Hox and ParaHox genes: A review on molluscs

Hox and ParaHox genes are involved in patterning the anterior‐posterior body axis in metazoans during embryo development. Body plan evolution and diversification are affected by variations in the number and sequence of Hox and ParaHox genes, as well as by their expression patterns. For this reason Hox and ParaHox gene investigation in the phylum Mollusca is of great interest, as this is one of the most important taxa of protostomes, characterized by a high morphological diversity. The comparison of the works reviewed here indicates that species of molluscs, belonging to different classes, share a similar composition of Hox and ParaHox genes. Therefore evidence suggests that the wide morphological diversity of this taxon could be ascribed to differences in Hox gene interactions and expressions and changes in the Hox downstream genes rather than to Hox cluster composition. Moreover the data available on Hox and ParaHox genes in molluscs compared with those of other Lophotrochozoa shed light on the complex and controversial evolutionary histories that these genes have undergone within protostomes. genesis 52:935–945, 2014. © 2014 Wiley Periodicals, Inc.     

Arterial Pulsation-driven Cerebrospinal Fluid Flow in the Perivascular Space: A Computational Model

This study was conducted to determine whether local arterial pulsations are sufficient to cause cerebrospinal fluid (CSF) flow along perivascular spaces (PVS) within the spinal cord. A theoretical model of the perivascular space surrounding a "typical" small artery was analysed using computational fluid dynamics. Systolic pulsations were modelled as travelling waves on the arterial wall. The effects of wave geometry and variable pressure conditions on fluid flow were investigated. Arterial pulsations induce fluid movement in the PVS in the direction of arterial wave travel. Perivascular flow continues even in the presence of adverse pressure gradients of a few kilopascals. Flow rates are greater with increasing pulse wave velocities and arterial deformation, as both an absolute amplitude and as a proportion of the PVS. The model suggests that arterial pulsations are sufficient to cause fluid flow in the perivascular space even against modest adverse pressure gradients. Local increases in flow in this perivascular pumping mechanism or reduction in outflow may be important in the etiology of syringomyelia.     

Agro-biology for bioregenerative Life Support Systems in long-term Space missions: General constraints and the Italian efforts

Abstract

Future Space stations and Space habitats/outposts should be envisioned as self-sufficient ecological closed or semi-closed systems. The Italian Space Agency (ASI) projects have involved many research groups from complementary areas with a final goal of designing a facility for plant cultivation in Space. It has been critical to (i) identify, for this particular environment, highly productive species able to optimize O₂ production/CO₂ consumption, and (ii) develop high-tech controlled environments. Research activities have included seedling production in simulated microgravity and in Space with the two-fold objective of (i) integrating the crew diet with fresh food, and (ii) studying specific biological phenomena. Another research topic concerned pollen biology as a critical component for seed-to-seed cycles but also for gametophytic selection. In this context, a review of the main scientific topics on plant Space biology and of the Italian efforts on agro-biology for bioregenerative Life Support Systems will be presented and discussed in this paper.     

Space: A Final Frontier for Vacuolar Pathogens

There is a fundamental gap in our understanding of how a eukaryotic cell apportions the limited space within its cell membrane. Upon infection, a cell competes with intracellular pathogens for control of this same precious resource. The struggle between pathogen and host provides us with an opportunity to uncover the mechanisms regulating subcellular space by understanding how pathogens modulate vesicular traffic and membrane fusion events to create a specialized compartment for replication. By comparing several important intracellular pathogens, we review the molecular mechanisms and trafficking pathways that drive two space allocation strategies, the formation of tight and spacious pathogen‐containing vacuoles. Additionally, we discuss the potential advantages of each pathogenic lifestyle, the broader implications these lifestyles might have for cellular biology and outline exciting opportunities for future investigation.      

Identification of cis-regulatory elements from the C. elegans Hox gene lin-39 required for embryonic expression and for regulation by the transcription factors LIN-1, LIN-31 and LIN-39

