Genome-wide survey and expression analysis of the bHLH-PAS genes in the amphioxus Branchiostoma floridae reveal both conserved and diverged expression patterns between cephalochordates and vertebrates

BACKGROUND: The bHLH-PAS transcription factors are found in both protostomes and deuterostomes. They are involved in many developmental and physiological processes, including regional differentiation of the central nervous system, tube-formation, hypoxia signaling, aromatic hydrocarbon sensing, and circadian rhythm regulation. To understand the evolution of these genes in chordates, we analyzed the bHLH-PAS genes of the basal chordate amphioxus (Branchiostoma floridae). RESULTS: From the amphioxus draft genome database, we identified ten bHLH-PAS genes, nine of which could be assigned to known orthologous families. The tenth bHLH-PAS gene could not be assigned confidently to any known bHLH family; however, phylogenetic analysis clustered this gene with arthropod Met family genes and two spiralian bHLH-PAS-containing sequences, suggesting that they may share the same ancestry. We examined temporal and spatial expression patterns of these bHLH-PAS genes in developing amphioxus embryos. We found that BfArnt, BfNcoa, BfSim, and BfHifα were expressed in the central nervous system in patterns similar to those of their vertebrate homologs, suggesting that their functions may be conserved. By contrast, the amphioxus BfAhr and BfNpas4 had expression patterns distinct from those in vertebrates. These results imply that there were changes in gene regulation after the divergence of cephalochordates and vertebrates. CONCLUSIONS: We have identified ten bHLH-PAS genes from the amphioxus genome and determined the embryonic expression profiles for these genes. In addition to the nine currently recognized bHLH-PAS families, our survey suggests that the BfbHLHPAS-orphan gene along with arthropod Met genes and the newly identified spiralian bHLH-PAS-containing sequences represent an ancient group of genes that were lost in the vertebrate lineage. In a comparison with the expression patterns of the vertebrate bHLH-PAS paralogs, which are the result of whole-genome duplication, we found that although several members seem to retain conserved expression patterns during chordate evolution, many duplicated paralogs may have undergone subfunctionalization and neofunctionalization in the vertebrate lineage. In addition, our survey of amphioxus bHLH-PAS gene models from genome browser with experimentally verified cDNA sequences calls into question the accuracy of the current in silico gene annotation of the B. floridae genome

Magnetic trapping of ultracold molecules at high density

Trapping ultracold molecules in conservative traps is essential for applications -- such as quantum state-controlled chemistry, quantum simulations, and quantum information processing. These applications require high densities or phase-space densities. We report magnetic trapping of NaLi molecules in the triplet ground state at high density ($\approx 10^{11} \; \rm{cm}^{-3}$) and ultralow temperature ($\approx 1\;{\rm \mu K}$). Magnetic trapping at these densities allows studies on both atom-molecule and molecule-molecule collisions in the ultracold regime in the absence of trapping light, which has often lead to undesired photo-chemistry. We measure the inelastic loss rates in a single spin sample and spin-mixtures of fermionic NaLi as well as spin-stretched NaLi$+$Na mixtures. We demonstrate sympathetic cooling of NaLi molecules in the magnetic trap by radio frequency evaporation of co-trapped Na atoms and observe an increase in the molecules' phase-space density by a factor of $\approx 16$.Comment: 8 pages, 4 figure

Tris(piperazinediium) phosphatododeca­molybo(V,VI)phosphate

The title compound, (C4H12N2)3[PMo12O40] or (H2pip)3[PMo12O40] (pip is piperazine), was prepared under hydro­thermal conditions. The asymmetric unit contains one-sixth of a mixed-valent Mo(V,VI) pseudo-Keggin-type [PMo12O40]6− anion and half a piperazinediium cation, (H2pip)2+. The discrete Keggin-type [PMo12O40]6- anion has site symmetry and the three (H2pip)2+ cations each have site symmetry at the centres of the mol­ecules. The central P atom is on special position , which is a roto-inversion position and generates the disorder of the PO4 tetra­hedron. Furthermore, six doubly bridging oxide groups are also disordered with an occupancy factor of 0.5 for each O atom. The anions and cations are linked by an extensive network of inter­molecular N—H⋯O and C—H⋯O hydrogen bonds