Hyper, a Hydrogen Peroxide Sensor, Indicates the Sensitivity of the Arabidopsis Root Elongation Zone to Aluminum Treatment

Emerging evidence indicates that some reactive oxygen species (ROS), such as the superoxide anion radical and hydrogen peroxide (H2O2), are central regulators of plant responses to biotic and abiotic stresses. Thus, the cellular levels of ROS are thought to be tightly regulated by an efficient and elaborate pro- and antioxidant system that modulates the production and scavenging of ROS. Until recently, studies of ROS in plant cells have been limited to biochemical assays and the use of fluorescent probes; however, the irreversible oxidation of these fluorescent probes makes it impossible to visualize dynamic changes in ROS levels. In this work, we describe the use of Hyper, a recently developed live cell probe for H2O2 measurements in living cells, to monitor oxidative stress in Arabidopsis roots subjected to aluminum treatment. Hyper consists of a circularly permuted YFP (cpYFP) inserted into the regulatory domain of the Escherichia coli hydrogen peroxide-binding protein (OxyR), and is a H2O2-specific ratiometric, and therefore quantitative, probe that can be expressed in plant and animal cells. Now we demonstrate that H2O2 levels drop sharply in the elongation zone of roots treated with aluminum. This response could contribute to root growth arrest and provides evidence that H2O2 is involved in early Al sensing

An Autophagy-Related Kinase Is Essential for the Symbiotic Relationship between Phaseolus vulgaris and Both Rhizobia and Arbuscular Mycorrhizal Fungi

Eukaryotes contain three types of lipid kinases that belong to the phosphatidylinositol 3-kinase (PI3K) family. In plants and Saccharomyces cerevisiae, only PI3K class III family members have been identified. These enzymes regulate the innate immune response, intracellular trafficking, autophagy, and senescence. Here, we report that RNAi-mediated downregulation of common bean (Phaseolus vulgaris) PI3K severely impaired symbiosis in composite P. vulgaris plants with endosymbionts such as Rhizobium tropici and Rhizophagus irregularis. Downregulation of Pv-PI3K was associated with a marked decrease in root hair growth and curling. Additionally, infection thread growth, root-nodule number, and symbiosome formation in root nodule cells were severely affected. Interestingly, root colonization by AM fungi and the formation of arbuscules were also abolished in PI3K loss-of-function plants. Furthermore, the transcript accumulation of genes encoding proteins known to interact with PI3K to form protein complexes involved in autophagy was drastically reduced in these transgenic roots. RNAi-mediated downregulation of one of these genes, Beclin1/Atg6, resulted in a similar phenotype as observed for transgenic roots in which Pv-PI3K had been downregulated. Our findings show that an autophagy-related process is crucial for the mutualistic interactions of P. vulgaris with beneficial microorganismsInstituto de Fisiología y Recursos Genéticos VegetalesFil: Estrada-Navarrete, Georgina. Universidad Nacional Autónoma de México. Instituto de Biotecnología. Departamento de Biología Molecular de Plantas; MéxicoFil: Cruz-Mireles, Neftaly. Universidad Nacional Autónoma de México. Instituto de Biotecnología. Departamento de Biología Molecular de Plantas; MéxicoFil: Lascano, Hernán Ramiro. Consejo Nacional de Investigaciones Científicas y Técnicas. Unidad de Estudios Agropecuarios (UDEA); ArgentinaFil: Lascano, Hernán Ramiro. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Fisiología y Recursos Genéticos Vegetales. ArgentinaFil: Alvarado-Affantranger, Xóchitl. Universidad Nacional Autónoma de México. Instituto de Biotecnología. Laboratorio Nacional de Microscopía Avanzada; MéxicoFil: Hernández-Barrera, Alejandra. Universidad Nacional Autónoma de México. Instituto de Biotecnología. Departamento de Biología Molecular de Plantas; MéxicoFil: Barraza, Aarón. Universidad Nacional Autónoma de México. Instituto de Biotecnología. Departamento de Biología Molecular de Plantas; MéxicoFil: Olivares, Juan E. Universidad Nacional Autónoma de México. Instituto de Biotecnología. Departamento de Biología Molecular de Plantas; MéxicoFil: Arthikala, Manoj-Kumar. Universidad Nacional Autónoma de México. Escuela Nacional de Estudios Superiores-Unidad León; MéxicoFil: Cárdenas, Luis. Universidad Nacional Autónoma de México. Instituto de Biotecnología. Departamento de Biología Molecular de Plantas; MéxicoFil: Quinto, Carmen. Universidad Nacional Autónoma de México. Instituto de Biotecnología. Departamento de Biología Molecular de Plantas; MéxicoFil: Sanchez, Federico. Universidad Nacional Autónoma de México. Instituto de Biotecnología. Departamento de Biología Molecular de Plantas; Méxic

