bluuebunny/crossref_metadata_2025 huggingface dataset:
DNA-Based Marker Systems to Determine Genetic Diversity of Weedy Species and Their Application to Biocontrol
Authors: Nissen Scott J. , Masters Robert A. , Lee Donald J. , Rowe Martha L.
Published: May 2019

DNA-based molecular markers may provide information about introduced weedy species that would be useful in biological weed control efforts. Chloroplast DNA restriction fragment length polymorphisms (cpDNA RFLP) and random amplified polymorphic DNA (RAPD) analysis are two DNA-based marker techniques that can provide estimates of genetic variation in native and introduced populations of weedy species. Profiles provided by these techniques could furnish the necessary information to determine the geographic origins of introduced species and provide evidence for multiple introductions. Although DNA-based markers would not necessarily identify the genetic basis for host-pest compatibility, they would enable identification of specific host genotypes. Current criteria for selecting a weedy species as a target for biological control are primarily political and economic. The importance of genetic diversity and population structure in determining the vulnerability of plant populations to insects or diseases has not been fully appreciated. Estimates of genetic diversity based on DNA marker analysis could be used as one criteria for determining which plants are targeted for biological control. The success of biological weed control efforts has been limited by the high levels of genetic diversity occurring in target weed specks and the lack of biocontrol agent and target weed compatibilities. DNA-based markers may be used to increase our understanding of these factors and contribute to the success of biological weed control by helping to target the most vulnerable species and provide more realistic expectations of the potential for success given available resources.
Absorption, Translocation, and Metabolism of Imazethapyr in Common Ragweed (Ambrosia artemisiifolia) and Giant Ragweed (Ambrosia trifida)
Authors: Ballard Thomas O. , Foley Michael E. , Bauman Thomas T.
Published: May 2019

Common and giant ragweed are important weeds of soybeans in Indiana. These two weeds respond differently to imazethapyr POST treatments with common ragweed demonstrating more tolerance than giant ragweed. Both plants show initial susceptibility to imazethapyr, but common ragweed can regrow 10 to 14 days following herbicide application. Laboratory studies were conducted to determine the factors that contribute to the differential control of common and giant ragweed with imazethapyr. Differential absorption was observed at 72 h, with common ragweed absorbing 52% of the applied14C-imazethapyr and giant ragweed absorbing 39%. The absorption of radioactivity was the same for both species by 672 h. Imazethapyr exhibited both xylem and phloem mobility by translocating both acropetally and basipetally from a treated leaf in giant and common ragweed. A higher percentage of the absorbed radioactivity accumulated in the lower foliage and roots of giant ragweed than common ragweed by 336 h. The rate of imazethapyr metabolism in common ragweed was greater than in giant ragweed. At 336 h, 81 and 68% of the identified radioactivity in the treated leaf was imazethapyr metabolites in common and giant ragweed, respectively. A higher level of the inactive glucose conjugate metabolite was found in the lower plant and root tissues of common ragweed than in giant ragweed. The differential control of common and giant ragweed with foliar applications of imazethapyr was attributed to differences in both translocation and metabolism.
Effects of Photoperiod on Reproductive Development in Velvetleaf (Abutilon theophrasti)
Authors: Patterson David T.
Published: May 2019

When velvetleaf plants from Mississippi and Minnesota populations were maintained in growth chambers with day/night temperatures of 29/23 C and photoperiods of 11, 12, 13, 14, and 15 h, flower buds and open flowers appeared first in the 12 h photoperiod. Buds and flowers appeared 2 to 4 d later at photoperiods of 11, 13, or 14 h. Increasing the photoperiod beyond 14 h to 15 h delayed bud appearance an additional 7 d in the MN plants and 12 d in the MS plants. Open flowers appeared four to five nodes higher, 10 d later at 15 than at 14 h in the MN plants and 20 d later in the MS plants. Vegetative shoot weight and fruit weight 73 d after emergence were greater in 13 h or longer photoperiods than at 11 or 12 h. In shorter photoperiods, MN plants produced more vegetative growth than MS plants, but the reverse occurred at longer photoperiods where MS plants were taller than MN plants. These growth differences occurred because earlier shifts in allocation to reproductive growth in MN plants limited their vegetative growth, particularly in the longest photoperiods. Differences in rate of reproductive development between populations were not evident until photoperiod exceeded 13 h. Reciprocal transfer of plants of the MS population between short and long photoperiods revealed the durations of the juvenile (pre-inductive), inductive, and post-inductive phases to be 3 to 5, 7 to 8 (short day) or 30 (long day), and 10 to 11 d, respectively. Differences in competitive ability among latitudinal biotypes of photoperiodically-sensitive weeds may depend on time of emergence in the field and consequent photoperiod exposure. Weed growth simulation models to be used in development of expert systems for weed management should take photoperiodic sensitivity into account.
Growth and Yield of Pea (Pisum sativumL.) and Lentil (Lens culinarisL.) Sprayed with Low Rates of Sulfonylurea and Phenoxy Herbicides
Authors: Gealy David R. , Boerboom Chris M. , Ogg Alex G.
Published: May 2019