Expression of the Caenorhabditis elegans Hox gene lin-39 begins in the embryo and continues in multiple larval cells, including the P cell lineages that generate ventral cord neurons (VCNs) and vulval precursor cells (VPCs). lin-39 is regulated by several factors and by Wnt and Ras signaling pathways; however, no cis-acting sites mediating lin-39 regulation have been identified. Here, we describe three elements controlling lin-39 expression: a 338-bp upstream fragment that directs embryonic expression in P5-P8 and their descendants in the larva, a 247-bp intronic region sufficient for VCN expression, and a 1.3-kb upstream cis-regulatory module that drives expression in the VPC P6.p in a Ras-dependent manner. Three trans-acting factors regulate expression via the 1.3-kb element. A single binding site for the ETS factor LIN-1 mediates repression in VPCs other than P6.p; however, loss of LIN-1 decreases expression in P6.p. Therefore, LIN-1 acts both negatively and positively on lin-39 in different VPCs. The Forkhead domain protein LIN-31 also acts positively on lin-39 in P6.p via this module. Finally, LIN-39 itself binds to this element, suggesting that LIN-39 autoregulates its expression in P6.p. Therefore, we have begun to unravel the cis-acting sites regulating lin-39 Hox gene expression and have shown that lin-39 is a direct target of the Ras pathway acting via LIN-1 and LIN-31.     

Microbe-I: fungal biota analyses of the Japanese experimental module KIBO of the International Space Station before launch and after being in orbit for about 460 days

In addition to the crew, microbes also find their way aboard the International Space Station (ISS). Therefore, microbial monitoring is necessary for the health and safety of the crew and for general maintenance of the facilities of this station. Samples were collected from three sites in the Japanese experimental module KIBO on the ISS (air diffuser, handrail, and surfaces) for analysis of fungal biota approximately 1 year after this module had docked with the ISS. Samples taken from KIBO before launch and from our laboratory were used as controls. In the case of KIBO, both microbe detection sheet (MDS) and swab culture tests of orbital samples were negative. The MDS were also examined by field emission-scanning electron microscopy; no microbial structures were detected. However, fungal DNAs were detected by real-time PCR and analyzed by the clone library method; Alternaria sp. and Malassezia spp. were the dominant species before launch and in space, respectively. The dominant species found in specimens from the air conditioner diffuser, lab bench, door push panel, and facility surfaces on our laboratory (ground controls) were Inonotus sp., Cladosporium sp., Malassezia spp., and Pezicula sp., respectively. The fungi in the KIBO were probably derived from contamination due to humans, while those in our laboratory came from the environment (e.g., the soil). In conclusion, the cleanliness in KIBO was equivalent to that in a clean room environment on the ground.     

Translation and the cytoskeleton: a mechanism for targeted protein synthesis

This review describes the critical evidence that in eukaryotic cells polyribosomes, mRNAs and components of the protein synthetic machinery are associated with the cytoskeleton. The role of microtubules, intermediate filaments and microfilaments are discussed; at present most evidence suggests that polyribosomes interact with the actin filaments. The use of non-ionic detergent/deoxycholate treatment in the isolation of cytoskeletal-bound polysomes is described and the conclusion reached that at low salt concentrations this leads to mixed preparations of polysomes derived from both the cytoskeleton and the endoplasmic reticulum. At present the best approach for isolation of cytoskeletal-bound polysomes appears to involve extraction with salt concentrations greater than 130 mM after an initial non-ionic detergent treatment. Such polysomes appear to be enriched in certain mRNAs and thus it is suggested that they are involved in translation of a unique set of proteins. The evidence for mRNA localisation is presented and the role of the cytoskeleton in transport and localisation of RNA discussed. Recent data on the role of the 3 untranslated region in the targeting of mRNAs both to particular regions of the cell and for translation on cytoskeletal-bound polysomes is described. The hypothesis is developed that the association of polysomes with the cytoskeleton is the basis of a mechanism for the targeting of mRNAs and the compartmentalization of protein synthesis.Abbreviations CBP cytoskeletal-bound polysomes - FP free polysomes - MBP membrane-bound polysomes - ER endoplasmic reticulum     

Time series analysis of magnetic susceptibility variations in deep marine sedimentary rocks: A test using the upper Danian–Lower Selandian proposed GSSP, Spain

