Maximum Matching in Turnstile Streams

We consider the unweighted bipartite maximum matching problem in the one-pass turnstile streaming model where the input stream consists of edge insertions and deletions. In the insertion-only model, a one-pass $2$-approximation streaming algorithm can be easily obtained with space $O(n \log n)$, where $n$ denotes the number of vertices of the input graph. We show that no such result is possible if edge deletions are allowed, even if space $O(n^{3/2-\delta})$ is granted, for every $\delta > 0$. Specifically, for every $0 \le \epsilon \le 1$, we show that in the one-pass turnstile streaming model, in order to compute a $O(n^{\epsilon})$-approximation, space $\Omega(n^{3/2 - 4\epsilon})$ is required for constant error randomized algorithms, and, up to logarithmic factors, space $O( n^{2-2\epsilon} )$ is sufficient. Our lower bound result is proved in the simultaneous message model of communication and may be of independent interest

Sparse {Fourier Transform} by Traversing {Cooley-Tukey FFT} Computation Graphs

Computing the dominant Fourier coefficients of a vector is a common task in many fields, such as signal processing, learning theory, and computational complexity. In the Sparse Fast Fourier Transform (Sparse FFT) problem, one is given oracle access to a $d$-dimensional vector $x$ of size $N$, and is asked to compute the best $k$-term approximation of its Discrete Fourier Transform, quickly and using few samples of the input vector $x$. While the sample complexity of this problem is quite well understood, all previous approaches either suffer from an exponential dependence of runtime on the dimension $d$ or can only tolerate a trivial amount of noise. This is in sharp contrast with the classical FFT algorithm of Cooley and Tukey, which is stable and completely insensitive to the dimension of the input vector: its runtime is $O(N\log N)$ in any dimension $d$. In this work, we introduce a new high-dimensional Sparse FFT toolkit and use it to obtain new algorithms, both on the exact, as well as in the case of bounded $\ell_2$ noise. This toolkit includes i) a new strategy for exploring a pruned FFT computation tree that reduces the cost of filtering, ii) new structural properties of adaptive aliasing filters recently introduced by Kapralov, Velingker and Zandieh'SODA'19, and iii) a novel lazy estimation argument, suited to reducing the cost of estimation in FFT tree-traversal approaches. Our robust algorithm can be viewed as a highly optimized sparse, stable extension of the Cooley-Tukey FFT algorithm. Finally, we explain the barriers we have faced by proving a conditional quadratic lower bound on the running time of the well-studied non-equispaced Fourier transform problem. This resolves a natural and frequently asked question in computational Fourier transforms. Lastly, we provide a preliminary experimental evaluation comparing the runtime of our algorithm to FFTW and SFFT 2.0

Leaf epidermal structure in the dwarf succulent genus Conophytum N.E. Br. (Aizoaceae)

The epidermal structure of 66 species and subspecies of the dwarf succulent genus Cono- phytum N.E. Br. was examined using scanning electron microscopy. Taxa within this genus pos- sess a number of adaptations to their arid envi- ronment including sunken stomata, a prominent wax layer and trichomes. The range of epidermal morphologies present in this genus is described and the use of these to inform infrageneric classi- fication in Conophytum is discussed. In many cases the epidermis of closely related species is similar but this is not always the case across the 16 sections that comprise the genus. Whilst this study confirms the assignment of several recently described taxa to existing sections it suggests that the infrageneric classification of Conophytum needs to be re-evaluated

A novel Botrytis species is associated with a newly emergent foliar disease in cultivated Hemerocallis.

Foliar tissue samples of cultivated daylilies (Hemerocallis hybrids) showing the symptoms of a newly emergent foliar disease known as 'spring sickness' were investigated for associated fungi. The cause(s) of this disease remain obscure. We isolated repeatedly a fungal species which proved to be member of the genus Botrytis, based on immunological tests. DNA sequence analysis of these isolates, using several different phyogenetically informative genes, indicated that they represent a new Botrytis species, most closely related to B. elliptica (lily blight, fire blight) which is a major pathogen of cultivated Lilium. The distinction of the isolates was confirmed by morphological analysis of asexual sporulating cultures. Pathogenicity tests on Hemerocallis tissues in vitro demonstrated that this new species was able to induce lesions and rapid tissue necrosis. Based on this data, we infer that this new species, described here as B. deweyae, is likely to be an important contributor to the development of 'spring sickness' symptoms. Pathogenesis may be promoted by developmental and environmental factors that favour assault by this necrotrophic pathogen. The emergence of this disease is suggested to have been triggered by breeding-related changes in cultivated hybrids, particularly the erosion of genetic diversity. Our investigation confirms that emergent plant diseases are important and deserve close monitoring, especially in intensively in-bred plants

Rubisco evolution in C₄ eudicots: an analysis of Amaranthaceae sensu lato.

