Identification of an l-Arabinose Reductase Gene in Aspergillus niger and Its Role in l-Arabinose Catabolism

The first enzyme in the pathway for l-arabinose catabolism in eukaryotic microorganisms is a reductase, reducing l-arabinose to l-arabitol. The enzymes catalyzing this reduction are in general nonspecific and would also reduce d-xylose to xylitol, the first step in eukaryotic d-xylose catabolism. It is not clear whether microorganisms use different enzymes depending on the carbon source. Here we show that Aspergillus niger makes use of two different enzymes. We identified, cloned, and characterized an l-arabinose reductase, larA, that is different from the d-xylose reductase, xyrA. The larA is up-regulated on l-arabinose, while the xyrA is up-regulated on d-xylose. There is however an initial up-regulation of larA also on d-xylose but that fades away after about 4 h. The deletion of the larA gene in A. niger results in a slow growth phenotype on l-arabinose, whereas the growth on d-xylose is unaffected. The l-arabinose reductase can convert l-arabinose and d-xylose to their corresponding sugar alcohols but has a higher affinity for l-arabinose. The K_m for l-arabinose is 54 ± 6 mm and for d-xylose 155 ± 15 mm.     

Long non‐coding RNA ELDR enhances oral cancer growth by promoting ILF3‐cyclin E1 signaling

Oral squamous cell carcinoma (OSCC) is the sixth most common cancer with a 5‐year overall survival rate of 50%. Thus, there is a critical need to understand the disease process, and to identify improved therapeutic strategies. Previously, we found the long non‐coding RNA (lncRNA) EGFR long non‐coding downstream RNA (ELDR) induced in a mouse tongue cancer model; however, its functional role in human oral cancer remained unknown. Here, we show that ELDR is highly expressed in OSCC patient samples and in cell lines. Overexpression of ELDR in normal non‐tumorigenic oral keratinocytes induces cell proliferation, colony formation, and PCNA expression. We also show that ELDR depletion reduces OSCC cell proliferation and PCNA expression. Proteomics data identifies the RNA binding protein ILF3 as an interacting partner of ELDR. We further show that the ELDR‐ILF3 axis regulates Cyclin E1 expression and phosphorylation of the retinoblastoma (RB) protein. Intratumoral injection of ELDR‐specific siRNA reduces OSCC and PDX tumor growth in mice. These findings provide molecular insight into the role of ELDR in oral cancer and demonstrate that targeting ELDR has promising therapeutic potential.     

Spatial control of lipid droplet proteins by the ERAD ubiquitin ligase Doa10

The endoplasmic reticulum (ER) plays a central role in the biogenesis of most membrane proteins. Among these are proteins localized to the surface of lipid droplets (LDs), fat storage organelles delimited by a phospholipid monolayer. The LD monolayer is often continuous with the membrane of the ER allowing certain membrane proteins to diffuse between the two organelles. In these connected organelles, how some proteins concentrate specifically at the surface of LDs is not known. Here, we show that the ERAD ubiquitin ligase Doa10 controls the levels of some LD proteins. Their degradation is dependent on the localization to the ER and appears independent of the folding state. Moreover, we show that by degrading the ER pool of these LD proteins, ERAD contributes to restrict their localization to LDs. The signals for LD targeting and Doa10‐mediated degradation overlap, indicating that these are competing events. This spatial control of protein localization is a novel function of ERAD that might contribute to generate functional diversity in a continuous membrane system.     

