention time on cellulose (avicel) as sole carbon and energy source. The reactor performance and microbial community structure was monitored during the establishment of the cellulose-degrading community.

Specialized proteomic responses and an ancient photoprotection mechanism sustain marine green algal growth during phosphate limitation.

Marine algae perform approximately half of global carbon fixation, but their growth is often limited by the availability of phosphate or other nutrients. As oceans warm, the area of phosphate-limited surface waters is predicted to increase, resulting in ocean desertification. Understanding the responses of key eukaryotic phytoplankton to nutrient limitation is therefore critical.

Physiological and proteomic analyses of Fe(III)-reducing co-cultures of Desulfotomaculum reducens MI-1 and Geobacter sulfurreducens PCA.

We established Fe(III)-reducing co-cultures of two species of metal-reducing bacteria, the Gram-positive Desulfotomaculum reducens MI-1 and the Gram-negative Geobacter sulfurreducens PCA. Co-cultures were given pyruvate, a substrate that D. reducens can ferment and use as electron donor for Fe(III) reduction.

Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode.

Internodes of grass stems function in mechanical support, transport, and, in some species, are a major sink organ for carbon in the form of cell wall polymers. This study reports cell wall composition, proteomic, and metabolite analyses of the rice elongating internode. Cellulose, lignin, and xylose increase as a percentage of cell wall material along eight segments of the second rice internode (internode II) at booting stage, from the younger to the older internode segments, indicating active cell wall synthesis.

T2 Magnetic Resonance Assay-Based Direct Detection of Three Lyme Disease-Related Borrelia Species in Whole-Blood Samples.

In early Lyme disease (LD), serologic testing is insensitive and seroreactivity may reflect active or past infection. In this study, we evaluated a novel assay for the direct detection of three species of spirochetes in whole blood. The T2 magnetic resonance (T2MR) assay platform was used to amplify DNA released from intact spirochetes and to detect amplicon.

Borrelia miyamotoi Infection in Patients from Upper Midwestern United States, 2014-2015.

We confirmed Borrelia miyamotoi infection in 7 patients who had contracted an illness while near La Crosse, Wisconsin, USA, an area where Ixodes scapularis ticks are endemic. B. miyamatoi infection should now be considered among differential diagnoses for patients from the midwestern United States who have signs and symptoms suggestive of tickborne illness.

Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants.

Background: Prasinophytes are widespread marine green algae that are related to plants. Cellular abundance of the prasinophyte Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these unicellular eukaryotes are important for marine ecology and for understanding Viridiplantae evolution and diversification.

Detection of IFN-γ Secretion by T Cells Collected Before and After Successful Treatment of Early Lyme Disease.

Background: Current serodiagnostics for Lyme disease lack sensitivity during early disease, and cannot determine treatment response. We evaluated an assay based on QuantiFERON technology utilizing peptide antigens derived from Borrelia burgdorferi to stimulate interferon-gamma (IFN-γ) release as an alternative to serodiagnosis for the laboratory detection of Lyme disease.

Methods: Blood was obtained from patients with erythema migrans before (n = 29) and 2 months after (n = 27) antibiotic therapy.

Comparative Proteomic Analysis of Desulfotomaculum reducens MI-1: Insights into the Metabolic Versatility of a Gram-Positive Sulfate- and Metal-Reducing Bacterium.

The proteomes of the metabolically versatile and poorly characterized Gram-positive bacterium Desulfotomaculum reducens MI-1 were compared across four cultivation conditions including sulfate reduction, soluble Fe(III) reduction, insoluble Fe(III) reduction, and pyruvate fermentation. Collectively across conditions, we observed at high confidence ~38% of genome-encoded proteins. Here, we focus on proteins that display significant differential abundance on conditions tested.

Evaluating Models of Cellulose Degradation by Fibrobacter succinogenes S85.

Fibrobacter succinogenes S85 is an anaerobic non-cellulosome utilizing cellulolytic bacterium originally isolated from the cow rumen microbial community. Efforts to elucidate its cellulolytic machinery have resulted in the proposal of numerous models which involve cell-surface attachment via a combination of cellulose-binding fibro-slime proteins and pili, the production of cellulolytic vesicles, and the entry of cellulose fibers into the periplasmic space. Here, we used a combination of RNA-sequencing, proteomics, and transmission electron microscopy (TEM) to further clarify the cellulolytic mechanism of F.

Molecular dissection of a putative iron reductase from Desulfotomaculum reducens MI-1.

Desulfotomaculum reducens MI-1 is a Firmicute strain capable of reducing a variety of heavy metal ions and has a great potential in heavy metal bioremediation. We recently identified Dred_2421 as a potential iron reductase through proteomic study of D. reducens.

The Emergence of Clinically Relevant Babesiosis in Southwestern Wisconsin.

Objective: To determine the frequency and characteristics of babesiosis cases, and to assess the impact of the introduction of a tick-borne infection diagnostic panel on babesiosis diagnosis in the region surrounding La Crosse, Wisconsin, where babesiosis in non-travelers was previously rare.

Methods: In the spring of 2013, we conducted a point-in-time survey of Ixodes scopuloris ticks for the presence of Babesia microti. We also conducted a retrospective study of all babesiosis cases diagnosed in our health system between January 1, 2004, and November 1, 2013.

Antibody responses to Borrelia burgdorferi outer surface proteins C and F in experimentally infected Beagle dogs.

Antibody levels to outer surface proteins C and F (OspC and OspF, respectively) in sera collected from laboratory Beagle dogs at 1, 2, and 4 months after challenge with infected black-legged ticks (Ixodes scapularis) were determined. Each dog was confirmed by culture to harbor Borrelia burgdorferi in the skin (n = 10) or the skin and joints (n = 14). Significant levels of immunoglobulin M (Ig)M or IgG anti-OspC antibodies were detected in single serum samples from only 3 (13%) dogs.