Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice

Nuclei of higher organisms are well structured and have multiple, distinct nuclear compartments or nuclear bodies. Paraspeckles are recently identified mammal-specific nuclear bodies ubiquitously found in most cells cultured in vitro. To investigate the physiological role of paraspeckles, we examined the in vivo expression patterns of two long noncoding RNAs, NEAT1_1 and NEAT1_2, which are essential for the architectural integrity of nuclear bodies. Unexpectedly, these genes were only strongly expressed in a particular subpopulation of cells in adult mouse tissues, and prominent paraspeckle formation was observed only in the cells highly expressing NEAT1_2. To further investigate the cellular functions of paraspeckles, we created an animal model lacking NEAT1 by gene targeting. These knockout mice were viable and fertile under laboratory growth conditions, showing no apparent phenotypes except for the disappearance of paraspeckles. We propose that paraspeckles are nonessential, subpopulation-specific nuclear bodies formed secondary to particular environmental triggers.     

PFPI-like genes are expressed in Leishmania major but are pseudogenes in other Leishmania species

Pyrococcus furiosus protease I (PFPI) is a multimeric cysteine peptidase from P. furiosus. Genome analyses indicate that orthologues are present in rather few other organisms, including Dictyostelium discoideum and several bacteria, Archaea and plants. An open reading frame (ORF) coding for a PFPI-like protein (PFP1) was identified in Leishmania major and Leishmania mexicana and full-length spliced and polyadenylated PFP1 mRNA detected for both species. Vestiges of a PFPI-like gene could also be identified in Leishmania braziliensis and Leishmania infantum, but no ORF remains owing to the presence of frame-shifts and stop codons. No evidence for a PFPI-like gene could be found in the syntenic region of Trypanosoma brucei or Trypanosoma cruzi, raising the possibility that the PFPI-like genes were acquired by a lateral gene transfer event after the divergence of trypanosomes and Leishmania. The gene may have subsequently degenerated into a pseudogene in some Leishmania species, owing to the loss of relevant biological function. However, antibodies raised against L. mexicana recombinant protein detected PFP1 in promastigote extracts of L. major, but not in L. mexicana promastigote or amastigote extracts. The expression of PFP1 in L. major suggests that PFP1 might contribute to the disease tropism that distinguishes this Leishmania species from others.     

Ideas are not replicators but minds are

An idea is not a replicator because it does not consist of coded self-assembly instructions. It may retain structure as it passes from one individual to another, but does not replicate it. The cultural replicator is not an idea but an associatively-structured network of them that together form an internal model of the world, or worldview. A worldview is a primitive, uncoded replicator, like the autocatalytic sets of polymers widely believed to be the earliest form of life. Primitive replicators generate self-similar structure, but because the process happens in a piecemeal manner, through bottom-up interactions rather than a top-down code, they replicate with low fidelity, and acquired characteristics are inherited. Just as polymers catalyze reactions that generate other polymers, the retrieval of an item from memory can in turn trigger other items, thus cross-linking memories, ideas, and concepts into an integrated conceptual structure. Worldviews evolve idea by idea, largely through social exchange. An idea participates in the evolution of culture by revealing certain aspects of the worldview that generated it, thereby affecting the worldviews of those exposed to it. If an idea influences seemingly unrelated fields this does not mean that separate cultural lineages are contaminating one another, because it is worldviews, not ideas, that are the basic unit of cultural evolution.     

液泡加工酶: 植物中具有胱天蛋白酶功能的蛋白酶

植物的液泡加工酶(VPE)是一类存在于液泡中的半胱氨酸蛋白酶家族,最近被发现与动物细胞的胱天蛋白酶(caspase)在调控细胞的PCD(细胞程序性死亡)方面具有相似性。文章综述了VPE调控植物细胞程序性死亡的研究进展,从结构、功能和作用机制方面讨论了液泡加工酶与胱天蛋白酶的相似性。     

