Identification and classification of 16 new kinesin superfamily (KIF) proteins in mouse genome

KIF (kinesin superfamily) proteins are microtubule-dependent molecular motors that play important roles in intracellular transport and cell division. The extent to which KIFs are involved in various transporting phenomena, as well as their regulation mechanism, are unknown. The identification of 16 new KIFs in this report doubles the existing number of KIFs known in the mouse. Conserved nucleotide sequences in the motor domain were amplified by PCR using cDNAs of mouse nervous tissue, kidney, and small intestine as templates. The new KIFs were studied with respect to their expression patterns in different tissues, chromosomal location, and molecular evolution. Our results suggest that (i) there is no apparent tendency among related subclasses of KIFs of cosegregation in chromosomal mapping, and (ii) according to their tissue distribution patterns, KIFs can be divided into two classes–i.e., ubiquitous and specific tissue-dominant. Further characterization of KIFs may elucidate unknown fundamental phenomena underlying intracellular transport. Finally, we propose a straightforward nomenclature system for the members of the mouse kinesin superfamily.

Australian lungfish neurohypophysial hormone genes encode vasotocin and [Phe2]mesotocin precursors homologous to tetrapod-type precursors

In view of the well-established role of neurohypophysial hormones in osmoregulation of terrestrial vertebrates, lungfishes are a key group for study of the molecular and functional evolution of the hypothalamo-neurohypophysial system. Here we report on the primary structure of the precursors encoding vasotocin (VT) and [Phe2]mesotocin ([Phe2]MT) of the Australian lungfish, Neoceratodus forsteri. Genomic sequence analysis and Northern blot analysis confirmed that [Phe2]MT is a native oxytocin family peptide in the Australian lungfish, although it has been reported that the lungfish neurohypophysis contains MT. The VT precursor consists of a signal peptide, VT, that is connected to a neurophysin by a Gly-Lys-Arg sequence, and a copeptin moiety that includes a Leu-rich core segment and a glycosylation site. In contrast, the [Phe2]MT precursor does not contain a copeptin moiety. These structural features of the lungfish precursors are consistent with those in tetrapods, but different from those in teleosts where both VT and isotocin precursors contain a copeptin-like moiety without a glycosylation site at the carboxyl terminals of their neurophysins. Comparison of the exon/intron organization also supports homology of the lungfish [Phe2]MT gene with tetrapod oxytocin/MT genes, rather than with teleost isotocin genes. Moreover, molecular phylogenetic analysis shows that neurohypophysial hormone genes of the lungfish are closely related to those of the toad. The present results along with previous morphological findings indicate that the hypothalamo-neurohypophysial system of the lungfish has evolved along the tetrapod lineage, whereas the teleosts form a separate lineage, both within the class Osteichthyes.

Antigen-driven CD4+ T cell and HIV-1 dynamics: Residual viral replication under highly active antiretroviral therapy

Antigen-induced stimulation of the immune system can generate heterogeneity in CD4+ T cell division rates capable of explaining the temporal patterns seen in the decay of HIV-1 plasma RNA levels during highly active antiretroviral therapy. Posttreatment increases in peripheral CD4+ T cell counts are consistent with a mathematical model in which host cell redistribution between lymph nodes and peripheral blood is a function of viral burden. Model fits to patient data suggest that, although therapy reduces HIV replication below replacement levels, substantial residual replication continues. This residual replication has important consequences for long-term therapy and the evolution of drug resistance and represents a challenge for future treatment strategies.

RNA-peptide fusions for the in vitro selection of peptides and proteins

Covalent fusions between an mRNA and the peptide or protein that it encodes can be generated by in vitro translation of synthetic mRNAs that carry puromycin, a peptidyl acceptor antibiotic, at their 3′ end. The stable linkage between the informational (nucleic acid) and functional (peptide) domains of the resulting joint molecules allows a specific mRNA to be enriched from a complex mixture of mRNAs based on the properties of its encoded peptide. Fusions between a synthetic mRNA and its encoded myc epitope peptide have been enriched from a pool of random sequence mRNA-peptide fusions by immunoprecipitation. Covalent RNA-peptide fusions should provide an additional route to the in vitro selection and directed evolution of proteins.

