Small RNA Derived from the Virulence Modulating Region of the Potato spindle tuber viroid Silences callose synthase Genes of Tomato Plants

The tomato (Solanum lycopersicum) callose synthase genes CalS11-like and CalS12-like encode proteins that are essential for the formation of callose, a major component of pollen mother cell walls; these enzymes also function in callose formation during pathogen infection. This article describes the targeting of these callose synthase mRNAs by a small RNA derived from the virulence modulating region of two Potato spindle tuber viroid variants. More specifically, viroid infection of tomato plants resulted in the suppression of the target mRNAs up to 1.5-fold, depending on the viroid variant used and the gene targeted. The targeting of these mRNAs by RNA silencing was validated by artificial microRNA experiments in a transient expression system and by RNA ligase-mediated rapid amplification of cDNA ends. Viroid mutants incapable of targeting callose synthase mRNAs failed to induce typical infection phenotypes, whereas a chimeric viroid obtained by swapping the virulence modulating regions of a mild and a severe variant of Potato spindle tuber viroid greatly affected the accumulation of viroids and the severity of disease symptoms. These data provide evidence of the silencing of multiple genes by a single small RNA derived from a viroid.     

Arabidopsis ATG4 cysteine proteases specificity toward ATG8 substrates

Macroautophagy (hereafter autophagy) is a regulated intracellular process during which cytoplasmic cargo engulfed by double-membrane autophagosomes is delivered to the vacuole or lysosome for degradation and recycling. Atg8 that is conjugated to phosphatidylethanolamine (PE) during autophagy plays an important role not only in autophagosome biogenesis but also in cargo recruitment. Conjugation of PE to Atg8 requires processing of the C-terminal conserved glycine residue in Atg8 by the Atg4 cysteine protease. The Arabidopsis plant genome contains 9 Atg8 (AtATG8a to AtATG8i) and 2 Atg4 (AtATG4a and AtATG4b) family members. To understand AtATG4’s specificity toward different AtATG8 substrates, we generated a unique synthetic substrate C-AtATG8-ShR (citrine-AtATG8-Renilla luciferase SuperhRLUC). In vitro analyses indicated that AtATG4a is catalytically more active and has broad AtATG8 substrate specificity compared with AtATG4b. Arabidopsis transgenic plants expressing the synthetic substrate C-AtAtg8a-ShR is efficiently processed by endogenous AtATG4s and targeted to the vacuole during nitrogen starvation. These results indicate that the synthetic substrate mimics endogenous AtATG8, and its processing can be monitored in vivo by a bioluminescence resonance energy transfer (BRET) assay. The synthetic Atg8 substrates provide an easy and versatile method to study plant autophagy during different biological processes.     

Diversity and ecology of algae from the Nahal Qishon river,northern Israel

In 59 samples of periphyton and phytoplankton collected in 2002 - 2003 from the Nahal Qishon (Qishon River), northern Israel, we found 178 species from seven divisions of algae and cyanoprocaryotes. Diatoms, clorophytes, and cyanoprocaryotes prevail. Nitzschia and Navicula (Bacillariophyta) are the most abundant. Most of the species are cosmopolitan or widespread, except Lagynion janei (Chrysophyta), which is endemic for the Mediterranean Realm. About 17% of species (26) are new for Israel and five of them represent the first recorded genera: Crinalium endophyticum Crow, Actinocyclus normanii (Gregory) Hustedt, Rhizoclonium hieroglyphicum (Agardh) Kütz (Chlorophyta), Lagynion janei Bourelly, and Stylococcus aureus Chodat. Most of them come from a rare riverine assemblage with red alga Audouinella pygmea, as well as from the estuarine assemblage. Alkaliphiles predominate among the indicators of acidity, with few acidophiles confined to the communities under the impact of industrial wastes. Among the indicators of salinity, most numerous are the oligohalobien-indifferents and species adapted to a moderate salinity level. The relative species richness of ecological groups and the indices of saprobity are correlated with changes in conductivity, pH, and N-nitrate concentration. Indicators of organic pollution fall in the range of betameso- to alfamesosaprobic self-purification grades. Our studies show ecological significance of the Nahal Qishon as a model for a strongly disturbed aquatic ecosystem in the coastal zone of eastern Mediterranean.     