Drift of sulfonylurea and phenoxy herbicides from spring cereal fields to nearby spring pea and lentil crops was simulated by spraying pea and lentil with 2,4-D or the 2:1 commercial mixture of thifensulfuron and tribenuron at rates of 0, 0.33, 1, 3.3, or 10% of the use rates (X) for spring cereal crops approximately 3 and 5 wk after planting pea and lentil. 2,4-D had minimal inhibitory effects on both crops at all rates tested. Lentil was slightly more sensitive than pea to 10% X 2,4-D. Thifensulfuron:tribenuron had no effect on either crop at rates less than 3.3% X. Two weeks after application of thifensulfuron:tribenuron, 10% X, and to a lesser degree 3.3% X rates, caused newly emerged leaves to become chlorotic, reducing chlorophyll content 25 to 50%. These treatments also reduced net photosynthesis by 37% and reduced or halted growth of the main stem. Early formation of leaves was reduced, thus tripling light penetration through the canopy. Five to six weeks after application, 10% X thifensulfuron:tribenuron had, in some treatments, more than tripled branching in pea, more than quadrupled branching in lentil, and reduced biomass as much as 42%. Flowering and maturity were delayed. Plants recovered from stunting by thifensulfuron:tribenuron to varying degrees depending on environmental conditions, and final seed yield generally was reduced less than 25%. In controlled greenhouse experiments, rate response to thifensulfuron generally was similar to that observed in field experiments. Pea was stunted less at 30 C than at 10 C, whereas lentil was affected similarly at these temperatures. Overall, visual symptoms from thifensulfuron:tribenuron exposure were more pronounced in pea than in lentil and were detectable at levels substantially lower than those that affected final seed yields.
Effect of Low Doses of Metamitron and Glyphosate on Growth and Chlorophyll Content of Common Lambsquarters (Chenopodium album)
Authors: Ketel David H.
Published: May 2019

Common lambsquarters was treated with metamitron (M) and glyphosate (G) to investigate chlorophyll content as a single, biological parameter for indicating sub-lethal-treated weeds. In three different greenhouse experiments the herbicides were applied at dose rates of 1/8, 1/4 and 1/2 times the M-recommended dose rate (= 0.7 kg ai ha−1), and 1/16, 1/8, and 1/4 times the G-recommended dose rate (= 1.44 kg ai ha−1), respectively. Three weeks after herbicide application the chlorophyll content in leaves of plants treated with 1/2 M was lower than the control. At the same time the chlorophyll content in leaves of plants treated with 1/8 and 1/4 M was higher than the control. The chlorophyll content in the leaves of plants treated with 1/16 and 1/8 G was also higher than the control, but the chlorophyll content in the leaves of plants treated with 1/4 G was equal to the control. A dose of 1/2 M killed 30% of available plants within 29 d, but most of the plants were still alive after 29 d when 1/4 M, 1/8 M, 1/4 G, 1/8 G and 1/16 G had been used. The fresh weight of the biomass reflected the fitness of the plants observed with time and was related to chlorophyll content. The dry weight of the biomass, however, was probably related to the typical action of metamitron and glyphosate. Measurements with a remote sensing technique supported the measurement of chlorophyll with a spectrophotometer confirming a significant discrepancy with time between a herbicide's affect on chlorophyll content and on plant growth. Because differences in chlorophyll content may have caused differences in the progress of plant degradation in sub-lethal- and lethal-treated plants, it is concluded that the chlorophyll content can be used as a single, biological parameter for indicating sub-lethal dose rates of metamitron and glyphosate.
Influence of Imazethapyr onRhizobiumGrowth and its Symbiosis with Pea (Pisum sativum)
Authors: Gonzalez A. , Gonzalez-Murua C. , Royuela M.
Published: May 2019

Imazethapyr is a selective herbicide used to control a wide spectrum of weeds in several legume crops, including pea. The effect of imazethapyr on pea-Rhizobiumsymbiosis was studied through its effect on microorganism growth, microorganism nodulation ability and plant growth. Symbiotic plants were damaged by imazethapyr concentrations higher than 1.73 μM applied preemergence. The number of nodules per plant was affected more than nodule size, suggesting a direct imazethapyr effect on the nodule initiation rather than on nodule development. However, imazethapyr did not directly affectRhizobiumbecause doses higher than 0.34 mM were required to cause slight effects onRhizobiumgrowth in a defined medium. Also, nodulation ability of bacteria treated with imazethapyr was not affected. These results suggest that imazethapyr inhibits the growth of the symbiotic plant rather than having a direct effect on the bacteria. Accordingly, symbiotic plants were less affected than the corresponding nitrate-reducing pea plants.
Reproductive Behaviour of Natural Populations of Meadow Salsify (Tragopogon pratensis)
Authors: QI Meiqin , Upadhyaya Mahesh K. , Turkington Roy
Published: May 2019

The reproductive characteristics of natural populations of meadow salsify were monitored between May 1990 and October 1991. Plants in even-aged populations did not produce seeds prior to the second winter and plants in uneven-aged populations died after seed production suggesting that meadow salsify at this site is a monocarpic perennial and not a true biennial. Delayed seed production may enhance abundance of this species by increasing the size of its bud bank. Plants of uneven-aged populations flowered over a range of root crown diameters; the percentage of plants bearing flowers increased with increasing root crown diameters. The minimum root crown diameter at which plants flowered in 1990 and 1991 was 0.2 and 0.6 cm respectively demonstrating that factor(s) other than plant size regulate flowering in this species. Seed production ranged between 100 to 850 seeds per plant. Total number of flower heads per plant and florets per plant were positively correlated with each other and with the root crown diameter. Root crown diameter is, therefore, a good indicator of potential fecundity in meadow salsify. Greater seed production by larger plants may compensate, at least in part, for the high juvenile mortality and longer generation time in this species. The results suggest that prolific seed production and long vegetative survival are important strategies in the maintenance of meadow salsify populations.
Seed Longevity of 41 Weed Species Buried 17 Years in Eastern and Western Nebraska
Authors: Burnside Orvin C. , Wilson Robert G. , Weisberg Sanford , Hubbard Kenneth G.
Published: May 2019