Amino Acid Isomerization in the Production of l-Phenylalanine from d-Phenylalanine by Bacteria

To establish an advantageous method for the production of l-amino acids, microbial isomerization of d- and dl-amino acids to l-amino acids was studied. Screening experiments on a number of microorganisms showed that cell suspensions of Pseudomonas fluorescens and P. miyamizu were capable of isomerizing d- and dl-phenylalanines to l-phenylalanine. Various conditions suitable for isomerization by these organisms were investigated. Cells grown in a medium containing d-phenylalanine showed highest isomerization activity, and almost completely converted d- or dl-phenylalanine into l-phenylalanine within 24 to 48 hr of incubation. Enzymatic studies on this isomerizing system suggested that the isomerization of d- or dl-phenylalanine is not catalyzed by a single enzyme, “amino acid isomerase,” but the conversion proceeds by a two step system as follows: d-pheylalanine is oxidized to phenylpyruvic acid by d-amino acid oxidase, and the acid is converted to l-phenylalanine by transamination or reductive amination.     

Pseudo‐repeats in doublecortin make distinct mechanistic contributions to microtubule regulation

Doublecortin (DCX) is a neuronal microtubule‐associated protein (MAP) indispensable for brain development. Its flexibly linked doublecortin (DC) domains—NDC and CDC—mediate microtubule (MT) nucleation and stabilization, but it is unclear how. Using high‐resolution time‐resolved cryo‐EM, we mapped NDC and CDC interactions with tubulin at different MT polymerization stages and studied their functional effects on MT dynamics using TIRF microscopy. Although coupled, each DC repeat within DCX appears to have a distinct role in MT nucleation and stabilization: CDC is a conformationally plastic module that appears to facilitate MT nucleation and stabilize tubulin–tubulin contacts in the nascent MT lattice, while NDC appears to be favored along the mature lattice, providing MT stabilization. Our structures of MT‐bound DC domains also explain in unprecedented detail the DCX mutation‐related brain defects observed in the clinic. This modular composition of DCX reflects a common design principle among MAPs where pseudo‐repeats of tubulin/MT binding elements chaperone or stabilize distinct conformational transitions to regulate distinct stages of MT dynamic instability.     

Ein Beitrag zur Nomenklatur sphinctozoider Schwämme (Porifera)

The sphinctozoid sponge generaFania Senowbari-Daryan 1990 andSpica Termier &Termier 1977 are preoccupied.Fania is replaced byFanthalamia nom. nov. andSpica by the younger synonymFistulispongia Termier &Termier 1977. The invalid subfamily name FaniinaeSenowbari-Daryan 1990 is replaced by Fanthalamiinae n. subfam. The invalid family and subfamily names SpicidaeTermier &Termier 1977 and SpicinaeSenowbari-Daryan 1990 respectively are replaced by FistulispongiidaeTermier atTermier 1977 and FistulispongiinaeSenowbari-Daryan 1990. The generaWaagenium de Laubenfels 1957 andCatubria Merla 1931 were previously overlooked.Waagenium DeLaubenfels 1957 is a younger synonym ofColospongia Laube 1865. The position ofCatubria Merla 1931 is uncertain. Most probablyCatubria is an alga.     

Conversion of the Extracellular Dextransucrase Isoenzymes from Leuconostoc mesenteroides NRRL B-1299

Effect of oxygen tension on l-lysine, l-threonine and l-isoleucine accumulation was investigated. Sufficient supply of oxygen to satisfy the cell’s oxygen demand was essential for the maximum production in each fermentation. The dissolved oxygen level must be controlled at greater than 0.01 atm in every fermentation, and the optimum redox potentials of culture media were above ?170 mV in l-lysine and l-threonine and above ?180 mV in l-isoleucine fermentations. The maximum concentrations of the products were 45.5 mg/ml for l-lysine, 10.3 mg/ml for l-threonine and 15.1 mg/ml for l-isoleucine. The degree of the inhibition due to oxygen limitation was slight in the fermentative production of l-lysine, l-threonine and l-isoleucine, whose biosynthesis is initiated with l-aspartic acid, in contrast to the accumulation of l-proline, l-glutamine and l-arginine, which is biosynthesized by way of l-glutamic acid.     

