Morphology and molecular relationships of Leptofauchea rhodymenioides (Rhodymeniales,Rhodophyta), a new record for Japan

Leptofauchea rhodymenioides Taylor (Faucheaceae, Rhodymeniales) is reported from Japan for the first time, based on detailed morphological studies and molecular phylogenetic analyses of nuclear‐encoded small subunit ribosomal RNA (SSU rRNA) and plastid‐encoded rbcL gene sequences. This is the first report of male gametophytes and detailed carposporophyte development in the genus Leptofauchea. This species is characterized as follows: (i) flat, membranous, and regularly and dichotomously branched thalli; (ii) the older blades are constricted below the apices; (iii) the cortex is composed of a continuous layer with an irregularly arranged outer layer, and the medulla of two to three incomplete layers; (iv) gametophytes are dioecious; (v) in males, the cortical cells cut off two to three spermatangial mother cells, which produce terminal spermatangia; (vi) in females, the procarp is composed of a three‐celled carpogonial branch and a two‐celled auxiliary cell branch; (vii) upon fertilization, the carpogonium directly contacts the auxiliary cell; (viii) the auxiliary mother cell fuses with vegetative cells, and forms a large trunk‐like fusion cell; (ix) gonimoblast filaments develop outwardly, and transform completely into carposporangia; (x) the carposporophyte is covered with a pericarp with a well‐defined tela arachnoidea; (xi) the mature cystocarp is spherical, has an ostiole, and protrudes from the blade margins; and (xii) the cruciately divided tetrasporangia are formed in nemathecia, produced laterally from paraphyses or terminally on short filaments. Molecular analyses suggest that Leptofauchea forms a strong sister alliance with the genus Webervanbossea. The families Faucheaceae and Lomentariaceae, and the genera Leptofauchea and Webervanbossea are monophyletic, but the latter two genera are not included in the Faucheaceae.     

Chamaebotrys prolifera sp. nov. (Rhodymeniaceae, Rhodophyta) from Puerto Rico, Caribbean Sea, based on morphology and small subunit rDNA sequences

A new rhodymeniacean species, Chamaebotrys prolifera , is described from a shallow water habitat in Puerto Rico, representing the first occurrence of the genus in the Atlantic Ocean. Plants, to 5 cm across, are decumbent and comprised of compressed vesicles that are originally proliferously branched at the perimeter. Older vesicles become branched from their dorsal surfaces as well. Branches are septate at their origin and become irregularly shaped with age. Anastomoses between adjacent vesicles is common. Individual vesicles measure to 15 mm in broadest dimension. Vesicle walls consist of two layers of medullary cells and two layers of cortical cells. Tetrasporangia, which occur in diffuse nemathecia, are spherical, to 30 µm in diameter and are cut off terminally from an inner cortical cell. Cystocarps are hemispherical measuring to 800 µm in diameter and 350 µm in height. Spermatangia are apparently cut off randomly from outer cortical cells across the thallus surface. Molecular evidence confirms placement of Chamaebotrys within the Rhodymeniaceae.     

Effects of chemical modification on the potency,serum stability,and immunostimulatory properties of short shRNAs

Small hairpin RNAs (shRNAs) with 19-base-pair, or shorter, stems (short shRNAs [sshRNAs]) have been found to constitute a class whose mechanism of action appears to be distinct from that of small interfering RNAs (siRNAs) or longer shRNAs. These sshRNAs can be as active as canonical siRNAs or longer shRNAs. Their activity is affected by whether the antisense strand is positioned 5′ or 3′ to the loop (L or R sshRNAs, respectively). Dicer seems not to be involved in the processing of sshRNAs, although the mechanism of target gene suppression by these hairpins is through Ago2-mediated mRNA cleavage. In this study, the effects of chemical modifications on the potency, serum stability, and innate immune response of sshRNAs were investigated. Deoxynucleotide substitution and 2′-O-methyl (2′-OMe) modification in the sense strand and loop did not affect silencing activity, but, unlike with siRNAs, when placed in the antisense strand these modifications were detrimental. Conjugation with bulky groups at the 5′-end of L sshRNAs or 3′-end of R sshRNAs had a negative impact on the potency. Unmodified sshRNAs in dimer form or with blunt ends were immunostimulatory. Some modifications such as 3′-end conjugation and phosphorothioate linkages on the backbone of the sshRNAs could also induce inflammatory cytokine production. However, 2′-OMe substitution of sshRNAs abrogated the innate immune response and improved the serum stability of the hairpins.     

Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway

In flies, small silencing RNAs are sorted between Argonaute1 (Ago1), the central protein component of the microRNA (miRNA) pathway, and Argonaute2 (Ago2), which mediates RNA interference. Extensive double-stranded character—as is found in small interfering RNAs (siRNAs)—directs duplexes into Ago2, whereas central mismatches, like those found in miRNA/miRNA* duplexes, direct duplexes into Ago1. Central to this sorting decision is the affinity of the small RNA duplex for the Dcr-2/R2D2 heterodimer, which loads small RNAs into Ago2. Here, we show that while most Drosophila miRNAs are bound to Ago1, miRNA* strands accumulate bound to Ago2. Like siRNA loading, efficient loading of miRNA* strands in Ago2 favors duplexes with a paired central region and requires both Dcr-2 and R2D2. Those miRNA and miRNA* sequences bound to Ago2, like siRNAs diced in vivo from long double-stranded RNA, typically begin with cytidine, whereas Ago1-bound miRNA and miRNA* disproportionately begin with uridine. Consequently, some pre-miRNA generate two or more isoforms from the same side of the stem that differentially partition between Ago1 and Ago2. Our findings provide the first genome-wide test for the idea that Drosophila small RNAs are sorted between Ago1 and Ago2 according to their duplex structure and the identity of their first nucleotide.     

Spatial and temporal variation of abundance,biomass and diversity within marine reserves in the Philippines

Aim The objective of this study was to investigate the influence of protection duration (years of fishing closure) and location (distance from shore) on reef fish diversity. Location Danajon Double Barrier Reef, Bohol, Philippines. Methods Reef fish abundance and size structure, by species, were obtained monthly using replicated underwater visual belt transects (n = 8; 70 × 5‐m belt transects) over 3 years (2002–2005) at eight sites that included six marine reserves and two unprotected reef areas. We analysed species accumulation curves, diversity indices and abundance–biomass comparison (ABC) curves within and across the study sites to assess the influence of protection duration and location. Results Analyses showed that longer protection duration impacted reef fish diversity at both inshore and offshore sites by shifting ABC curves from higher abundance than biomass curves at fished sites to higher biomass than abundance curves at most of the protected sites. Protection duration did not significantly influence either the rate of species accumulation within sites or the 12 diversity indices measured across the study sites. The offshore sites consistently showed higher rates of species accumulation and diversity indices values than inshore sites with similar protection duration. One protected offshore young marine reserve site that has been assessed as the least well‐managed showed patterns more consistent with the fished sites. Main conclusions Analyses showed that protection duration mainly impacted diversity by increasing the dominance of large‐bodied species and enhancing total biomass. Besides protection duration, reserve location influenced species accumulation curves and diversity indices.     

Somatic mosaicism in cases with small supernumerary marker chromosomes

Somatic mosaicism is something that is observed in everyday lives of cytogeneticists. Chromosome instability is one of the leading causes of large-scale genome variation analyzable since the correct human chromosome number was established in 1956. Somatic mosaicism is also a well-known fact to be present in cases with small supernumerary marker chromosomes (sSMC), i.e. karyotypes of 47,+mar/46. In this study, the data available in the literature were collected concerning the frequency mosaicism in different subgroups of patients with sSMC. Of 3124 cases with sSMC 1626 (52%) present with somatic mosaicism. Some groups like patients with Emanuel-, cat-eye- or i(18p)- syndrome only tend rarely to develop mosaicism, while in Pallister-Killian syndrome every patient is mosaic. In general, acrocentric and non-acrocentric derived sSMCs are differently susceptible to mosaicism; non-acrocentric derived ones are hereby the less stable ones. Even though, in the overwhelming majority of the cases, somatic mosaicism does not have any detectable clinical effects, there are rare cases with altered clinical outcomes due to mosaicism. This is extremely important for prenatal genetic counseling. Overall, as mosaicism is something to be considered in at least every second sSMC case, array-CGH studies cannot be offered as a screening test to reliably detect this kind of chromosomal aberration, as low level mosaic cases and cryptic mosaics are missed by that.     

Natural ligand binding and transfer from liver fatty acid binding protein (LFABP) to membranes

Liver fatty acid-binding protein (LFABP) is distinctive among fatty acid-binding proteins because it binds more than one molecule of long-chain fatty acid and a variety of diverse ligands. Also, the transfer of fluorescent fatty acid analogues to model membranes under physiological ionic strength follows a different mechanism compared to most of the members of this family of intracellular lipid binding proteins. Tryptophan insertion mutants sensitive to ligand binding have allowed us to directly measure the binding affinity, ligand partitioning and transfer to model membranes of natural ligands. Binding of fatty acids shows a cooperative mechanism, while acyl-CoAs binding presents a hyperbolic behavior. Saturated fatty acids seem to have a stronger partition to protein vs. membranes, compared to unsaturated fatty acids. Natural ligand transfer rates are more than 200-fold higher compared to fluorescently-labeled analogues. Interestingly, oleoyl-CoA presents a markedly different transfer behavior compared to the rest of the ligands tested, probably indicating the possibility of specific targeting of ligands to different metabolic fates.     

