Inactivation of Complement by <Emphasis Type="SmallCaps">L</Emphasis>-Asparaginase Preparations not Correlated with Enzyme Content

DELÁGE et al.¹ recently reported that L-asparaginase (L-A) in vitro inhibits human and guinea-pig whole serum complement and that L-A is a potent activator of C1. They therefore proposed that their results may “give a clue to the severe anaphylactic reactions noted in some patients on administration of the drug”. Because guinea-pig serum contains L-A in high quantities and Deláge et al. used reagents and methods that make their data difficult to interpret on a molecular basis, we have reinvestigated the effect of L-A preparations on human and guinea-pig complement.     

Regulatory Properties of Intergeneric Hybrids of Aspartate Transcarbamylase

THE regulatory enzyme aspartate transcarbamylase (ATCase) from Escherichia coli contains two non-identical protein sub-units, one the catalytic subunit which provides the active sites of the enzyme and the other the regulatory subunit which provides the binding sites for nucleotide inhibitors and activators^1,2. The catalytic subunit is a trimer of “C” polypeptide chains, associated by three heterologous c: c domains of bonding (terminology given by Monod et al.³ and Cohlberg et al.⁴). The regulatory subunit is a dimer of “R” chains, associated by an isologous r: r domain. Two catalytic and three regulatory subunits interact specifically across six r: c domains of inter-subunit bonding to complete the quaternary structure of the ATCase molecule.     

Chemical shift assignments of Ribosomal protein S1 from <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis>

RpsA, also known as ribosomal protein S1, is an essential protein required for translation initiation of mRNAs when their Shine-Dalgarno sequence is degenerated (Sorensen et al. 1998). In addition, RpsA of Mycobacterium tuberculosis (M. tb) is involved in trans-translation, which is an effective system mediated by tmRNA-SmpB to release stalled ribosomes from mRNA in the presence of rare codons (Keiler 2008). Shi et al. found that POA binds to RpsA of Mtb and disrupts the formation of RpsA–tmRNA complex (Shi et al. 2011) and mutations at the C-terminus of RpsA confer PZA resistance. The previous work reported the pyrazinoic acid-binding domain of RpsA (Yang et al. Mol Microbiol 95:791–803, 2015). However, the HSQC spectra of the isolated S1 domain does not overlap with that of MtRpsA280-438, suggesting that substantial interactions occur between the flexible C-terminus and the S1 domain in MtRpsA .To further study the PZA resistance and how substantial interactions influence/affect protein structure, using heteronuclear NMR spectroscopy, we have completed backbone and side-chain ¹H, ¹⁵N, ¹³C chemical shift assignments of MtRpsA280-438 which contains S1 domain and the flexible C-terminus. These NMR resonance assignments provide the framework for detailed characterization of the solution-state protein structure determination, dynamic studies of this domain, as well as NMR-based drug discovery efforts.     

On new Jurassic Rissooidea and Zygopleuroidea convergently similar to them (Gastropoda: Pectinibranchia)

A new genus, Boreomica gen. nov., is established; it comprises small-sized gastropods widespread in the Jurassic of the Russian Plate, the taxonomic position of which was ambiguously treated by previous authors. The new genus is assigned to the family Rissoidae. The species composition and stratigraphical and geographical distribution of the genus and its species are discussed. From the Jurassic of the Russian Plate, Callovian Boreomica exigua (Gerasimov, 1992), the type species of the genus, and Kimmeridgian–Volgian Boreomica undulata (Tullberg, 1881), and members of the genus without species status from the Bathonian and Upper Oxfordian are described. Conchological polymorphism of species connected with their eurybiontic characteristics is discussed. Based on the study of samples of the species B. exigua from different types of facies, two subspecies are recognized, B. exigua exigua and B. exigua arenosa subsp. nov. Finds of gastropods morphologically similar to Boreomica are discussed: Katosira? sp. from Mitta et al., 2004, “Procerithium?” volgense Gerasimov, 1955, “Eulima” pusilla Tullberg, 1881, and “Hudlestonella” caleptra sensu Gerasimov, 1992 are considered. It is concluded that E. pusilla and H. caleptra are unknown zygopleurids, Katosira? sp. is likely a poorly preserved Katosira, and “Procerithium?” volgense is represented by a mixture of several species belonging to different genera: several zygopleurid species, the rissoids Boreomica undulata and Bralitzia. Shells of P. volgense in the P.A. Gerasimov’s collection from the Craspedites nodiger Zone are described as Laevipleura sp.     