Fragmentation of Contaminant and Endogenous DNA in Ancient Samples Determined by Shotgun Sequencing; Prospects for Human Palaeogenomics

Despite the successful retrieval of genomes from past remains, the prospects for human palaeogenomics remain unclear because of the difficulty of distinguishing contaminant from endogenous DNA sequences. Previous sequence data generated on high-throughput sequencing platforms indicate that fragmentation of ancient DNA sequences is a characteristic trait primarily arising due to depurination processes that create abasic sites leading to DNA breaks

The effects of forest degradation on arboreal primates within Sikundur, the Gunung Leuser Ecosystem, Northern Sumatra

Abstract of a paper given at the 87th Annual Meeting of the American Association of Physical Anthropologists held at Austin, Texas, 11-14 April 201

Search for a Light Charged Higgs Boson Decaying to a W Boson and a CP-Odd Higgs Boson in Final States with eμμ or μμμ in Proton-Proton Collisions at √s=13 TeV

A search for a light charged Higgs boson (H+) decaying to a W boson and a CP-odd Higgs boson (A) in final states with eμμ or μμμ is performed using data from pp collisions at √s=13  TeV, recorded by the CMS detector at the LHC and corresponding to an integrated luminosity of 35.9  fb−1. In this search, it is assumed that the H+ boson is produced in decays of top quarks, and the A boson decays to two oppositely charged muons. The presence of signals for H+ boson masses between 100 and 160 GeV and A boson masses between 15 and 75 GeV is investigated. No evidence for the production of the H+ boson is found. Upper limits at 95% confidence level are obtained on the combined branching fraction for the decay chain, t→bH+→bW+A→bW+μ+μ−, of 1.9×10−6 to 8.6×10−6, depending on the masses of the H+ and A bosons. These are the first limits for these decay modes of the H+ and A bosons.Peer reviewe

Search for dark matter particles produced in association with a Higgs boson in proton-proton collisions at √s = 13 TeV

© 2020, The Author(s). A search for dark matter (DM) particles is performed using events with a Higgs boson candidate and large missing transverse momentum. The analysis is based on proton- proton collision data at a center-of-mass energy of 13 TeV collected by the CMS experiment at the LHC in 2016, corresponding to an integrated luminosity of 35.9 fb−1. The search is performed in five Higgs boson decay channels: h → b b ¯ , γγ, τ+τ−, W+W−, and ZZ. The results from the individual channels are combined to maximize the sensitivity of the analysis. No significant excess over the expected standard model background is observed in any of the five channels or in their combination. Limits are set on DM production in the context of two simplified models. The results are also interpreted in terms of a spin-independent DM-nucleon scattering cross section and compared to those from direct-detection DM experiments. This is the first search for DM particles produced in association with a Higgs boson decaying to a pair of W or Z bosons, and the first statistical combination based on five Higgs boson decay channels. [Figure not available: see fulltext.].SCOAP

An empirical evaluation of genotype imputation of ancient DNA

With capabilities of sequencing ancient DNA to high coverage often limited by sample quality or cost, imputation of missing genotypes presents a possibility to increase the power of inference as well as cost-effectiveness for the analysis of ancient data. However, the high degree of uncertainty often associated with ancient DNA poses several methodological challenges, and performance of imputation methods in this context has not been fully explored. To gain further insights, we performed a systematic evaluation of imputation of ancient data using Beagle v4.0 and reference data from phase 3 of the 1000 Genomes project, investigating the effects of coverage, phased reference, and study sample size. Making use of five ancient individuals with high-coverage data available, we evaluated imputed data for accuracy, reference bias, and genetic affinities as captured by principal component analysis. We obtained genotype concordance levels of over 99% for data with 1× coverage, and similar levels of accuracy and reference bias at levels as low as 0.75×. Our findings suggest that using imputed data can be a realistic option for various population genetic analyses even for data in coverage ranges below 1×. We also show that a large and varied phased reference panel as well as the inclusion of low- to moderate-coverage ancient individuals in the study sample can increase imputation performance, particularly for rare alleles. In-depth analysis of imputed data with respect to genetic variants and allele frequencies gave further insight into the nature of errors arising during imputation, and can provide practical guidelines for postprocessing and validation prior to downstream analysis.eSSENC

