Editorial: The Atlantic Meridional Transect programme (1995-2023)

Since 1995 the Atlantic Meridional Transect (AMT) has undertaken measurements of oceanographic and atmospheric variables during 30 research cruises on a passage between the UK and destinations in the South Atlantic (Aiken and Bale, 2000; Robinson et al., 2006; Robinson et al., 2009; Rees et al., 2017). The transect spans more than 100° of latitude, samples to ocean depths of up to 1000 m and crosses a range of ecosystems from sub-polar to tropical, from eutrophic shelf seas and upwelling systems, to oligotrophic mid-ocean gyres. AMT has enabled the acquisition of repeat measurements of several Essential Ocean Variables and other ecosystem parameters and rate processes at a resolution of ~160 km (over ~13000 km). In delivering these activities AMT has facilitated long-term collaborations with NASA and ESA for the calibration and validation of satellite ocean colour sensors; with the UK Met-Office, NOC, NOAA, SOCCOM and University of Washington for ARGO and Bio-ARGO float deployment; and has maintained a long-term mooring in the South Atlantic Gyre (2009 to 2023). AMT data is archived and managed by the British Oceanographic Data Centre (BODC), whilst key data are also directed to other focus specific databases (e.g. NASA SeaBASS, ESA OC-CCI, SOCAT, CDIAC, SeaDataNet). The generation of sustained observations of ocean biogeochemical variables is invaluable in monitoring ecosystem function and health during this period of rapid climate and environmental change. Globally there are a number of initiatives which aim to make repeated observations which include ship transects such as GO-SHIP and GEOTRACES and deployment of hydrodynamical and biogeochemical sensors as part of the ARGO programme. Examples of fixed point observations in the Atlantic include: The European Station for Time-Series in the Ocean (ESTOC) which has provided observations of the eastern sub-tropical Atlantic for more than twenty five years (González-Dávila and Santana-Casiano, 2023), the Bermuda Atlantic Time Series (BATS) in the western sub�tropical Atlantic, which, since 1988 has documented increases in temperature, ocean acidification and decreasing oxygen (Bates and Johnson, 2021); In the north-east Atlantic,the Western Channel Observatory (WCO) has records dating to the early 20th century and in recent decades has further evidenced climate related shifts in plankton communities alongside increases in temperature and ocean acidification (McEvoy et al., 2023); the Estación Permanente de Estudios Ambientale (EPEA) in the western South Atlantic has evidenced increases in chlorophyll associated with an increased proportion of small celled phytoplankton (Lutz et al., 2023). The AMT offers a unique and alternative approach by making repeat measurements along a transect which incorporates the latitudinal range of all these fixed-point stations. AMT provides an inclusive platform for multi-disciplinary ocean research with cruise berths open to the international community upon request. The thirty research expeditions to date have involved 310 sea-going scientists from 81 institutes representing 31 countries, resulting in 400 refereed papers which are available here

Limitation of dimethylsulfoniopropionate synthesis at high irradiance in natural phytoplankton communities of the Tropical Atlantic

Predictions of the ocean-atmosphere flux of dimethyl sulfide will be improved by understanding what controls seasonal and regional variations in dimethylsulfoniopropionate (DMSP) production. To investigate the influence of high levels of irradiance including ultraviolet radiation (UVR), on DMSP synthesis rates (μDMSP) and inorganic carbon fixation (μPOC) by natural phytoplankton communities, nine experiments were carried out at different locations in the low nutrient, high light environment of the northeastern Tropical Atlantic. Rates of μDMSP and μPOC were determined by measuring the incorporation of inorganic 13C into DMSP and particulate organic carbon. Based on measurements over discrete time intervals during the day, a unique μDMSP vs. irradiance (P vs. E) relationship was established. Comparison is made with the P vs. E relationship for μPOC, indicating that light saturation of μDMSP occurs at similar irradiance to μPOC and is closely coupled to carbon fixation on a diel basis. Photoinhibition during the middle of the day was exacerbated by exposure to UVR, causing an additional 55–60% inhibition of both μDMSP and μPOC at the highest light levels. In addition, decreased production of DMSP in response to UVR-induced photoxidative stress, contrasted with the increased net synthesis of photoprotective xanthophyll pigments. Together these results indicate that DMSP production by phytoplankton in the tropical ocean is not regulated in the short term by the necessity to control increasing photooxidative stress as irradiance increases during the day. The study provides new insight into the regulation of resource allocation into this biogeochemically important, multi-functional compatible solute

