Pinus baileyi (section Pinus, Pinaceae) from the Paleogene of Idaho, USA

Pinus baileyi from the Paleogene of Idaho was initially related to the bristlecone pine P. longaeva (subgen. Strobus, sect. Parrya, subsect. Balfourianae) from western North America. Unlike the centromucronate condition in P. longaeva, P. baileyi cones have raised umbos that are excentromucronate, i.e., the mucro positioned in the upper umbo field above the keel. Cone size and scale morphology shows that P. baileyi more closely resembles excentromucronate pines of subsects. Halepenses and Pinus sensu Gernandt et al. (2005, Taxon 54: 29-42), but is most similar to P. resinosa, P. kesiya, and P. massoniana of subsect. Pinus. Morphologically, P. baileyi resembles the fossil species P. princetonensis and P. arnoldii from the Eocene Princeton Chert, British Columbia, Canada. Pinus baileyi extends the western North American range of ovulate cones resembling subsect. Pinus from the middle Eocene of British Columbia, Canada and Washington, USA to the Oligocene of Idaho, USA. Pinus baileyi, and possibly P. princetonensis and P. arnoldii, indicates the presence of early populations of subsect. Pinus-type pines in the western cordillera of North America, raising the possibility that P. resinosa and P. tropicalis may have evolved from this group.     

Proteomic analysis of the potato tuber life cycle

The tuber of potato (Solanum tuberosum) is commonly used as a model for underground storage organs. In this study, changes in the proteome were followed from tuberization, through tuber development and storage into the sprouting phase. Data interrogation using principal component analysis was able to clearly discriminate between the various stages of the tuber life cycle. Moreover, five well-defined protein expression patterns were found by hierarchical clustering. Altogether 150 proteins showing highly significant differences in abundance between specific stages in the life cycle were highlighted; 59 of these were identified. In addition, 50 proteins with smaller changes in abundance were identified, including several novel proteins. Most noticeably, the development process was characterized by the accumulation of the major storage protein patatin isoforms and enzymes involved in disease and defense reactions. Furthermore, enzymes involved in carbohydrate and energy metabolism and protein processing were associated with development but decreased during tuber maturation. These results represent the first comprehensive picture of many proteins involved in the tuber development and physiology.     

Reduction of image artifacts in mice by bladder flushing with a novel double-lumen urethral catheter

In electron paramagnetic resonance imaging (EPRI), the accumulation of contrast agent in the bladder can create a very large source of signal, often far greater than that of the organ of interest. Mouse model images have become increasingly important in preclinical testing. To minimize bladder accumulation on mouse images, we developed a novel, minimally invasive, MRI/EPRI-friendly procedure for flushing a female mouse bladder. It is also applicable to other imaging techniques, for example, PET, SPECT, etc., where contrast agent accumulation in the bladder is also undesirable. A double-lumen urethral catheter was developed, using a standard IV catheter with a silicone tube extension, having a polyethylene tube threaded into the IV catheter. Flushing of the bladder provides a substantial reduction in artifacts, as shown in images of tumors in mice.     

Phylogeny,niche conservatism and the latitudinal diversity gradient in mammals

Biologists have long searched for mechanisms responsible for the increase in species richness with decreasing latitude. The strong correlation between species richness and climate is frequently interpreted as reflecting a causal link via processes linked to energy or evolutionary rates. Here, we investigate how the aggregation of clades, as dictated by phylogeny, can give rise to significant climate–richness gradients without gradients in diversification or environmental carrying capacity. The relationship between climate and species richness varies considerably between clades, regions and time periods in a global-scale phylogenetically informed analysis of all terrestrial mammal species. Many young clades show negative richness–temperature slopes (more species at cooler temperatures), with the ages of these clades coinciding with the expansion of temperate climate zones in the late Eocene. In carnivores, we find steeply positive richness–temperature slopes in clades with restricted distributions and tropical origins (e.g. cat clade), whereas widespread, temperate clades exhibit shallow, negative slopes (e.g. dog–bear clade). We show that the slope of the global climate–richness gradient in mammals is driven by aggregating Chiroptera (bats) with their Eutherian sister group. Our findings indicate that the evolutionary history should be accounted for as part of any search for causal links between environment and species richness.     

Contribution of nematodes to the structure and function of the soil food web

As carbon and energy flow through the soil food web they are depleted by the metabolic and production functions of organisms. To be sustained, a "long" food web, with a large biomass at higher trophic levels, must receive a high rate of rhizodeposition or detrital subsidy, or be top-populated by organisms of slow growth and long life cycle. Disturbed soil food webs tend to be bottom heavy and recalcitrant to restoration due to the slow growth of upper predator populations, physical and chemical constraints of the soil matrix, biological imbalances, and the relatively low mobility and invasion potential of soil organisms. The functional roles of nematodes, determined by their metabolic and behavioral activities, may be categorized as ecosystem services, disservices or effect-neutral. Among the disservices attributable to nematodes are overgrazing, which diminishes services of prey organisms, and plant-damaging herbivory, which reduces carbon fixation and availability to other organisms in the food web. Unfortunately, management to ameliorate potential disservices of certain nematodes results in unintended but long-lasting diminution of the services of others. Beneficial roles of nematodes may be enhanced by environmental stewardship that fosters greater biodiversity and, consequently, complementarity and continuity of their services.     

