35 research outputs found
Retention and splicing complex (RES) - the importance of cooperativity.
One of the great challenges to structural biologists lies in explaining the complexities of the spliceosome - a ribosome-sized molecular machine that is assembled in a step-wise manner and is responsible for pre-mRNA splicing. The spliceosome is both fascinating and difficult to work with, because of its dynamic nature. At each discrete step of splicing tens of proteins come and go orchestrating the functional transition through massive structural rearrangements. The retention and splicing complex (RES) is an important splicing factor interacting with pre-mRNA at the onset of the first transesterification reaction. RES is a specific splicing factor for a number of genes and is important for controlling pre-mRNA retention in the nucleus. RES is a 71kDa heterotrimer composed of the 3 proteins Pml1p, Bud13p and Snu17p. We solved the 3-dimensional structure of the core of the RES complex as well as the 2 dimers, Snu17p-Bud13p and Snu17p-Pml1p. Further biophysical analysis revealed an astounding cooperativity that governs the assembly of this trimeric complex as well as its interaction with pre-mRNA. The more than 100-fold cooperativity originates from the progressive rigidification of Snu17p upon coupled binding-and-folding of protein regions, which are disordered in the unbound state. Our work highlights the role of cooperativity in the spliceosome and poses new questions about the structure and assembly of the spliceosome
Robust deep labeling of radiological emphysema subtypes using squeeze and excitation convolutional neural networks: The MESA Lung and SPIROMICS Studies
Pulmonary emphysema, the progressive, irreversible loss of lung tissue, is
conventionally categorized into three subtypes identifiable on pathology and on
lung computed tomography (CT) images. Recent work has led to the unsupervised
learning of ten spatially-informed lung texture patterns (sLTPs) on lung CT,
representing distinct patterns of emphysematous lung parenchyma based on both
textural appearance and spatial location within the lung, and which aggregate
into 6 robust and reproducible CT Emphysema Subtypes (CTES). Existing methods
for sLTP segmentation, however, are slow and highly sensitive to changes in CT
acquisition protocol. In this work, we present a robust 3-D
squeeze-and-excitation CNN for supervised classification of sLTPs and CTES on
lung CT. Our results demonstrate that this model achieves accurate and
reproducible sLTP segmentation on lung CTscans, across two independent cohorts
and independently of scanner manufacturer and model
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The Anatomy of a Buried Submarine Hydrothermal System, Clark Volcano, Kermadec Arc, New Zealand
Clark volcano of the Kermadec arc, northeast of New Zealand, is a large stratovolcano comprised of two coalescing volcanic cones; an apparently younger, more coherent, twin-peaked edifice to the northwest and a relatively older, more degraded and tectonized cone to the southeast. High-resolution water column surveys show an active hydrothermal system at the summit of the NW cone largely along a ridge spur connecting the two peaks, with activity also noted at the head of scarps related to sector collapse. Clark is the only known cone volcano along the Kermadec arc to host sulfide mineralization. Volcano-scale gravity and magnetic surveys over Clark show that it is highly magnetized, and that a strong gravity gradient exists between the two edifices. Modeling suggests that a crustal-scale fault lies between these two edifices, with thinner crust beneath the NW cone. Locations of regional earthquake epicenters show a southwest-northeast trend bisecting the two Clark cones, striking northeastward into Tangaroa volcano. Detailed mapping of magnetics above the NW cone summit shows a highly magnetized “ring structure” ~350 m below the summit that is not apparent in the bathymetry; we believe this structure represents the top of a caldera. Oblate zones of low (weak) magnetization caused by hydrothermal fluid upflow, here termed “burn holes,” form a pattern in the regional magnetization resembling Swiss cheese. Presumably older burn holes occupy the inner margin of the ring structure and show no signs of hydrothermal activity, while younger burn holes are coincident with active venting on the summit. A combination of mineralogy, geochemistry, and seafloor mapping of the NW cone shows that hydrothermal