ALBERT

Description: For $q$ an odd prime power with $q 〉 169,$ we prove that there are always three consecutive primitive elements in the finite field $\mathbb {F}_{q}$ . Indeed, there are precisely eleven values of $q \leq 169$ for which this is false. For $4\leq n \leq 8,$ we present conjectures on the size of $q_{0}(n)$ such that $q 〉 q_{0}(n)$ guarantees the existence of $n$ consecutive primitive elements in $\mathbb {F}_{q}$ , provided that $\mathbb {F}_{q}$ has characteristic at least $n$ . Finally, we improve the upper bound on $q_{0}(n)$ for all $n\geq 3$ .

Description: Summer droughts are likely to increase in frequency and intensity across Europe, yet long-lived trees may have a limited ability to tolerate drought. It is therefore critical that we improve our understanding of phenotypic plasticity to drought in natural populations for ecologically and economically important trees such as Populus nigra L. A common garden experiment was conducted using ~500 wild P. nigra trees, collected from 11 river populations across Europe. Phenotypic variation was found across the collection, with southern genotypes from Spain and France characterized by small leaves and limited biomass production. To examine the relationship between phenotypic variation and drought tolerance, six genotypes with contrasting leaf morphologies were subjected to a water deficit experiment. ‘North eastern’ genotypes were collected at wet sites and responded to water deficit with reduced biomass growth, slow stomatal closure and reduced water use efficiency (WUE) assessed by 13 C. In contrast, ‘southern’ genotypes originating from arid sites showed rapid stomatal closure, improved WUE and limited leaf loss. Transcriptome analyses of a genotype from Spain (Sp2, originating from an arid site) and another from northern Italy (Ita, originating from a wet site) revealed dramatic differences in gene expression response to water deficit. Transcripts controlling leaf development and stomatal patterning, including SPCH , ANT , ER , AS1 , AS2 , PHB , CLV1 , ERL1–3 and TMM , were down-regulated in Ita but not in Sp2 in response to drought.

Description: For isohydric trees mid-day water uptake is stable and depends on soil water status, reflected in pre-dawn leaf water potential ( pd ) and mid-day stem water potential ( md ), tree hydraulic conductance and a more-or-less constant leaf water potential ( l ) for much of the day, maintained by the stomata. Stabilization of l can be represented by a linear relationship between canopy resistance ( R c ) and vapor pressure deficit ( D ), and the slope ( B D ) is proportional to the steady-state water uptake. By analyzing sap flow (SF), meteorological and md measurements during a series of wetting and drying ( D / W ) cycles in a nectarine orchard, we found that for the range of md relevant for irrigated orchards the slope of the relationship of R c to D , B D is a linear function of md . R c was simulated using the above relationships, and its changes in the morning and evening were simulated using a rectangular hyperbolic relationship between leaf conductance and photosynthetic irradiance, fitted to leaf-level measurements. The latter was integrated with one-leaf, two-leaf and integrative radiation models, and the latter gave the best results. Simulated R c was used in the Penman–Monteith equation to simulate tree transpiration, which was validated by comparing with SF from a separate data set. The model gave accurate estimates of diurnal and daily total tree transpiration for the range of md s used in regular and deficit irrigation. Diurnal changes in tree water content were determined from the difference between simulated transpiration and measured SF . Changes in water content caused a time lag of 90–105 min between transpiration and SF for md between –0.8 and –1.55 MPa, and water depletion reached 3 l h –1 before noon. Estimated mean diurnal changes in water content were 5.5 l day –1  tree –1 at md of –0.9 MPa and increased to 12.5 l day –1  tree –1 at –1.45 MPa, equivalent to 6.5 and 16.5% of daily tree water use, respectively. Sixteen percent of the dynamic water volume was in the leaves. Inversion of the model shows that md can be predicted from D and R c , which may have some importance for irrigation management to maintain target values of md . That relationship will be explored in future research.

Description: This article describes the use of continuous vector space models for reasoning with a formal knowledge base. The practical significance of these models is that they support fast, approximate but robust inference and hypothesis generation, which is complementary to the slow, exact, but sometimes brittle behaviour of more traditional deduction engines such as theorem provers. The article explains the way logical connectives can be used in semantic vector models, and summarizes the development of Predication-based Semantic Indexing, which involves the use of Vector Symbolic Architectures to represent the concepts and relationships from a knowledge base of subject-predicate-object triples. Experiments show that the use of continuous models for formal reasoning is not only possible, but already demonstrably effective for some recognized informatics tasks, and showing promise in other traditional problem areas. Examples described in this article include: predicting new uses for existing drugs in biomedical informatics; removing unwanted meanings from search results in information retrieval and concept navigation; type inference from attributes; comparing words based on their orthography; and representing tabular data, including modelling numerical values. The algorithms and techniques described in this article are all publicly released and freely available in the Semantic Vectors open-source software package. 1

Description: Proteins adhere to DNA at locations and with strengths that depend on the protein conformation, the underlying DNA sequence and the ionic content of the solution. A facile technique to probe the positions and strengths of protein-DNA binding would aid in understanding these important interactions. Here, we describe a ‘DNA pulley’ for position-resolved nano-mechanical measurements of protein-DNA interactions. A molecule of DNA is tethered by one end to a glass surface, and by the other end to a magnetic bead. The DNA is stretched horizontally by a magnet, and a nanoscale knife made of silicon nitride is manipulated to contact, bend and scan along the DNA. The mechanical profile of the DNA at the contact with the knife is probed via nanometer-precision optical tracking of the magnetic bead. This system enables detection of protein bumps on the DNA and localization of their binding sites. We study theoretically the technical requirements to detect mechanical heterogeneities in the DNA itself.

