BoGH13ASus from Bacteroides ovatus represents a novel α-amylase used for Bacteroides starch breakdown in the human gut.

Members of the Bacteroidetes phylum in the human colon deploy an extensive number of proteins to capture and degrade polysaccharides. Operons devoted to glycan breakdown and uptake are termed polysaccharide utilization loci or PUL. The starch utilization system (Sus) is one such PUL and was initially described in Bacteroides thetaiotaomicron (Bt). BtSus is highly conserved across many species, except for its extracellular α-amylase, SusG. In this work, we show that the Bacteroides ovatus (Bo) extracellular α-amylase, BoGH13ASus, is distinguished from SusG in its evolutionary origin and its domain architecture and by being the most prevalent form in Bacteroidetes Sus. BoGH13ASus is the founding member of both a novel subfamily in the glycoside hydrolase family 13, GH13_47, and a novel carbohydrate-binding module, CBM98. The BoGH13ASus CBM98-CBM48-GH13_47 architecture differs from the CBM58 embedded within the GH13_36 of SusG. These domains adopt a distinct spatial orientation and invoke a different association with the outer membrane. The BoCBM98 binding site is required for Bo growth on polysaccharides and optimal enzymatic degradation thereof. Finally, the BoGH13ASus structure features bound Ca2+ and Mn2+ ions, the latter of which is novel for an α-amylase. Little is known about the impact of Mn2+ on gut bacterial function, much less on polysaccharide consumption, but Mn2+ addition to Bt expressing BoGH13ASus specifically enhances growth on starch. Further understanding of bacterial starch degradation signatures will enable more tailored prebiotic and pharmaceutical approaches that increase starch flux to the gut.

Infrared Photoactivation Enables Improved Native Top-Down Mass Spectrometry of Transmembrane Proteins.

Membrane proteins are often challenging targets for native top-down mass spectrometry experimentation. The requisite use of membrane mimetics to solubilize such proteins necessitates the application of supplementary activation methods to liberate protein ions prior to sequencing, which typically limits the sequence coverage achieved. Recently, infrared photoactivation has emerged as an alternative to collisional activation for the liberation of membrane proteins from surfactant micelles. However, much remains unknown regarding the mechanism by which IR activation liberates membrane protein ions from such micelles, the extent to which such methods can improve membrane protein sequence coverage, and the degree to which such approaches can be extended to support native proteomics. Here, we describe experiments designed to evaluate and probe infrared photoactivation for membrane protein sequencing, proteoform identification, and native proteomics applications. Our data reveal that infrared photoactivation can dissociate micelles composed of a variety of detergent classes, without the need for a strong IR chromophore by leveraging the relatively weak association energies of such detergent clusters in the gas phase. Additionally, our data illustrate how IR photoactivation can be extended to include membrane mimetics beyond micelles and liberate proteins from nanodiscs, liposomes, and bicelles. Finally, our data quantify the improvements in membrane protein sequence coverage produced through the use of IR photoactivation, which typically leads to membrane protein sequence coverage values ranging from 40 to 60%.

Development of an Automated, High-Throughput Methodology for Native Mass Spectrometry and Collision-Induced Unfolding.

Native ion mobility mass spectrometry (nIM-MS) has emerged as a useful technology for the rapid evaluation of biomolecular structures. When combined with collisional activation in a collision-induced unfolding (CIU) experiment, nIM-MS experimentation can be leveraged to gain greater insight into biomolecular conformation and stability. However, nIM-MS and CIU remain throughput limited due to nonautomated sample preparation and introduction. Here, we explore the use of a RapidFire robotic sample handling system to develop an automated, high-throughput methodology for nMS and CIU. We describe native RapidFire-MS (nRapidFire-MS) capable of performing online desalting and sample introduction in as little as 10 s per sample. When combined with CIU, our nRapidFire-MS approach can be used to collect CIU fingerprints in 30 s following desalting by using size exclusion chromatography cartridges. When compared to nMS and CIU data collected using standard approaches, ion signals recorded by nRapidFire-MS exhibit identical ion collision cross sections, indicating that the same conformational populations are tracked by the two approaches. Our data further suggest that nRapidFire-MS can be extended to study a variety of biomolecular classes, including proteins and protein complexes ranging from 5 to 300 kDa and oligonucleotides. Furthermore, nRapidFire-MS data acquired for biotherapeutics suggest that nRapidFire-MS has the potential to enable high-throughput nMS analyses of biopharmaceutical samples. We conclude by discussing the potential of nRapidFire-MS for enabling the development of future CIU assays capable of catalyzing breakthroughs in protein engineering, inhibitor discovery, and formulation development for biotherapeutics.