Seed of 41 economically important weed species of the Great Plains region of the United States were buried 20 cm deep in soil in eastern and western Nebraska in 1976. The 41 species consisted of 11 annual grass, 14 annual broadleaf, 4 biennial broadleaf, and 12 perennial broadleaf species. Weed seeds were exhumed annually for germination tests the first 9 yr, then after 12 and 17 yr. Germination percentages at the two burial locations averaged over 0, 1 to 4, 5 to 8, and 9 to 17 yr of burial were 57, 28, 9, and 4% for annual grass; 47, 26, 16, and 11 % for annual broadleaf; 52, 49, 44, and 30 % for biennial broadleaf; 36, 18, 13, and 8% for perennial broadleaf; and 47, 26, 16, and 10% for all 41 weed species, respectively. Biennial broadleaf weeds showed the greatest seed germination over years. Annual grass weeds showed less seed germinability over 17 yr of burial than annual broadleaf weeds and perennial broadleaf weed species were intermediate. Weed seed germinability in soil was greater in the reduced rainfall and more moderate soil temperatures of western Nebraska than in the greater rainfall and more fluctuating soil temperatures of eastern Nebraska. The greatest seed survival among the 41 weed species was shown by common mullein, which had 95% germination after 17 yr of burial in western Nebraska. Decay rates of individual weed species in soil will be of most value to weed scientists, agriculturalists, and modelers evaluating past or designing future weed management systems.
Canada Thistle (Cirsium arvense) Effects on Yield Components of Spring Wheat (Triticum aestivum)
Authors: Donald William W. , Khan Mohammad
Published: May 2019

The effect of Canada thistle on major yield components of spring wheat was characterized using path coefficient analysis, which provides insight concerning which yield components are most sensitive to Canada thistle competition. Increasing Canada thistle density decreased wheat stand in each of three years. Canada thistle also reduced spikes per plant and seed per spike to varying extents depending on year, but Canada thistle had comparatively little effect on wheat seed weight per 1000 seed. In the path coefficient model proposed, Canada thistle was assumed to reduce yield by directly reducing wheat yield components and through them, indirectly reducing yield. Path coefficient correlation analysis showed that Canada thistle reduced spring wheat yield chiefly by indirect effects of decreasing wheat density, the earliest formed yield component. Canada thistle reduced wheat density which, in turn, reduced wheat yield. These data suggest that Canada thistle must be controlled either before or shortly after wheat emergence if detrimental effects on wheat yield are to be minimized.
Diurnally Alternating Temperatures Stimulate Sprouting of Purple Nutsedge (Cyperus rotundus) Tubers
Authors: Miles Joel E. , Nishimoto Roy K. , Kawabata Osamu
Published: May 2019

Experiments were conducted to determine the response of purple nutsedge tuber sprouting to diurnally alternating temperature. These experiments compared the response to alternating and constant temperatures and determined the effect of the amplitude of alternation and time of exposure to the maximum temperature. Tuber sprouting was more rapid and complete with alternating temperatures than with constant temperatures. Increasing temperature fluctuation from 0 to 6 C for 12 h daily linearly increased total tuber sprouting. As little as 30 min exposure to high temperature per day provided nearly the same level of sprouting as a 12 h alternating temperature cycle. This phenomenon should be considered when conducting studies to describe tuber temperature responses or when predicting tuber sprouting and emergence.
Cotton (Gossypium hirsutum) Response to Imazaquin and Imazethapyr Soil Residues
Authors: Johnson David H. , Talbert Ronald E.
Published: May 2019

The effects of imazaquin and imazethapyr on cotton planted the year following application to soybean were studied on one silt loam and two clay soils in Arkansas from 1989 to 1991. Imazaquin was applied to soybean at 0.07 kg ai ha−1PPI and POST, 0.14 kg ha−1PPI, PRE, and POST, and sequentially PPI or PRE followed by POST at 0.14 kg ha−1per application. Imazethapyr was applied at 0.035 kg ha−1PPI and POST, 0.07 kg ha−1PPI, PRE, and POST, and sequentially PPI or PRE followed by POST at 0.07 kg ha−1per application. Soil residues of 0.07 kg ha−1imazaquin and imazethapyr did not injure cotton at any location. Residues of 0.14 kg ha−1imazaquin applied sequentially reduced cotton shoot dry weight for 6 wk after emergence on clay but not on silt loam soil. The PPI followed by POST sequential imazaquin treatment (0.28 kg ha−1total imazaquin) delayed initiation of fruiting and reduced yield and lint quality.
Sorption and Mobility of Bentazon in Coastal Plain Soils
Authors: Grey Timothy L. , Wehtje Glenn R. , Hajek Ben F. , Walker Robert H.
Published: May 2019