A Fungal Sarcolemmal Membrane-Associated Protein (SLMAP) Homolog Plays a Fundamental Role in Development and Localizes to the Nuclear Envelope,Endoplasmic Reticulum,and Mitochondria

Sarcolemmal membrane-associated protein (SLMAP) is a tail-anchored protein involved in fundamental cellular processes, such as myoblast fusion, cell cycle progression, and chromosomal inheritance. Further, SLMAP misexpression is associated with endothelial dysfunctions in diabetes and cancer. SLMAP is part of the conserved striatin-interacting phosphatase and kinase (STRIPAK) complex required for specific signaling pathways in yeasts, filamentous fungi, insects, and mammals. In filamentous fungi, STRIPAK was initially discovered in Sordaria macrospora, a model system for fungal differentiation. Here, we functionally characterize the STRIPAK subunit PRO45, a homolog of human SLMAP. We show that PRO45 is required for sexual propagation and cell-to-cell fusion and that its forkhead-associated (FHA) domain is essential for these processes. Protein-protein interaction studies revealed that PRO45 binds to STRIPAK subunits PRO11 and SmMOB3, which are also required for sexual propagation. Superresolution structured-illumination microscopy (SIM) further established that PRO45 localizes to the nuclear envelope, endoplasmic reticulum, and mitochondria. SIM also showed that localization to the nuclear envelope requires STRIPAK subunits PRO11 and PRO22, whereas for mitochondria it does not. Taken together, our study provides important insights into fundamental roles of the fungal SLMAP homolog PRO45 and suggests STRIPAK-related and STRIPAK-unrelated functions.     

Regulation of sulfate uptake by amino acids in cultured tobacco cells

The sulfur requirements of tobacco (Nicotiana tabacum L. var. Xanthi) XD cells grown in chemically defined liquid media can be satisfied by sulfate, thiosulfate, l-cyst(e)ine, l-methionine or glutathione, and somewhat less effectively by d-cyst (e) ine, d-methionine or dl-homocyst (e)ine. Sulfate uptake is inhibited after a 2 hr lag by l-cyst (e)ine, l-methionine, l-homocyst(e)ine or l-isoleucine, but not by any of the other protein amino acids, nor by d-cyst(e)ine. l-cyst(e)ine is neither a competitive nor a non-competitive inhibitor of sulfate uptake. Its action most closely resembles apparent uncompetitive inhibition. Inhibition of sulfate uptake by l-cyst(e)ine can be partially prevented by equimolar l-arginine, l-lysine, l-leucine, l-phenylalanine, l-tyrosine or l-tryptophan, but is little affected by any of the other protein amino acids. The effective amino acids are apparent competitive inhibitors of l-cyst(e)ine uptake after a 2 hr lag. Inhibition of sulfate uptake by l-methionine cannot be prevented, nor can uptake of l-methionine be inhibited by any single protein amino acid. The results suggest the occurrence of negative feedback control of sulfate assimilation by the end products, the sulfur amino acids, in cultured tobacco cells.     

AutoMoDe-<Emphasis FontCategory="NonProportional" Type="Bold">Chocolate</Emphasis>: automatic design of control software for robot swarms

We present two empirical studies on the design of control software for robot swarms. In Study A, Vanilla and EvoStick, two previously published automatic design methods, are compared with human designers. The comparison is performed on five swarm robotics tasks that are different from those on which Vanilla and EvoStick have been previously tested. The results show that, under the experimental conditions considered, Vanilla performs better than EvoStick, but it is not able to outperform human designers. The results indicate that Vanilla ’s weak element is the optimization algorithm employed to search the space of candidate designs. To improve over Vanilla and with the final goal of obtaining an automatic design method that performs better than human designers, we introduce Chocolate, which differs from Vanilla only in the fact that it adopts a more powerful optimization algorithm. In Study B, we perform an assessment of Chocolate. The results show that, under the experimental conditions considered, Chocolate outperforms both Vanilla and the human designers. Chocolate is the first automatic design method for robot swarms that, at least under specific experimental conditions, is shown to outperform a human designer.     