On oviposition in weevils of the genus <Emphasis Type="Italic">Larinus</Emphasis> Dej. (Coleoptera,Curculionidae)

The following actions performed by females of several Larinus Dej. species during egg laying are described: search of an appropriate place on the plant, making the hole for the egg, oviposition proper, and sealing the hole. The hole preparation takes the longest time and the greatest effort. Only one individual usually completes development in one flower head. Females of Larinus vulpes Ol. prefer larger flower heads for oviposition and occasionally lay eggs into stems. The ability of females to distinguish the flower heads with already laid eggs is discussed. Species of Larinus may be divided into two groups with “early” and “late” oviposition. The evolution of egg laying in the genus Larinus is discussed.     

Induced Bivalent Interlocking and the Course of Meiotic Chromosome Synapsis

WHEN chromosomes pair at meiosis the bivalents so formed do not normally interlock. Heat-treatments can, however, induce bivalent interlocking in the locust Locusta migratoria. Only the longest bivalents interlock and usually only two are found per cell; two “rod” bivalents, with single chiasmata, two “ring” bivalents, each with two or three chiasmata, or one “rod” and one “ring” bivalent (Fig. 1a, b and c). The nature of this interlocking and the metaphase orientational and congressional properties of interlocked bivalents are analysed in detail elsewhere¹.     

Genome-wide identification and expression analysis of the molecular chaperone binding protein <Emphasis Type="Italic">BiP</Emphasis> genes in <Emphasis Type="Italic">Citrus</Emphasis>

Here, we report for the first time the genome-wide identification and expression analysis of the molecular chaperone BiP genes in Citrus. Six genes encoding the conserved protein domain family GPR78/BiP/KAR2 were identified in the genome of Citrus sinensis and C. clementina. Two of them, named here as CsBiP1 and CsBiP2, were classified as true BiPs based on their deduced amino acid sequences. Alignment of the deduced amino acid sequences of CsBiP1 and CsBiP2 with BiP homologs from soybean and Arabidopsis showed that they contain all the conserved functional motifs of BiPs. Analysis of the promoter region of CsBiPs revealed the existence of cis-acting regulatory sequences involved in abiotic, heat-shock, and endoplasmic reticulum (ER) stress responses. Publicly available RNA-seq data indicated that CsBiP1 is abundantly expressed in leaf, flower, fruit, and callus, whereas CsBiP2 expression is rarely detected in any tissues under normal conditions. Comparative quantitative real-time PCR (qPCR) analysis of expression of these genes between C. sinensis grafted on the drought-tolerant “Rangpur” lime (C. limonia) and -sensitive “Flying Dragon” trifoliate orange (Poncirus trifoliata) rootstocks showed that CsBiP1 was upregulated by drought stress on the former but downregulated on the latter, whereas the CsBiP2 mRNA levels were downregulated on drought-stressed “Flying Dragon,” but remained constant on “Rangpur.” CsBiP2 upregulation was only observed in C. sinensis seedlings subjected to osmotic and cold treatments. Taken together, these results indicate the existence of two highly conserved BiP genes in Citrus that are differentially regulated in the different tissues and in response to abiotic stresses.     

High-throughput sequencing of <Emphasis Type="Italic">Prunus ferganensis</Emphasis> indicates that it is a geographical population of <Emphasis Type="Italic">P. persica</Emphasis>

Peach belongs to the genus Prunus, which includes Prunus persica and its relative species, P. mira, P. davidiana, P. kansuensis, and P. ferganensis. Of these, P. ferganensis have been classified as a species, subspecies, or geographical population of P. persica. To explore the genetic difference between P. ferganensis and P. persica, high-throughput sequencing was used in different peach accessions belonging to different species. First, low-depth sequencing data of peach accessions belonging to four categories revealed that similarity between P. ferganensis and P. persica was similar to that between P. persica accessions from different geographical populations. Then, to further detect the genomic variation in P. ferganensis, the P. ferganensis accession “Xinjiang Pan Tao 1” and the P. persica accession “Xia Miao 1” were sequenced with high depth, and sequence reads were assembled. The results showed that the collinearity of “Xinjiang Pan Tao 1” with the reference genome “Lovell” was higher than that of “Xia Miao 1” and “Lovell” peach. Additionally, the number of genetic variants, including single nucleotide polymorphisms (SNPs), structural variations (SVs), and the specific genes annotated from unmapped sequence in “Xia Miao 1” was higher than that in “Xinjiang Pan Tao 1” peach. The data showed that there was a close distance between “Xinjiang Pan Tao 1” (P. ferganensis) and reference genome which belong to P. persica, comparing “Xia Miao 1” (P. persica) and reference ones. The results accompany with phylogenetic tree and structure analysis confirmed that P. ferganensis should be considered as a geographic population of P. persica rather than a subspecies or a distinct species. Furthermore, gene ontology analysis was performed using the gene comprising large-effect variation to understand the phenotypic difference between two accessions. The result revealed that the pathways of gene function affected by SVs but SNPs and insertion-deletions markedly differed between the two peach accessions.     