Performance evaluation of in-source ion activation hardware for collision-induced unfolding of proteins and protein complexes on a drift tube ion mobility-mass spectrometer.

Native ion mobility-mass spectrometry (IM-MS) has emerged as an information-rich technique for gas phase protein structure characterization; however, IM resolution is currently insufficient for the detection of subtle structural differences in large biomolecules. This challenge has spurred the development of collision-induced unfolding (CIU) which utilizes incremental gas phase activation to unfold a protein in order to expand the number of measurable descriptors available for native protein ions. Although CIU is now routinely used in native mass spectrometry studies, the interlaboratory reproducibility of CIU has not been established. Here we evaluate the reproducibility of the CIU data produced across three laboratories (University of Michigan, Texas A&M University, and Vanderbilt University). CIU data were collected for a variety of protein ions ranging from 8.6-66 kDa. Within the same laboratory, the CIU fingerprints were found to be repeatable with root mean square deviation (RMSD) values of less than 5%. Collision cross section (CCS) values of the CIU intermediates were consistent across the laboratories, with most features exhibiting an interlaboratory reproducibility of better than 1%. In contrast, the activation potentials required to induce protein CIU transitions varied between the three laboratories. To address these differences, three source assemblies were constructed with an updated ion activation hardware design utilizing higher mechanical tolerance specifications. The production-grade assemblies were found to produce highly consistent CIU data for intact antibodies, exhibiting high precision ion CCS and CIU transition values, thus opening the door to establishing databases of CIU fingerprints to support future biomolecular classification efforts.

Spatiotemporal variation in the fecal microbiota of mule deer is associated with proximate and future measures of host health.

BACKGROUND: Mule deer rely on fat and protein stored prior to the winter season as an energy source during the winter months when other food sources are sparse. Since associated microorganisms ('microbiota') play a significant role in nutrient metabolism of their hosts, we predicted that variation in the microbiota might be associated with nutrient storage and overwintering in mule deer populations. To test this hypothesis we performed a 16S rRNA marker gene survey of fecal samples from two deer populations in the western United States before and after onset of winter. RESULTS: PERMANOVA analysis revealed the deer microbiota varied interactively with geography and season. Further, using metadata collected at the time of sampling, we were able to identify different fecal bacterial taxa that could potentially act as bioindicators of mule deer health outcomes. First, we identified the abundance of Collinsella (family: Coriobacteriaceae) reads as a possible predictor of poor overwintering outcomes for deer herds in multiple locations. Second, we showed that reads assigned to the Bacteroides and Mollicutes Order RF39 were both positively correlated with deer protein levels, leading to the idea that these sequences might be useful in predicting mule deer protein storage. CONCLUSIONS: These analyses confirm that variation in the microbiota is associated with season-dependent health outcomes in mule deer, which may have useful implications for herd management strategies.

Lesions of Mycobacterium avium spp. hominissuis Infection Resembling M. bovis Lesions in a Wild Mule Deer, Canada1.

We used molecular analyses to confirm Mycobacterium avium spp. hominissuis infection in lung granulomas and pyogranulomas in the tracheobronchial lymph node in a wild mule deer in Banff, Canada. These lesions are similar to those found in M. bovis-infected animals, emphasizing the critical need for disease surveillance in wildlife populations.