An ancestral MADS-box gene duplication occurred before the divergence of plants and animals

Changes in genes encoding transcriptional regulators can alter development and are important components of the molecular mechanisms of morphological evolution. MADS-box genes encode transcriptional regulators of diverse and important biological functions. In plants, MADS-box genes regulate flower, fruit, leaf, and root development. Recent sequencing efforts in Arabidopsis have allowed a nearly complete sampling of the MADS-box gene family from a single plant, something that was lacking in previous phylogenetic studies. To test the long-suspected parallel between the evolution of the MADS-box gene family and the evolution of plant form, a polarized gene phylogeny is necessary. Here we suggest that a gene duplication ancestral to the divergence of plants and animals gave rise to two main lineages of MADS-box genes: TypeI and TypeII. We locate the root of the eukaryotic MADS-box gene family between these two lineages. A novel monophyletic group of plant MADS domains (AGL34 like) seems to be more closely related to previously identified animal SRF-like MADS domains to form TypeI lineage. Most other plant sequences form a clear monophyletic group with animal MEF2-like domains to form TypeII lineage. Only plant TypeII members have a K domain that is downstream of the MADS domain in most plant members previously identified. This suggests that the K domain evolved after the duplication that gave rise to the two lineages. Finally, a group of intermediate plant sequences could be the result of recombination events. These analyses may guide the search for MADS-box sequences in basal eukaryotes and the phylogenetic placement of new genes from other plant species.

Modification of Carbon Partitioning, Photosynthetic Capacity, and O2 Sensitivity in Arabidopsis Plants with Low ADP-Glucose Pyrophosphorylase Activity1

Wild-type Arabidopsis plants, the starch-deficient mutant TL46, and the near-starchless mutant TL25 were evaluated by noninvasive in situ methods for their capacity for net CO2 assimilation, true rates of photosynthetic O2 evolution (determined from chlorophyll fluorescence measurements of photosystem II), partitioning of photosynthate into sucrose and starch, and plant growth. Compared with wild-type plants, the starch mutants showed reduced photosynthetic capacity, with the largest reduction occurring in mutant TL25 subjected to high light and increased CO2 partial pressure. The extent of stimulation of CO2 assimilation by increasing CO2 or by reducing O2 partial pressure was significantly less for the starch mutants than for wild-type plants. Under high light and moderate to high levels of CO2, the rates of CO2 assimilation and O2 evolution and the percentage inhibition of photosynthesis by low O2 were higher for the wild type than for the mutants. The relative rates of 14CO2 incorporation into starch under high light and high CO2 followed the patterns of photosynthetic capacity, with TL46 showing 31% to 40% of the starch-labeling rates of the wild type and TL25 showing less than 14% incorporation. Overall, there were significant correlations between the rates of starch synthesis and CO2 assimilation and between the rates of starch synthesis and cumulative leaf area. These results indicate that leaf starch plays an important role as a transient reserve, the synthesis of which can ameliorate any potential reduction in photosynthesis caused by feedback regulation.

Signals and signs in the nervous system: The dynamic anatomy of electrical activity is probably information-rich

The dichotomy between two groups of workers on neuroelectrical activity is retarding progress. To study the interrelations between neuronal unit spike activity and compound field potentials of cell populations is both unfashionable and technically challenging. Neither of the mutual disparagements is justified: that spikes are to higher functions as the alphabet is to Shakespeare and that slow field potentials are irrelevant epiphenomena. Spikes are not the basis of the neural code but of multiple codes that coexist with nonspike codes. Field potentials are mainly information-rich signs of underlying processes, but sometimes they are also signals for neighboring cells, that is, they exert influence. This paper concerns opportunities for new research with many channels of wide-band (spike and slow wave) recording. A wealth of structure in time and three-dimensional space is different at each scale—micro-, meso-, and macroactivity. The depth of our ignorance is emphasized to underline the opportunities for uncovering new principles. We cannot currently estimate the relative importance of spikes and synaptic communication vs. extrasynaptic graded signals. In spite of a preponderance of literature on the former, we must consider the latter as probably important. We are in a primitive stage of looking at the time series of wide-band voltages in the compound, local field, potentials and of choosing descriptors that discriminate appropriately among brain loci, states (functions), stages (ontogeny, senescence), and taxa (evolution). This is not surprising, since the brains in higher species are surely the most complex systems known. They must be the greatest reservoir of new discoveries in nature. The complexity should not deter us, but a dose of humility can stimulate the flow of imaginative juices.