NMDA receptors are movin' in

Dynamic modulation of the number of postsynaptic glutamate receptors is considered one of the main mechanisms for altering the strength of excitatory synapses in the central nervous system (CNS). However, until recently N-methyl-d-aspartate (NMDA) receptors were considered relatively stable once in the plasma membrane, especially in comparison with alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA) receptors that are internalized at a high rate. A series of recent studies has changed this viewpoint by revealing that NMDA receptors are subject to constitutive as well as agonist-induced internalization through clathrin-mediated endocytosis. Surprisingly, agonist-induced internalization is not dependent on current flow through the NMDA channel, and the receptors are primed for this type of internalization by selective stimulation of the glycine site but not of the glutamate site. Endocytosis of NMDA receptors provides a fundamental mechanism for dynamic regulation of the number of NMDA receptors at synapses, which might be important for physiological and pathological functioning of the CNS.     

Skeletal development--Wnts are in control

Approximately 200 individual skeletal elements, which differ in shape and size, are the building blocks of the vertebrate skeleton. Various features of the individual skeletal elements, such as their location, shape, growth and differentiation rate, are being determined during embryonic development. A few skeletal elements, such as the lateral halves of the clavicle and parts of the skull are formed by a process called intramembranous ossification, whereby mesenchymal cells differentiate directly into osteoblasts, while the majority of skeletal elements are formed via endochondral ossification. The latter process starts with the formation of a cartilaginous template, which eventually is being replaced by bone. This requires co-regulation of differentiation of the cell-types specific for cartilage and bone, chondrocytes and osteoblasts, respectively. In recent years it has been demonstrated that Wnt family members and their respective intracellular pathways, such as non-canonical and the canonical Wnt/beta-catenin pathway, play important and diverse roles during different steps of vertebrate skeletal development. Based on the recent discoveries modulation of the canonical Wnt-signaling pathway could be an interesting approach to direct stem cells into certain skeletal lineages.     

Predators are rare even when they are small

A recent review of published studies revealed that predators generally have lower population densities than non-predators in a variety of communities. We report here similar results for a highly replicated study of macroinvertebrates that colonized very uniform detrital microcosms in an old field. This pattern persisted even though predators usually were smaller than non-predators, as determined by body length and volume.     

Three of four pseudoknots in tmRNA are interchangeable and are substitutable with single-stranded RNAs

A novel translation, trans-translation, is facilitated by a highly structured RNA molecule, tmRNA. This molecule has two structural domains, a tRNA domain and an mRNA domain, the latter including four pseudoknot structures (PK1 to PK4). Here, we show that replacement of each of these pseudoknots, except PK1, in Escherichia coli tmRNA with a single stranded RNA did not seriously affect the functions as an alanine tRNA and as an mRNA. Furthermore, these three pseudoknots were interchangeable with only small losses of the two functions. These findings suggest that neither PK2, PK3 nor PK4 interacts in a functional manner with ribosome during the trans-translation process. Together with an earlier study showing the significance of PK1, it is concluded that among the four pseudoknots, PK1 is the most functional.     

Zeolites are effective ROS-scavengers in vitro

We report on the use of zeolites to limit the effects of reactive oxygen species (ROS) on human albumin under in vitro conditions. Zeolites of different structure type, channel size, channel polarity, and charge-compensating cation were screened for the elimination of ROS, notably HO, resulting from the Fenton reaction. A test based on ischemia-modified albumin (IMA) was used as a marker to monitor the activity of HO after co-exposure of human serum to these zeolites. Two commercial zeolites, faujasite (FAU 13×, channel opening 0.74 × 0.74 nm with Na⁺ as charge-compensating cation) and ferrierite (FER, channel opening 0.54 × 0.42 nm with H⁺ as charge-compensating cation), were found to reduce IMA formation by more than 65% due to removal of HO relative to reference values. It was established that partial ion exchange of the zeolites’ respective charge-compensating cation vs. Fe³⁺ implicated in the Fenton reaction plays a major role in HO deactivation process. Moreover, our results show that no saturation of the respective zeolite active sites occurred. This is possible only when ROS are actively converted to water molecules within the zeolite void system, which generates H⁺ ion transport.Because zeolites cannot be administered in blood, their use in medicine should be limited to extra corporeal circuits. Zeolites could be of use during cardiopulmonary bypass or hemodialysis procedures.     

