Channel Axis Research Articles

A proteolytic AAA+ machine poised to unfold protein substrates

AAA+ proteolytic machines unfold proteins before degrading them. Here, we present cryoEM structures of ClpXP-substrate complexes that reveal a postulated but heretofore unseen intermediate in substrate unfolding/degradation. A ClpX hexamer draws natively folded substrates tightly against its axial channel via interactions with a fused C-terminal degron tail and ClpX-RKH loops that flexibly conform to the globular substrate. The specific ClpX-substrate contacts observed vary depending on the substrate degron and affinity tags, helping to explain ClpXP’s ability to unfold/degrade a wide array of different cellular substrates. Some ClpX contacts with native substrates are enabled by upward movement of the seam subunit in the AAA+ spiral, a motion coupled to a rearrangement of contacts between the ClpX unfoldase and ClpP peptidase. Our structures additionally highlight ClpX’s ability to translocate a diverse array of substrate topologies, including the co-translocation of two polypeptide chains.

Data-Driven Analysis of Ocean Fronts’ Impact on Acoustic Propagation: Process Understanding and Machine Learning Applications, Focusing on the Kuroshio Extension Front

Ocean fronts, widespread across the global ocean, cause abrupt shifts in physical properties such as temperature, salinity, and sound speed, significantly affecting underwater acoustic communication and detection. While past research has concentrated on qualitative analysis and small-scale research on ocean front sections, a comprehensive analysis of ocean fronts’ characteristics and their impact on underwater acoustics is lacking. This study employs high-resolution reanalysis data and in situ observations to accurately identify ocean fronts, sound speed structures, and acoustic propagation features from over six hundred thousand Kuroshio Extension Front (KEF) sections. Utilizing marine big data statistics and machine learning evaluation metrics such as out-of-bag (OOB) error and Shapley values, this study quantitatively assesses the variations in sound speed structures across the KEF and their effects on acoustic propagation shifts. This study’s key findings reveal that differences in sound speed structure are significantly correlated with KEF strength, with the channel axis depth and conjugate depth increasing with front strength, while the thermocline intensity and depth excess decrease. Acoustic propagation features in the KEF environment exhibit notable seasonal variations.

Bedform development in confined and unconfined settings of the Carchuna Canyon (Alboran Sea, western Mediterranean Sea): An example of cyclic steps in shelf-incised canyons

Newly acquired high-resolution multibeam bathymetry in combination with sub-bottom acoustic profiles, surficial sediment samples, and three-dimensional flow simulations made possible the characterization of bedforms along the axial channel and depositional lobe of the shelf-incised Carchuna Canyon (Alboran Sea, western Mediterranean Sea). This study aims to describe the erosional and depositional bedforms in confined and unconfined settings of the Carchuna Canyon in order to determine the genetic constraints on sedimentary processes leading to bedform development along the canyon in recent times.The straight Carchuna Canyon, deeply incised in the shelf up to 200 m off the coastline, hosts: (1) crescentic-shaped bedforms (CSBs) that exhibit distinctive crest concavities, asymmetries, and lengths along the axial channel; (2) continuous lateral levees and; (3) a channel bend with three depressed stretches of the levee crest that are less than 20 m high. A set of concentric sediment waves and two scour trails were identified proximal to the channel bend on the open slope east of the Carchuna Canyon. Two distinct acoustic groups consisting of four acoustic units with distinct acoustic patterns were defined along the sediment wave field. The sediment transport simulation shows the highest flow velocities along the Carchuna Canyon thalweg, while along the overbank deposition the highest velocity values occur along the top of the bedform crests, with the higher Froude values being found over the bedform lee sides.The occurrence of CSBs along the canyon axial channel suggests the imprint of confined sediment-laden gravity flows descending from the canyon head and exhibiting a flow variability along the canyon induced by local variations of slope gradient and/or sediment concentration. A spatial relationship is identified between the development of sediment waves over the overbank deposit and lowered levee crest heights at the channel bend. In contrast, more energetic downstream turbiditic flows exceed the levee crest at the channel bend, focusing the overflow and promoting erosion of the overbank deposit, thereby generating the scour trains. Based on the recent history of overbank deposition, two alternating scenarios of flow behavior can be interpreted. In a high-density turbidity current setting, erosion would prevail along the axial channel. Widespread spillover flows of coarse-grained sediments would occur in both levees, forming heterogeneous sedimentary patterns that change downslope within the depositional lobe due to lesser turbulence of spillover turbidity currents and gentler slope gradients. In contrast, in a low-density turbidity current setting, turbidity currents flowing along the Carchuna Canyon would form depositional bedforms in the axial channel, while spillover processes would be localized at the channel bend, forming either depositional or erosional bedforms over the depositional lobe according to the frequency, magnitude and focusing of turbiditic flows.

