Canonical Products Research Articles

Strengthening of Gaisin’s lemma on the minimum modulus of even canonical products

Strengthening of Gaisin’s lemma on the minimum modulus of even canonical products

Impaired ribosome-associated quality control of C9orf72 arginine-rich dipeptide-repeat proteins.

Protein quality control pathways have evolved to ensure the fidelity of protein synthesis and efficiently clear potentially toxic protein species. Defects in ribosome-associated quality control and its associated factors have been implicated in the accumulation of aberrant proteins and neurodegeneration. C9orf72 repeat-associated non-AUG translation has been suggested to involve inefficient translation elongation, lead to ribosomal pausing and activation of ribosome-associated quality control pathways. However, the role of the ribosome-associated quality control complex in the processing of proteins generated through this non-canonical translation is not well understood. Here we use reporter constructs containing the C9orf72-associated hexanucleotide repeat, ribosome-associated quality control complex deficient cell models and stain for ribosome-associated quality control markers in C9orf72-expansion carrier human tissue to understand its role in dipeptide-repeat protein pathology. Our studies show that canonical ribosome-associated quality control substrates products are efficiently cleared by the ribosome-associated quality control complex in mammalian cells. Furthermore, using stalling reporter constructs, we show that repeats associated with the C9orf72-expansion induce ribosomal stalling when arginine (R)-rich dipeptide-repeat proteins are synthesized in a length-dependent manner. However, despite triggering this pathway, these arginine-rich dipeptide-repeat proteins are not efficiently processed by the core components of the ribosome-associated quality control complex (listerin, nuclear-export mediator factor and valosin containing protein) partly due to lack of lysine residues, which precludes ubiquitination. Deficient processing by this complex may be implicated in C9orf72-expansion associated disease as dipeptide-repeat protein inclusions were observed to be predominantly devoid of ubiquitin and co-localize with nuclear-export mediator factor in mutation carriers' frontal cortex and cerebellum tissue. These findings suggest that impaired processing of these arginine-rich dipeptide-repeat proteins derived from repeat-associated non-AUG translation by the ribosome-associated quality control complex may contribute to protein homeostasis dysregulation observed in C9orf72-expansion amyotrophic lateral sclerosis and frontotemporal degeneration neuropathogenesis.

The SPTLC1 p.S331 mutation bridges sensory neuropathy and motor neuron disease and has implications for treatment.

SPTLC1-related disorder is a late onset sensory-autonomic neuropathy associated with perturbed sphingolipid homeostasis which can be improved by supplementation with the serine palmitoyl-CoA transferase (SPT) substrate, l-serine. Recently, a juvenile form of motor neuron disease has been linked to SPTLC1 variants. Variants affecting the p.S331 residue of SPTLC1 cause a distinct phenotype, whose pathogenic basis has not been established. This study aims to define the neuropathological and biochemical consequences of the SPTLC1 p.S331 variant, and test response to l-serine in this specific genotype. We report clinical and neurophysiological characterisation of two unrelated children carrying distinct p.S331 SPTLC1 variants. The neuropathology was investigated by analysis of sural nerve and skin innervation. To clarify the biochemical consequences of the p.S331 variant, we performed sphingolipidomic profiling of serum and skin fibroblasts. We also tested the effect of l-serine supplementation in skin fibroblasts of patients with p.S331 mutations. In both patients, we recognised an early onset phenotype with prevalent progressive motor neuron disease. Neuropathology showed severe damage to the sensory and autonomic systems. Sphingolipidomic analysis showed the coexistence of neurotoxic deoxy-sphingolipids with an excess of canonical products of the SPT enzyme. l-serine supplementation in patient fibroblasts reduced production of toxic 1-deoxysphingolipids but further increased the overproduction of sphingolipids. Our findings suggest that p.S331 SPTLC1 variants lead to an overlap phenotype combining features of sensory and motor neuropathies, thus proposing a continuum in the spectrum of SPTLC1-related disorders. l-serine supplementation in these patients may be detrimental.

