scholarly journals An Initiation Process of Tropical Depression-type Disturbances under the Influence of Upper-level Troughs

2021 ◽  
Author(s):  
Yuya Hamaguchi ◽  
Yukari N. Takayabu
Keyword(s):  
Large Scale ◽  
Convective Available Potential Energy ◽  
Three Dimensional ◽  
Lower Troposphere ◽  
Dimensional Structure ◽  
Convective Heating ◽  
Upper Troposphere ◽  
Tropical Depression ◽  
Upper Level ◽  
Extratropical Forcing

AbstractIn this study, the statistical relationship between tropical upper-tropospheric troughs (TUTTs) and the initiation of summertime tropical-depression type disturbances (TDDs) over the western and central North Pacific is investigated. By applying a spatiotemporal filter to the 34-year record of brightness temperature and using JRA-55 reanalysis products, TDD-event initiations are detected and classified as trough-related (TR) or non-trough-related (non-TR). The conventional understanding is that TDDs originate primarily in the lower-troposphere; our results refine this view by revealing that approximately 30% of TDDs in the 10°N-20°N latitude ranges are generated under the influence of TUTTs. Lead-lag composite analysis of both TR- and non-TR-TDDs clarifies that TR-TDDs occur under relatively dry and less convergent large-scale conditions in the lower-troposphere. This result suggests that TR-TDDs can form in a relatively unfavorable low-level environment. The three-dimensional structure of the wave activity flux reveals southward and downward propagation of wave energy in the upper troposphere that converges at the mid-troposphere around the region where TR-TDDs occur, suggesting the existence of extratropical forcing. Further, the role of dynamic forcing associated with the TUTT on the TR-TDD-initiation is analyzed using the quasi-geostrophic omega equation. The result reveals that moistening in the mid-to-upper troposphere takes place in association with the sustained dynamical ascent at the southeast side of the TUTT, which precedes the occurrence of deep convective heating. Along with a higher convective available potential energy due to the destabilizing effect of TUTTs, the moistening in the mid-to-upper troposphere also helps to prepare the environment favorable to TDDs initiation.

Interaction of Tropical Deep Convection with the Large-Scale Circulation in the MJO

2010 ◽  
Vol 23 (7) ◽  
pp. 1837-1853 ◽  
Author(s):  
Eric Tromeur ◽  
William B. Rossow
Keyword(s):  
Large Scale ◽  
Deep Convection ◽  
Lower Troposphere ◽  
Surface Fluxes ◽  
Convective Heating ◽  
Large Scale Circulation ◽  
Tropical Deep Convection ◽  
Upper Level ◽  
Almost All ◽  
Cloud Regimes

Abstract To better understand the interaction between tropical deep convection and the Madden–Julian oscillation (MJO), tropical cloud regimes are defined by cluster analysis of International Satellite Cloud Climatology Project (ISCCP) cloud-top pressure—optical thickness joint distributions from the D1 dataset covering 21.5 yr. An MJO index based solely on upper-level wind anomalies is used to study variations of the tropical cloud regimes. The MJO index shows that MJO events are present almost all the time; instead of the MJO event being associated with “on or off” deep convection, it is associated with weaker or stronger mesoscale organization of deep convection. Atmospheric winds and humidity from NCEP–NCAR reanalysis 1 are used to characterize the large-scale dynamics of the MJO; the results show that the large-scale motions initiate an MJO event by moistening the lower troposphere by horizontal advection. Increasingly strong convection transports moisture into the upper troposphere, suggesting a reinforcement of the convection itself. The change of convection organization shown by the cloud regimes indicates a strong interaction between the large-scale circulation and deep convection. The analysis is extended to the complete atmospheric diabatic heating by precipitation, radiation, and surface fluxes. The wave organizes stronger convective heating of the tropical atmosphere, which results in stronger winds, while there is only a passive response of the surface, directly linked to cloud radiative effects. Overall, the results suggest that an MJO event is an amplification of large-scale wave motions by stronger convective heating, which results from a dynamic reorganization of scattered deep convection into more intense mesoscale systems.

scholarly journals A Simple Multicloud Parameterization for Convectively Coupled Tropical Waves. Part I: Linear Analysis

