Synthesis of some new pyrimidine and pyridopyrimidine derivatives

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A comparative analysis of metacommunity types in the freshwater realm

Most metacommunity studies have taken a direct mechanistic approach, aiming to model the effects of local and regional processes on local communities within a metacommunity. An alternative approach is to focus on emergent patterns at the metacommunity level through applying the elements of metacommunity structure (EMS; Oikos, 97, 2002, 237) analysis. The EMS approach has very rarely been applied in the context of a comparative analysis of metacommunity types of main microbial, plant, and animal groups. Furthermore, to our knowledge, no study has associated metacommunity types with their potential ecological correlates in the freshwater realm. We assembled data for 45 freshwater metacommunities, incorporating biologically highly disparate organismal groups (i.e., bacteria, algae, macrophytes, invertebrates, and fish). We first examined ecological correlates (e.g., matrix properties, beta diversity, and average characteristics of a metacommunity, including body size, trophic group, ecosystem type, life form, and dispersal mode) of the three elements of metacommunity structure (i.e., coherence, turnover, and boundary clumping). Second, based on those three elements, we determined which metacommunity types prevailed in freshwater systems and which ecological correlates best discriminated among the observed metacommunity types. We found that the three elements of metacommunity structure were not strongly related to the ecological correlates, except that turnover was positively related to beta diversity. We observed six metacommunity types. The most common were Clementsian and quasi-nested metacommunity types, whereas Random, quasi-Clementsian, Gleasonian, and quasi-Gleasonian types were less common. These six metacommunity types were best discriminated by beta diversity and the first axis of metacommunity ecological traits, ranging from metacommunities of producer organisms occurring in streams to those of large predatory organisms occurring in lakes. Our results showed that focusing on the emergent properties of multiple metacommunities provides information additional to that obtained in studies examining variation in local community structure within a metacommunity.Peer reviewe

Four-Round Concurrent Non-Malleable Commitments from One-Way Functions

How many rounds and which assumptions are required for concurrent non-malleable commitments? The above question has puzzled researchers for several years. Pass in [TCC 2013] showed a lower bound of 3 rounds for the case of black-box reductions to falsifiable hardness assumptions with respect to polynomial-time adversaries. On the other side, Goyal [STOC 2011], Lin and Pass [STOC 2011] and Goyal et al. [FOCS 2012] showed that one-way functions (OWFs) are sufficient with a constant number of rounds. More recently Ciampi et al. [CRYPTO 2016] showed a 3-round construction based on subexponentially strong one-way permutations. In this work we show as main result the first 4-round concurrent non-malleable commitment scheme assuming the existence of any one-way function. Our approach builds on a new security notion for argument systems against man-in-the-middle attacks: Simulation-Witness-Independence. We show how to construct a 4-round one-many simulation-witnesses-independent argument system from one-way functions. We then combine this new tool in parallel with a weak form of non-malleable commitments constructed by Goyal et al. in [FOCS 2014] obtaining the main result of our work

The Sum Can Be Weaker Than Each Part

International audienceIn this paper we study the security of summing the outputs of two independent hash functions, in an effort to increase the security of the resulting design, or to hedge against the failure of one of the hash functions. The exclusive-or (XOR) combiner H1(M)⊕H2(M) is one of the two most classical combiners, together with the concatenation combiner H1(M) H2(M). While the security of the concatenation of two hash functions is well understood since Joux's seminal work on multicollisions, the security of the sum of two hash functions has been much less studied. The XOR combiner is well known as a good PRF and MAC combiner, and is used in practice in TLS versions 1.0 and 1.1. In a hash function setting, Hoch and Shamir have shown that if the compression functions are modeled as random oracles, or even weak random oracles (i.e. they can easily be inverted – in particular H1 and H2 offer no security), H1 ⊕ H2 is indifferentiable from a random oracle up to the birthday bound. In this work, we focus on the preimage resistance of the sum of two narrow-pipe n-bit hash functions, following the Merkle-Damgård or HAIFA structure (the internal state size and the output size are both n bits). We show a rather surprising result: the sum of two such hash functions, e.g. SHA-512 ⊕ Whirlpool, can never provide n-bit security for preimage resistance. More precisely, we present a generic preimage attack with a complexity of O(2 5n/6). While it is already known that the XOR combiner is not preserving for preimage resistance (i.e. there might be some instantiations where the hash functions are secure but the sum is not), our result is much stronger: for any narrow-pipe functions, the sum is not preimage resistant. Besides, we also provide concrete preimage attacks on the XOR combiner (and the concatenation combiner) when one or both of the compression functions are weak; this complements Hoch and Shamir's proof by showing its tightness for preimage resistance. Of independent interests, one of our main technical contributions is a novel structure to control simultaneously the behavior of independent hash computations which share the same input message. We hope that breaking the pairwise relationship between their internal states will have applications in related settings