Studies of ultrastructure, gene expression, and marker analysis reveal that mouse bladder PDGFRA+ interstitial cells are fibroblasts.

Fibroblasts are crucial to normal and abnormal organ and tissue biology, yet we lack basic insights into the fibroblasts that populate the bladder wall. Candidates may include bladder interstitial cells (also referred to as myofibroblasts, telocytes, and interstitial cells of Cajal-like cells), which express the fibroblast-associated marker PDGFRA along with VIM and CD34 but whose form and function remain enigmatic. By applying the latest insights in fibroblast transcriptomics, coupled with studies of gene expression, ultrastructure, and marker analysis, we observe the following: 1) that mouse bladder PDGFRA+ cells exhibit all of the ultrastructural hallmarks of fibroblasts including spindle shape, lack of basement membrane, abundant endoplasmic reticulum and Golgi, and formation of homotypic cell-cell contacts (but not heterotypic ones); 2) that they express multiple canonical fibroblast markers (including Col1a2, CD34, LY6A, and PDGFRA) along with the universal fibroblast genes Col15a1 and Pi16 but they do not express Kit; and 3) that PDGFRA+ fibroblasts include suburothelial ones (which express ACTA2, CAR3, LY6A, MYH10, TNC, VIM, Col1a2, and Col15a1), outer lamina propria ones (which express CD34, LY6A, PI16, VIM, Col1a2, Col15a1, and Pi16), intermuscular ones (which express CD34, VIM, Col1a2, Col15a1, and Pi16), and serosal ones (which express CD34, PI16, VIM, Col1a2, Col15a1, and Pi16). Collectively, our study revealed that the ultrastructure of PDFRA+ interstitial cells combined with their expression of multiple canonical and universal fibroblast-associated gene products indicates that they are fibroblasts. We further propose that there are four regionally distinct populations of fibroblasts in the bladder wall, which likely contribute to bladder function and dysfunction.NEW & NOTEWORTHY We currently lack basic insights into the fibroblasts that populate the bladder wall. By exploring the ultrastructure of mouse bladder connective tissue cells, combined with analyses of their gene and protein expression, our study revealed that PDGRA+ interstitial cells (also referred to as myofibroblasts, telocytes, and interstitial cells of Cajal-like cells) are fibroblasts and that the bladder wall contains multiple, regionally distinct populations of these cells.

Finite Blaschke products and the golden ratio

Geometric properties of finite Blaschke products have been intensively studied by many different aspects. In this paper, our aim is to study geometric properties of finite Blaschke products related to the golden ratio $\alpha =\frac{1+\sqrt{5}}{2}$. Mainly, we focus on the relationships between the zeros of canonical finite Blaschke products of lower degree and the golden ratio. We show that the geometric notions such as "golden triangle, "golden ellipse" and "golden rectangle" are closely related to the geometry of finite Blaschke products.

Secondary cup and cap products in coarse geometry

We construct secondary cup and cap products on coarse (co-)homology theories from given cross and slant products. They are defined for coarse spaces relative to weak generalized controlled deformation retracts. On ordinary coarse cohomology, our secondary cup product agrees with a secondary product defined by Roe. For coarsifications of topological coarse (co-)homology theories, our secondary cup and cap products correspond to the primary cup and cap products on Higson dominated coronas via transgression maps. And in the case of coarse mathrm {K}-theory and -homology, the secondary products correspond to canonical primary products between the mathrm {K}-theories of the stable Higson corona and the Roe algebra under assembly and co-assembly.

Childhood amyotrophic lateral sclerosis caused by excess sphingolipid synthesis.