Toward a plant genomics initiative: Thoughts on the value of cross-species and cross-genera comparisons in the grasses

Comparative genomics offers unparalleled opportunities to integrate historically distinct disciplines, to link disparate biological kingdoms, and to bridge basic and applied science. Cross-species, cross-genera, and cross-kingdom comparisons are proving key to understanding how genes are structured, how gene structure relates to gene function, and how changes in DNA have given rise to the biological diversity on the planet. The application of genomics to the study of crop species offers special opportunities for innovative approaches for combining sequence information with the vast reservoirs of historical information associated with crops and their evolution. The grasses provide a particularly well developed system for the development of tools to facilitate comparative genetic interpretation among members of a diverse and evolutionarily successful family. Rice provides advantages for genomic sequencing because of its small genome and its diploid nature, whereas each of the other grasses provides complementary genetic information that will help extract meaning from the sequence data. Because of the importance of the cereals to the human food chain, developments in this area can lead directly to opportunities for improving the health and productivity of our food systems and for promoting the sustainable use of natural resources.

Oceanic minerals: Their origin, nature of their environment, and significance

The chemical and isotopic compositions of oceanic biogenic and authigenic minerals contain invaluable information on the evolution of seawater, hence on the history of interaction between tectonics, climate, ocean circulation, and the evolution of life. Important advances and greater understanding of (a) key minor and trace element cycles with various residence times, (b) isotopic sources and sinks and fractionation behaviors, and (c) potential diagenetic problems, as well as developments in high-precision instrumentation, recently have been achieved. These advances provided new compelling evidence that neither gradualism nor uniformitarianism can explain many of the new important discoveries obtained from the chemistry and isotopic compositions of oceanic minerals. Presently, the best-developed geochemical proxies in biogenic carbonates are 18O/16O and Sr/Ca ratios (possibly Mg/Ca) for temperature; 87Sr/86Sr for input sources, Cd/Ca and Ba/Ca ratios for phosphate and alkalinity concentrations, respectively, thus also for ocean circulation; 13C/12C for ocean productivity; B isotopes for seawater pH;, U, Th isotopes, and 14C for dating; and Sr and Mn concentrations for diagenesis. The oceanic authigenic minerals most widely used for chemical paleoceanography are barite, evaporite sulfates, and hydrogenous ferromanganese nodules. Marine barite is an effective alternative monitor of seawater 87Sr/86Sr, especially where carbonates are diagenetically altered or absent. It also provides a high-resolution record of seawater sulfate S isotopes, (evaporite sulfates only carry an episodic record), with new insights on factors affecting the S and C cycles and atmospheric oxygen. High-resolution studies of Sr, Nd, and Pb isotopes of well-dated ferromanganese nodules contain invaluable records on climate driven changes in oceanic circulation.

Complexity, contingency, and criticality.

Complexity originates from the tendency of large dynamical systems to organize themselves into a critical state, with avalanches or "punctuations" of all sizes. In the critical state, events which would otherwise be uncoupled become correlated. The apparent, historical contingency in many sciences, including geology, biology, and economics, finds a natural interpretation as a self-organized critical phenomenon. These ideas are discussed in the context of simple mathematical models of sandpiles and biological evolution. Insights are gained not only from numerical simulations but also from rigorous mathematical analysis.

Breaking the silence ceiling: how gender violence became into a social problem in Spain through media and politics

This research presents the explanatory model of the process of reconstruction of the ʺsocial problemʺ of Intimate Partner Violence (I.P.V) in Spain during last five years, with special attention to the role of media in this process. Using a content analysis of the three more diffused general newspapers, a content analysis of the minutes of the Parliament, and the statistics of the police reports and murders, from January of 1997 to December of 2001, it observes the relationship between the evolution of the incidence of Intimate Partner Violence (I.P.V) (measured by the number of deaths and the number of police reports) and the evolution of stories about this topic in press. It also studies the interconnection of the two previous variables with the political answer to the problem (measured by the interventions on the I.P.V. in the Senate and in the Congress). Data shows that, even though police reports have increased due to the contribution of politics and media, I.P.V murders keep on growing up.

Triassic redbeds in the Malaguide Complex (Betic Cordillera — Spain): petrography, geochemistry and geodynamic implications