Poly(A)-Binding Protein 1 Partially Relocalizes to the Nucleus during Herpes Simplex Virus Type 1 Infection in an ICP27-Independent Manner and Does Not Inhibit Virus Replication

Infection of cells by herpes simplex virus type 1 (HSV-1) triggers host cell shutoff whereby mRNAs are degraded and cellular protein synthesis is diminished. However, virus protein translation continues because the translational apparatus in HSV-infected cells is maintained in an active state. Surprisingly, poly(A)-binding protein 1 (PABP1), a predominantly cytoplasmic protein that is required for efficient translation initiation, is partially relocated to the nucleus during HSV-1 infection. This relocalization occurred in a time-dependent manner with respect to virus infection. Since HSV-1 infection causes cell stress, we examined other cell stress inducers and found that oxidative stress similarly relocated PABP1. An examination of stress-induced kinases revealed similarities in HSV-1 infection and oxidative stress activation of JNK and p38 mitogen-activated protein (MAP) kinases. Importantly, PABP relocalization in infection was found to be independent of the viral protein ICP27. The depletion of PABP1 by small interfering RNA (siRNA) knockdown had no significant effect on viral replication or the expression of selected virus late proteins, suggesting that reduced levels of cytoplasmic PABP1 are tolerated during infection.The lytic replication cycle of herpes simplex virus type 1 (HSV-1) can be divided into three phases, immediate-early (IE), early (E), and late (L), that occur in a coordinated sequential gene expression program. IE proteins can regulate E and L gene expression, which produces proteins involved in DNA replication, capsid production, and virion assembly. HSV infection results in host cell shutoff to facilitate the efficient production of viral proteins. First, mRNA is degraded by the virion-associated vhs protein, and then ICP27, a multifunctional regulator of gene expression, inhibits pre-mRNA splicing. As most viral mRNAs are intronless, this abrogates the production of stable cellular mRNAs that can be exported to the cytoplasm and compete for translation with viral mRNAs (44).HSV mRNAs are capped and polyadenylated and so are translated via a normal cap-dependent mechanism. Translation initiation, during which translationally active ribosomes are assembled, is a tightly regulated process (21). Eukaryotic initiation factor 4F (eIF4F) (composed of eIF4E, eIF4G, and eIF4A) that binds the cap at the 5′ end of the mRNA promotes the recruitment of the 40S ribosomal subunit and associated factors, including eIF2-GTP initiator tRNA. The recognition of the start codon then promotes large ribosomal subunit joining. Poly(A)-binding protein 1 (PABP1), which binds and multimerizes on mRNA poly(A) tails, enhances translation initiation through interactions with the eIF4G component of the eIF4F cap-binding complex (20, 29, 32, 51) to circularize the mRNA in a “closed-loop” conformation (24). Key protein-RNA and protein-protein interactions in the translation initiation complex are strengthened by this PABP1-mediated circularization (12).HSV-1 maintains active viral translation in the face of host translational shutoff. Infection activates protein kinase R (PKR), which phosphorylates eIF2α, resulting in translation inhibition. However, HSV-1 ICP34.5 redirects protein phosphatase 1α to reverse eIF2α phosphorylation, abrogating the block to translation (17, 38). In addition, the HSV-1 US11 protein inhibits PKR and may also block PKR-mediated eIF2α phosphorylation (40, 42). HSV-1 infection also enhances eIF4F assembly in quiescent cells by the phosphorylation and proteasome-mediated degradation of the eIF4E-binding protein (4E-BP), which, when hypophosphorylated, can negatively regulate eIF4F complex formation (54). However, ICP6 may also contribute to eIF4F assembly by binding to eIF4G (55). Finally, ICP6 is required for Mnk-1 phosphorylation of eIF4E, but the mechanisms behind this remain unclear (54). ICP27 has also been implicated in translation regulation during HSV infection (6, 8, 10, 30) and may also activate p38 mitogen-activated protein (MAP) kinase that can phosphorylate eIF4E (16, 59).PABP1 appears to be a common cellular target of RNA and DNA viruses. PABP1 can undergo proteolysis, intracellular relocalization, or modification of its interaction with other translation factors in response to infection. For example, poliovirus induces host cell shutoff by cleaving PABP1, thus disrupting certain PABP1-containing complexes (28, 29). The rotavirus NSP3 protein can displace PABP1 from translation initiation complexes (41). However, NSP3 also interacts with a cellular protein, RoXaN, which is required to relocate PABP1 to the nucleus (13). Similarly, the Kaposi''s sarcoma herpesvirus (KSHV) SOX protein plays a role in relocating PABP1, its cofactor in cellular mRNA decay, to the nucleus (33). Although steady-state levels of PABP1 are highest in the cytoplasm of normal cells, where it has cytoplasmic functions, it is a nucleocytoplasmic shuttling protein (1). However, it is unclear how PABP1 enters or exits the nucleus, as it contains neither a canonical nuclear export nor an import signal.Here we describe the loss of PABP1 from cap-binding complexes and the partial relocation of PABP1 to the nucleus in HSV-1-infected cells in a time-dependent manner. Relocation is specific for PABP1, as other translation factors remained in the cytoplasm. Cells undergo stress during HSV-1 infection, and analysis of a variety of cell stresses revealed that PABP relocalization was also observed upon oxidative stress. Paxillin, a potential PABP1 nuclear chaperone, was phosphorylated, and the paxillin-PABP1 interaction was reduced during virus infection. However, the interaction was weak and cell type dependent, indicating that other effectors of PABP1 relocation in the infected cell must exist. Recently, the HSV-1 ICP27 protein was suggested to alter the PABP1 cellular location (6). However, infections with ICP27-null mutant viruses clearly demonstrated that ICP27 is not required for PABP1 nuclear relocation in the context of infection. Although HSV-1 mRNAs are translated by a normal cap-dependent mechanism known to be enhanced by PABP1, small interfering RNA (siRNA) knockdown of PABP1 indicated that at late times of infection, the translation of certain virus late proteins tolerates very low levels of PABP1.