Estimation of Fish Biomass Using Environmental DNA

Environmental DNA (eDNA) from aquatic vertebrates has recently been used to estimate the presence of a species. We hypothesized that fish release DNA into the water at a rate commensurate with their biomass. Thus, the concentration of eDNA of a target species may be used to estimate the species biomass. We developed an eDNA method to estimate the biomass of common carp (Cyprinus carpio L.) using laboratory and field experiments. In the aquarium, the concentration of eDNA changed initially, but reached an equilibrium after 6 days. Temperature had no effect on eDNA concentrations in aquaria. The concentration of eDNA was positively correlated with carp biomass in both aquaria and experimental ponds. We used this method to estimate the biomass and distribution of carp in a natural freshwater lagoon. We demonstrated that the distribution of carp eDNA concentration was explained by water temperature. Our results suggest that biomass data estimated from eDNA concentration reflects the potential distribution of common carp in the natural environment. Measuring eDNA concentration offers a non-invasive, simple, and rapid method for estimating biomass. This method could inform management plans for the conservation of ecosystems

Effects of Total Resources, Resource Ratios, and Species Richness on Algal Productivity and Evenness at Both Metacommunity and Local Scales

The study of the interrelationship between productivity and biodiversity is a major research field in ecology. Theory predicts that if essential resources are heterogeneously distributed across a metacommunity, single species may dominate productivity in individual metacommunity patches, but a mixture of species will maximize productivity across the whole metacommunity. It also predicts that a balanced supply of resources within local patches should favor species coexistence, whereas resource imbalance would favor the dominance of one species. We performed an experiment with five freshwater algal species to study the effects of total supply of resources, their ratios, and species richness on biovolume production and evenness at the scale of both local patches and metacommunities. Generally, algal biovolume increased, whereas algal resource use efficiency (RUE) and evenness decreased with increasing total supply of resources in mixed communities containing all five species. In contrast to predictions for biovolume production, the species mixtures did not outperform all monocultures at the scale of metacommunities. In other words, we observed no general transgressive overyielding. However, RUE was always higher in mixtures than predicted from monocultures, and analyses indicate that resource partitioning or facilitation in mixtures resulted in higher-than-expected productivity at high resource supply. Contrasting our predictions for the local scale, balanced supply of resources did not generally favor higher local evenness, however lowest evenness was confined to patches with the most imbalanced supply. Thus, our study provides mixed support for recent theoretical advancements to understand biodiversity-productivity relationships

Discovery of Pod Shatter-Resistant Associated SNPs by Deep Sequencing of a Representative Library Followed by Bulk Segregant Analysis in Rapeseed

Background: Single nucleotide polymorphisms (SNPs) are an important class of genetic marker for target gene mapping. As of yet, there is no rapid and effective method to identify SNPs linked with agronomic traits in rapeseed and other crop species. Methodology/Principal Findings: We demonstrate a novel method for identifying SNP markers in rapeseed by deep sequencing a representative library and performing bulk segregant analysis. With this method, SNPs associated with rapeseed pod shatter-resistance were discovered. Firstly, a reduced representation of the rapeseed genome was used. Genomic fragments ranging from 450–550 bp were prepared from the susceptible bulk (ten F2 plants with the silique shattering resistance index, SSRI,0.10) and the resistance bulk (ten F2 plants with SSRI.0.90), and also Solexa sequencingproduced 90 bp reads. Approximately 50 million of these sequence reads were assembled into contigs to a depth of 20-fold coverage. Secondly, 60,396 ‘simple SNPs ’ were identified, and the statistical significance was evaluated using Fisher’s exact test. There were 70 associated SNPs whose –log10p value over 16 were selected to be further analyzed. The distribution of these SNPs appeared a tight cluster, which consisted of 14 associated SNPs within a 396 kb region on chromosome A09. Our evidence indicates that this region contains a major quantitative trait locus (QTL). Finally, two associated SNPs from this region were mapped on a major QTL region

