Intercomparing drifts from eddy-resolving and cycling floats in the deep western boundary current along the Mid-Atlanic Ridge

The Lagrangian nature of cycling floats is evaluated in the framework defined by the Deep Western Boundary Current of the Mid-Atlantic Ridge. In a statistical approach, speeds and drifts are estimated for an APEX cycling float and compared with the velocities inferred from a park ensemble of four eddy-resolving RAFOS floats. They were deployed at the same location and ballasted for drifting at the same mission depth. Displacement errors induced by geostrophic shear and wind forced currents are analyzed. We observe that the velocity estimated from the RAFOS floats is not statistically different from the velocity estimated from the APEX float. Likewise, the initial separation between the cycling float and a simultaneously deployed RAFOS float has been studied in terms of the turbulent diffusivity. Though the performance of this study in comparable cases without a mean current field may be limited, these oceanic observations support exploiting the Lagrangian nature of the cycling floats

On the Atomic Photoeffect in Non-relativistic QED

In this paper we present a mathematical analysis of the photoelectric effect for one-electron atoms in the framework of non-relativistic QED. We treat photo-ionization as a scattering process where in the remote past an atom in its ground state is targeted by one or several photons, while in the distant future the atom is ionized and the electron escapes to spacial infinity. Our main result shows that the ionization probability, to leading order in the fine-structure constant, $\alpha$, is correctly given by formal time-dependent perturbation theory, and, moreover, that the dipole approximation produces an error of only sub-leading order in $\alpha$. In this sense, the dipole approximation is rigorously justified.Comment: 25 page

The Needle Component of the Type III Secreton of Shigella Regulates the Activity of the Secretion Apparatus

Gram-negative bacteria commonly interact with eukaryotic host cells by using type III secretion systems (TTSSs or secretons). TTSSs serve to transfer bacterial proteins into host cells. Two translocators, IpaB and IpaC, are first inserted with the aid of IpaD by Shigella into the host cell membrane. Then at least two supplementary effectors of cell invasion, IpaA and IpgD, are transferred into the host cytoplasm. How TTSSs are induced to secrete is unknown, but their activation appears to require direct contact of the external distal tip of the apparatus with the host cell. The extracellular domain of the TTSS is a hollow needle protruding 60 nm beyond the bacterial surface. The monomeric unit of the Shigella flexneri needle, MxiH, forms a superhelical assembly. To probe the role of the needle in the activation of the TTSS for secretion, we examined the structure-function relationship of MxiH by mutagenesis. Most point mutations led to normal needle assembly, but some led to polymerization or possible length control defects. In other mutants, secretion was constitutively turned “on.” In a further set, it was “constitutively on” but experimentally “uninducible.” Finally, upon induction of secretion, some mutants released only the translocators and not the effectors. Most types of mutants were defective in interactions with host cells. Together, these data indicate that the needle directly controls the activity of the TTSS and suggest that it may be used to “sense” host cells

HP1 drives de novo 3D genome reorganization in early Drosophila embryos

Fundamental features of 3D genome organization are established de novo in the early embryo, including clustering of pericentromeric regions, the folding of chromosome arms and the segregation of chromosomes into active (A-) and inactive (B-) compartments. However, the molecular mechanisms that drive de novo organization remain unknown. Here, by combining chromosome conformation capture (Hi-C), chromatin immunoprecipitation with high-throughput sequencing (ChIP–seq), 3D DNA fluorescence in situ hybridization (3D DNA FISH) and polymer simulations, we show that heterochromatin protein 1a (HP1a) is essential for de novo 3D genome organization during Drosophila early development. The binding of HP1a at pericentromeric heterochromatin is required to establish clustering of pericentromeric regions. Moreover, HP1a binding within chromosome arms is responsible for overall chromosome folding and has an important role in the formation of B-compartment regions. However, depletion of HP1a does not affect the A-compartment, which suggests that a different molecular mechanism segregates active chromosome regions. Our work identifies HP1a as an epigenetic regulator that is involved in establishing the global structure of the genome in the early embryo