2006 ◽  
Vol 63 (4) ◽  
pp. 1308-1323 ◽  
Author(s):  
Boualem Khouider ◽  
Andrew J. Majda
Keyword(s):  
Large Scale ◽  
Deep Convection ◽  
Convective Available Potential Energy ◽  
Lower Troposphere ◽  
Kelvin Waves ◽  
Dynamical Analysis ◽  
Convective Precipitation ◽  
Convective Heating ◽  
Cumulus Clouds

Abstract Recent observational analysis reveals the central role of three multicloud types, congestus, stratiform, and deep convective cumulus clouds, in the dynamics of large-scale convectively coupled Kelvin waves, westward-propagating two-day waves, and the Madden–Julian oscillation. A systematic model convective parameterization highlighting the dynamic role of the three cloud types is developed here through two baroclinic modes of vertical structure: a deep convective heating mode and a second mode with low-level heating and cooling corresponding respectively to congestus and stratiform clouds. A systematic moisture equation is developed where the lower troposphere moisture increases through detrainment of shallow cumulus clouds, evaporation of stratiform rain, and moisture convergence and decreases through deep convective precipitation. A nonlinear switch is developed that favors either deep or congestus convection depending on the relative dryness of the troposphere; in particular, a dry troposphere with large convective available potential energy (CAPE) has no deep convection and only congestus clouds. The properties of the multicloud model parameterization are tested by linearized analysis in a two-dimensional setup with no rotation with constant sea surface temperature. In particular, the present study reveals new mechanisms for the large-scale instability of moist gravity waves with features resembling observed convectively coupled Kelvin waves in realistic parameter regimes without any effect of wind-induced surface heat exchange (WISHE). A detailed dynamical analysis for the linear waves is given herein and idealized nonlinear numerical simulations are reported in a companion paper. A maximum congestus heating leads during the dry phase of the wave. It is followed by an increase of the boundary layer θe, that is, CAPE, and lower troposphere moistening that precondition the upper troposphere for the next deep convective episode. In turn, deep convection consumes CAPE and removes moisture, thus yielding the dry episode.

scholarly journals Biophysical and biochemical investigations of RNA catalysis in the hammerhead ribozyme

1999 ◽  
Vol 32 (3) ◽  
pp. 241-284 ◽  
Author(s):  
William G. Scott
Keyword(s):  
Metal Ions ◽  
Conformational Change ◽  
Large Scale ◽  
Enzyme Inhibitor ◽  
Hammerhead Ribozyme ◽  
Three Dimensional ◽  
Chemical Mechanism ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Hammerhead Rna

1. How do ribozymes work? 2412. The hammerhead RNA as a prototype ribozyme 2422.1 RNA enzymes 2422.2 Satellite self-cleaving RNAs 2422.3 Hammerhead RNAs and hammerhead ribozymes 2443. The chemical mechanism of hammerhead RNA self-cleavage 2463.1 Phosphodiester isomerization via an SN2(P) reaction 2473.2 The canonical role of divalent metal ions in the hammerhead ribozyme reaction 2513.3 The hammerhead ribozyme does not actually require metal ions for catalysis 2543.4 Hammerhead RNA enzyme kinetics 2574. Sequence requirements for hammerhead RNA self-cleavage 2604.1 The conserved core, mutagenesis and functional group modifications 2604.2 Ground-state vs. transition-state effects 2615. The three-dimensional structure of the hammerhead ribozyme 2625.1 Enzyme–inhibitor complexes 2625.2 Enzyme–substrate complex in the initial state 2645.3 Hammerhead ribozyme self-cleavage in the crystal 2645.4 The requirement for a conformational change 2655.5 Capture of conformational intermediates using crystallographic freeze-trapping 2665.6 The structure of a hammerhead ribozyme ‘early’ conformational intermediate 2675.7 The structure of a hammerhead ribozyme ‘later’ conformational intermediate 2685.8 Is the conformational change pH dependent? 2695.9 Isolating the structure of the cleavage product 2715.10 Evidence for and against additional large-scale conformation changes 2745.11 NMR spectroscopic studies of the hammerhead ribozyme 2786. Concluding remarks 2807. Acknowledgements 2818. References 2811. How do ribozymes work? 241The discovery that RNA can be an enzyme (Guerrier-Takada et al. 1983; Zaug & Cech, 1986) has created the fundamental question of how RNA enzymes work. Before this discovery, it was generally assumed that proteins were the only biopolymers that had sufficient complexity and chemical heterogeneity to catalyze biochemical reactions. Clearly, RNA can adopt sufficiently complex tertiary structures that make catalysis possible. How does the three- dimensional structure of an RNA endow it with catalytic activity? What structural and functional principles are unique to RNA enzymes (or ribozymes), and what principles are so fundamental that they are shared with protein enzymes?