Application and microbial preparation of <Emphasis Type="SmallCaps">d</Emphasis>-valine

d-Valine is an important organic chiral source and has extensive industrial application, which is used as intermediate for the synthesis of agricultural pesticides, semi-synthetic veterinary antibiotics and pharmaceutical drugs. Its derivatives have shown great activity in clinical use, such as penicillamine for the treatment of immune-deficiency diseases, and actinomycin D for antitumor therapy. Fluvalinate, a pyrethroid pesticide made from d-valine, is a broad-spectrum insecticide with low mammalian toxicity. Valnemulin, a semi-synthetic pleuromutilin derivative synthesized from d-valine, is an antibiotic for animals. Moreover, d-valine is also used in cell culture for selectively inhibiting fibroblasts proliferation. Due to its widespread application, d-valine is gaining more and more attention and some approaches for d-valine preparation have been investigated. In comparison with other approaches, microbial preparation of d-valine is more competitive and promising because of its high stereo selectivity, mild reaction conditions and environmental friendly process. So far, microbial preparation of d-valine can be mainly classified into three categories: microbial asymmetric degradation of dl-valine, microbial stereoselective hydrolysis of N-acyl-dl-valine by d-aminoacylase, and microbial specific hydrolysis of dl-5-isopropylhydantoin by d-hydantoinase coupled with d-carbamoylase. In this paper, the industrial application of d-valine and its microbial preparation are reviewed.     

On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo

For various species, high quality sequences and complete genomes are nowadays available for many individuals. This makes data analysis challenging, as methods need not only to be accurate, but also time efficient given the tremendous amount of data to process. In this article, we introduce an efficient method to infer the evolutionary history of individuals under the multispecies coalescent model in networks (MSNC). Phylogenetic networks are an extension of phylogenetic trees that can contain reticulate nodes, which allow to model complex biological events such as horizontal gene transfer, hybridization and introgression. We present a novel way to compute the likelihood of biallelic markers sampled along genomes whose evolution involved such events. This likelihood computation is at the heart of a Bayesian network inference method called SnappNet, as it extends the Snapp method inferring evolutionary trees under the multispecies coalescent model, to networks. SnappNet is available as a package of the well-known beast 2 software.Recently, the MCMC_BiMarkers method, implemented in PhyloNet, also extended Snapp to networks. Both methods take biallelic markers as input, rely on the same model of evolution and sample networks in a Bayesian framework, though using different methods for computing priors. However, SnappNet relies on algorithms that are exponentially more time-efficient on non-trivial networks. Using simulations, we compare performances of SnappNet and MCMC_BiMarkers. We show that both methods enjoy similar abilities to recover simple networks, but SnappNet is more accurate than MCMC_BiMarkers on more complex network scenarios. Also, on complex networks, SnappNet is found to be extremely faster than MCMC_BiMarkers in terms of time required for the likelihood computation. We finally illustrate SnappNet performances on a rice data set. SnappNet infers a scenario that is consistent with previous results and provides additional understanding of rice evolution.     