New insights on cultural dualism and population structure in the Middle Neolithic Funnel Beaker culture on the island of Gotland

In recent years it has been shown that the Neolithization of Europe was partly driven by migration of farming groups admixing with local hunter-gatherer groups as they dispersed across the continent. However, little research has been done on the cultural duality of contemporaneous foragers and farming populations in the same region. Here we investigate the demographic history of the Funnel Beaker culture [Trichterbecherkultur or TRB, c. 4000–2800 cal BCE], and the sub-Neolithic Pitted Ware culture complex [PWC, c. 3300–2300 cal BCE] during the Nordic Middle Neolithic period on the island of Gotland, Sweden. We use a multidisciplinary approach to investigate individuals buried in the Ansarve dolmen, the only confirmed TRB burial on the island. We present new radiocarbon dating, isotopic analyses for diet and mobility, and mitochondrial DNA haplogroup data to infer maternal inheritance. We also present a new Sr-baseline of 0.71208 ± 0.0016 for the local isotope variation. We compare and discuss our findings together with that of contemporaneous populations in Sweden and the North European mainland. The radiocarbon dating and Strontium isotopic ratios show that the dolmen was used between c. 3300–2700 cal BCE by a population which displayed local Sr-signals. Mitochondrial data show that the individuals buried in the Ansarve dolmen had maternal genetic affinity to that of other Early and Middle Neolithic farming cultures in Europe, distinct from that of the contemporaneous PWC on the island. Furthermore, they exhibited a strict terrestrial and/or slightly varied diet in contrast to the strict marine diet of the PWC. The findings indicate that two different contemporary groups coexisted on the same island for several hundred years with separate cultural identity, lifestyles, as well as dietary patterns

The stone cist conundrum: a multidisciplinary approach to investigate Late Neolithic/Early Bronze Age population demography on the island of Gotland

The Late Neolithic period in Scandinavia [LN, c. 2350–1700 cal BCE] marks a time of considerable changes in settlement patterns, economy, and material culture. This shift also lays the foundation for the demographic developments in the Early Bronze Age [EBA, c. 1700–1100 cal BCE]. However, little is presently known regarding the developments from these time-periods on the island of Gotland in the Baltic Sea. During the Middle Neolithic period [MN, c. 3300–2350 cal BCE], Gotland was inhabited by groups associated with the Funnel Beaker culture [TRB, c. 4000–2700 cal BCE], and the sub-Neolithic Pitted Ware culture [PWC, c. 3300–2300 cal BCE]. Some indications of connections with the Battle Axe/Corded Ware cultures [BAC/CWC, c. 2800–2300 cal BCE] have also been found, but no typical BAC/CWC burials have been located on the island to date. Here, we investigate the chronological and internal relationship of twenty-three individuals buried in four LN/EBA stone cist burials; Häffinds, Hägur, Suderkvie, and Utalskog on Gotland. We present eleven mitochondrial genomes [from 23 X to 1271 X coverage], and twenty-three new radiocarbon dates, as well as stable isotope data for diet. We examine the local Sr-baseline range for Gotland, and present new Sr-data to discuss mobility patterns of the individuals. The genetic results are compared and discussed in light of earlier cultural periods from Gotland [TRB and PWC], and CWC from the European continent, as well as contemporaneous LN secondary burials in the MN Ansarve dolmen. We find that all burials were used into the EBA, but only two of the cists showed activity already during the LN. We also see some mobility to Gotland during the LN/EBA period based on Strontium and mitochondrial data. We see a shift in the dietary pattern compared to the preceding period on the island [TRB and PWC], and the two LN individuals from the Ansarve dolmen exhibited different dietary and mobility patterns compared to the individuals from the LN/EBA stone cist burials. We find that most of the cist burials were used by individuals local to the area of the burials, with the exception of the large LN/EBA Häffinds cist burial which showed higher levels of mobility. Our modeling of ancestral mitochondrial contribution from chronologically older individuals recovered in the cultural contexts of TRB, PWC and CWC show that the best model is a 55/45 mix of CWC and TRB individuals. A 3-way model with a slight influx from PWC [5%] also had a good fit. This is difficult to reconcile with the current archaeological evidence on the island. We suggest that the maternal CWC/TRB contribution we see in the local LN/EBA individuals derives from migrants after the Scandinavian MN period, which possible also admixed with smaller local groups connected with the PWC. Further genomic analyses of these groups on Gotland will help to clarify the demographic history during the MN to EBA time periods