Simulation Approaches for the Study of the Oil Flow Rate Distribution in Lubricating Systems with Rotating Shafts

This study addresses the issue of predicting the distribution of lubricant flow through the outlets of a rotating shaft used in vehicle power transmission. A typical geometry with closely spaced rows of holes, suitable for the lubrication of multi-disk clutches, was considered. Both lumped parameter and computational fluid dynamics approaches were applied and compared. The test rig for model validation was designed with a variable speed shaft featuring an axial oil inlet and three equally spaced pairs of radial outlet holes. The main characteristic of the experimental facility is the possibility to selectively measure the flow rates through each outlet. It was found that the three-dimensional model based on the multiple reference frame approach provides a reliable prediction of how the flow rate is distributed. Generally, the flow rate is lower through the outlet closest to the inlet and is maximum at the farthest exit. The flow distribution is minimally affected by the shaft speed. The influence of geometric parameters on making the flow distribution more uniform was studied. It was found that a better flow balance is obtained with a low ratio between the diameter of the radial holes and that of the axial channel. The results obtained offer best-practice guidelines for accurately simulating comparable systems, in order to optimize reliability of the mechanical transmission and energy efficiency of the flow generation unit.

Confinement Modulates Axial Patterning in Regenerating Hydra

The establishment of the body plan is a major step in animal morphogenesis. The role of mechanical forces and feedback in patterning the body plan remains unclear. Here we explore this question by studying regenerating Hydra tissues confined in narrow cylindrical channels, which constrain their morphology. We find that frustration between the orientation of the channel and the inherited axis in the regenerating tissues can lead to the formation of a multiaxial body plan. The morphological outcome is directly related to the pattern of nematic topological defects that emerges in the organization of the supracellular actomyosin fibers. When the inherited axis, which can be read out from the initial alignment of the supracellular fibers in the confined spheroid, is parallel to the channel's axis, the tissue regenerates normally into animals with a single body axis aligned with the channel. However, regenerating spheroids that are confined in a frustrated perpendicular configuration often develop excess defects (including negatively charged −1/2 defects) and regenerate into multiaxial morphologies. The influence of mechanical constraints on the regenerated body plan argues against an axial patterning mechanism that is based solely on inherited gradients of biochemical morphogens. We further show that the dependence of the regeneration outcomes on the initial tissue orientation can be recapitulated by a biophysical model, which considers the coupled dynamics of the nematic organization of the actomyosin fibers and a morphogen concentration field, incorporating a mechanochemical feedback loop involving strain-dependent morphogen production at defect sites. Published by the American Physical Society 2024

Single turnover transient state kinetics reveals processive protein unfolding catalyzed by Escherichia coli ClpB

Escherichia coli ClpB and Saccharomyces cerevisiae Hsp104 are AAA+ motor proteins essential for proteome maintenance and thermal tolerance. ClpB and Hsp104 have been proposed to extract a polypeptide from an aggregate and processively translocate the chain through the axial channel of its hexameric ring structure. However, the mechanism of translocation and if this reaction is processive remains disputed. We reported that Hsp104 and ClpB are non-processive on unfolded model substrates. Others have reported that ClpB is able to processively translocate a mechanically unfolded polypeptide chain at rates over 240 amino acids (aa) per second. Here, we report the development of a single turnover stopped-flow fluorescence strategy that reports on processive protein unfolding catalyzed by ClpB. We show that when translocation catalyzed by ClpB is challenged by stably folded protein structure, the motor enzymatically unfolds the substrate at a rate of ~0.9 aa s−1 with a kinetic step-size of ~60 amino acids at sub-saturating [ATP]. We reconcile the apparent controversy by defining enzyme catalyzed protein unfolding and translocation as two distinct reactions with different mechanisms of action. We propose a model where slow unfolding followed by fast translocation represents an important mechanistic feature that allows the motor to rapidly translocate up to the next folded region or rapidly dissociate if no additional fold is encountered.