Sorption and mobility of14C-bentazon were evaluated using soil solution and soil-thin-layer chromatography, respectively on three Coastal Plain soils. The proportion of bentazon adsorbed, was pH and concentration dependent and ranged between 28 to 47, 31 to 61, and 17 to 68% for the Dothan loamy sand, Greenville clay, and Troup loamy sand, respectively. Bentazon sorption decreased as soil pH increased from 5.4 to 5.8 on the Troup loamy sand, regardless of bentazon concentration. Sorption of 1 and 10 ppm bentazon decreased as soil pH increased from 5.0 to 5.7 on the Greenville clay and 6.1 to 6.4 on the Dothan loamy sand. Bentazon was least mobile on the Greenville clay and mobility increased as pH increased. Mobility of bentazon was greatest on the Troup loamy sand and was not pH dependent. Bentazon mobility decreased as soil pH increased for the Dothan loamy sand.
Knowledge of the Transmission of Tuberculosis and Infection Control Measures for Tuberculosis Among Healthcare Workers
Authors: Lai Kwan Kew , Fontecchio Sally A. , Kelley Anita L. , Melvin Zita S.
Published: May 2019

Two hundred seventy-five of 325 (85%) healthcare workers (HCWs) completed a questionnaire testing their knowledge of transmission of tuberculosis (TB) and infection control measures for TB. Of the 75 HCWs with no patient contact, 49 (65%) felt that masks should be worn, and 40 (53%) would use gowns. In contrast, 175 (88%) of 200 HCWs having contact with patients thought masks should be worn, and 70 (35%) would use gowns (P=.0001 and .0085, respectively). Only 87% of HCWs with patient contact felt that respiratory precautions should be instituted for TB patients. The results of our sur vey showed that HCWs should be reeducated about TB.
Comparative Killing Kinetics of Methicillin-Resistant Staphylococcus aureus by Bacitracin or Mupirocin
Authors: Chapnick Edward K. , Gradon Jeremy D. , Kreiswirth Barry , Lutwick Larry I. , Schaffer Benjamin C. , Schiano Thomas D. , Levi Michael H.
Published: May 2019

The in vitro activities of bacitracin and mupirocin were compared for seven different strains of methicillin-resistant Staphylococcus aureus. Six of seven strains showed bacitracin minimum inhibitory concentrations (MICs) of 0.5 to 1.0 units/mL, and all seven had mupirocin MICs of 0.5 to 2 μg/mL. Time-kill studies revealed 2.6- to 4.5-log reduction in 24 hours with strains susceptible to bacitracin (4 units/mL) and 0 to 2.2 reduction with mupirocin (16 μg/mL). Bacitracin should be considered further for in vivo studies because of enhanced bacteriocidal effect and lower cost.
Determining Key Influences on Patient Ability to Successfully Manage Noncommunicable Disease After Natural Disaster
Authors: Ryan Benjamin J. , Franklin Richard C. , Burkle Frederick M. , Smith Erin C. , Aitken Peter , Leggat Peter A.
Published: May 2019

Introduction:

Natural disasters often damage or destroy the protective public health service infrastructure (PHI) required to maintain the health and well-being of people with noncommunicable diseases (NCDs). This interruption increases the risk of an acute exacerbation or complication, potentially leading to a worse long-term prognosis or even death. Disaster-related exacerbations of NCDs will continue, if not increase, due to an increasing prevalence and sustained rise in the frequency and intensity of disasters, along with rapid unsustainable urbanization in flood plains and storm-prone coastal zones. Despite this, the focus of disaster and health systems preparedness and response remains on communicable diseases, even when the actual risk of disease outbreaks post-disaster is low, particularly in developed countries. There is now an urgent need to expand preparedness and response beyond communicable diseases to include people with NCDs.

Hypothesis/Problem:

The developing evidence-base describing the risk of disaster-related exacerbation of NCDs does not incorporate the perspectives, concerns, and challenges of people actually living with the conditions. To help address this gap, this research explored the key influences on patient ability to successfully manage their NCD after a natural disaster.

Methods:

A survey of people with NCDs in Queensland, Australia collected data on demographics, disease, disaster experience, and primary concern post-disaster. Descriptive statistics and chi-square tests with a Bonferroni-adjustment were used to analyze data.

Results:

There were 118 responses to the survey. Key influences on the ability to self-manage post-disaster were access to medication, medical services, water, treatment and care, power, and food. Managing disease-specific symptoms associated with cardiovascular disease, diabetes, mental health, and respiratory diseases were primary concerns following a disaster. Stress and anxiety, loss of sleep, weakness or fatigue, and shortness of breath were common concerns for all patients with NCDs. Those dependent on care from others were most worried about shortness of breath and slow healing sores. Accessing medication and medical services were priorities for all patients post-disaster.

Conclusion:

The key influences on successful self-management post-disaster for people with NCDs must be reflected in disaster plans and strategies. Achieving this will reduce exacerbations or complications of disease and decrease demand for emergency health care post-disaster.
Building a Conservative State: Partisan Polarization and the Redeployment of Administrative Power
Authors: Jacobs Nicholas F. , King Desmond , Milkis Sidney M.
Published: May 2019

It is commonplace to equate the arrival of a new conservative administration in Washington, DC, with the “rolling back” of the federal activities. We disagree with this conventional perspective, and seek to demonstrate that the equation of conservative Republicanism and retrenchment elides a critical change in the relationship between party politics and State power—a relationship that Donald Trump seems determined to nurture. Drawing on primary research, we argue that partisanship in the United States is no longer a struggle over the size of the State; rather it is a contest to control national administrative power. Since the late 1960s, conservative administrations have sought to redeploy rather than dismantle or roll back state power. Through “redeployment,” conservative presidents have sustained previous levels of State spending or State activity, but in a way reflecting a new administration’s ideology.
Millennial‐Scale Age Offsets Within Fossil Assemblages: Result of Bioturbation Below the Taphonomic Active Zone and Out‐of‐Phase Production
Authors: Tomašových A. , Kidwell S. M. , Alexander C. R. , Kaufman D. S.
Published: May 2019