Amyotrophic lateral sclerosis (ALS) is a progressive, neurodegenerative disease of the lower and upper motor neurons with sporadic or hereditary occurrence. Age of onset, pattern of motor neuron degeneration and disease progression vary widely among individuals with ALS. Various cellular processes may drive ALS pathomechanisms, but a monogenic direct metabolic disturbance has not been causally linked to ALS. Here we show SPTLC1 variants that result in unrestrained sphingoid base synthesis cause a monogenic form of ALS. We identified four specific, dominantly acting SPTLC1 variants in seven families manifesting as childhood-onset ALS. These variants disrupt the normal homeostatic regulation of serine palmitoyltransferase (SPT) by ORMDL proteins, resulting in unregulated SPT activity and elevated levels of canonical SPT products. Notably, this is in contrast with SPTLC1 variants that shift SPT amino acid usage from serine to alanine, result in elevated levels of deoxysphingolipids and manifest with the alternate phenotype of hereditary sensory and autonomic neuropathy. We custom designed small interfering RNAs that selectively target the SPTLC1 ALS allele for degradation, leave the normal allele intact and normalize sphingolipid levels in vitro. The role of primary metabolic disturbances in ALS has been elusive; this study defines excess sphingolipid biosynthesis as a fundamental metabolic mechanism for motor neuron disease.

Detecting circRNA in purified spliceosomal P complex.

Circular RNAs (circRNAs) generated from back-splicing of exons have been found in a wide range of eukaryotic species and exert a variety of biological functions. Unlike canonical splicing, the mechanism of back-splicing has long remained elusive. We recently determined the cryo-EM structure of the yeast spliceosomal E complex assembled on introns, leading us to hypothesize that the same E complex can assemble across an exon forming the exon-definition complex. This complex, when assembled on long exons, goes through the splicing cycle and catalyzes back-splicing to generate circRNAs. Supporting this hypothesis, we purified the yeast post-catalytic spliceosomal P complex (the best complex in the splicing cycle to trap splicing products and intermediates) and detected canonical and back-splicing products as well as splicing intermediates. Here we describe in detail this procedure, which may be applied to other organisms to facilitate research on the biogenesis and regulation of circRNA.

Interpolation Problems of A. F. Leontiev Type

In this paper, we discuss free interpolation in the spaces of entire and analytic finite-order functions in the upper half-plane. A review of problems and basic results related to such problems is given. Solvability criteria are formulated in terms of canonical products of interpolation nodes and in terms of the measure determined by these nodes.

Biological Filtering and Substrate Promiscuity Prediction for Annotating Untargeted Metabolomics.

Mass spectrometry coupled with chromatography separation techniques provides a powerful platform for untargeted metabolomics. Determining the chemical identities of detected compounds however remains a major challenge. Here, we present a novel computational workflow, termed extended metabolic model filtering (EMMF), that aims to engineer a candidate set, a listing of putative chemical identities to be used during annotation, through an extended metabolic model (EMM). An EMM includes not only canonical substrates and products of enzymes already cataloged in a database through a reference metabolic model, but also metabolites that can form due to substrate promiscuity. EMMF aims to strike a balance between discovering previously uncharacterized metabolites and the computational burden of annotation. EMMF was applied to untargeted LC–MS data collected from cultures of Chinese hamster ovary (CHO) cells and murine cecal microbiota. EMM metabolites matched, on average, to 23.92% of measured masses, providing a > 7-fold increase in the candidate set size when compared to a reference metabolic model. Many metabolites suggested by EMMF are not catalogued in PubChem. For the CHO cell, we experimentally confirmed the presence of 4-hydroxyphenyllactate, a metabolite predicted by EMMF that has not been previously documented as part of the CHO cell metabolic model.