Effect of cumulative polymery of tomato keeping life genes

Results from works involving the study of hetero-and homozygous interaction of the keeping quality genes alc, nor, and rin in tomato plants are presented. It is shown that cumulative polymery leading to the formation of a new “long ripening” phenotype is observed in the double heterozygotes alc/alc ⁺//nor/nor ⁺, nor/nor ⁺//rin/rin ⁺, and alc/alc ⁺//rin/rin ⁺. Strong inhibition of processes of ripeness and synthesis of carotenoids occurs with nonallelic interaction in the double homozygotes alc/alc//rin/rin, nor/nor//rin/rin, and alc/alc//nor/nor. This promotes the formation of a new “non-ripening” phenotype with the absence of visual signs of ripeness, i.e., a whitish-green coloring of the fruit.     

Relationship of Plasminogen Activator to Fibrin

THERE are two principal theories of the mechanism of thrombus dissolution by the fibrinolytic system. Alkjaersig et al.¹ suggested that as fibrin polymerizes, plasminogen is adsorbed preferentially to the fibrin and is available in large quantities within a thrombus which is comparatively free of antiplasmin. When an activator enters the circulation it diffuses into the clot converting the plasminogen to plasmin in situ and so promotes lysis. Ambrus and Markus², however, proposed that when plasmin forms in the circulation naturally or during infusion of an activator it is normally bound to the excess antiplasmin present in blood. They suggested that this plasmin/antiplasmin complex is reversible and dissociates in the presence of fibrin, its preferred substrate, so allowing the plasmin to bring about fibrin dissolution by “external lysis”. Neither of these theories, however, is supported by an observed phenomena.     

Floral ontogeny and vasculature in Xyridaceae,with particular reference to staminodes and stylar appendages

We provide a detailed comparative study of floral ontogeny and vasculature in Xyridaceae, including Xyris, Abolboda and Orectanthe. We evaluate these data in the context of a recent well-resolved phylogenetic analysis of Poales to compare floral structures within the xyrid clade (Xyridaceae and Eriocaulaceae). Xyrids are relatively diverse in both flower structure and anatomy; many species incorporate diverse and unusual floral structures such as staminodes and stylar appendages. Xyridaceae possess three generally epipetalous stamens in a single whorl; the “missing” stamen whorl is either entirely absent or transformed into staminodes. Fertile stamens each receive a single vascular bundle diverged from the median petal bundle. In Xyris, the stamen bundle diverges at the flower base, but it diverges at upper flower levels in both Abolboda and Orectanthe. In species of Abolboda that possess staminodes, staminode vasculature is closely associated with the lateral vasculature of each petal. Despite the likely sister-group relationship between Eriocaulaceae and Xyridaceae, our character optimization indicates that the stylar appendages that characterize some Xyridaceae (except Xyris and Achlyphila) are non-homologous with those of some Eriocaulaceae. On the other hand, it remains equivocal whether the loss of a fertile outer androecial whorl occurred more than once during the evolutionary history of the xyrid clade; this transition occurred either once followed by a reversal to fertile stamens in Eriocauloideae and staminodes in some Xyridaceae, or twice independently within both Xyridaceae and Eriocaulaceae.     

Hardness maximization or equalization? New insights and quantitative relations between hardness increase and bond dissociation energy

It has been overlooked that the change of hardness, η, upon bonding is intimately connected to thermochemical cycles, which determine whether hardness is increased according to Pearson’s “maximum hardness principle” (MHP) or equalized, as expected by Datta’s “hardness equalization principle” (HEP). So far the performances of these likely incompatible “structural principles” have not been compared. Computational validations have been inconclusive because the hardness values and even their qualitative trends change drastically and unsystematically at different levels of theory. Here I elucidate the physical basis of both rules, and shed new light on them from an elementary experimental source. The difference, Δη = η _mol – <η _at>, of the molecular hardness, η _mol, and the averaged atomic hardness, <η _at>, is determined by thermochemical cycles involving the bond dissociation energies D of the molecule, D ⁺ of its cation, and D ^? of its anion. Whether the hardness is increased, equalized or even reduced is strongly influenced by ΔD = 2D – D ⁺  ? D ^?. Quantitative expressions for Δη are obtained, and the principles are tested on 90 molecules and the association reactions forming them. The Wigner-Witmer symmetry constraints on bonding require the valence state (VS) hardness, η _VS, instead of the conventional ground state (GS) hardness, η _GS. Many intriguingly “unpredictable” failures and systematic shortcomings of said “principles” are understood and overcome for the first time, including failures involving exotic and/or challenging molecules, such as Be_2, B₂, O₃, and transition metal compounds. New linear relationships are discovered between the MHP hardness increase Δη _VS and the intrinsic bond dissociation energy D _i . For bond formations, MHP and HEP are not compatible, and HEP does not qualify as an ordering rule.     