Endogenous and Transplanted Small Hepatocytes in Retrorsine-treated/Partially Hepatectomized Rat Liver Show Differences in Growth, Phenotype, and Proximity to Clusters of ��-Glutamyl Transpeptidase-positive Host Hepatocytes

In the present report, we have compared the phenotype and growth of small hepatocyte progenitors (SHPs) induced by retrorsine/partial hepatectomy (R/PH) and small hepatocytes (SHs) isolated from normal adult liver. SHs were isolated by a combination of differential centrifugation and Percoll isodensity fractionation from a liver cell suspension prepared by collagenase perfusion of a dipeptidyl peptidase IV (DPPIV)–positive Fischer F344 rat liver. Following further purification by flow cytometry, the SH-R3 fraction was transplanted via the portal vein into R/PH–treated, DPPIV-negative Fischer F344 rats. Frozen sections from tissue harvested at 5, 7, and 21 days after transplantation were analyzed by indirect immunofluorescence to compare the phenotypic characteristics of colonies formed by exogenous SH-R3s and endogenous SHPs. Colonies of transplanted SHs and endogenous SHPs displayed similar histologies and phenotypes but were distinguished from surrounding hepatocytes by their elevated expression of transferrin receptor. SH-R3 colonies were frequently located within clusters of γ-glutamyl transpeptidase–positive host hepatocytes. Although significantly smaller at 5 and 7 days after PH, by day 21, SH-R3 colonies were similar in size to those formed by SHPs. The present results suggest that endogenous SHPs are derived, at least in part, from SHPs. (J Histochem Cytochem 58:61–72, 2010)     

Description of Paratetrahymena parawassi n. sp. using Morphological and Molecular Evidence and a Phylogenetic Analysis of Paratetrahymena and Other Taxonomically Ambiguous Genera in the Order Loxocephalida (Ciliophora,Oligohymenophorea)

ABSTRACT. The marine scuticociliate Paratetrahymena parawassi n. sp. is described on the basis of morphology, especially infraciliature, and the sequence of its small subunit (SSU) rRNA gene to become the second known member of its genus. Paratetrahymena and other ciliates in the order Loxocephalida possess a mixture of morphological and morphogenetic features characteristic of the subclasses Hymenostomatia and Scuticociliatia. Accordingly, we used SSU rRNA sequences to analyze the phylogeny of Paratetrahymena and three other loxocephalid genera. Paratetrahymena and Cardiostomatella vermiformis formed a moderately well‐supported clade that diverged at a deep level from all other scuticociliates, supporting separation of loxocephalids from other scuticociliates as a suprafamilial taxon. Sathrophilus holtae was a sister taxon to Paratetrahymena and Cardiostomatella in a poorly supported, unresolved relationship; nevertheless, association of all three genera into a single clade was supported by an approximately unbiased (AU) test. Any association of these genera singly or as a group with the Hymenostomatia was rejected decisively by AU tests and by a complete absence in the loxocephalids of the unique nucleotide identities that distinguish hymenostomes. Therefore, the morphological and morphogenetic similarities of loxocephalids to hymenostomes may be plesiomorphies, and the conflicting mix of scuticociliate and hymenostome characteristics seen in loxocephalids may result from differing rates of character evolution. Dexiotrichides pangi and Urocentrum, which is currently classified as a peniculid, formed a small clade that associated with hymenostomes and peritrichs. Monophyly of the Loxocephalida with Dexiotrichides and/or Urocentrum included was not rejected by AU; however, inclusion of Urocentrum in the Peniculia was rejected by AU tests. A hypothesis is offered to explain the lack of resolution of loxocephalid ciliates and Urocentrum in phylogenetic trees, namely that their phylogenetic positions are influenced by a combination of heterogeneous data and long‐branch attraction caused by poor representation of taxa in analyses. The well‐known genus Cyclidium, a member of the order Pleuronematida, was revealed to be polyphyletic as a byproduct of our analyses of loxocephalids. In particular, Cyclidium porcatum appears to fall outside the clade containing typical members of the subclass Scuticociliatia and thus invites investigation as a possible member of the order Loxocephalida.