activity today is largely manifest by widespread diffuse venting, with temperatures ranging between 56° and 106°C. Numerous, small (≤30 cm high) chimneys populate the summit area, with one site host to the ~7-m-tall “Twin Towers” chimneys with maximum vent fluid temperatures of 221°C (pH 4.9), consistent with δ³⁴S[subscript anhydrite-pyrite] values indicating formation temperatures of ~228° to 249°C. Mineralization is dominated by pyrite-marcasite-barite-anhydrite. Radiometric dating using the ²²⁸Ra/²²⁶Ra and ²²⁶Ra/Ba methods shows active chimneys to be <20 with most <2 years old. However, the chimneys at Clark show evidence for mixing with, and remobilizing of, barite as old as 19,000 years. This is consistent with Nd and Sr isotope compositions of Clark chimney and sulfate crust samples that indicate mixing of ~40% seawater with a vent fluid derived from low K lavas. Similarly, REE data show the hydrothermal fluids have interacted with a plagioclase-rich source rock. A holistic approach to the study of the Clark hydrothermal system has revealed a two-stage process whereby a caldera-forming volcanic event preceded a later cone-building event. This ensured a protracted (at least 20 ka yrs) history of hydrothermal activity and associated mineral deposition. If we assume at least 200-m-high walls for the postulated (buried) caldera, then hydrothermal fluids would have exited the seafloor 20 ka years ago at least 550 m deeper than they do today, with fluid discharge temperatures potentially much hotter (~350°C). Subsequent to caldera infilling, relatively porous volcaniclastic and other units making up the cone acted as large-scale filters, enabling ascending hydrothermal fluids to boil and mix with seawater subseafloor, effectively removing the metals (including remobilized Cu) in solution before they reached the seafloor. This has implications for estimates for the metal inventory of seafloor hydrothermal systems pertaining to arc hydrothermal systems.This is the publisher’s final pdf. The published article is copyrighted by the Society of Economic Geologists and can be found at: http://economicgeology.org
Structures of intermediates during RES complex assembly.
The action of the spliceosome depends on the stepwise cooperative assembly and disassembly of its components. Very strong cooperativity was observed for the RES (Retention and Splicing) hetero-trimeric complex where the affinity from binary to tertiary interactions changes more than 100-fold and affects RNA binding. The RES complex is involved in splicing regulation and retention of not properly spliced pre-mRNA with its three components-Snu17p, Pml1p and Bud13p-giving rise to the two possible intermediate dimeric complexes Pml1p-Snu17p and Bud13p-Snu17p. Here we determined the three-dimensional structure and dynamics of the Pml1p-Snu17p and Bud13p-Snu17p dimers using liquid state NMR. We demonstrate that localized as well as global changes occur along the RES trimer assembly pathway. The stepwise rigidification of the Snu17p structure following the binding of Pml1p and Bud13p provides a basis for the strong cooperative nature of RES complex assembly
( 210 Pb/ 226 Ra) variations during the 1994-2001 intracaldera volcanism at Rabaul Caldera
Determining the timing and source of gas transfer during intermittent intracaldera volcanism can aid in our understanding of degassing in these large systems. Using (210Pb/226Ra) ratios, (parentheses denote activity ratios) as a time-sensitive tracer, injections of 222Rn and the subsequent time scales of gas accumulation and loss can be determined. Variations in (210Pb/226Ra) have been measured for 15 volcanic products erupted at Rabaul Caldera over the period 1994 to 2001. In addition, one basaltic enclave from the 1937 eruption was also analyzed. Water and carbon dioxide contents determined from olivine hosted melt inclusions erupted in 1997 are < 1% and suggest extensive shallow-level degassing. Both 210Pb excesses and deficits are found in andesites and dacites, whereas the basaltic enclave displays an (210Pb/226Ra)0 ratio of 7. Between 1994 and 1997 three samples with (210Pb/226Ra) deficits were erupted which indicate open system gas loss since 1992 and 1994. No correlation exists between (210Pb/226Ra) and lava chemistry, eruptive style or date. 210Pb excesses are more common than deficits in Rabaul samples but cannot be explained by plagioclase feldspar accumulation, Pb sublimate accumulation or differentiation. Instead, a model of intra-magma 222Rn transfer can produce 210Pb excesses of the appropriate magnitude if gas transfer occurs over 1-5 years from an underlying body of magma that is 2-10 times larger than the volume of erupted material and that is consistent with geophysical estimates. Although intermittent gas transfer events can be inferred by the development of 210Pb excess, there is no evidence at Rabaul for a direct link between eruptive style, gas flux and (210Pb/226Ra)