It has been clearly demonstrated that past climate fluctuations are recorded in marine sedimentary rocks. However, for many reasons, extracting the climate signature is difficult. Initial low-field mass-specific magnetic susceptibility (MS) data can potentially provide a measure of climate variability and thus become a proxy characterizing climate cyclicity in a wide range of marine sediments. This is due to the fact that climate change (warm, wet versus cold, dry) drives cyclic weathering and erosional variations that are recorded as the detrital components of marine sediment that dominates the MS. To test the utility of MS to yield climate proxies in marine sediments showing major changes in lithology, we have sampled the well-studied Danian/Selandian boundary interval (Lower Paleocene) at Zumaia (Zumaya), Spain. This interval represents a dramatic, rapid lithologic change from Danian carbonate-dominated limestone–marl couplets to a detrital-dominated marl-shale sequence in the Selandian, indicating onset of a major regression-erosional event beginning in the lowest Selandian. Sampling included a continuous sequence from the uppermost Danian Stage (3.71 m) into the lowermost Selandian Stage (5.2 m), a suite of 175 samples collected at 5 cm intervals. Our results indicate that MS measurements reflect changes in detrital sediment at the site, first by closely tracking high-frequency limestone–marl couplets, second with a large, rapid shift toward higher MS values beginning at the Danian/Selandian boundary resulting from a major regression, and third by tracking low-frequency climate-controlled variations known to have occurred during deposition of these sediments. MS zones developed from the cyclicity observed throughout the sequence, supported by time series analysis using Fourier Transform (FT) methods applied to the MS results, exhibit Milankovitch cyclicities in the precessional (19–24 kyr), obliquity (41–54 kyr) and eccentricity bands (100 kyr). This is in excellent agreement with previous FT work on the section using measured variations in cyclic bed thicknesses. With the new MS data set and FT results, we then developed a Floating Point Time Scale (FPTS) for the sequence sampled (covering  550 kyr through the Danian/Selandian boundary interval), yielding a time-scale resolution for the uppermost Danian to  10,000 years. However, only the  100,000 year eccentricity band for the Selandian is sufficiently well developed for an FPTS estimate, and yields a time-scale resolution of  50,000 years. Our test of the utility of MS data sets in this varying depositional setting demonstrated that these data can provide a climate proxy that is not disrupted by large lithologic changes.     

A recombinogenic targeting method to modify large-inserts for cis-regulatory analysis in transgenic mice: construction and expression of a 100-kb, zebrafish Hoxa-11b-lacZ reporter gene

The identification of cis-sequences responsible for spatiotemporal patterns of gene expression often requires the functional analysis of large genomic regions. In this study a 100-kb zebrafish Hoxa-11b-lacZ reporter gene was constructed and expressed in transgenic mice. PAC clone 10-O19, containing a portion of the zebrafish HoxA-b cluster, was captured into the yeast-bacterial shuttle vector, pPAC-ResQ, by recombinogenic targeting. A lacZ reporter gene was then inserted in-frame into exon 1 of the zfHoxa-11b locus by a second round of recombinogenic targeting. Expression of the zfHoxa-11b-lacZ reporter gene in 10.5 d.p.f. transgenic mouse embryos was observed only in the posterior portion of the A-P axis, in the paraxial mesoderm, neural tube, and somites. These findings demonstrate the utility of recombinogenic targeting for the modification and expression of large inserts captured from P1/PAC clones. Received: 22 June 1999 / Accepted: 1 September 1999     

Proton Hopping: A Proposed Mechanism for Myelinated Axon Nerve Impulses

Myelinated axon nerve impulses travel 100 times more rapidly than impulses in non‐myelinated axons. Increased speed is currently believed to be due to ‘hopping’ or ‘saltatory propagation’ along the axon, but the mechanism by which impulses flow has never been adequately explained. We have used modeling approaches to simulate a role for proton hopping in the space between the plasma membrane and myelin sheath as the mechanism of nerve action‐potential flow.     

RT—PCR测定大鼠妊娠早期子宫孕激素受体基因的表达

孕激素在妊娠的建立和维持过程中起着非常重要的作用,但目前为止未见有关大鼠子宫 激素受体（ＰＲ）基因在该过程中表达情况的系统报道。本和反转偶联聚合酶链式反应（ＲＴ－ＰＣＲ）方法测定了大鼠动情周期和妊娠早期子宫孕激素受体基因的转录,结果表明：１．动情周期中,子吕ＰＲｍＲＮＡ水平在动情期最高,在动情后期最低,动情期水平约为动情后期的２倍。２．妊娠开始后,子宫ＰＲｍＲＮＡ水平迅速上地ｄ３－ｄ４（着床前）达     

A Mechanism for Histone Chaperoning Activity of Nucleoplasmin: Thermodynamic and Structural Models