Single turnover transient state kinetics reveals processive protein unfolding catalyzed by Escherichia coli ClpB.

Escherichia coli ClpB and Saccharomyces cerevisiae Hsp104 are AAA+ motor proteins essential for proteome maintenance and thermal tolerance. ClpB and Hsp104 have been proposed to extract a polypeptide from an aggregate and processively translocate the chain through the axial channel of its hexameric ring structure. However, the mechanism of translocation and if this reaction is processive remains disputed. We reported that Hsp104 and ClpB are non-processive on unfolded model substrates. Others have reported that ClpB is able to processively translocate a mechanically unfolded polypeptide chain at rates over 240 amino acids (aa) per second. Here, we report the development of a single turnover stopped-flow fluorescence strategy that reports on processive protein unfolding catalyzed by ClpB. We show that when translocation catalyzed by ClpB is challenged by stably folded protein structure, the motor enzymatically unfolds the substrate at a rate of ~0.9 aa s-1 with a kinetic step-size of ~60 amino acids at sub-saturating [ATP]. We reconcile the apparent controversy by defining enzyme catalyzed protein unfolding and translocation as two distinct reactions with different mechanisms of action. We propose a model where slow unfolding followed by fast translocation represents an important mechanistic feature that allows the motor to rapidly translocate up to the next folded region or rapidly dissociate if no additional fold is encountered.

Non-negligible buoyancy effect on bubbles travelling in horizontal microchannels of comparable size at small Bond numbers

When a gas bubble is transported by a liquid flow confined within a horizontal channel of comparable size, buoyancy effects are usually assumed to be negligible if the Bond number of the flow is less than unity. However, recent experimental studies showed that buoyancy may still significantly impact the bubble dynamics even when Bo≪1, provided that the flow speed is sufficiently small, such that the viscous and inertial forces are weak. To derive a new criterion to assess the significance of buoyancy on the flow of small bubbles in horizontal microchannels, we have performed systematic numerical simulations using the free software Basilisk, covering a wide range of Bond, capillary and Reynolds numbers, Bo=0.004−0.4, Ca=10−4−0.5 and Re=0−100, and exploring the bubble-to-channel diameter ratios db/D=0.2−0.9. We demonstrate that the nondimensional group Bo(db/D)2/Ca is effective in assessing the importance of buoyancy in flows with negligible inertial effects. When Bo(db/D)2/Ca<0.1, buoyancy effects are negligible and the bubble travels along the channel axis. When Bo(db/D)2/Ca>10, buoyancy effects dominate and the bubble travels in the vicinity of the upper wall. For intermediate values, bubbles take equilibrium positions between the channel centre and the wall, and the threshold Bo(db/D)2/Ca=1 is effective in predicting whether bubbles will travel closer to the channel centre or to the wall. The capillary number at the denominator describes the lift force generated by the deformation of the bubble due to viscous shear, which acts towards the channel centre thus opposing buoyancy. Inertial forces significantly alter the shape and equilibrium position of the bubble when the Weber number of the flow exceeds unity and Bo/We<1. Under the action of inertia, bubbles of size comparable to the channel diameter become elongated but remain centred. Smaller bubbles migrate towards the channel wall and do not exhibit a preferential near-wall circumferential position.

How the double-ring ClpAP protease motor grips the substrate to unfold and degrade stable proteins

Loops in the axial channels of ClpAP and other AAA+ proteases bind a short peptide degron connected by a linker to the N- or C-terminal residue of a native protein to initiate degradation. ATP hydrolysis then powers pore-loop movements that translocate these segments through the channel until a native domain is pulled against the narrow channel entrance, creating an unfolding force. Substrate unfolding is thought to depend on strong contacts between pore loops and a subset of amino acids in the unstructured sequence directly preceding the folded domain. Here, we identify such contact sequences that promote grip for ClpAP and use ClpA structures to place these sequences within ClpA's two AAA+ rings. The positions and chemical nature of certain residues within an unstructured segment that are positioned to interact with the D2 ring have major positive effects on substrate unfolding, whereas segments located within the D1 ring have little consequence. Within the D2-bound segment, two short elements are critical for accelerating degradation; one is at the 'top' of D2 and consists of at least two properly positioned non-slippery residues. In contrast, the second D2 element, which can be as short as one residue, is positioned to contact pore loops near the 'bottom' of this ring. Comparison with similar studies for ClpXP reveals that positioning a well-gripped substrate sequence within the major unfoldase motor is more important than its proximity to the folded domain and that charged, polar, and hydrophobic residues all contribute favorable contacts to substrate grip.