scholarly journals Crystal structure of a tankyrase 1–telomere repeat factor 1 complex

2016 ◽  
Vol 72 (4) ◽  
pp. 320-327 ◽  
Author(s):  
Bo Li ◽  
Ruihong Qiao ◽  
Zhizhi Wang ◽  
Weihong Zhou ◽  
Xin Li ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Large Scale ◽  
Sparse Matrix ◽  
Critical Role ◽  
Three Dimensional ◽  
Mitotic Cell ◽  
Ankyrin Repeat ◽  
Dimensional Structure ◽  
Telomere Repeat ◽  
Tankyrase 1

Telomere repeat factor 1 (TRF1) is a subunit of shelterin (also known as the telosome) and plays a critical role in inhibiting telomere elongation by telomerase. Tankyrase 1 (TNKS1) is a poly(ADP-ribose) polymerase that regulates the activity of TRF1 through poly(ADP-ribosyl)ation (PARylation). PARylation of TRF1 by TNKS1 leads to the release of TRF1 from telomeres and allows telomerase to access telomeres. The interaction between TRF1 and TNKS1 is thus important for telomere stability and the mitotic cell cycle. Here, the crystal structure of a complex between the N-terminal acidic domain of TRF1 (residues 1–55) and a fragment of TNKS1 covering the second and third ankyrin-repeat clusters (ARC2-3) is presented at 2.2 Å resolution. The TNKS1–TRF1 complex crystals were optimized using an `oriented rescreening' strategy, in which the initial crystallization condition was used as a guide for a second round of large-scale sparse-matrix screening. This crystallographic and biochemical analysis provides a better understanding of the TRF1–TNKS1 interaction and the three-dimensional structure of the ankyrin-repeat domain of TNKS.

scholarly journals SVFX: a machine-learning framework to quantify the pathogenicity of structural variants

2019 ◽  
Author(s):  
Sushant Kumar ◽  
Arif Harmanci ◽  
Jagath Vytheeswaran ◽  
Mark B. Gerstein
Keyword(s):  
Machine Learning ◽  
Large Scale ◽  
Three Dimensional ◽  
Point Mutations ◽  
Dimensional Structure ◽  
Rapid Decline ◽  
Ras Signaling ◽  
Cancer Genes ◽  
Structural Variations ◽  
Pathogenic Variants

AbstractA rapid decline in sequencing cost has made large-scale genome sequencing studies feasible. One of the fundamental goals of these studies is to catalog all pathogenic variants. Numerous methods and tools have been developed to interpret point mutations and small insertions and deletions. However, there is a lack of approaches for identifying pathogenic genomic structural variations (SVs). That said, SVs are known to play a crucial role in many diseases by altering the sequence and three-dimensional structure of the genome. Previous studies have suggested a complex interplay of genomic and epigenomic features in the emergence and distribution of SVs. However, the exact mechanism of pathogenesis for SVs in different diseases is not straightforward to decipher. Thus, we built an agnostic machine-learning-based workflow, called SVFX, to assign a “pathogenicity score” to somatic and germline SVs in various diseases. In particular, we generated somatic and germline training models, which included genomic, epigenomic, and conservation-based features for SV call sets in diseased and healthy individuals. We then applied SVFX to SVs in six different cancer cohorts and a cardiovascular disease (CVD) cohort. Overall, SVFX achieved high accuracy in identifying pathogenic SVs. Moreover, we found that predicted pathogenic SVs in cancer cohorts were enriched among known cancer genes and many cancer-related pathways (including Wnt signaling, Ras signaling, DNA repair, and ubiquitin-mediated proteolysis). Finally, we note that SVFX is flexible and can be easily extended to identify pathogenic SVs in additional disease cohorts.