Fire, rodent herbivory, and plant competition: implications for invasion and altered fire regimes in the Mojave Desert.

Biological invasions are responsive to changing wildfire regimes related to human activities that are altering biological communities. Our objective was to investigate how fire, rodent activity, and competition among plant species modify plant community structure, invasion patterns, and vulnerability to altered fire regimes. We imposed experimental fires, and reduced rodent density using fencing in a full factorial design and quantified competitive interactions among plant species in the northeast Mojave Desert that has experienced dramatic increases in plant invasion and fire in recent years. Vegetation surveys were conducted in the experimental plots to determine plant density, cover, and biomass of herbaceous plants over a 5-year period. Rodent exclusion increased the density, cover, and biomass of Bromus rubens, an invasive annual grass, and density of forb species. In contrast, rodent exclusion decreased the density, cover, and biomass of Schismus spp. another dominant annual invader. Fire increased Schismus spp. and forb species density, cover, and biomass but decreased B. rubens density. Negative spatial correlation between B. rubens and Schismus spp., and forbs indicated interspecific competition among the dominant plant species. Fire reduced rodent community diversity (Shannon's) 2.5-fold, which was correlated with increases in B. rubens cover and biomass, and native forb diversity. Fire, high rodent diversity, and competition from the other plant species may decrease fire potential in our study system by reducing the density and biomass of B. rubens, which because of its taller growth form tends to ignite and carry fire better than Schismus spp. and forbs.

Measurement of the Effective Weak Mixing Angle in pp[over ¯]→Z/γ

We present a measurement of the effective weak mixing angle parameter sin^{2}θ_{eff}^{ℓ} in pp[over ¯]→Z/γ^{*}→µ^{+}µ^{-} events at a center-of-mass energy of 1.96 TeV, collected by the D0 detector at the Fermilab Tevatron Collider and corresponding to 8.6 fb^{-1} of integrated luminosity. The measured value of sin^{2}θ_{eff}^{ℓ}[µµ]=0.23016±0.00064 is further combined with the result from the D0 measurement in pp[over ¯]→Z/γ^{*}→e^{+}e^{-} events, resulting in sin^{2}θ_{eff}^{ℓ}[comb]=0.23095±0.00040. This combined result is the most precise measurement from a single experiment at a hadron collider and is the most precise determination using the coupling of the Z/γ^{*} to light quarks.

Spatial processes decouple management from objectives in a heterogeneous landscape: predator control as a case study.

Predator control is often implemented with the intent of disrupting top-down regulation in sensitive prey populations. However, ambiguity surrounding the efficacy of predator management, as well as the strength of top-down effects of predators in general, is often exacerbated by the spatially implicit analytical approaches used in assessing data with explicit spatial structure. Here, we highlight the importance of considering spatial context in the case of a predator control study in south-central Utah. We assessed the spatial match between aerial removal risk in coyotes (Canis latrans) and mule deer (Odocoileus hemionus) resource selection during parturition using a spatially explicit, multi-level Bayesian model. With our model, we were able to evaluate spatial congruence between management action (i.e., coyote removal) and objective (i.e., parturient deer site selection) at two distinct scales: the level of the management unit and the individual coyote removal. In the case of the former, our results indicated substantial spatial heterogeneity in expected congruence between removal risk and parturient deer site selection across large areas, and is a reflection of logistical constraints acting on the management strategy and differences in space use between the two species. At the level of the individual removal, we demonstrated that the potential management benefits of a removed coyote were highly variable across all individuals removed and in many cases, spatially distinct from parturient deer resource selection. Our methods and results provide a means of evaluating where we might anticipate an impact of predator control, while emphasizing the need to weight individual removals based on spatial proximity to management objectives in any assessment of large-scale predator control. Although we highlight the importance of spatial context in assessments of predator control strategy, we believe our methods are readily generalizable in any management or large-scale experimental framework where spatial context is likely an important driver of outcomes.

The impact of education, country, race and ethnicity on the self-report of postpartum depression using the Edinburgh Postnatal Depression Scale.