The Impact of Special Marine Environments Such as the Kuroshio on Hydroacoustic Detection Equipment

In order to study the impact of acoustic propagation characteristics in the northeastern South China Sea, GEBCO08 global terrain grid data and Argo data were used to numerically simulate the acoustic transmission characteristics of two stations in the northeast South China Sea affected by the Kuroshio. The impact of different marine environments on acoustic transmission characteristics was analyzed. The results show that increasing the deployment depth of a sound source within a certain range will reduce the transmission loss; deploying a sound source near the axis of the surface acoustic channel or the deep-sea acoustic channel will also greatly increase the propagation distance of sound signals; and the presence of topography such as undersea mountains will increase the transmission loss.

Two serial filters control P2X7 cation selectivity, Ser342 in the central pore and lateral acidic residues at the cytoplasmic interface.

The human P2X7 receptor (hP2X7R) is a homotrimeric cell surface receptor gated by extracellular ATP4- with two transmembrane helices per subunit, TM1 and TM2. A ring of three S342 residues, one from each pore-forming TM2 helix, located halfway across the membrane bilayer, functions to close and open the gate in the apo and ATP4--bound open states, respectively. The hP2X7R is selective for small inorganic cations, but can also conduct larger organic cations such as Tris+. Here, we show by voltage-clamp electrophysiology in Xenopus laevis oocytes that mutation of S342 residues to positively charged lysines decreases the selectivity for Na+ over Tris+, but maintains cation selectivity. Deep in the membrane, laterally below the S342 ring are nine acidic residues arranged as an isosceles triangle consisting of residues E14, D352, and D356 on each side, which do not move significantly during gating. When the E14K mutation is combined with lysine substitutions of D352 and/or D356, cation selectivity is lost and permeation of the small anion Cl- is allowed. Lysine substitutions of S342 together with D352 or E14 plus D356 in the acidic triangle convert the hP2X7R mutant to a fully Cl--selective ATP4--gated receptor. We conclude that the ion selectivity of wild-type hP2X7R is determined by two sequential filters in one single pathway: (i) a primary size filter, S342, in the membrane center and (ii) three cation filters lateral to the channel axis, one per subunit interface, consisting of a total of nine acidic residues at the cytoplasmic interface.

Elucidating the Architectural dynamics of MuB filaments in bacteriophage Mu DNA transposition

MuB is a non-specific DNA-binding protein and AAA+ ATPase that significantly influences the DNA transposition process of bacteriophage Mu, especially in target DNA selection for transposition. While studies have established the ATP-dependent formation of MuB filament as pivotal to this process, the high-resolution structure of a full-length MuB protomer and the underlying molecular mechanisms governing its oligomerization remain elusive. Here, we use cryo-EM to obtain a 3.4-Å resolution structure of the ATP(+)-DNA(+)-MuB helical filament, which encapsulates the DNA substrate within its axial channel. The structure categorizes MuB within the initiator clade of the AAA+ protein family and precisely locates the ATP and DNA binding sites. Further investigation into the oligomeric states of MuB show the existence of various forms of the filament. These findings lead to a mechanistic model where MuB forms opposite helical filaments along the DNA, exposing potential target sites on the bare DNA and then recruiting MuA, which stimulates MuB’s ATPase activity and disrupts the previously formed helical structure. When this happens, MuB generates larger ring structures and dissociates from the DNA.

Simulation and Analysis of Pressure Waves in Flow Channels of Axial and Radial Gas Wave Ejectors