Proteins are polyisoprenylated in Arabidopsis thaliana

Isoprenoid lipids were found to be covalently linked to proteins of Arabidopsis thaliana. Their identity (polyprenols: Prenol-9-11 with Pren-10 dominating and dolichols: Dol-15-17 with Dol-16 dominating) was confirmed by means of HPLC/ESI-MS with application of the multiple reaction monitoring technique as well as metabolic labeling of Arabidopsis plants with [³H]mevalonate and other precursors. The occurrence of typical farnesol-, geranylgeraniol-, and phytol-modified proteins was also noted. Radioisotopic labeling allowed detection of several proteins that were covalently bound to mevalonate-derived isoprenoid alcohols. A significant portion of polyisoprenylated proteins was recovered in the cytosolic/light vesicular fraction of Arabidopsis cells upon subfractionation. Taken together our data prove that a subset of plant proteins is polyisoprenylated.     

Animal cells in culture are microorganisms

Pick up any textbook with ‘Microbiology’ in the title and observe the scant to nonexistent treatment of animal cells in culture. Viruses do not suffer from such an exclusion. Chapters abound regaling the molecular niceties of the complex dances their components undergo while infecting bacteria or animal cells in culture. Indeed, it is normally in the latter sense only that any recognition is given to the existence of animal cells in culture. Such views pervade even the minds of those who initiate and direct activities of societies whoseraison d’être is the growth and exploitation of animal cells in culture. The author of this editorial was appointed to a Chair in Microbiology at the University of Surrey in 1983 and has worked on the growth and use of animal cells in culture continuously since 1970; he, therefore, had to reconcile his position in the university with his chosen calling. In this he was helped by undergraduates too numerous to mention who struggled mightily with essays which asked the question; are animal cells in culture microorganisms? What follows is a digest of their efforts and the views of the author.     

Postreproductive lifespans are rare in mammals

A species has a post‐reproductive stage if, like humans, a female entering the adult population can expect to live a substantial proportion of their life after their last reproductive event. However, it is conceptually and statistically challenging to distinguish these true post‐reproductive stages from the usual processes of senescence, which can result in females occasionally surviving past their last reproductive event. Hence, despite considerable interest, the taxonomic prevalence of post‐reproductive stages remains unclear and debated. In this study we use life tables constructed from published data on wild populations of mammals, and statistical measures of post‐reproductive lifespans, to distinguish true post‐reproductive stages from artefacts of senescence and demography in 52 species. We find post‐reproductive stages are rare in mammals and are limited to humans and a few species of toothed whales. By resolving this long‐standing debate, we hope to provide clarity for researchers in the field of evolutionary biology and a solid foundation for further studies investigating the evolution and adaptive significance of this unusual life history trait.     

Golgi enzymes are enriched in perforated zones of golgi cisternae but are depleted in COPI vesicles

In the most widely accepted version of the cisternal maturation/progression model of intra-Golgi transport, the polarity of the Golgi complex is maintained by retrograde transport of Golgi enzymes in COPI-coated vesicles. By analyzing enzyme localization in relation to the three-dimensional ultrastructure of the Golgi complex, we now observe that Golgi enzymes are depleted in COPI-coated buds and 50- to 60-nm COPI-dependent vesicles in a variety of different cell types. Instead, we find that Golgi enzymes are concentrated in the perforated zones of cisternal rims both in vivo and in a cell-free system. This lateral segregation of Golgi enzymes is detectable in some stacks during steady-state transport, but it was significantly prominent after blocking endoplasmic reticulum-to-Golgi transport. Delivery of transport carriers to the Golgi after the release of a transport block leads to a diminution in Golgi enzyme concentrations in perforated zones of cisternae. The exclusion of Golgi enzymes from COPI vesicles and their transport-dependent accumulation in perforated zones argues against the current vesicle-mediated version of the cisternal maturation/progression model.