Unique Properties of Eukaryote-Type Actin and Profilin Horizontally Transferred to Cyanobacteria

A eukaryote-type actin and its binding protein profilin encoded on a genomic island in the cyanobacterium Microcystis aeruginosa PCC 7806 co-localize to form a hollow, spherical enclosure occupying a considerable intracellular space as shown by in vivo fluorescence microscopy. Biochemical and biophysical characterization reveals key differences between these proteins and their eukaryotic homologs. Small-angle X-ray scattering shows that the actin assembles into elongated, filamentous polymers which can be visualized microscopically with fluorescent phalloidin. Whereas rabbit actin forms thin cylindrical filaments about 100 µm in length, cyanobacterial actin polymers resemble a ribbon, arrest polymerization at 5-10 µm and tend to form irregular multi-strand assemblies. While eukaryotic profilin is a specific actin monomer binding protein, cyanobacterial profilin shows the unprecedented property of decorating actin filaments. Electron micrographs show that cyanobacterial profilin stimulates actin filament bundling and stabilizes their lateral alignment into heteropolymeric sheets from which the observed hollow enclosure may be formed. We hypothesize that adaptation to the confined space of a bacterial cell devoid of binding proteins usually regulating actin polymerization in eukaryotes has driven the co-evolution of cyanobacterial actin and profilin, giving rise to an intracellular entity

QTL for phytosterol and sinapate ester content in Brassica napus L. collocate with the two erucic acid genes

Improving oil and protein quality for food and feed purposes is an important goal in rapeseed (Brassica napus L.) breeding programs. Rapeseed contains phytosterols, used to enrich food products, and sinapate esters, which are limiting the utilization of rapeseed proteins in the feed industry. Increasing the phytosterol content of oil and lowering sinapate ester content of meal could increase the value of the oilseed rape crop. The objective of the present study was to identify quantitative trait loci (QTL) for phytosterol and sinapate ester content in a winter rapeseed population of 148 doubled haploid lines, previously found to have a large variation for these two traits. This population also segregated for the two erucic acid genes. A close negative correlation was found between erucic acid and phytosterol content (Spearman’s rank correlation, rs = −0.80**). For total phytosterol content, three QTL were detected, explaining 60% of the genetic variance. The two QTL with the strongest additive effects were mapped on linkage groups N8 and N13 within the confidence intervals of the two erucic acid genes. For sinapate ester content four QTL were detected, explaining 53% of the genetic variance. Again, a close negative correlation was found between erucic acid and sinapate ester content (rs = −0.66**) and the QTL with the strongest additive effects mapped on linkage groups N8 and N13 within the confidence intervals of the two erucic acid genes. The results suggests, that there is a pleiotropic effect of the two erucic acid genes on phytosterol and sinapate ester content; the effect of the alleles for low erucic acid content is to increase phytosterol and sinapate ester content. Possible reasons for this are discussed based on known biosynthetic pathways

How to Record Quantum Queries, and Applications to Quantum Indifferentiability

The quantum random oracle model (QROM) has become the standard model in which to prove the post-quantum security of random-oracle-based constructions. Unfortunately, none of the known proof techniques allow the reduction to record information about the adversary\u27s queries, a crucial feature of many classical ROM proofs, including all proofs of indifferentiability for hash function domain extension. In this work, we give a new QROM proof technique that overcomes this ``recording barrier\u27\u27. Our central observation is that when viewing the adversary\u27s query and the oracle itself in the Fourier domain, an oracle query switches from writing to the adversary\u27s space to writing to the oracle itself. This allows a reduction to simulate the oracle by simply recording information about the adversary\u27s query in the Fourier domain. We then use this new technique to show the indifferentiability of the Merkle-Damgard domain extender for hash functions. We also give a proof of security for the Fujisaki-Okamoto transformation; previous proofs required modifying the scheme to include an additional hash term. Given the threat posed by quantum computers and the push toward quantum-resistant cryptosystems, our work represents an important tool for efficient post-quantum cryptosystems