Hsp70 sequences indicate that choanoflagellates are closely related to animals

AbstractOver 130 years ago, James-Clark [1, 2] noted a remarkable structural similarity between the feeding cells of sponges (choanocytes) and a group of free-living protists, the choanoflagellates. Both cell types possess a single flagellum surrounded by a collar of fine tentacles [3]. The similarity led to the hypothesis that sponges, and, by implication, other animals, evolved from choanoflagellate-like ancestors. Phylogenetic analysis of ribosomal DNA neither supports nor refutes this hypothesis [4–6]. Here, we report the sequence of an hsp70 gene and pseudogene from the freshwater choanoflagellate Monosiga ovata. These represent the first nuclear-encoded protein-coding sequences reported for any choanoflagellate. We find that Monosiga and most bilaterian hsp70 genes have high GC contents that may distort phylogenetic tree construction; therefore, protein sequences were used for phylogenetic reconstruction. Our analyses indicate that Monosiga is more closely related to animals than to fungi. We infer that animals and at least some choanoflagellates are part of a clade that excludes the fungi. This is consistent with the origin of animals from a choanoflagellate-like ancestor

Partially Adaptive STAP Algorithm Approaches to Functional MRI

In this work, the architectures of three partially adaptive STAP algorithms are introduced, one of which is explored in detail, that reduce dimensionality and improve tractability over fully adaptive STAP when used in construction of brain activation maps in fMRI. Computer simulations incorporating actual MRI noise and human data analysis indicate that element space partially adaptive STAP can attain close to the performance of fully adaptive STAP while significantly decreasing processing time and maximum memory requirements, and thus demonstrates potential in fMRI analysis

Parameter identifiability in a class of random graph mixture models

We prove identifiability of parameters for a broad class of random graph mixture models. These models are characterized by a partition of the set of graph nodes into latent (unobservable) groups. The connectivities between nodes are independent random variables when conditioned on the groups of the nodes being connected. In the binary random graph case, in which edges are either present or absent, these models are known as stochastic blockmodels and have been widely used in the social sciences and, more recently, in biology. Their generalizations to weighted random graphs, either in parametric or non-parametric form, are also of interest in many areas. Despite a broad range of applications, the parameter identifiability issue for such models is involved, and previously has only been touched upon in the literature. We give here a thorough investigation of this problem. Our work also has consequences for parameter estimation. In particular, the estimation procedure proposed by Frank and Harary for binary affiliation models is revisited in this article

Global impacts of energy demand on the freshwater resources of nations

The growing geographic disconnect between consumption of goods, the extraction and processing of resources, and the environmental impacts associated with production activities makes it crucial to factor global trade into sustainability assessments. Using an empirically validated environmentally extended global trade model, we examine the relationship between two key resources underpinning economies and human well-being—energy and freshwater. A comparison of three energy sectors (petroleum, gas, and electricity) reveals that freshwater consumption associated with gas and electricity production is largely confined within the territorial boundaries where demand originates. This finding contrasts with petroleum, which exhibits a varying ratio of territorial to international freshwater consumption, depending on the origin of demand. For example, although the United States and China have similar demand associated with the petroleum sector, international freshwater consumption is three times higher for the former than the latter. Based on mapping patterns of freshwater consumption associated with energy sectors at subnational scales, our analysis also reveals concordance between pressure on freshwater resources associated with energy production and freshwater scarcity in a number of river basins globally. These energy-driven pressures on freshwater resources in areas distant from the origin of energy demand complicate the design of policy to ensure security of fresh water and energy supply. Although much of the debate around energy is focused on greenhouse gas emissions, our findings highlight the need to consider the full range of consequences of energy production when designing policy

TREX exposes the RNA binding domain of Nxf1 to enable mRNA export

The metazoan TREX complex is recruited to mRNA during nuclear RNA processing and functions in exporting mRNA to the cytoplasm. Nxf1 is an mRNA export receptor, which binds processed mRNA and transports it through the nuclear pore complex. At present, the relationship between TREX and Nxf1 is not understood. Here we show that Nxf1 uses an intramolecular interaction to inhibit its own RNA binding activity. When the TREX subunits Aly and Thoc5 make contact with Nxf1, Nxf1 is driven into an open conformation, exposing its RNA binding domain, allowing RNA binding. Moreover, the combined knockdown of Aly and Thoc5 drastically reduces the amount of Nxf1 bound to mRNA in vivo and also causes a severe mRNA export block. Together, our data indicate that TREX provides a license for mRNA export by driving Nxf1 into a conformation capable of binding mRNA