Human Identity and the Evolution of Societies

Human societies are examined as distinct and coherent groups. This trait is most parsimoniously considered a deeply rooted part of our ancestry rather than a recent cultural invention. Our species is the only vertebrate with society memberships of significantly more than 200. We accomplish this by using society-specific labels to identify members, in what I call an anonymous society. I propose that the human brain has evolved to permit not only the close relationships described by the social brain hypothesis, but also, at little mental cost, the anonymous societies within which such alliances are built. The human compulsion to discover or invent labels to “mark” group memberships may originally have been expressed in hominins as vocally learned greetings only slightly different in function from chimpanzee pant hoots (now known to be society-specific). The weight of evidence suggests that at some point, conceivably early in the hominin line, the distinct groups composed of several bands that were typical of our ancestors came to be distinguished by their members on the basis of multiple labels that were socially acquired in this way, the earliest of which would leave no trace in the archaeological record. Often overlooked as research subjects, these sizable fission-fusion communities, in recent egalitarian hunter-gatherers sometimes 2,000 strong, should consistently be accorded the status of societies, in the same sense that this word is used to describe tribes, chiefdoms, and other cultures arising later in our history. The capacity of hunter-gatherer societies to grow sufficiently populous that not all members necessarily recognize one another would make the transition to larger agricultural societies straightforward. Humans differ from chimpanzees in that societal labels are essential to the maintenance of societies and the processes giving birth to new ones. I propose that anonymous societies of all kinds can expand only so far as their labels can remain sufficiently stable.     

BRACHYURY and CDX2 mediate BMP-induced differentiation of human and mouse pluripotent stem cells into embryonic and extraembryonic lineages

BMP is thought to induce hESC differentiation toward multiple lineages including mesoderm and trophoblast. The BMP-induced trophoblast phenotype is a long-standing paradox in stem cell biology. Here we readdressed BMP function in hESCs and mouse epiblast-derived cells. We found that BMP4 cooperates with FGF2 (via ERK) to induce mesoderm and to inhibit endoderm differentiation. These conditions induced cells with high levels of BRACHYURY (BRA) that coexpressed CDX2. BRA was necessary for and preceded CDX2 expression; both genes were essential for expression not only of mesodermal genes but also of trophoblast-associated genes. Maximal expression of the latter was seen in the absence of FGF but these cells coexpressed mesodermal genes and moreover they differed in cell surface and epigenetic properties from placental trophoblast. We conclude that BMP induces human and mouse pluripotent stem cells primarily to form mesoderm, rather than trophoblast, acting through BRA and CDX2.     

MicroRNA expression profiling identifies activated B cell status in chronic lymphocytic leukemia cells

Chronic lymphocytic leukemia (CLL) is thought to be a disease of resting lymphocytes. However, recent data suggest that CLL cells may more closely resemble activated B cells. Using microRNA (miRNA) expression profiling of highly-enriched CLL cells from 38 patients and 9 untransformed B cells from normal donors before acute CpG activation and 5 matched B cells after acute CpG activation, we demonstrate an activated B cell status for CLL. Gene set enrichment analysis (GSEA) identified statistically-significant similarities in miRNA expression between activated B cells and CLL cells including upregulation of miR-34a, miR-155, and miR-342-3p and downregulation of miR-103, miR-181a and miR-181b. Additionally, decreased levels of two CLL signature miRNAs miR-29c and miR-223 are associated with ZAP70(+) and IgV(H) unmutated status and with shorter time to first therapy. These data indicate an activated B cell status for CLL cells and suggest that the direction of change of individual miRNAs may predict clinical course in CLL.     

Sexual dimorphism in relative sacral breadth among catarrhine primates

As the sacrum contributes to the size and shape of the birth canal, the sexually dimorphic sacrum of humans is frequently interpreted within obstetric contexts. However, while the human sacrum has been extensively studied, comparatively little is known about sacral morphology in nonhuman primates. Thus, it remains unclear whether sacral sexual dimorphism exists in other primates, and whether potential dimorphism is primarily related to obstetrics or other factors such as body size dimorphism. In this study, sacra of Homo sapiens, Hylobates lar, Nasalis larvatus, Gorilla gorilla, Pongo pygmaeus, Pan troglodytes, and Pan paniscus were evaluated for sexual dimorphism in relative sacral breadth (i.e., the ratio of overall sacral breadth to first sacral vertebral body breadth). Homo sapiens, H. lar, N. larvatus, and G. gorilla exhibit dimorphism in this ratio. Of these, the first three species have large cephalopelvic proportions, whereas G. gorilla has small cephalopelvic proportions. P. pygmaeus, P. troglodytes, and P. paniscus, which all have small cephalopelvic proportions, were not dimorphic for relative sacral breadth. We argue that among species with large cephalopelvic proportions, wide sacral alae in females facilitate birth by increasing the pelvic inlet's transverse diameter. However, given the small cephalopelvic proportions among gorillas, an obstetric basis for dimorphism in relative sacral breadth appears unlikely. This raises the possibility that sacral dimorphism in gorillas is attributable to selection for relatively narrow sacra in males rather than relatively broad sacra in females. Accordingly, these results have implications for interpreting pelvic dimorphism among fossil primates, including hominins. Am J Phys Anthropol 152:435–446, 2013. © 2013 Wiley Periodicals, Inc.     