Introduction: As an efficient energy transfer technology, the gas wave ejector (GWE) holds several patents poised to address the challenges of low-carbon energy. These patents find applications in numerous fields. Traditional axial-flow GWE patents encounter limitations under certain application conditions, whereas radial-flow GWE patents offer an effective solution to these issues. However, the mechanisms behind the performance differences between these two types of GWEs have not yet been studied. Objective: Since pressure waves are central to energy transfer in wave rotors, this study analyzes the coupling effects of centrifugal forces and pressure waves. By examining the differences in pressure wave intensity and propagation velocity within two types of wave rotor channels, the mechanisms underlying the performance disparities are elucidated. Method: Fluent was utilized for numerical simulations, and Response Surface Methodology was employed to model the influence of various factors. Result and Discussion: It can be observed that the propagation velocity and intensity of pressure waves changed under the influence of centrifugal forces. The propagation velocities of S1 and E2, which propagate in the same direction as the fluid flow within the rotor, increase 9% and 32% respectively, whereas the propagation speed of E1, which propagates in the opposite direction of the fluid flow, decreases 15%. Regarding the intensity of each pressure wave, the coupling effect of centrifugal force resulted in an increase of 1.04 to 2.55 kPa. This paper is the first to fit a relational expression for the speed differential of pressure wave propagation within axial and radial flow channels, correlating the main pressure wave velocities (S1, E1, E2) with flow channel length, rotational speed, compression ratio, and expansion ratio, thus providing a reference for GWE design and analysis. Through analysis of variance and significance tests, it is evident that each parameter significantly contributes to the fitting degree of the pressure wave propagation velocity difference (p &lt; 0.01). Furthermore, the inadequacy test (F-value=2.36~3.56) suggests a low level of discrepancy. Conclusion: The fundamental reason for the performance disparity between the two types of gas wave ejectors (GWE) lies in the discrepancies in pressure wave intensity and propagation velocity resulting from centrifugal force effects. Based on the fitted relationships, theoretical foundations can be provided for subsequent wave rotor design and performance analysis. For example, the differences in pressure wave propagation speed can inform the design and analysis of corresponding pressure ports.

Robot-LDA Plane Measurements And Smoke Investigations On A 30° Inclined Flat Plate In An Open Wind Channel With And Without Plasma Actuation Effect

Active flow control is a relatively new approach to influence the velocity vector field for plane airfoils or process engineering applications with a plasma source. The goal is to positively effect the point of separation to increase the lift/drag ratio or increase separation efficiency and to reduce pressure drop. In the presented study two approaches, the Robot-LDA measurements and smoke investigations, are chosen to find out whether the plasma source has an effect on the velocity vector field on a 30°inclined flat plate and the separation point. A flow rate of 250 m³/h resulting in a Reynolds number of 100 000 is chosen, since this is typical for already presented results within the field of plasma source investigations. With Robot-LDA in total 825 measurements points of the axial wind channel velocity components are captured twice, with and without activated plasma source. The measurement plane was set 80 mm x 50 mm orthogonal to the flat plate in the middle of the wind channel axis. The plasma source was powered with 14 kVp−p and 5 kHz. Due to stability of the plasma actuator, the LDA measurements were subdivided into eight regions. For the same configurations smoke investigations are performed. A chromium-nickel wire with a diameter of 0.213 mm is heated by an electronic circuit including capacitor and power source to vaporize liquid paraffin. The flow field is captured by a highspeed camera. Robot-LDA measurement results show a free-stream axial wind channel velocity component of about 15 m/s. In the shadow region of the 30°inclined flat plate a recirculation zone is found due to negative velocity components. At a distance up to 12 mm close to the plat plate, wall reflections dominated and to find valid LDA measurement results were not possible. With and without activated plasma source velocity differences between -0.5 m/s and 0.5 m/s are found. The biggest velocity differences are in the region of 15 mm to 45 mm relative to the tip of the inclined flat plate. For post-processing purposes, the 3D wind channel geometry and the Robot-LDA measurement results are loaded in ParaView 5.10.1. Smoke investigations show that the plasma source minimally attach the flow to the flat plate. This effect is higher with smaller flow rates (50 m³/h) than with 250 m³/h. Robot-LDA and smoke measurement results are promising that flow influence due to plasma has potential in various applications in future.

Deep attention network for identifying ligand-protein binding sites

One of the critical aspects of structure-based drug design is to choose important druggable binding sites in the protein's crystallography structures. As experimental processes are costly and time-consuming, computational drug design using machine learning algorithms is recommended. Over recent years, deep learning methods have been utilized in a wide variety of research applications such as binding site prediction. In this study, a new combination of attention blocks in the 3D U-Net model based on semantic segmentation methods is used to improve localization of pocket prediction. The attention blocks are tuned to find which point and channel of features should be emphasized along spatial and channel axes. Our model's performance is evaluated through extensive experiments on several datasets from different sources, and the results are compared to the most recent deep learning-based models. The results indicate the proposed attention model (Att-UNet) can predict binding sites accurately, i.e. the overlap of the predicted pocket using the proposed method with the true binding site shows statistically significant improvement when compared to other state-of-the-art models. The attention blocks may help the model focus on the target structure by suppressing features in irrelevant regions.