Cadherins and catenins in dendrite and synapse morphogenesis

Neurons are highly polarized specialized cells. Neuronal integrity and functional roles are critically dependent on dendritic architecture and synaptic structure, function and plasticity. The cadherins are glycosylated transmembrane proteins that form cell adhesion complexes in various tissues. They are associated with a group of cytosolic proteins, the catenins. While the functional roles of the complex have been extensively investigates in non-neuronal cells, it is becoming increasingly clear that components of the complex have critical roles in regulating dendritic and synaptic architecture, function and plasticity in neurons. Consistent with these functional roles, aberrations in components of the complex have been implicated in a variety of neurodevelopmental disorders. In this review, we discuss the roles of the classical cadherins and catenins in various aspects of dendrite and synapse architecture and function and their relevance to human neurological disorders. Cadherins are glycosylated transmembrane proteins that were initially identified as Ca²⁺-dependent cell adhesion molecules. They are present on plasma membrane of a variety of cell types from primitive metazoans to humans. In the past several years, it has become clear that in addition to providing mechanical adhesion between cells, cadherins play integral roles in tissue morphogenesis and homeostasis. The cadherin family is composed of more than 100 members and classified into several subfamilies, including classical cadherins and protocadherins. Several of these cadherin family members have been implicated in various aspects of neuronal development and function.^1-3 Deans, MR, Krol A, Abraira VE, Copley CO, Tucker AF, Goodrich LV. Control of neuronal morphology by the atypical cadherin Fat3. Neuron 2011; 71:820-32; PMID:21903076; http://dx.doi.org/10.1016/j.neuron.2011.06.026 S0896-6273(11)00556-3 [pii] Matsunaga E, Nambu S, Oka M, Iriki A. Differential cadherin expression in the developing postnatal telencephalon of a New World monkey. J Comp Neurol 2013; 521:4027-60; PMID:23784870; http://dx.doi.org/10.1002/cne.23389 Li Y, Xiao H, Chiou TT, Jin H, Bonhomme B, Miralles CP, Pinal N, Ali R, Chen WV, Maniatis T, De Blas AL, et al. Molecular and functional interaction between protocadherin-gammaC5 and GABAA receptors. J Neurosci 2012; 32:11780-97; PMID:22915120; http://dx.doi.org/10.1523/JNEUROSCI.0969-12.2012 32/34/11780 [pii]  The classical cadherins are associated with a group of cytosolic proteins, collectively called the catenins. While the functional roles of the cadherin-catenin cell adhesion complex have been extensively investigated in epithelial cells, it is now clear that components of the complex are well expressed in central neurons at different stages during development.^4,5 McLachlan IG, Heiman MG. Shaping dendrites with machinery borrowed from epithelia. Curr Opin Neurobiol 2013; 23:1005-10; PMID:23871793; http://dx.doi.org/10.1016/j.conb.2013.06.011 S0959-4388(13)00130-X [pii] Hirano S, Takeichi M. Cadherins in brain morphogenesis and wiring. Physiol Rev 2012; 92:597-634; PMID:22535893; http://dx.doi.org/10.1152/physrev.00014.2011 92/2/597 [pii] (2012)  Recent exciting studies have shed some light on the functional roles of cadherins and catenins in central neurons. In this review, we will provide a brief overview of the cadherin superfamily, describe cadherin family members expressed in central neurons, cadherin-catenin complexes in central neurons and then focus on role of the cadherin-catenin complex in dendrite morphogenesis and synapse morphogenesis, function and plasticity. The final section is dedicated to discussion of the emerging list of neural disorders linked to cadherins and catenins. While the roles of cadherins and catenins have been examined in several different types of neurons, the focus of this review is their role in mammalian central neurons, particularly those of the cortex and hippocampus. Accompanying this review is a series of excellent reviews targeting the roles of cadherins and protocadherins in other aspects of neural development.     

Integrative genomics positions MKRN1 as a novel ribonucleoprotein within the embryonic stem cell gene regulatory network

In embryonic stem cells (ESCs), gene regulatory networks (GRNs) coordinate gene expression to maintain ESC identity; however, the complete repertoire of factors regulating the ESC state is not fully understood. Our previous temporal microarray analysis of ESC commitment identified the E3 ubiquitin ligase protein Makorin‐1 (MKRN1) as a potential novel component of the ESC GRN. Here, using multilayered systems‐level analyses, we compiled a MKRN1‐centered interactome in undifferentiated ESCs at the proteomic and ribonomic level. Proteomic analyses in undifferentiated ESCs revealed that MKRN1 associates with RNA‐binding proteins, and ensuing RIP‐chip analysis determined that MKRN1 associates with mRNAs encoding functionally related proteins including proteins that function during cellular stress. Subsequent biological validation identified MKRN1 as a novel stress granule‐resident protein, although MKRN1 is not required for stress granule formation, or survival of unstressed ESCs. Thus, our unbiased systems‐level analyses support a role for the E3 ligase MKRN1 as a ribonucleoprotein within the ESC GRN.     