Relationships among habitat quality and measured condition variables in Gulf of Mexico mangroves

Ecosystem condition assessments were conducted for 12 mangrove sites in the northern Gulf of Mexico. Nine sites were selected randomly; three were selected a priori based on best professional judgment to represent a poor, intermediate and good environmental condition. During single visits a visual assessment generated numerical scores for each site relative to the reference condition range. Relationships were examined among variables to evaluate relevance of visual observations and empirical data of environmental condition. Sites in poorest visual condition possessed low concentrations of soil contaminants as hydrological attributes that restricted contaminant inflow lowered visual scores. Bacterial abundance related to the greatest number of variables, and was the only indicator that correlated with the visually derived score (0.60, p < 0.05). Soil enzymatic activity ratios within classes provided estimates of microbial nutrient status. Low peptidases/phosphatase and glycosidases/phosphatase ratios supported the conclusion reached from the molar ratios of nutrients, that mangrove soils were phosphorous limited. A positive correlation (0.71, p < 0.05) observed between C:N ratios in leaf tissue and soil from all mangrove sites indicated that relative molar ratios of major nutrients in leaf tissue were reflective of limitations in the soil. Principal components analysis guided a reduction in variables retained for analysis, and provided an ordination of the sites which grouped into three clusters and two outliers. Grouping was primarily influenced by soil C:N. In future studies measuring major nutrients in soil, C:N:P, could possibly function as a single, cost effective indicator to validate rapid visual condition assessments of mangroves.     

Cell death mediated by the N-terminal domains of a unique and highly conserved class of NB-LRR protein

Plant genomes encode large numbers of nucleotide-binding, leucine-rich repeat (NB-LRR) proteins, many of which are active in pathogen detection and defense response induction. NB-LRR proteins fall into two broad classes: those with a Toll and interleukin-1 receptor (TIR) domain at their N-terminus and those with a coiled-coil (CC) domain at the N-terminus. Within CC-NB-LRR-encoding genes, one basal clade is distinguished by having CC domains resembling the Arabidopsis thaliana RPW8 protein, which we refer to as CCR domains. Here, we show that CCR-NB-LRR-encoding genes are present in the genomes of all higher plants surveyed, and that they comprise two distinct subgroups: one typified by the Nicotiana benthamiana N-required gene 1 (NRG1) protein and the other typified by the Arabidopsis activated disease resistance gene 1 (ADR1) protein. We further report that, in contrast to CC-NB-LRR proteins, the CCR domains of both NRG1- and ADR1-like proteins are sufficient for the induction of defense responses, and that this activity appears to be SGT1-independent. Additionally, we report the apparent absence of both NRG1 homologs and TIR-NB-LRR-encoding genes from the dicot Aquilegia coerulea and the dicotyledonous order Lamiales as well as from monocotyledonous species. This strong correlation in occurrence is suggestive of a functional relationship between these two classes of NB-LRR proteins.     

ARGONAUTE2 mediates RNA-silencing antiviral defenses against Potato virus X in Arabidopsis

RNA-silencing mechanisms control many aspects of gene regulation including the detection and degradation of viral RNA through the action of, among others, Dicer-like and Argonaute (AGO) proteins. However, the extent to which RNA silencing restricts virus host range has been difficult to separate from other factors that can affect virus-plant compatibility. Here we show that Potato virus X (PVX) can infect Arabidopsis (Arabidopsis thaliana), which is normally a nonhost for PVX, if coinfected with a second virus, Pepper ringspot virus. Here we show that the pepper ringspot virus 12K protein functions as a suppressor of silencing that appears to enable PVX to infect Arabidopsis. We also show that PVX is able to infect Arabidopsis Dicer-like mutants, indicating that RNA silencing is responsible for Arabidopsis nonhost resistance to PVX. Furthermore, we find that restriction of PVX on Arabidopsis also depends on AGO2, suggesting that this AGO protein has evolved to specialize in antiviral defenses.