TiF1-Gamma Plays an Essential Role in Murine Hematopoiesis and Regulates Transcriptional Elongation of Erythroid Genes

Transcriptional regulators play critical roles in the regulation of cell fate during hematopoiesis. Previous studies in zebrafish have identified an essential role for the transcriptional intermediary factor TIF1γ in erythropoiesis by regulating the transcription elongation of erythroid genes. To study if TIF1γ plays a similar role in murine erythropoiesis and to assess its function in other blood lineages, we generated mouse models with hematopoietic deletion of TIF1γ. Our results showed a block in erythroid maturation in the bone marrow following tif1γ deletion that was compensated with enhanced spleen erythropoiesis. Further analyses revealed a defect in transcription elongation of erythroid genes in the bone marrow. In addition, loss of TIF1γ resulted in defects in other blood compartments, including a profound loss of B cells, a dramatic expansion of granulocytes and decreased HSC function. TIF1γ exerts its functions in a cell-autonomous manner as revealed by competitive transplantation experiments. Our study therefore demonstrates that TIF1γ plays essential roles in multiple murine blood lineages and that its function in transcription elongation is evolutionally conserved.Stem Cell and Regenerative Biolog

Photoelectron angular distributions from rotationally resolved autoionizing states of N2

The single-photon, photoelectron-photoion coincidence spectrum of N2 has been recorded at high (~1.5 cm–1 ) resolution in the region between the N2+ X 2Σg+, v+ = 0 and 1 ionization thresholds by using a double-imaging spectrometer and intense vacuum-ultraviolet light from the Synchrotron SOLEIL. This approach provides the relative photoionization cross section, the photoelectron energy distribution, and the photoelectron angular distribution as a function of photon energy. The region of interest contains autoionizing valence states, vibrationally autoionizing Rydberg states converging to vibrationally excited levels of the N2+ X 2Σg+ ground state, and electronically autoionizing states converging to the N2+ A 2Π and B 2Σu+ states. The wavelength resolution is sufficient to resolve rotational structure in the autoionizing states, but the electron energy resolution is insufficient to resolve rotational structure in the photoion spectrum. A simplified approach based on multichannel quantum defect theory is used to predict the photoelectron angular distribution parameters, β, and the results are in reasonably good agreement with experiment

Photoelectron angular distributions from rotationally resolved autoionizing states of N2

The single-photon, photoelectron-photoion coincidence spectrum of N2 has been recorded at high (~1.5 cm–1 ) resolution in the region between the N2+ X 2Σg+, v+ = 0 and 1 ionization thresholds by using a double-imaging spectrometer and intense vacuum-ultraviolet light from the Synchrotron SOLEIL. This approach provides the relative photoionization cross section, the photoelectron energy distribution, and the photoelectron angular distribution as a function of photon energy. The region of interest contains autoionizing valence states, vibrationally autoionizing Rydberg states converging to vibrationally excited levels of the N2+ X 2Σg+ ground state, and electronically autoionizing states converging to the N2+ A 2Π and B 2Σu+ states. The wavelength resolution is sufficient to resolve rotational structure in the autoionizing states, but the electron energy resolution is insufficient to resolve rotational structure in the photoion spectrum. A simplified approach based on multichannel quantum defect theory is used to predict the photoelectron angular distribution parameters, β, and the results are in reasonably good agreement with experiment

Genomic Scans across Three Eucalypts Suggest that Adaptation to Aridity is a Genome-Wide Phenomenon

Widespread species spanning strong environmental (e.g., climatic) gradients frequently display morphological and physiological adaptations to local conditions. Some adaptations are common to different species that occupy similar environments. However, the genomic architecture underlying such convergent traits may not be the same between species. Using genomic data from previous studies of three widespread eucalypt species that grow along rainfall gradients in southern Australia, our probabilistic approach provides evidence that adaptation to aridity is a genome-wide phenomenon, likely to involve multiple and diverse genes, gene families and regulatory regions that affect a multitude of complex genetic and biochemical processes