(²¹⁰Pb/²²⁶Ra) variations during the 1994-2001 intracaldera volcanism at Rabaul Caldera
Determining the timing and source of gas transfer during intermittent intracaldera volcanism can aid in our understanding of degassing in these large systems. Using (²¹⁰Pb/²²⁶Ra) ratios, (parentheses denote activity ratios) as a time-sensitive tracer, injections of ²²²Rn and the subsequent time scales of gas accumulation and loss can be determined. Variations in (²¹⁰Pb/²²⁶Ra) have been measured for 15 volcanic products erupted at Rabaul Caldera over the period 1994 to 2001. In addition, one basaltic enclave from the 1937 eruption was also analyzed. Water and carbon dioxide contents determined from olivine hosted melt inclusions erupted in 1997 are < 1% and suggest extensive shallow-level degassing. Both ²¹⁰Pb excesses and deficits are found in andesites and dacites, whereas the basaltic enclave displays an (²¹⁰Pb/²²⁶Ra)0 ratio of 7. Between 1994 and 1997 three samples with (²¹⁰Pb/²²⁶Ra) deficits were erupted which indicate open system gas loss since 1992 and 1994. No correlation exists between (²¹⁰Pb/²²⁶Ra) and lava chemistry, eruptive style or date. ²¹⁰Pb excesses are more common than deficits in Rabaul samples but cannot be explained by plagioclase feldspar accumulation, Pb sublimate accumulation or differentiation. Instead, a model of intra-magma ²²²Rn transfer can produce ²¹⁰Pb excesses of the appropriate magnitude if gas transfer occurs over 1–5 years from an underlying body of magma that is 2–10 times larger than the volume of erupted material and that is consistent with geophysical estimates. Although intermittent gas transfer events can be inferred by the development of ²¹⁰Pb excess, there is no evidence at Rabaul for a direct link between eruptive style, gas flux and (²¹⁰Pb/²²⁶Ra).11 page(s
Cooperative structure of the heterotrimeric pre-mRNA retention and splicing complex.
The precursor mRNA (pre-mRNA) retention and splicing (RES) complex is a spliceosomal complex that is present in yeast and humans and is important for RNA splicing and retention of unspliced pre-mRNA. Here, we present the solution NMR structure of the RES core complex from Saccharomyces cerevisiae. Complex formation leads to an intricate folding of three components-Snu17p, Bud13p and Pml1p-that stabilizes the RNA-recognition motif (RRM) fold of Snu17p and increases binding affinity in tertiary interactions between the components by more than 100-fold compared to that in binary interactions. RES interacts with pre-mRNA within the spliceosome, and through the assembly of the RES core complex RNA binding efficiency is increased. The three-dimensional structure of the RES core complex highlights the importance of cooperative folding and binding in the functional organization of the spliceosome
NMR Solution Structure of a Photoswitchable Apoptosis Activating Bak Peptide Bound to Bcl-x(L)
The Bcl-2 family of proteins includes the major regulators and effectors of the intrinsic apoptosis pathway. Cancers are frequently formed when activation of the apoptosis mechanism is compromised either by misregulated expression of prosurvival family members or, more frequently, by damage to the regulatory pathways that trigger intrinsic apoptosis. Short peptides derived from the pro-apoptotic members of the Bcl-2 family can activate mechanisms that ultimately lead to cell death. The recent development of photocontrolled peptides that are able to change their conformation and activity upon irradiation with an external light source has provided new tools to target cells for apoptosis induction with temporal and spatial control. Here, we report the first NMR solution structure of a photoswitchable peptide derived from the proapoptotic protein Bak in complex with the antiapoptotic protein Bcl-xL. This structure provides insight into the molecular mechanism, by which the increased affinity of such photopeptides compared to their native forms is achieved, and offers a rationale for the large differences in the binding affinities between the helical and nonhelical states