Oceanographic and evolutionary inferences based on fossil assemblages can be obscured by age offsets among co‐occurring shells (i.e., time averaging). To identify the contributions of sedimentation, mixing, durability, and production to within‐ and between‐species age offsets, we analyze downcore changes in the age‐frequency distributions of two bivalves on the California shelf. Within‐species age offsets are ~50–2,000 years for Parvilucina and ~2,000–4,000 years for Nuculana and between‐species offsets are 1,000–4,000 years within the 10‐ to 25‐cm‐thick stratigraphic units. Shells within the top 20–24 cm of the seabed are age‐homogeneous, defining the thickness of the surface completely‐mixed layer (SML), and have strongly right‐skewed age‐frequency distributions, indicating fast shell disintegration. The SML thus coincides with the taphonomic active zone and extends below the redoxcline at ~10 cm. Shells >2,000–3,000 years old occurring within the SML have been exhumed from subsurface shell‐rich units rich where disintegration is negligible (sequestration zone, SZ). Burrowers (callianassid shrimps) penetrate 40–50 cm below the seafloor into this SZ. The millennial offsets within each increment result from the advection of old shells from the SZ, combined with an out‐of‐phase change in species production. Age unmixing reveals that Parvilucina was abundant during the transgressive phase, rare during the highstand phase, and increased steeply in the twentieth century in response to wastewater. Nuculana was abundant during the highstand phase and has declined over the past two centuries. This sequestration‐exhumation dynamic accentuates age offsets by allowing both the persistence of shells below the SML and their later admixing with younger shells within the SML.
Experimental and computational analyses reveal that environmental restrictions shape HIV-1 spread in 3D cultures
Authors: Imle Andrea , Kumberger Peter , Schnellbächer Nikolas D. , Fehr Jana , Carrillo-Bustamante Paola , Ales Janez , Schmidt Philip , Ritter Christian , Godinez William J. , Müller Barbara , Rohr Karl , Hamprecht Fred A. , Schwarz Ulrich S. , Graw Frederik , Fackler Oliver T.
Published: May 2019

Pathogens face varying microenvironments in vivo, but suitable experimental systems and analysis tools to dissect how three-dimensional (3D) tissue environments impact pathogen spread are lacking. Here we develop an Integrative method to Study Pathogen spread by Experiment and Computation within Tissue-like 3D cultures (INSPECT-3D), combining quantification of pathogen replication with imaging to study single-cell and cell population dynamics. We apply INSPECT-3D to analyze HIV-1 spread between primary human CD4 T-lymphocytes using collagen as tissue-like 3D-scaffold. Measurements of virus replication, infectivity, diffusion, cellular motility and interactions are combined by mathematical analyses into an integrated spatial infection model to estimate parameters governing HIV-1 spread. This reveals that environmental restrictions limit infection by cell-free virions but promote cell-associated HIV-1 transmission. Experimental validation identifies cell motility and density as essential determinants of efficacy and mode of HIV-1 spread in 3D. INSPECT-3D represents an adaptable method for quantitative time-resolved analyses of 3D pathogen spread.
PFA ependymoma-associated protein EZHIP inhibits PRC2 activity through a H3 K27M-like mechanism
Authors: Jain Siddhant U. , Do Truman J. , Lund Peder J. , Rashoff Andrew Q. , Diehl Katharine L. , Cieslik Marcin , Bajic Andrea , Juretic Nikoleta , Deshmukh Shriya , Venneti Sriram , Muir Tom W. , Garcia Benjamin A. , Jabado Nada , Lewis Peter W.
Published: May 2019

Posterior fossa type A (PFA) ependymomas exhibit very low H3K27 methylation and express high levels of EZHIP (Enhancer of Zeste Homologs Inhibitory Protein, also termed CXORF67). Here we find that a conserved sequence in EZHIP is necessary and sufficient to inhibit PRC2 catalytic activity in vitro and in vivo. EZHIP directly contacts the active site of the EZH2 subunit in a mechanism similar to the H3 K27M oncohistone. Furthermore, expression of H3 K27M or EZHIP in cells promotes similar chromatin profiles: loss of broad H3K27me3 domains, but retention of H3K27me3 at CpG islands. We find that H3K27me3-mediated allosteric activation of PRC2 substantially increases the inhibition potential of EZHIP and H3 K27M, providing a mechanism to explain the observed loss of H3K27me3 spreading in tumors. Our data indicate that PFA ependymoma and DIPG are driven in part by the action of peptidyl PRC2 inhibitors, the K27M oncohistone and the EZHIP ‘oncohistone-mimic’, that dysregulate gene silencing to promote tumorigenesis.
TUBG1 missense variants underlying cortical malformations disrupt neuronal locomotion and microtubule dynamics but not neurogenesis
Authors: Ivanova Ekaterina L. , Gilet Johan G. , Sulimenko Vadym , Duchon Arnaud , Rudolf Gabrielle , Runge Karen , Collins Stephan C. , Asselin Laure , Broix Loic , Drouot Nathalie , Tilly Peggy , Nusbaum Patrick , Vincent Alexandre , Magnant William , Skory Valerie , Birling Marie-Christine , Pavlovic Guillaume , Godin Juliette D. , Yalcin Binnaz , Hérault Yann , Dráber Pavel , Chelly Jamel , Hinckelmann Maria-Victoria
Published: May 2019