Sandstone petrography and mudstone mineralogy and geochemistry of Triassic mudstones and sandstones from continental redbeds of the Malaguide Complex (Betic Cordillera, southern Spain) provide useful information on provenance, palaeoclimate and geodynamics during the early stages of the Pangea break-up, and on their diagenetic evolution. The sandstones are quartzarenites to sub-litharenites, with minor lithic fragments and rare feldspars. The mudstone samples show a PAAS like elemental distribution. The samples likely record recycling processes from their metasedimentary basement rocks that significantly affected the weathering indices, and monitors cumulative effects, including a first cycle of weathering at the source rocks. Sandstone composition and chemical–mineralogical features of mudstones record a provenance derived from continental block and recycled orogen that were weathered under warm and episodically wet climate. Source areas were located towards the east of the present-day Malaguide outcrops, and were formed by fairly silicic rock types, made up mainly of Palaezoic metasedimentary rocks, similar to those of the Paleozoic underlying series, with subordinate contributions from magmatic–metamorphic sources, and a rare supply from mafic metavolcanic rocks. Clay-mineral distribution of mudstones is dominated by illite and illite/smectite mixed-layer that result from differences in provenance, weathering, and burial/temperature history. Illite crystallinity values, illitization of kaolinite, occurrence of typical authigenic minerals and apatite fission-track studies, coupled with a subsidence analysis of the whole Malaguide succession suggest burial depths of at least 4–6 km with temperatures of 140–160 °C, typical of the burial diagenetic stage, and confirm the Middle Miocene exhumation of the Betic Internal Domain tectonic stack topped by the Malaguide Complex.

The imprint of the crustal magnetic field on the thermal spectra and pulse profiles of isolated neutron stars

Isolated neutron stars (NSs) show a bewildering variety of astrophysical manifestations, presumably shaped by the magnetic field strength and topology at birth. Here, using state-of-the-art calculations of the coupled magnetic and thermal evolution of NSs, we compute the thermal spectra and pulse profiles expected for a variety of initial magnetic field configurations. In particular, we contrast models with purely poloidal magnetic fields to models dominated by a strong internal toroidal component. We find that, while the former displays double-peaked profiles and very low pulsed fractions, in the latter, the anisotropy in the surface temperature produced by the toroidal field often results in a single pulse profile, with pulsed fractions that can exceed the 50–60 per cent level even for perfectly isotropic local emission. We further use our theoretical results to generate simulated ‘observed’ spectra, and show that blackbody (BB) fits result in inferred radii that can be significantly smaller than the actual NS radius, even as low as ∼1–2 km for old NSs with strong internal toroidal fields and a high absorption column density along their line of sight. We compute the size of the inferred BB radius for a few representative magnetic field configurations, NS ages and magnitudes of the column density. Our theoretical results are of direct relevance to the interpretation of X-ray observations of isolated NSs, as well as to the constraints on the equation of state of dense matter through radius measurements.

Feedbacks between vegetation pattern and resource loss dramatically decrease ecosystem resilience and restoration potential in a simple dryland model

Conceptual frameworks of dryland degradation commonly include ecohydrological feedbacks between landscape spatial organization and resource loss, so that decreasing cover and size of vegetation patches result in higher water and soil losses, which lead to further vegetation loss. However, the impacts of these feedbacks on dryland dynamics in response to external stress have barely been tested. Using a spatially-explicit model, we represented feedbacks between vegetation pattern and landscape resource loss by establishing a negative dependence of plant establishment on the connectivity of runoff-source areas (e.g., bare soils). We assessed the impact of various feedback strengths on the response of dryland ecosystems to changing external conditions. In general, for a given external pressure, these connectivity-mediated feedbacks decrease vegetation cover at equilibrium, which indicates a decrease in ecosystem resistance. Along a gradient of gradual increase of environmental pressure (e.g., aridity), the connectivity-mediated feedbacks decrease the amount of pressure required to cause a critical shift to a degraded state (ecosystem resilience). If environmental conditions improve, these feedbacks increase the pressure release needed to achieve the ecosystem recovery (restoration potential). The impact of these feedbacks on dryland response to external stress is markedly non-linear, which relies on the non-linear negative relationship between bare-soil connectivity and vegetation cover. Modelling studies on dryland vegetation dynamics not accounting for the connectivity-mediated feedbacks studied here may overestimate the resistance, resilience and restoration potential of drylands in response to environmental and human pressures. Our results also suggest that changes in vegetation pattern and associated hydrological connectivity may be more informative early-warning indicators of dryland degradation than changes in vegetation cover.

Self-heating and deicing conductive cement. Experimental study and modeling

This research studies the self-heating produced by the application of an electric current to conductive cement pastes with carbonaceous materials. The main parameters studied were: type and percentage of carbonaceous materials, effect of moisture, electrical resistance, power consumption, maximum temperature reached and its evolution and ice melting kinetics are the main parameters studied. A mathematical model is also proposed, which predicts that the degree of heating is adjustable with the applied voltage. Finally, the results have been applied to ensure that cementitious materials studied are feasible to control ice layers in transportation infrastructures.