Nucleoplasmin (NP), a histone chaperone, acts as a reservoir for histones H2A-H2B in Xenopus laevis eggs and can displace sperm nuclear basic proteins and linker histones from the chromatin fiber of sperm and quiescent somatic nuclei. NP has been proposed to mediate the dynamic exchange of histones during the expression of certain genes and assists the assembly of nucleosomes by modulating the interaction between histones and DNA. Here, solution structural models of full-length NP and NP complexes with the functionally distinct nucleosomal core and linker histones are presented for the first time, providing a picture of the physical interactions between the nucleosomal and linker histones with NP core and tail domains. Small-angle X-ray scattering and isothermal titration calorimetry reveal that NP pentamer can accommodate five histones, either H2A-H2B dimers or H5, and that NP core and tail domains are intimately involved in the association with histones. The analysis of the binding events, employing a site-specific cooperative model, reveals a negative cooperativity-based regulatory mechanism for the linker histone/nucleosomal histone exchange. The two histone types bind with drastically different intrinsic affinity, and the strongest affinity is observed for the NP variant that mimicks the hyperphosphorylated active protein. The different “affinity windows” for H5 and H2A-H2B might allow NP to fulfill its histone chaperone role, simultaneously acting as a reservoir for the core histones and a chromatin decondensing factor. Our data are compatible with the previously proposed model where NP facilitates nucleosome assembly by removing the linker histones and depositing H2A-H2B dimers onto DNA.     

BIMLR: A method for constructing rooted phylogenetic networks from rooted phylogenetic trees

Rooted phylogenetic trees constructed from different datasets (e.g. from different genes) are often conflicting with one another, i.e. they cannot be integrated into a single phylogenetic tree. Phylogenetic networks have become an important tool in molecular evolution, and rooted phylogenetic networks are able to represent conflicting rooted phylogenetic trees. Hence, the development of appropriate methods to compute rooted phylogenetic networks from rooted phylogenetic trees has attracted considerable research interest of late. The C_ASS algorithm proposed by van Iersel et al. is able to construct much simpler networks than other available methods, but it is extremely slow, and the networks it constructs are dependent on the order of the input data. Here, we introduce an improved C_ASS algorithm, BIMLR. We show that BIMLR is faster than C_ASS and less dependent on the input data order. Moreover, BIMLR is able to construct much simpler networks than almost all other methods. BIMLR is available at http://nclab.hit.edu.cn/wangjuan/BIMLR/.     

The Double-Water-Film Electrode: A Device for Measuring the Resistance and the Capacitance of the Internode/Node Interface of Chara as Functions of Time and Temperature

Abstract A ``double-water-film electrode technique' has been developed for the long-term characterization of the electrical properties across the interface between the nodal (N) and internodal (A or B) cells and the vacuole along the length of an internode of Chara as a function of time and temperature. The electrode unit consisted of a pair of the water-film electrodes described elsewhere (Chilcott 1988; Chilcott and others 1983; Coster and others 1984; Lucas 1985; and Ogata 1983). The distance between two water-film probes was fixed at 1.0 cm. By scanning the electrode unit, the spatial variations in electrical resistance and capacitance along the longitudinal axis of Chara were observed. Analysis was performed by applying an electrical equivalent circuit for the biomembrane (Philippson 1921). Across the internode (−A or −B)/central nodal cells interface, the specific parallel resistance (Rm) and the parallel capacitance (Cm) at 20°C were 30 ± 5 × 10⁻³Ωm² and 1.5 ± 0.5 × 10⁻¹Fm⁻² (at 30 Hz), respectively. And the series resistance, corresponding to the vacuole of the internode was 8 × 10⁻³Ωm². Study of temperature dependencies of Rm and Cm suggested that a dynamic homeostatic regulation was operating at the interface where numerous plasmodesmata were observed with an electron microscope (Pickett-Heaps 1967; Spanswick and Costerton 1967). Assuming that the individual cylinder of plasmodesma was filled only with cytoplasm, the number of plasmodesma per interface was estimated at 2.6 × 10⁵. Received 19 January 2000; accepted 16 March 2000     

Histamine: A Neurotransmitter Candidate for Drosophila Photoreceptors

Recent experimental evidence suggests that histamine might be the synaptic transmitter used by invertebrate photoreceptors. In the present study, we have examined whether histamine is a transmitter candidate for Drosophila photoreceptors. Our findings are as follows: (a) Large amounts of histamine are synthesized by wild-type heads, whereas heads from the eye-deficient mutants, eyes absent and sine oculis, show reduced histamine synthesis. (b) Histidine decarboxylase activity is approximately 10-fold higher in extracts of normal heads compared with that in the mutants. (c) Histamine taken up by fly heads is metabolized into N-acetylhistamine and imidazole-4-acetic acid. (d) Immunostaining of normal and sevenless heads with histamine-specific antisera demonstrates that histamine is present in photoreceptors R1-6 and R8. (e) Histamine synthesized from exogenously supplied [3H]histidine can be released by depolarization with 50 mM K+, and the release is Ca2+ dependent. These observations strongly suggest that histamine is a major neurotransmitter used by Drosophila photoreceptors.