De novo heterozygous missense variants in the γ-tubulin gene TUBG1 have been linked to human malformations of cortical development associated with intellectual disability and epilepsy. Here, we investigated through in-utero electroporation and in-vivo studies, how four of these variants affect cortical development. We show that TUBG1 mutants affect neuronal positioning, disrupting the locomotion of new-born neurons but without affecting progenitors’ proliferation. We further demonstrate that pathogenic TUBG1 variants are linked to reduced microtubule dynamics but without major structural nor functional centrosome defects in subject-derived fibroblasts. Additionally, we developed a knock-in Tubg1Y92C/+ mouse model and assessed consequences of the mutation. Although centrosomal positioning in bipolar neurons is correct, they fail to initiate locomotion. Furthermore, Tubg1Y92C/+ animals show neuroanatomical and behavioral defects and increased epileptic cortical activity. We show that Tubg1Y92C/+ mice partially mimic the human phenotype and therefore represent a relevant model for further investigations of the physiopathology of cortical malformations.
GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions
Authors: Farhat Maha R. , Freschi Luca , Calderon Roger , Ioerger Thomas , Snyder Matthew , Meehan Conor J. , de Jong Bouke , Rigouts Leen , Sloutsky Alex , Kaur Devinder , Sunyaev Shamil , van Soolingen Dick , Shendure Jay , Sacchettini Jim , Murray Megan
Published: May 2019

Drug resistance diagnostics that rely on the detection of resistance-related mutations could expedite patient care and TB eradication. We perform minimum inhibitory concentration testing for 12 anti-TB drugs together with Illumina whole-genome sequencing on 1452 clinical Mycobacterium tuberculosis (MTB) isolates. We evaluate genome-wide associations between mutations in MTB genes or non-coding regions and resistance, followed by validation in an independent data set of 792 patient isolates. We confirm associations at 13 non-canonical loci, with two involving non-coding regions. Promoter mutations are measured to have smaller average effects on resistance than gene body mutations. We estimate the heritability of the resistance phenotype to 11 anti-TB drugs and identify a lower than expected contribution from known resistance genes. This study highlights the complexity of the genomic mechanisms associated with the MTB resistance phenotype, including the relatively large number of potentially causal loci, and emphasizes the contribution of the non-coding portion of the genome.
The structural basis of translational control by eIF2 phosphorylation
Authors: Adomavicius Tomas , Guaita Margherita , Zhou Yu , Jennings Martin D. , Latif Zakia , Roseman Alan M. , Pavitt Graham D.
Published: May 2019

Protein synthesis in eukaryotes is controlled by signals and stresses via a common pathway, called the integrated stress response (ISR). Phosphorylation of the translation initiation factor eIF2 alpha at a conserved serine residue mediates translational control at the ISR core. To provide insight into the mechanism of translational control we have determined the structures of eIF2 both in phosphorylated and unphosphorylated forms bound with its nucleotide exchange factor eIF2B by electron cryomicroscopy. The structures reveal that eIF2 undergoes large rearrangements to promote binding of eIF2α to the regulatory core of eIF2B comprised of the eIF2B alpha, beta and delta subunits. Only minor differences are observed between eIF2 and eIF2αP binding to eIF2B, suggesting that the higher affinity of eIF2αP for eIF2B drives translational control. We present a model for controlled nucleotide exchange and initiator tRNA binding to the eIF2/eIF2B complex.
Publisher Correction: Rabies-based vaccine induces potent immune responses against Nipah virus
Authors: Keshwara Rohan , Shiels Thomas , Postnikova Elena , Kurup Drishya , Wirblich Christoph , Johnson Reed F. , Schnell Matthias J.
Published: May 2019

In the original published version of this Article, the figure legends were attached to the wrong figures. The legend for Fig. 2 was moved to Fig. 4, the legend for Fig. 3 was moved to Fig. 2, and the legend for Fig. 4 was moved to Fig. 3. The PDF and HTML versions of the Article have been corrected.
Flow and detailed 3D morphodynamic data from laboratory experiments of fluvial dike breaching
Authors: Rifai Ismail , El kadi Abderrezzak Kamal , Erpicum Sébastien , Archambeau Pierre , Violeau Damien , Pirotton Michel , Dewals Benjamin
Published: May 2019

This paper presents a dataset obtained from fifty four laboratory experiments of the breaching of fluvial dikes due to flow overtopping. Data were collected on two complementary experimental setups, each consisting of a main channel representing the river, an erodible lateral dike and a floodplain. The dataset covers seven test series, involving varying hydraulic boundary conditions (e.g. inflow discharge, downstream boundary conditions), main channel dimensions, as well as bottom and dike material. The following experimental data were produced: time series of water levels in the main channel, time series of flow discharges in the main channel and through the breach, as well as high resolution 3D reconstructions of the breach geometry during its expansion. The latter measurements were performed using a novel non-intrusive laser profilometry technique developed for this research. Reuse of the collected data will support efforts to improve our understanding of the physical processes underpinning fluvial dike breaching. It will also enable benchmarking the accuracy of conceptual or detailed numerical models for the prediction of dike breaching, which is central to flood risk management.
A global, empirical, harmonised dataset of soil organic carbon changes under perennial crops
Authors: Ledo Alicia , Hillier Jonathan , Smith Pete , Aguilera Eduardo , Blagodatskiy Sergey , Brearley Francis Q. , Datta Ashim , Diaz-Pines Eugenio , Don Axel , Dondini Marta , Dunn Jennifer , Feliciano Diana Marisa , Liebig Mark A. , Lang Rong , Llorente Mireia , Zinn Yuri Lopes , McNamara Niall , Ogle Stephen , Qin Zhangcai , Rovira Pere , Rowe Rebecca , Vicente-Vicente José Luis , Whitaker Jeanette , Yue Qian , Zerihun Ayalsew
Published: May 2019