Expansions of the Real Field by Canonical Products

AbstractWe consider expansions of o-minimal structures on the real field by collections of restrictions to the positive real line of the canonical Weierstrass products associated with sequences such as$(-n^{s})_{n>0}$(for$s>0$) and$(-s^{n})_{n>0}$(for$s>1$), and also expansions by associated functions such as logarithmic derivatives. There are only three possible outcomes known so far: (i) the expansion is o-minimal (that is, definable sets have only finitely many connected components); (ii) every Borel subset of each$\mathbb{R}^{n}$is definable; (iii) the expansion is interdefinable with a structure of the form$(\mathfrak{R}^{\prime },\unicode[STIX]{x1D6FC}^{\mathbb{Z}})$where$\unicode[STIX]{x1D6FC}>1$,$\unicode[STIX]{x1D6FC}^{\mathbb{Z}}$is the set of all integer powers of$\unicode[STIX]{x1D6FC}$, and$\mathfrak{R}^{\prime }$is o-minimal and defines no irrational power functions.

Elucidating CO2 Chemisorption in Diamine-Appended Metal-Organic Frameworks.

The widespread deployment of carbon capture and sequestration as a climate change mitigation strategy could be facilitated by the development of more energy-efficient adsorbents. Diamine-appended metal-organic frameworks of the type diamine-M2(dobpdc) (M = Mg, Mn, Fe, Co, Ni, Zn; dobpdc4- = 4,4'-dioxidobiphenyl-3,3'-dicarboxylate) have shown promise for carbon-capture applications, although questions remain regarding the molecular mechanisms of CO2 uptake in these materials. Here we leverage the crystallinity and tunability of this class of frameworks to perform a comprehensive study of CO2 chemisorption. Using multinuclear nuclear magnetic resonance (NMR) spectroscopy experiments and van-der-Waals-corrected density functional theory (DFT) calculations for 13 diamine-M2(dobpdc) variants, we demonstrate that the canonical CO2 chemisorption products, ammonium carbamate chains and carbamic acid pairs, can be readily distinguished and that ammonium carbamate chain formation dominates for diamine-Mg2(dobpdc) materials. In addition, we elucidate a new chemisorption mechanism in the material dmpn-Mg2(dobpdc) (dmpn = 2,2-dimethyl-1,3-diaminopropane), which involves the formation of a 1:1 mixture of ammonium carbamate and carbamic acid and accounts for the unusual adsorption properties of this material. Finally, we show that the presence of water plays an important role in directing the mechanisms for CO2 uptake in diamine-M2(dobpdc) materials. Overall, our combined NMR and DFT approach enables a thorough depiction and understanding of CO2 adsorption within diamine-M2(dobpdc) compounds, which may aid similar studies in other amine-functionalized adsorbents in the future.

Asymptotic behaviour of even canonical products with slight abnormalities in the distribution of the set of zeros, which has positive density

The asymptotic behaviour of even canonical products with zeros on the real axis is considered. It is assumed that the set of zeros has density (the sequence has density). Sharp asymptotic estimates for the logarithm of the modulus of the canonical product are obtained under certain restrictions on the rate of convergence of the ratio to its limit. Bibliography: 8 titles.

Γ–structures and symmetric spaces

$\Gamma$-structures are weak forms of multiplications on closed oriented manifolds. As shown by Hopf the rational cohomology algebras of manifolds admitting $\Gamma$-structures are free over odd degree generators. We prove that this condition is also sufficient for the existence of $\Gamma$-structures on manifolds which are nilpotent in the sense of homotopy theory. This includes homogeneous spaces with connected isotropy groups. Passing to a more geometric perspective we show that on compact oriented Riemannian symmetric spaces with connected isotropy groups and free rational cohomology algebras the canonical products given by geodesic symmetries define $\Gamma$-structures. This extends work of Albers, Frauenfelder and Solomon on $\Gamma$-structures on Lagrangian Grassmannians.