Eocene to Miocene sediment provenance features and evolution history of the western slope area in the Xihu Sag of the East China Sea Continental Shelf Basin

Rift basins are commonly characterised by multiple sediment sources (e.g. transverse and longitudinal) that change over time during different rifting evolution stages. Therefore, tracing sediment provenance to decipher the sedimentary source-to-sink analyses processes in rift basins is important to predict sandy reservoirs. The Xihu Sag in the East China Sea Shelf Basin, particularly its western slope, features large-scale sand bodies of unclear origin. We used petrography, heavy minerals and geochemistry to study sediment provenance in the Eocene Baoshi to Miocene Longjing formations. Our work suggests there are three distinct areas (namely zones A, B and C) affected by different source areas. Zone A, influenced by the Hupijiao uplift, primarily contains metamorphic rock minerals; Zone B, affected by the Haijiao and Hupijiao uplifts, contains igneous and metamorphic rock minerals; and Zone C, dominated by the Haijiao uplift, features igneous with some metamorphic sources, which increase over time, indicating stronger sediment input from the northern Hupijiao uplift. Rare earth element analysis suggests a continental margin and island arc setting, primarily with intermediate–acid felsic rock sources. However, a Eu negative anomaly in Eocene upper Pinghu Formation to the Miocene Longjing Formation indicates some basic source contributions, possibly from a volcanic belt east of the South Yellow Sea. This intermediate–basic volcanic rock belt is located to the northwest of the Hupijiao uplift and may provide clasts for zones A and B through axial channels. These findings indicate that varied sediment sources in the different zones and basin evolution stages with a growing extra-basinal contribution from the Eocene to Miocene, which align with the tectonic shift from the rifting to post-rift period, are essential for understanding the sedimentary filling in this area.

Construction of an Axial Charge Transfer Channel Between Single-Atom Fe Sites and Nitrogen-Doped Carbon Supports for Boosting Oxygen Reduction.

The introduction of axial-coordinated heteroatoms in Fe─N─C single-atom catalysts enables the significant enhancement of their oxygen reduction reaction (ORR) performance. However, the interaction relationship between the axial-coordinated heteroatoms and their carbon supports is still unclear. In this work, a gas phase surface treatment method is proposed to prepare a series of X─Fe─N─C (X = O, P, and S) single-atom catalysts with axial X-coordination on graphitic-N-rich carbon supports. Synchrotron-based X-ray absorption near-edge structure spectra and X-ray photoelectron spectroscopy indicate the formation of an axial charge transfer channel between the graphitic-N-rich carbon supports and single-atom Fe sites by axial O atoms in O─Fe─N─C. As a result, the O─Fe─N─C exhibits excellent ORR performance with a half-wave potential of 0.905V versus RHE and a high specific capacity of 884 mAh g-1 for zinc-air battery, which is superior to other X─Fe─N─C catalysts without axial charge transfer and the commercial Pt/C catalyst. This work not only demonstrates a general synthesis strategy for the preparation of single-atom catalysts with axial-coordinated heteroatoms, but also presents insights into the interaction between single-atom active sites and doped carbon supports.

Classification of sound speed fields in the Western Pacific Ocean based on tensor decomposition

The three-dimensional (3-D) sound speed structure of the ocean is a fundamental environmental element in studying underwater sound propagation modeling and forecasting. The accurate classification of the sound speed fields (SSFs) provides a comprehensive understanding and analysis of the sound propagation pattern. To take advantage of the 3-D structure of the ocean SSFs, this paper presents a quick method based on tensor decomposition for classifying the ocean 3-D SSFs. Utilizing the WOA18 dataset, High Order Iterative Orthogonal (HOOI) decomposition of the 3-D SSFs is executed so as to accurately extract the characteristic information of the SSFs. The Fuzzy C-Means clustering (FCM) method is applied to classify the feature tensors, partitioning of regional categories in different seasons and revealing the typical SSFs structures. By combining the BELLHOP model with analysis of the characteristics of the first convergence zone of each category, it is concluded that there are six categories of SSFs in the Western Pacific Ocean. The SSFs across all categories are primarily latitudinally distributed, featuring distinct sound channel axes and surface sound speed variations.