A global, unified dataset on Soil Organic Carbon (SOC) changes under perennial crops has not existed till now. We present a global, harmonised database on SOC change resulting from perennial crop cultivation. It contains information about 1605 paired-comparison empirical values (some of which are aggregated data) from 180 different peer-reviewed studies, 709 sites, on 58 different perennial crop types, from 32 countries in temperate, tropical and boreal areas; including species used for food, bioenergy and bio-products. The database also contains information on climate, soil characteristics, management and topography. This is the first such global compilation and will act as a baseline for SOC changes in perennial crops. It will be key to supporting global modelling of land use and carbon cycle feedbacks, and supporting agricultural policy development.
Changes in bone metabolic profile associated with pregnancy or lactation
Authors: Miyamoto Takeshi , Miyakoshi Kei , Sato Yuiko , Kasuga Yoshifumi , Ikenoue Satoru , Miyamoto Kana , Nishiwaki Yuji , Tanaka Mamoru , Nakamura Masaya , Matsumoto Morio
Published: May 2019

Calcium and nutrients are transferred from mothers to fetuses or infants during pregnancy or lactation, respectively, promoting metabolic changes in the mother, many uncharacterized. To evaluate these changes, we undertook two parallel studies. In one we analyzed fourteen clinical cases of vertebral fragility fractures, at or before three months after partum, in mothers who breastfed their infants. In the other, we enrolled 79 additional pregnant subjects, some who chose to breastfeed and others who did not, and analyzed changes in bone metabolic status starting between 34 and 36 weeks of gestation and ending one month after partum. In the larger group, bone-resorbing and bone-forming parameters such as serum TRACP5b and osteocalcin, respectively, significantly increased after partum. Among parameters that changed after partum, serum PTH and the bone-resorbing markers serum TRACP5b and urine NTX were significantly higher in mothers who only breastfed infants compared to mothers who fed infants formula or a mix of both. However, bone-forming parameters were comparable between breastfeeding and non-breast-feeding groups after partum, suggesting that elevated bone-resorption occurs only in the breastfeeding group. Radiographic analysis after partum demonstrated that no subject among the 79 analyzed showed vertebral fractures, even those who breastfed exclusively. Among fracture cases analyzed, subjects exhibited significantly lower bone mineral density than did non-fracture cases in breastfeeding-only subjects. We conclude that bone metabolic status significantly changes over the period between pregnancy and post-partum lactation, and that low bone mineral density seen in a small subset of breastfeeding-only cases likely causes post-partum vertebral fragility fractures.
From jamming to fast compaction dynamics in granular binary mixtures
Authors: Pillitteri Salvatore , Lumay Geoffroy , Opsomer Eric , Vandewalle Nicolas
Published: May 2019

Binary granular mixtures are known to show various packing arrangements depending on both fractions and size ratios of their components. While the final packing fraction can be estimated by geometrical arguments, the dynamics of the pile submitted to gentle vibrations towards a dense state is seen to be highly size ratio dependent. We observe experimentally a diverging compaction characteristic time close to a critical size ratio, such that the grain mobility in the packing is the lowest close to the percolation threshold, when small particles can pass through the voids left by the large ones. Moreover, we evidence a fast compaction dynamics regime when the grain size ratio is large enough.
Gender-specific mediators of the association between parental education and adiposity among adolescents: the HEIA study
Authors: Gebremariam Mekdes K. , Arah Onyebuchi A. , Bergh Ingunn H. , Andersen Lene F. , Ommundsen Yngvar , Totland Torunn H. , Bjelland Mona , Grydeland May , Lien Nanna
Published: May 2019

Identifying the mechanisms behind socioeconomic inequalities in adiposity among youth is vital for efforts aimed at combating these inequalities. The study explored whether a broad range of behavioral and familial factors mediated the associations between parental education and indicators of adiposity among adolescents. Baseline data from a school-based intervention study conducted in 2007 among 11-year-old adolescents were used. Anthropometric outcomes, physical activity and sedentary time among adolescents were objectively measured. Other behavioral variables and parental waist circumference were self-reported. Mediation analyses were conducted. Among boys, maternal waist circumference (WC), paternal WC and TV viewing mediated 16%, 11.5% and 13% of the association between parental education and adolescent WC. The respective proportions when body fat percentage was used as the outcome variable were 22.5%, 16% and 21%. Among girls, maternal and paternal WC mediated 20% and 14% of the association between parental education and WC. The respective proportions when body fat percentage was used as the outcome variable were 14% and 10%. Other included variables did not play any mediating role. Parental WC was found to be a mediator of socioeconomic differences in adiposity in both genders; underlying mechanisms were however not investigated. Among boys, reducing TV time could contribute to the reduction of social inequalities in adiposity.
Age-related changes in molecular organization of type I collagen in tendon as probed by polarized SHG and Raman microspectroscopy
Authors: Van Gulick Laurence , Saby Charles , Morjani Hamid , Beljebbar Abdelilah
Published: May 2019