BACKGROUND: Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses the key reaction in the photosynthetic assimilation of CO₂. In C₄ plants CO₂ is supplied to Rubisco by an auxiliary CO₂-concentrating pathway that helps to maximize the carboxylase activity of the enzyme while suppressing its oxygenase activity. As a consequence, C₄ Rubisco exhibits a higher maximum velocity but lower substrate specificity compared with the C₃ enzyme. Specific amino-acids in Rubisco are associated with C₄ photosynthesis in monocots, but it is not known whether selection has acted on Rubisco in a similar way in eudicots. METHODOLOGY/PRINCIPAL FINDINGS: We investigated Rubisco evolution in Amaranthaceae sensu lato (including Chenopodiaceae), the third-largest family of C₄ plants, using phylogeny-based maximum likelihood and Bayesian methods to detect Darwinian selection on the chloroplast rbcL gene in a sample of 179 species. Two Rubisco residues, 281 and 309, were found to be under positive selection in C₄ Amaranthaceae with multiple parallel replacements of alanine by serine at position 281 and methionine by isoleucine at position 309. Remarkably, both amino-acids have been detected in other C₄ plant groups, such as C₄ monocots, illustrating a striking parallelism in molecular evolution. CONCLUSIONS/SIGNIFICANCE: Our findings illustrate how simple genetic changes can contribute to the evolution of photosynthesis and strengthen the hypothesis that parallel amino-acid replacements are associated with adaptive changes in Rubisco

Probing a Complex of Cytochromecand Cardiolipin by Magnetic Circular Dichroism Spectroscopy: Implications for the Initial Events in Apoptosis

Oxidation of cardiolipin (CL) by its complex with cytochrome c (cyt c) plays a crucial role in triggering apoptosis. Through a combination of magnetic circular dichroism spectroscopy and potentiometric titrations, we show that both the ferric and ferrous forms of the heme group of a CL:cyt c complex exist as multiple conformers at a physiologically relevant pH of 7.4. For the ferric state, these conformers are His/Lys- and His/OH–-ligated. The ferrous state is predominantly high-spin and, most likely, His/–. Interconversion of the ferric and ferrous conformers is described by a single midpoint potential of -80 ± 9 mV vs SHE. These results suggest that CL oxidation in mitochondria could occur by the reaction of molecular oxygen with the ferrous CL:cyt c complex in addition to the well-described reaction of peroxides with the ferric form

Coevolution of amino acid residues in the key photosynthetic enzyme Rubisco

<p>Abstract</p> <p>Background</p> <p>One of the key forces shaping proteins is coevolution of amino acid residues. Knowing which residues coevolve in a particular protein may facilitate our understanding of protein evolution, structure and function, and help to identify substitutions that may lead to desired changes in enzyme kinetics. Rubisco, the most abundant enzyme in biosphere, plays an essential role in the process of carbon fixation through photosynthesis, thus facilitating life on Earth. This makes Rubisco an important model system for studying the dynamics of protein fitness optimization on the evolutionary landscape. In this study we investigated the selective and coevolutionary forces acting on large subunit of land plants Rubisco using Markov models of codon substitution and clustering approaches applied to amino acid substitution histories.</p> <p>Results</p> <p>We found that both selection and coevolution shape Rubisco, and that positively selected and coevolving residues have their specifically favored amino acid composition and pairing preference. The mapping of these residues on the known Rubisco tertiary structures showed that the coevolving residues tend to be in closer proximity with each other compared to the background, while positively selected residues tend to be further away from each other. This study also reveals that the residues under positive selection or coevolutionary force are located within functionally important regions and that some residues are targets of both positive selection and coevolution at the same time.</p> <p>Conclusion</p> <p>Our results demonstrate that coevolution of residues is common in Rubisco of land plants and that there is an overlap between coevolving and positively selected residues. Knowledge of which Rubisco residues are coevolving and positively selected could be used for further work on structural modeling and identification of substitutions that may be changed in order to improve efficiency of this important enzyme in crops.</p

Positively selected amino acid replacements within the RuBisCO enzyme of oak trees are associated with ecological adaptations

Phylogenetic analysis by maximum likelihood (PAML) has become the standard approach to study positive selection at the molecular level, but other methods may provide complementary ways to identify amino acid replacements associated with particular conditions. Here, we compare results of the decision tree (DT) model method with ones of PAML using the key photosynthetic enzyme RuBisCO as a model system to study molecular adaptation to particular ecological conditions in oaks (Quercus). We sequenced the chloroplast rbcL gene encoding RuBisCO large subunit in 158 Quercus species, covering about a third of the global genus diversity. It has been hypothesized that RuBisCO has evolved differentially depending on the environmental conditions and leaf traits governing internal gas diffusion patterns. Here, we show, using PAML, that amino acid replacements at the residue positions 95, 145, 251, 262 and 328 of the RuBisCO large subunit have been the subject of positive selection along particular Quercus lineages associated with the leaf traits and climate characteristics. In parallel, the DT model identified amino acid replacements at sites 95, 219, 262 and 328 being associated with the leaf traits and climate characteristics, exhibiting partial overlap with the results obtained using PAML