The occurrence of a rich subtidal macrobenthic fauna in through-flow residential marina canals, and the potential of such systems to be managed as biodiversity assets

The subtidal soft-sediment macrobenthos of a residential coastal marina's 25 ha through-flow canal system was investigated in relation to that in the adjacent natural waterways. The marina, developed from a polluted brownfield island in a warm-temperate estuarine bay, straddles the interface between the axial estuarine channel and a smaller backwater creek separating the island from the mainland, one entrance/exit connecting the canals to each water mass. Although they shared a common pool of taxa, an epibenthic cerithioid microgastropod dominated the axial channel as a whole, a subsurface paraonid polychaete likewise the backwater creek, whilst, unusually, sediment/water interface crustaceans dominated the whole marina canal system, especially the amphipods Ampelisca and Grandidierella. In contrast, the abundance of opportunistic annelids in the marina was very low. Whilst coastal marinas have generally been considered ecological disasters, biodiversity in this one's canals was unusually high at 104 observed invertebrate taxa; 97% of those achieving >25 m−2 in the local axial estuarine channel also occurred in the marina, and additionally its canals supported a number of uncommon taxa not otherwise known from the estuarine bay. This South African marina atypically appears to constitute a biodiversity asset, the more valuable because of its brownfield-site origin; and such appropriately constructed and managed through-flow marinas could form potential refuges for threatened estuarine and coastal soft-sediment benthos. It is concluded that only new marinas with a through water flow should be permitted to be located in ecologically sensitive or conservationally important areas and that regular monitoring of soft-sediment benthos should form an essential part of marina management regimes.

Epigenetic changes to the carotid body drive hypertension in perinatal nicotine exposed rats

Background: Epigenetic changes can be shaped by a wide array of environmental cues as well as maternal health and behaviors. One of the most detrimental behaviors to the developing fetus is nicotine exposure. Perinatal nicotine exposure remains as a significant risk factor for cardiovascular health and in particular, hypertension, as it has been shown to alter angiotensin signaling. Hypothesis: We hypothesized that perinatal nicotine exposure alters carotid body angiotensin signaling to induce hypertension in adult life. Methods: Pregnant Sprague-Dawley rats were exposed to nicotine (2mg/kg SQ, or PBS- control) from estrous day 6 to post-natal day (PND) 21. Experiments on pups took place from PND 56-90. Carotid bodies were harvested pooled together for RNAseq and confirmation of unbiased transcriptomics was conducted with qPCR. Blood pressure was measured with indwelling telemetry. ELISA assessed serum angiotensin. PC12 cells were used a surrogate for carotid body glomus cells and were used for calcium imaging. Results: Unbiased RNAseq of carotid bodies from nicotine exposed pups compared to saline control pups showed that KEGG pathways with significant angiotensin signaling components including Neuroactive ligand-receptor interaction (Log2FC=2.4, p=7.5x10−8) and Dopaminergic synapse (Log2FC=2.3, p=0.0007) were significantly upregulated. qPCR of carotid bodies demonstrated that Angiotensin II type 1 receptor (56%↑), Angiotensin II type 2 receptor (15%↑) and TRPV1 channels (63%↑) were upregulated in nicotine exposed pups compared to controls. Blood pressure measured in nicotine exposed pups was suppressed 1 day after bilateral carotid body denervation. Circulating angiotensin assessed from serum was similar between nicotine exposed and control pups. Calcium imaging of PC12 cells showed that nicotine significantly increased spike frequency in response to nicotine (0.2mg/ml). Incubation with nicotine + Angiotensin (50ng/ml) did not further increase spike frequency. This increased excitation was suppressed with losartan (3μM), AMG9810 (TRPV1 antagonist, 10μM) and combined blockade (p&lt;0.05). Conclusion: Our data demonstrate that adverse maternal behaviors produce epigenetic changes to carotid bodies of offspring resulting in neurogenic hypertension. The epigenetic changes involve an Angiotensin-Angiotensin II type 1 receptor-TRPV1 channel axis in the carotid body without any significant systemic changes. We suggest carotid body modulation may have a significant health impact on offspring with adverse perinatal environmental exposures. UCOP TRDRP T32IP4707, T32KT4708. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.