BACKGROUND: Universal screening for postpartum depression is recommended in many countries. Knowledge of whether the disclosure of depressive symptoms in the postpartum period differs across cultures could improve detection and provide new insights into the pathogenesis. Moreover, it is a necessary step to evaluate the universal use of screening instruments in research and clinical practice. In the current study we sought to assess whether the Edinburgh Postnatal Depression Scale (EPDS), the most widely used screening tool for postpartum depression, measures the same underlying construct across cultural groups in a large international dataset. METHOD: Ordinal regression and measurement invariance were used to explore the association between culture, operationalized as education, ethnicity/race and continent, and endorsement of depressive symptoms using the EPDS on 8209 new mothers from Europe and the USA. RESULTS: Education, but not ethnicity/race, influenced the reporting of postpartum depression [difference between robust comparative fit indexes (∆*CFI) 0.01), but not between European countries (∆*CFI < 0.01). CONCLUSIONS: Investigators and clinicians should be aware of the potential differences in expression of phenotype of postpartum depression that women of different educational backgrounds may manifest. The increasing cultural heterogeneity of societies together with the tendency towards globalization requires a culturally sensitive approach to patients, research and policies, that takes into account, beyond rhetoric, the context of a person's experiences and the context in which the research is conducted.

Rodent herbivory differentially affects mortality rates of 14 native plant species with contrasting life history and growth form traits.

Ecosystems are transformed by changes in disturbance regimes including wildfire and herbivory. Rodent consumers can have strong top-down effects on plant community assembly through seed predation, but their impacts on post-germination seedling establishment via seedling herbivory need better characterization, particularly in deserts. To test the legacy effects of fire history, and native rodent consumers on seedling establishment, we evaluated factorial combinations of experimental exclusion of rodents and fire history (burned vs. unburned) on seedling survival of 14 native plant species that vary in their life history strategies and growth form in the Mojave Desert. Seedlings were placed into the experimental plots, and seedling survival was monitored daily for 8 days. The legacy effects of fire history had minimal effects on seedling survival, but rodent exclusion, year, and their interaction were strongly significant. Seedling survival rates were nearly sixfold greater in rodent exclusion plots compared to control plots in 2012 (53 vs. 9%) and 17-fold greater in 2013 (17 vs. 1%). The dramatic increase in seedling mortality from 2012 to 2013 was likely driven by an increase in rodent abundance and an outbreak of grasshoppers that appears to have intensified the rodent effect. There was strong variability in plant species survival in response to rodent herbivory with annual plants and forb species showing lower survival than perennial plants and shrub species. These results indicate that rodent consumers can strongly regulate seedling survival of native plant species with potentially strong regulatory effects on plant community development.

Use of stereotactic body radiotherapy for prostate cancer in the United States from 2004 through 2012.

BACKGROUND: Stereotactic body radiotherapy (SBRT) is a newer treatment option for patients with localized prostate cancer. The rates of diffusion of this technology across the United States are unknown. The goal of the current study was to describe the use of SBRT among patients with prostate cancer based on different risk groups (low, intermediate, or high risk) and by type of facility (community cancer program, comprehensive community cancer program, or academic program) in which patients were treated. METHODS: Using the National Cancer Data Base, a national registry that contains approximately 70% of patients with cancer in the United States, the authors identified 274,466 men between the ages of 40 to 80 years who were diagnosed from 2004 to 2012 with localized prostate cancer and received radiation therapy (RT) as their initial treatment. The authors described the prevalence of SBRT use each year, and multivariable analysis was used to examine factors associated with the receipt of SBRT. RESULTS: In 2004, SBRT use was low (<1% in all patient groups), and was observed to increase steadily each year. By 2012, 8.8% of low-risk patients treated at academic centers with RT received SBRT. Uptake of SBRT was highest in patients with low-risk or intermediate-risk disease. Multivariable analysis demonstrated that year of diagnosis, type of center, risk group, and race were all significantly associated with the use of SBRT. CONCLUSIONS: To the authors' knowledge, the current study is the first report of the adoption of SBRT for localized prostate cancer across the United States. Diffusion was noted to be slowest at community cancer programs, reflecting potential barriers of cost or expertise for this new technology. Adoption of SBRT was found to be highest among patients with low-risk or intermediate-risk disease, in accordance with the bulk of patients included in published SBRT studies. Cancer 2016;122:2234-41. © 2016 American Cancer Society.