Type I Collagen is one of the most abundant proteins of the extracellular matrix of the most organs. During chronological aging or in diseases, type I collagen undergoes biochemical and structural changes which can impact biomechanical and physiological properties of organs. In this study, we have investigated the age-related changes in the molecular organization of type I collagen in rat tails tendon using polarized Raman spectroscopy. Our results show that Amide I, amide III as well as the bands related to proline and hydroxyproline are highly sensitive to polarization and age-related. On the other hand, 1453 and 1270 cm−1 do not show any preferential orientation. Depolarization and anisotropic ratios were used to provide information about the changes in orientation of collagen fibers with aging. The anisotropy degree of Raman bands increase from adult to old collagen, indicating a higher collagen fibers alignment to the fascicle backbone axis in old tendons, and consequently a higher straightness of collagen fibers. These data were correlated to those obtained using polarized second harmonic generation technique. Polarized Raman mapping showed a more homogeneous spatial distribution of collagen fibers alignment to the fascicle axis in old tendon. This confirms a higher straightness of collagen fiber with aging.
Hybrid Nanostructured Porous Silicon-Silver Layers for Wideband Optical Absorption
Authors: Martín-Palma Raúl J. , McAtee Patrick D. , Ramadan Rehab , Lakhtakia Akhlesh
Published: May 2019

As subwavelength nanostructures are receiving increasing attention for photonic and plasmonic applications, we grew nanostructured porous silicon (n-PS) and hybrid n-PS/Ag layers onto silicon substrates and measured their reflection and absorption characteristics as functions of the wavelength, angle of incidence, and polarization state of incident light. The experimental results show that the absorption characteristics of the hybrid n-PS/Ag layer can be controlled by selecting the appropriate combination of its thickness and porosity, together with the density of infiltrant silver nanoparticles. The observed wideband optical absorption characteristics of the hybrid n-PS/Ag layers might be useful in light-harvesting devices and photodetectors, since the overall efficiency will be increased as a result of increased field-of-view for both s- and p-polarization states of incident light.
Acceleration of the precession frequency for optically-oriented electron spins in ferromagnetic/semiconductor hybrids
Authors: Moraes F. C. D. , Ullah S. , Balanta M. A. G. , Iikawa F. , Danilov Y. A. , Dorokhin M. V. , Vikhrova O. V. , Zvonkov B. N. , Hernandez F. G. G.
Published: May 2019

Time-resolved Kerr rotation measurements were performed in InGaAs/GaAs quantum wells nearby a doped Mn delta layer. Our magneto-optical results show a typical time evolution of the optically-oriented electron spin in the quantum well. Surprisingly, this is strongly affected by the Mn spins, resulting in an increase of the spin precession frequency in time. This increase is attributed to the variation in the effective magnetic field induced by the dynamical relaxation of the Mn spins. Two processes are observed during electron spin precession: a quasi-instantaneous alignment of the Mn spins with photo-excited holes, followed by a slow alignment of Mn spins with the external transverse magnetic field. The first process leads to an equilibrium state imprinted in the initial precession frequency, which depends on pump power, while the second process promotes a linear frequency increase, with acceleration depending on temperature and external magnetic field. This observation yields new information about exchange process dynamics and on the possibility of constructing spin memories, which can rapidly respond to light while retaining information for a longer period.
A Targeted Mass Spectrometric Assay for Reliable Sensitive Hepcidin Quantification
Authors: Moghieb Ahmed , Tesfay Lia , Nie Song , Gritsenko Marina , Fillmore Thomas L. , Jacobs Jon M. , Smith Richard D. , Torti Frank M. , Torti Suzy V. , Shi Tujin , Ansong Charles
Published: May 2019

Hepcidin, a cysteine-rich peptide hormone, secreted mainly by the liver, plays a central role in iron metabolism regulation. Emerging evidence suggests that disordered iron metabolism is a risk factor for various types of diseases including cancers. However, it remains challenging to apply current mass spectrometry (MS)-based hepcidin assays for precise quantification due to the low fragmentation efficiency of intact hepcidin as well as synthesis difficulties for the intact hepcidin standard. To address these issues we recently developed a reliable sensitive targeted MS assay for hepcidin quantification from clinical samples that uses fully alkylated rather than intact hepcidin as the internal standard. Limits of detection and quantification were determined to be <0.5 ng/mL and 1 ng/mL, respectively. Application of the alkylated hepcidin assay to 70 clinical plasma samples (42 non-cancerous and 28 ovarian cancer patient samples) enabled reliable detection of endogenous hepcidin from the plasma samples, as well as conditioned culture media. The hepcidin concentrations ranged from 0.0 to 95.6 ng/mL across non-cancerous and cancer plasma specimens. Interestingly, cancer patients were found to have significantly higher hepcidin concentrations compared to non-cancerous patients (mean: 20.6 ng/ml for cancer; 5.94 ng/ml for non-cancerous) (p value < 0.001). Our results represent the first application of the alkylated hepcidin assay to clinical samples and demonstrate that the developed assay has better sensitivity and quantification accuracy than current MS-based hepcidin assays without the challenges in synthesis of intact hepcidin standard and accurately determining its absolute amount.