Do calcium buffers always slow down the propagation of calcium waves?

Calcium buffers are large proteins that act as binding sites for free cytosolic calcium. Since a large fraction of cytosolic calcium is bound to calcium buffers, calcium waves are widely observed under the condition that free cytosolic calcium is heavily buffered. In addition, all physiological buffered excitable systems contain multiple buffers with different affinities. It is thus important to understand the properties of waves in excitable systems with the inclusion of buffers. There is an ongoing controversy about whether or not the addition of calcium buffers into the system always slows down the propagation of calcium waves. To solve this controversy, we incorporate the buffering effect into the generic excitable system, the FitzHugh–Nagumo model, to get the buffered FitzHugh–Nagumo model, and then to study the effect of the added buffer with large diffusivity on traveling waves of such a model in one spatial dimension. We can find a critical dissociation constant ( $K=K(a)$ ) characterized by system excitability parameter $a$ such that calcium buffers can be classified into two types: weak buffers ( $K\in (K(a),\infty )$ ) and strong buffers ( $K\in (0,K(a))$ ). We analytically show that the addition of weak buffers or strong buffers but with its total concentration $b_0^1$ below some critical total concentration $b_{0,c}^1$ into the system can generate a traveling wave of the resulting system which propagates faster than that of the origin system, provided that the diffusivity $D_1$ of the added buffers is sufficiently large. Further, the magnitude of the wave speed of traveling waves of the resulting system is proportional to $\sqrt{D_1}$ as $D_1\rightarrow \infty $ . In contrast, the addition of strong buffers with the total concentration $b_0^1>b_{0,c}^1$ into the system may not be able to support the formation of a biologically acceptable wave provided that the diffusivity $D_1$ of the added buffers is sufficiently large.     

Description of a new Aelurillus species from Khorasan province of Iran,with comments on A. concolor Kulczyński, 1901 (Araneae: Salticidae)

A new species Aelurillus khorasanicus sp.n. (♂♀) is described from north-east Iran. Aelurillus muganicus Dunin, 1984 Dunin, P. M. (1984): Fauna and ecology of spiders (Aranei) of Apsheron Peninsula [in Russian]. pp. 45–60. In: Utochkin, A. S. et al. (eds.), Fauna i ekologiya paukoobraznykh. Perm: PGU Press. [Google Scholar] is synonymised with A. concolor Kulczyński, 1901 Kulczyński, W. (1901): Arachnoidea. pp. 311–369. In: Horvath, G. (ed.), Zoologische Ergebnisse der dritten asiatischen Forschungsreise des Grafen Eugen Zichy. Volume 2. Budapest. [Google Scholar]. A distribution map of the two species is provided.     

A network with tunable clustering, degree correlation and degree distribution, and an epidemic thereon

A random network model which allows for tunable, quite general forms of clustering, degree correlation and degree distribution is defined. The model is an extension of the configuration model, in which stubs (half-edges) are paired to form a network. Clustering is obtained by forming small completely connected subgroups, and positive (negative) degree correlation is obtained by connecting a fraction of the stubs with stubs of similar (dissimilar) degree. An SIR (Susceptible $\rightarrow $ Infective $\rightarrow $ Recovered) epidemic model is defined on this network. Asymptotic properties of both the network and the epidemic, as the population size tends to infinity, are derived: the degree distribution, degree correlation and clustering coefficient, as well as a reproduction number $R_*$ , the probability of a major outbreak and the relative size of such an outbreak. The theory is illustrated by Monte Carlo simulations and numerical examples. The main findings are that (1) clustering tends to decrease the spread of disease, (2) the effect of degree correlation is appreciably greater when the disease is close to threshold than when it is well above threshold and (3) disease spread broadly increases with degree correlation $\rho $ when $R_*$ is just above its threshold value of one and decreases with $\rho $ when $R_*$ is well above one.