Description: We provide radio spectral properties at high frequencies (1≤ (GHz) ≤ 20) for 65 planetary nebulae in the Australia Telescope 20 GHz (AT20G) survey, identified from our list of sources that show flat-spectrum (α 〉 –0.5) and are well resolved at 0.15 arcsec angular size scale. We show that this method very effectively identifies thermal sources like planetary nebulae (and H ii regions). In our analysis of the radio spectra of a subset of 37 planetary nebulae, we find no clear evidence of either the excess flux in the optically thin region proposed in the literature, or non-thermal emission. Using a combination of radio spectra, radio interferometric technique and infrared spectra from Wide-field Infrared Survey Explorer , we provide an effective method of identifying further candidates and we list a total of six new planetary nebulae that require follow-up. Together with the list of planetary nebula candidates and the planetary nebulae from the AT20G survey presented in this paper, we provide radio spectra for a complete radio flux limited sample of planetary nebulae at | b | 〉 1.5 deg in the Southern hemisphere at 20 GHz.

Description: Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis -antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of non-coding RNAs in a given organism is challenging, especially since some of these RNAs were attributed to ‘transcriptional noise’. To allow the search for conserved transcriptomic elements we produced comparative transcriptome maps for multiple species across the microbial tree of life. These transcriptome maps are detailed in annotations, comparable by gene families, and BLAST-searchable by user provided sequences. Our transcriptome collection includes 18 model organisms spanning 10 phyla/subphyla of bacteria and archaea that were sequenced using standardized RNA-seq methods. The utility of the comparative approach, as implemented in our web server, is demonstrated by highlighting genes with exceptionally long 5'UTRs across species, which correspond to many known riboswitches and further suggest novel putative regulatory elements. Our study provides a standardized reference transcriptome to major clinically and environmentally important microbial phyla. The viewer is available at http://exploration.weizmann.ac.il/TCOL , setting a framework for comparative studies of the microbial non-coding genome.

Description: Stars orbiting within 1 arcsec of the supermassive black hole in the Galactic Centre, Sgr A*, are notoriously difficult to detect due to obscuration by gas and dust. We show that some stars orbiting this region may be detectable via synchrotron emission. In such instances, a bow shock forms around the star and accelerates the electrons. We calculate that around the 10 GHz band (radio) and at 10 14  Hz (infrared) the luminosity of a star orbiting the black hole is comparable to the luminosity of Sgr A*. The strength of the synchrotron emission depends on a number of factors including the star's orbital velocity. Thus, the ideal time to observe the synchrotron flux is when the star is at pericentre. The star S2 will be ~0.015 arcsec from Sgr A* in 2018, and is an excellent target to test our predictions.

Description: Roots interact with soil properties and irrigation water quality leading to changes in root growth, structure and function. We studied these interactions in an orchard and in lysimeters with clay and sandy loam soils. Minirhizotron imaging and manual sampling showed that root growth was three times lower in the clay relative to sandy loam soil. Treated wastewater (TWW) led to a large reduction in root growth with clay (45–55%) but not with sandy loam soil (〈20%). Treated wastewater increased salt uptake, membrane leakage and proline content, and decreased root viability, carbohydrate content and osmotic potentials in the fine roots, especially in clay. These results provide evidence that TWW challenges and damages the root system. The phenology and physiology of root orders were studied in lysimeters. Soil type influenced diameter, specific root area, tissue density and cortex area similarly in all root orders, while TWW influenced these only in clay soil. Respiration rates were similar in both soils, and root hydraulic conductivity was severely reduced in clay soil. Treated wastewater increased respiration rate and reduced hydraulic conductivity of all root orders in clay but only of the lower root orders in sandy loam soil. Loss of hydraulic conductivity increased with root order in clay and clay irrigated with TWW. Respiration and hydraulic properties of all root orders were significantly affected by sodium-amended TWW in sandy loam soil. These changes in root order morphology, anatomy, physiology and hydraulic properties indicate rapid and major modifications of root systems in response to differences in soil type and water quality.

Description: MicroRNAs play important roles in a large variety of biological systems and processes through their regulation of target mRNA expression, and show promise as clinical biomarkers. However, their small size presents challenges for tagging or direct detection. Innovation in techniques to sense and quantify microRNAs may aid research into novel aspects of microRNA biology and contribute to the development of diagnostics. By introducing an additional stem loop into the fluorescent RNA Spinach and altering its 3' and 5' ends, we have generated a new RNA, Pandan, that functions as the basis for a microRNA sensor. Pandan contains two sequence-variable stem loops that encode complementary sequence for a target microRNA of interest. In its sensor form, it requires the binding of a target microRNA in order to reconstitute the RNA scaffold for fluorophore binding and fluorescence. Binding of the target microRNA resulted in large changes in fluorescence intensity. The median fold change in fluorescence observed for the sensors tested was ~50-fold. Pandan RNA sensors exhibit good signal-to-noise ratios, and can detect their target microRNAs within complex RNA mixtures.