A quasi-synoptic survey of the thermocline circulation and water mass distribution within the Canary Basin

Shipboard hydrographic measurements and moored current meters are used to infer both the large-scale and mesoscale water mass distribution and features of the general circulation in the Canary Basin. We found a convoluted current system dominated by the time-dependent meandering of the eastward flowing Azores Current and the formation of mesoscale eddies. At middepths, several distinctly different water masses are identified: Subpolar Mode and Labrador Sea Water are centered in the northwest, Subantarctic Intermediate Water is centered in the southeast, and the saltier, warmer Mediterranean tongue lies between them. Mesoscale structures of these water masses suggest the presence of middepth meanders and detached eddies which may be caused by fluctuations of the Azores Current

Inferring and perturbing cell fate regulomes in human brain organoids

Self-organizing neural organoids grown from pluripotent stem cells(1-3) combined with single-cell genomic technologies provide opportunities to examine gene regulatory networks underlying human brain development. Here we acquire single-cell transcriptome and accessible chromatin data over a dense time course in human organoids covering neuroepithelial formation, patterning, brain regionalization and neurogenesis, and identify temporally dynamic and brain-region-specific regulatory regions. We developed Pando-a flexible framework that incorporates multi-omic data and predictions of transcription-factor-binding sites to infer a global gene regulatory network describing organoid development. We use pooled genetic perturbation with single-cell transcriptome readout to assess transcription factor requirement for cell fate and state regulation in organoids. We find that certain factors regulate the abundance of cell fates, whereas other factors affect neuronal cell states after differentiation. We show that the transcription factor GLI3 is required for cortical fate establishment in humans, recapitulating previous research performed in mammalian model systems. We measure transcriptome and chromatin accessibility in normal or GLI3-perturbed cells and identify two distinct GLI3 regulomes that are central to telencephalic fate decisions: one regulating dorsoventral patterning with HES4/5 as direct GLI3 targets, and one controlling ganglionic eminence diversification later in development. Together, we provide a framework for how human model systems and single-cell technologies can be leveraged to reconstruct human developmental biology

Recent changes in the surface salinity of the North Atlantic subpolar gyre

Sea surface salinity (SSS) was measured since 1896 along 60°N between Greenland and the North Sea and since 1993 between Iceland and Newfoundland. Along 60°N away from the shelves, and north of 53°N, the amplitude of the seasonal cycle is comparable to or less than interannual variability. In these parts of the North Atlantic subpolar gyre, large-scale deviations from the seasonal cycle correlate from one season to the next. This suggests that in these regions, summer and autumn surface data are useful for monitoring changes in upper ocean salinity best diagnosed from less common winter surface data. Further south near the subarctic front, the Labrador Current or near shelves where seasonal variability is strong, this is not the case. Along 60°N, the multiannual low-frequency variability is well correlated across the basin and exhibits fresher surface water since the mid 1970s than in the late 1920s to 1960s. SSS in the Irminger Sea along 60°N lags by 1-year SSS farther east in the Iceland Basin. Variability between Iceland and Newfoundland within the Irminger Sea north of 54°N presents similar characteristics to what is observed along 60°N. Variability near the northwest corner of the North Atlantic Current (52°N/45°W) is larger and is not correlated to what is found further north. Maps of SSS were constructed for a few recent seasons between July 1996 and June 2000, which illustrate the fresh conditions found usually during that period across the whole North Atlantic subpolar gyre, although this includes an episode of higher salinity. The SSS anomaly maps have large uncertainties but suggest that the highest SSS occurred before the spring of 1998 in the Iceland Basin, and after that, in the Irminger Sea. This is followed by fresher conditions, first in the Labrador and Iceland Basin, reaching recently the Irminger Sea