scholarly journals Modeling the transport of very short-lived substances into the tropical upper troposphere and lower stratosphere

2009 ◽  
Vol 9 (5) ◽  
pp. 18511-18543 ◽  
Author(s):  
J. Aschmann ◽  
B. M. Sinnhuber ◽  
E. L. Atlas ◽  
S. M. Schauffler
Keyword(s):  
Large Scale ◽  
Lower Stratosphere ◽  
Transport Model ◽  
Three Dimensional ◽  
Chemical Transport Model ◽  
Heating Rates ◽  
Model Calculations ◽  
Upper Troposphere ◽  
Mass Fluxes ◽  
Tropical Upper Troposphere

Abstract. The transport of very short-lived substances into the tropical upper troposphere and lower stratosphere is investigated by a three-dimensional chemical transport model using archived convective updraft mass fluxes (or detrainment rates) from the European Centre for Medium-Range Weather Forecast's ERA-Interim reanalysis. Large-scale vertical velocities are calculated from diabatic heating rates. With this approach we explicitly model the large scale subsidence in the tropical troposphere with convection taking place in fast and isolated updraft events. The model calculations agree generally well with observations of bromoform and methyl iodide from aircraft campaigns and with ozone and water vapor from sonde and satellite observations. Using a simplified treatment of dehydration and bromine product gas washout we give a range of 1.6 to 3 ppt for the contribution of bromoform to stratospheric bromine, assuming a uniform source in the boundary layer of 1 ppt. We show that the most effective region for VSLS transport into the stratosphere is the West Pacific, accounting for about 55% of the bromine from bromoform transported into the stratosphere under the supposition of a uniformly distributed source.

scholarly journals Eurasian Cooling Linked with Arctic Warming: Insights from PV Dynamics

2020 ◽  
Vol 33 (7) ◽  
pp. 2627-2644
Author(s):  
Yongkun Xie ◽  
Guoxiong Wu ◽  
Yimin Liu ◽  
Jianping Huang
Keyword(s):  
Vertical Structure ◽  
Diabatic Heating ◽  
Linear Trend ◽  
Three Dimensional ◽  
Lower Troposphere ◽  
The Arctic ◽  
Arctic Warming ◽  
Circulation Change ◽  
General Dynamics ◽  
Upper Level

AbstractThe three-dimensional connections between Eurasian cooling and Arctic warming since 1979 were investigated using potential vorticity (PV) dynamics. We found that Eurasian cooling can be regulated by Arctic warming through PV adaptation and PV advection. Here, PV adaptation refers to the adaptation of PV to forcing and coherent dynamic–thermodynamic adaptation to PV change. In a PV perspective, first, the anticyclonic circulation change over the Arctic is produced by a negative PV change through PV adaptation, in which the change means the linear trend from 1979 to 2017. The negative PV change is directly regulated by Arctic warming because the vertical structure of Arctic warming is stronger at lower levels, which generates a negative PV change through the diabatic heating effect. Second, the circulation change produces a change in horizontal PV advection due to the existence of climatological PV gradients. Thus, as a balanced result, both the circulation change and PV change extend to the midlatitudes through horizontal PV advection and PV adaptation. Eventually, Eurasian cooling at the surface and in the lower troposphere is dominated by PV changes at the surface through PV adaptation. Meanwhile, enhanced Eurasian cooling in the middle troposphere is dominated by top-down influences of upper-level PV change through PV adaptation. Nevertheless, the upper-level PV changes are still contributed to by horizontal PV advection associated with Arctic warming. Overall, the general dynamics connecting Eurasian cooling with Arctic warming are demonstrated in a PV view.