Evidence for a B_{s}

We report evidence for a narrow structure, X(5568), in the decay sequence X(5568)→B_{s}^{0}π^{±}, B_{s}^{0}→J/ψϕ, J/ψ→µ^{+}µ^{-}, ϕ→K^{+}K^{-}. This is evidence for the first instance of a hadronic state with valence quarks of four different flavors. The mass and natural width of this state are measured to be m=5567.8±2.9(stat)_{-1.9}^{+0.9}(syst) MeV/c^{2} and Γ=21.9±6.4(stat)_{-2.5}^{+5.0}(syst) MeV/c^{2}. If the decay is X(5568)→B_{s}^{*}π^{±}→B_{s}^{0}γπ^{±} with an unseen γ, m(X(5568)) will be shifted up by m(B_{s}^{*})-m(B_{s}^{0})∼49 MeV/c^{2}. This measurement is based on 10.4 fb^{-1} of pp[over ¯] collision data at sqrt[s]=1.96 TeV collected by the D0 experiment at the Fermilab Tevatron collider.

Evidence for Simultaneous Production of J/ψ and ϒ Mesons.

We report evidence for the simultaneous production of J/ψ and ϒ mesons in 8.1 fb^{-1} of data collected at sqrt[s]=1.96 TeV by the D0 experiment at the Fermilab pp[over ¯] Tevatron Collider. Events with these characteristics are expected to be produced predominantly by gluon-gluon interactions. In this analysis, we extract the effective cross section characterizing the initial parton spatial distribution, σ_{eff}=2.2±0.7(stat)±0.9(syst) mb.

Inclusive Production of the X(4140) State in pp[over ¯] Collisions at D0.

We present a study of the inclusive production of the X(4140) state with the decay to the J/ψϕ final state in hadronic collisions. Based on 10.4 fb^{-1} of pp[over ¯] collision data collected by the D0 experiment at the Fermilab Tevatron collider, we report the first evidence for the prompt production of an X(4140) state and find the fraction of X(4140) events originating from b hadrons to be f_{b}=0.39±0.07(stat)±0.10(syst). The ratio of the nonprompt X(4140) production rate to the B_{s}^{0} yield in the same channel is R=0.19±0.05(stat)±0.07(syst). The values of the mass M=4152.5±1.7(stat)_{-5.4}^{+6.2}(syst) MeV and width Γ=16.3±5.6(stat)±11.4(syst) MeV are consistent with previous measurements.

Search for Violation of CPT and Lorentz Invariance in Bs(0) Meson Oscillations.

We present the first search for CPT-violating effects in the mixing of Bs(0) mesons using the full Run II data set with an integrated luminosity of 10.4 fb(-1) of proton-antiproton collisions collected using the D0 detector at the Fermilab Tevatron Collider. We measure the CPT-violating asymmetry in the decay Bs(0)→µ(±)Ds(±) as a function of celestial direction and sidereal phase. We find no evidence for CPT-violating effects and place limits on the direction and magnitude of flavor-dependent CPT- and Lorentz-invariance violating coupling coefficients. We find 95% confidence intervals of Δa⊥<1.2×10(-12) GeV and (-0.8<ΔaT-0.396ΔaZ<3.9)×10(-13) GeV.