Hypercalcified segmented sponges (“sphinctozoans”) from the Upper Triassic (Norian) reef boulders of Taurus Mountains (southern Turkey)

Upper Triassic Norian reef boulders, exposed in a locality near the fountain “Tavuk Cesme” (“Chicken Fountain”) in Taurus Mountains, southern Turkey yielded a large number of hypercalcified sponges, including “sphinctozoans”, “inozoans”, “spongiomorphids”, and “chaetetids”. The sphinctozoans from this locality are described in this paper. Geologically, this locality belongs to the Anamas-Akseki autochthonous. The reef boulders of this locality are exposed near the “Tavuk Cesme” fountain, located at the road, leading from the town of Aksu to Yenisarbademli. The following taxa are described: Amblysiphonella taurica nov. sp., Anthalythalamia riedeli Senowbari-Daryan, Calabrisiphonella sphaerica nov. sp., Calabrisiphonella cuifi nov. sp., Cinnabaria minima Senowbari-Daryan, Colospongia recta nov. sp., Colospongia sp. 1, Colospongia sp. 2, Colospongia sp. 3, Cryptocoelia compacta nov. sp., Cryptocoelia? sp., Deningeria crassireticulata Senowbari-Daryan, Zühlke, Bechstädt and Flügel, Discosiphonella minima Senowbari-Daryan and Link, Gigantothalamia ovoidalis Senowbari-Daryan, Hajarispongia dipoyrazensis nov. sp., Hajarispongia cortexifera nov. sp., Kashanella irregularis Senowbari-Daryan, Kashanella cylindrica nov. sp., Parauvanella ferdowsensis Senowbari-Daryan, Parastylothalamia cylindrica nov. gen., nov. sp., Asiphothalamia polyosculata nov. gen, nov. sp., Sollasia norica nov. sp., and Thaumastocoelia sphaeroida Senowbari-Daryan. The most abundant sponge is Amblysiphonella taurica nov. sp. followed by Hajarispongia dipoyrazensis nov. sp., Colospongia and Discosiphonella minima Senowbari-Daryan and Link are also relatively abundant. The stylothalamid sponge Parastylothalamia nov. gen. is an abundant sponge genus in other Norian reefs of the Taurus Mountains, but is rare at the “Tavuk Cesme” locality.     

Entry of facultative pathogen <Emphasis Type="Italic">Serratia grimesii</Emphasis> into Hela cells. Electron microscopic analysis

Facultative pathogens Serratia grimesii are able to invade eukaryotic cells where they have been found in vacuoles and free in the cytoplasm (Efremova et al., 2001; Bozhokina et al., 2011). However, efficiency of this invasion is low, and the mechanisms of the invasion related to the initial steps of the process are not known. In the present study, we have increased the invasion efficiency by a 24-h-incubation of HeLa cells with N-acetylcysteine (NAC) preceding the infection. In the NAC-pretreated cells, two modes of S. grimesii to enter HeLa cells were observed. In the most cases, the penetration of S. grimesii into the cell was consistent with the “zipper mechanism”, which first step involves specific interaction of bacterial invasin with a host cell surface receptor. However, in some cases, bacteria were trapped by filopodia probably induced by injected bacterial proteins that trigger the bacterial uptake process, as described in the “trigger mechanism” of invasion. To clarify whether two different mechanisms or a predominant one operate during S. grimesii invasion, further elucidation of bacterial and cellular factors involved in the bacteria-host cell interaction should be performed.     

Function of the <Emphasis Type="Italic">rel</Emphasis> Gene in <Emphasis Type="Italic">Escherichia coli</Emphasis>

Sokawa et al. suggest that rel^- strains of Escherichia coli possess abnormal protein synthesizing machinery, which cannot carry out normal protein synthesis when the supply of amino-acids is limited.     

A method for decomposing multivariate time series into a causal hierarchy within specific frequency bands

We propose a method - Frequency extracted hierarchical decomposition (FEHD) - for studying multivariate time series that identifies linear combinations of its components that possess a causally hierarchical structure - the method orders the components so that those at the “top” of the hierarchy drive those below. The method shares many of the features of the “hierarchical decomposition” method of Repucci et al. (Annals of Biomedical Engineering, 29, 1135–1149, 2001) but makes a crucial advance - the proposed method is capable of determining this causal hierarchy over arbitrarily specified frequency bands. Additionally, a novel minimization strategy is used to generate the decomposition resulting in an increase in stability, reliability, and an improvement in the sensitivity to model parameters. We demonstrate the utility of the method by applying it to both artificial time series constructed to have specific causal graphs, and to the EEG of healthy volunteers and patient subjects who are recovering from a severe brain injury.