Deletion of Type I glutamine synthetase deregulates nitrogen metabolism and increases ethanol production in Clostridium thermocellum

Clostridium thermocellum rapidly deconstructs cellulose and ferments resulting hydrolysis products into ethanol and other products, and is thus a promising platform organism for the development of cellulosic biofuel production via consolidated bioprocessing. While recent metabolic engineering strategies have targeted eliminating canonical fermentation products (acetate, lactate, formate, and H2), C. thermocellum also secretes amino acids, which has limited ethanol yields in engineered strains to approximately 70% of the theoretical maximum. To investigate approaches to decrease amino acid secretion, we attempted to reduce ammonium assimilation by deleting the Type I glutamine synthetase (glnA) in an essentially wild type strain of C. thermocellum. Deletion of glnA reduced levels of secreted valine and total amino acids by 53% and 44% respectively, and increased ethanol yields by 53%. RNA-seq analysis revealed that genes encoding the RNF-complex were more highly expressed in ΔglnA and may have a role in improving NADH-availability for ethanol production. While a significant up-regulation of genes involved in nitrogen assimilation and urea uptake suggested that deletion of glnA induces a nitrogen starvation response, metabolomic analysis showed an increase in intracellular glutamine levels indicative of nitrogen-rich conditions. We propose that deletion of glnA causes deregulation of nitrogen metabolism, leading to overexpression of nitrogen metabolism genes and, in turn, elevated glutamine levels. Here we demonstrate that perturbation of nitrogen assimilation is a promising strategy to redirect flux from the production of nitrogenous compounds toward biofuels in C. thermocellum.

Building ProteomeTools based on a complete synthetic human proteome.

We describe ProteomeTools, a project building molecular and digital tools from the human proteome to facilitate biomedical research. Here we report the generation and multimodal liquid chromatography-tandem mass spectrometry analysis of >330,000 synthetic tryptic peptides representing essentially all canonical human gene products, and we exemplify the utility of these data in several applications. The resource (available at http://www.proteometools.org) will be extended to >1 million peptides, and all data will be shared with the community via ProteomicsDB and ProteomeXchange.

Mesh-free canonical tensor products for six-dimensional density matrix: computation of kinetic energy

The computation of a six-dimensional density matrix is the crucial step for the evaluation of kinetic energy in electronic structure calculations. For molecules with heavy nuclei, one has to consider a very refined mesh in order to deal with the nuclear cusps. This leads to high computational time and needs huge memory for the computation of the density matrix. To reduce the computational complexity and avoid discretization errors in the approximation, we use mesh-free canonical tensor products in electronic structure calculations. In this paper, we approximate the six-dimensional density matrix in an efficient way and then compute the kinetic energy. Accuracy is examined by comparing our computed kinetic energy with the exact computation of the kinetic energy.

Distribution of the zeros of canonical products and weighted condensation index

Canonical products with symmetrically positioned real zeros are considered. The question of the measurability of the sequence of zeros in terms of the weighted condensation index is treated. A natural class of weight functions, for which a finite condensation index ensures that the sequence of zeros is measurable, is distinguished. The main condition characterizing this class is shown to be sharp. Bibliography: 31 titles.

Distribution of the zeros of canonical products and weighted condensation index

Рассматриваются канонические произведения с симметричными вещественными нулями. Изучается вопрос об измеримости последовательности нулей в терминах весового индекса конденсации. Выделен естественный класс весовых функций, для которых конечность индекса конденсации гарантирует измеримость последовательности нулей. Показана точность основного условия, характеризующего упомянутый класс. Библиография: 31 название.

Задача кратной интерполяции в классе аналитических функций нулевого порядка в полуплоскости

In the paper we consider the problem of multiple interpolation in a class of functions of a zero order and type not exceeding normal in the upper half-plane of the complex variable. This problem belongs to the class of problems of free interpolation considered initially by A.F. Leont'ev. We find necessary and sufficient solvability conditions for this problem. The found criteria are formulated in terms of the canonical products constructed on interpolation nodes, and in terms of the Nevanlinna measure determined by these nodes. The work is a continuation of researches of the second author considered similar problems in classes of analytic functions in the upper half-plane of a nonzero order.