Measurement of the Effective Weak Mixing Angle in pp[over ¯]→Z/γ

We present a measurement of the fundamental parameter of the standard model, the weak mixing angle sin^{2}θ_{eff}^{ℓ} which determines the relative strength of weak and electromagnetic interactions, in pp[over ¯]→Z/γ^{*}→e^{+}e^{-} events at a center of mass energy of 1.96 TeV, using data corresponding to 9.7 fb^{-1} of integrated luminosity collected by the D0 detector at the Fermilab Tevatron. The effective weak mixing angle is extracted from the forward-backward charge asymmetry as a function of the invariant mass around the Z boson pole. The measured value of sin^{2}θ_{eff}^{ℓ}=0.23147±0.00047 is the most precise measurement from light quark interactions to date, with a precision close to the best LEP and SLD results.

Measurement of the forward-backward asymmetry in the production of B(±) mesons in pp̄ collisions at √s=1.96 TeV.

We present a measurement of the forward-backward asymmetry in the production of B(±) mesons, A(FB)(B(±)), using B(±)→J/ψK(±) decays in 10.4 fb(-1) of pp̄ collisions at sqrt[s]=1.96 TeV collected by the D0 experiment during Run II of the Tevatron collider. A nonzero asymmetry would indicate a preference for a particular flavor, i.e., b quark or ̄b antiquark, to be produced in the direction of the proton beam. We extract A(FB)(B(±)) from a maximum likelihood fit to the difference between the numbers of forward- and backward-produced B(±) mesons. We measure an asymmetry consistent with zero: A(FB)(B(±))=[-0.24±0.41 (stat)±0.19 (syst)]%.

Measurement of the B(s)(0) lifetime in the flavor-specific decay channel B(s)(0)→D(s)(-)µ(+)νX.

We present an updated measurement of the B(s)(0) lifetime using the semileptonic decays B(s)(0)→D(s)(-)µ(+)νX, with D(s)(-)→ϕπ(-) and ϕ→K(+)K(-) (and the charge conjugate process). This measurement uses the full Tevatron Run II sample of proton-antiproton collisions at √[s]=1.96 TeV, comprising an integrated luminosity of 10.4 fb(-1). We find a flavor-specific lifetime τ(fs)(B(s)(0))=1.479±0.010(stat)±0.021(syst) ps. This technique is also used to determine the B(0) lifetime using the analogous B(0)→D(-)µ(+)νX decay with D(-)→ϕπ(-) and ϕ→K(+)K(-), yielding τ(B(0))=1.534±0.019(stat)±0.021(syst) ps. Both measurements are consistent with the current world averages, and the B(s)(0) lifetime measurement is one of the most precise to date. Taking advantage of the cancellation of systematic uncertainties, we determine the lifetime ratio τ(fs)(B(s)(0))/τ(B(0))=0.964±0.013(stat)±0.007(syst).

The role of radiotherapy in node-positive prostate cancer.

Node-positive prostate cancer represents 12% of newly diagnosed prostate cancer cases in the United States; with decreasing use of screening, this proportion is likely to increase. However, very few clinical trials have specifically compared treatment options for this group of patients. Radiotherapy has a potential role as both definitive therapy and adjuvant therapy for node-positive prostate cancer. In regard to definitive treatment, retrospective studies comparing androgen deprivation therapy (ADT) alone vs ADT plus radiotherapy consistently demonstrated better survival associated with radiotherapy. In addition, two secondary analyses of clinical trial data compared radiotherapy alone vs radiotherapy plus ADT in this setting, and showed combination treatment achieved better survival. In terms of adjuvant treatment after prostatectomy in the setting of pathologic node-positive disease, the Eastern Cooperative Oncology Group (ECOG) 3886 trial established ADT as a standard of care. Institutional retrospective studies showed that ADT plus radiotherapy was associated with improved overall survival compared with ADT alone, but an analysis of the population-based Surveillance, Epidemiology and End Results-Medicare linked data did not show a benefit from radiotherapy. Because current management is informed by mostly retrospective studies, clinical trials are needed to more definitively guide treatment decisions for patients with node-positive disease. Off trial, radiotherapy with ADT should be offered to patients with this very aggressive form of prostate cancer.