Hepatocyte Aggregate Culture Technique for Bioreactors in Hybrid Liver Support Systems

1993 ◽  
Vol 16 (12) ◽  
pp. 843-846 ◽  
Author(s):  
J.C. Gerlach ◽  
K. Klöppel ◽  
C. MÜller ◽  
N. Schnoy ◽  
M.D. Smith ◽  
...  
Keyword(s):  
High Performance ◽  
Large Scale ◽  
Support Systems ◽  
Three Dimensional ◽  
Culture Technique ◽  
Dimensional Structure ◽  
Cell Aggregates ◽  
Liver Support ◽  
Aggregate Culture

Utilizing a modified culture technique for hepatocytes, a high performance suspension culture is possible in which hepatocytes spontaneously form cell aggregates. The aggregates of 20-100 cells have been histologically confirmed to hold a three-dimensional structure, they show a long-term external metabolism and a survival time comparable with standard adhesion cultures. This technique has several advantages in the construction of large scale bioreactors for hybrid liver support systems.

scholarly journals Influence of the Monsoon Trough on Westward-Propagating Tropical Waves over the Western North Pacific. Part I: Observations

2015 ◽  
Vol 28 (18) ◽  
pp. 7108-7127 ◽  
Author(s):  
Liang Wu ◽  
Zhiping Wen ◽  
Renguang Wu
Keyword(s):  
Interannual Variability ◽  
North Pacific ◽  
Western North Pacific ◽  
Three Dimensional ◽  
Marked Change ◽  
Monsoon Trough ◽  
Dimensional Structure ◽  
Tropical Depression ◽  
Tropical Waves ◽  
East West

Abstract The present study investigates the possible linkage between the monsoon trough and the interannual variability of the activity of westward-propagating tropical waves (WTW) over the western North Pacific (WNP) during July–November for the period 1979–2007. It is shown that the interannual variability of WTW activity is closely related to the location of the monsoon trough. During the years when the enhanced (weakened) monsoon trough extends eastward (retreats westward), the lower-tropospheric WTW activity is above (below) normal within the southeastern quadrant of the WNP. Furthermore, this study evaluates different wave structures and dynamics of two types of WTWs, equatorial Rossby (ER) waves and mixed Rossby–gravity (MRG)–tropical depression (TD)-type waves, in strong monsoon trough (S-MT) and weak monsoon trough (W-MT) years over the WNP. There is a significant change in the three-dimensional structure as those waves propagate westward to the east of the monsoon trough. For the TD–MRG waves, an apparent transition from MRG waves to off-equatorial TD disturbances is identified in the region of the monsoon trough. For the ER waves, their amplitudes have a faster growth, but their structures and propagation characters have no marked change. Differences in the location of the monsoon trough may lead to an east–west contrast in the WTWs. In a companion study (Part II), diagnostics of energetics and numerical experiments are conducted to explain the observed results in the present study.

scholarly journals Study of Clear Air Turbulence Related to Tropopause Folding over the Romanian Airspace

Atmosphere ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1099
Author(s):  
Sabina Ștefan ◽  
Bogdan Antonescu ◽  
Ana Denisa Urlea ◽  
Livius Buzdugan ◽  
Meda Daniela Andrei ◽  
...  
Keyword(s):  
Large Scale ◽  
Lower Stratosphere ◽  
Meteorological Data ◽  
Horizontal Temperature Gradient ◽  
Jet Streams ◽  
Mountain Waves ◽  
Upper Troposphere ◽  
Air Turbulence ◽  
Upper Level ◽  
Tropopause Folding

Clear air turbulence (CAT) poses a significant threat to aviation. CAT usually occurs in the lower stratosphere and the upper troposphere. It is generally associated with large scale waves, mountain waves, jet streams, upper-level fronts and tropopause folds. Aircraft can experience CAT when flying in proximity of a tropopause fold. To better understand and diagnose tropopause fold- associated CAT we selected a series of cases from among those reported by pilots between June 2017 and December 2018 in the Romanian airspace. Data on turbulence were used in conjunction with meteorological data, satellite imagery, and vertical profiles. Additionally, a set of indices as Ellrod, horizontal temperature gradient, Dutton, and Brown were computed to diagnose CAT associated with tropopause folding. These indices were also analyzed to test the physics mechanisms that may explain the occurrence of severe turbulence. Results show that out of the 420 cases announced by pilots, severe turbulence was reported in 80 cases of which 13 were associated with tropopause folding.

Sign in / Sign up

Export Citation Format

Share Document