Determining Atlantic Ocean province contrasts and variations

The Atlantic Meridional Transect (AMT) series of twenty-five cruises over the past twenty years has produced a rich depth-resolved biogeochemical in situ data resource consisting of a wealth of core variables. These multiple core datasets, key to the operation of AMT, such as temperature, salinity, oxygen and inorganic nutrients, are often only used as ancillary measurements for contextualising hypothesis-driven process studies. In this paper these core in situ variables, alongside data drawn from satellite Earth Observation (EO) and modelling, have been analysed to determine characteristic oceanic province variations encountered over the last twenty years on the AMT through the Atlantic Ocean. The EO and modelling analysis shows the variations of key environmental variables in each province, such as surface currents, the net heat flux and subsequent large scale biological responses, such as primary production. The in situ core dataset analysis allows the variation in features such as the tropical oxygen minimum zone to be quantified as well as showing clear contrasts between the provinces in nutrient stoichiometry. Such observations and relationships can be used within basin scale biogeochemical models to set realistic variation ranges

Insights from year-long measurements of air–water CH4 and CO2 exchange in a coastal environment

Air–water CH4 and CO2 fluxes were directly measured using the eddy covariance technique at the Penlee Point Atmospheric Observatory on the southwest coast of the United Kingdom from September 2015 to August 2016. The high-frequency, year-long measurements provide unprecedented detail on the variability of these greenhouse gas fluxes from seasonal to diurnal and to semi-diurnal (tidal) timescales. Depending on the wind sector, fluxes measured at this site are indicative of air–water exchange in coastal seas as well as in an outer estuary. For the open-water sector when winds were off the Atlantic Ocean, CH4 flux was almost always positive (annual mean of ∼0.05 mmol m−2 d−1) except in December and January, when CH4 flux was near zero. At times of high rainfall and river flow rate, CH4 emission from the estuarine-influenced Plymouth Sound sector was several times higher than emission from the open-water sector. The implied CH4 saturation (derived from the measured fluxes and a wind-speed-dependent gas transfer velocity parameterization) of over 1000 % in the Plymouth Sound is within range of in situ dissolved CH4 measurements near the mouth of the river Tamar. CO2 flux from the open-water sector was generally from sea to air in autumn and winter and from air to sea in late spring and summer, with an annual mean flux of near zero. A diurnal signal in CO2 flux and implied partial pressure of CO2 in water (pCO2) are clearly observed for the Plymouth Sound sector and also evident for the open-water sector during biologically productive periods. These observations suggest that coastal CO2 efflux may be underestimated if sampling strategies are limited to daytime only. Combining the flux data with seawater pCO2 measurements made in situ within the flux footprint allows us to estimate the CO2 transfer velocity. The gas transfer velocity and wind speed relationship at this coastal location agrees reasonably well with previous open-water parameterizations in the mean but demonstrates considerable variability. We discuss the influences of biological productivity, bottom-driven turbulence and rainfall on coastal air–water gas exchange

Identification of hip fracture patients from radiographs using Fourier analysis of the trabecular structure: a cross-sectional study

Peer reviewedPublisher PD

Overt is no better than covert when rehearsing visuo-spatial information in working memory

In the present study, we examined whether eye movements facilitate retention of visuo-spatial information in working memory. In two experiments, participants memorised the sequence of the spatial locations of six digits across a retention interval. In some conditions, participants were free to move their eyes during the retention interval, but in others they either were required to remain fixated or were instructed to move their eyes exclusively to a selection of the memorised locations. Memory performance was no better when participants were free to move their eyes during the memory interval than when they fixated a single location. Furthermore, the results demonstrated a primacy effect in the eye movement behaviour that corresponded with the memory performance. We conclude that overt eye movements do not provide a benefit over covert attention for rehearsing visuo-spatial information in working memory

Molecular basis of FIR-mediated c-myc transcriptional control

The far upstream element (FUSE) regulatory system promotes a peak in the concentration of c-Myc during cell cycle. First, the FBP transcriptional activator binds to the FUSE DNA element upstream of the c-myc promoter. Then, FBP recruits its specific repressor (FIR), which acts as an on/off transcriptional switch. Here we describe the molecular basis of FIR recruitment, showing that the tandem RNA recognition motifs of FIR provide a platform for independent FUSE DNA and FBP protein binding and explaining the structural basis of the reversibility of the FBP-FIR interaction. We also show that the physical coupling between FBP and FIR is modulated by a flexible linker positioned sequentially to the recruiting element. Our data explain how the FUSE system precisely regulates c-myc transcription and suggest that a small change in FBP-FIR affinity leads to a substantial effect on c-Myc concentration.MRC Grant-in-aid U11757455

A structurally distinct TGF-β mimic from an intestinal helminth parasite potently induces regulatory T cells

Helminth parasites defy immune exclusion through sophisticated evasion mechanisms, including activation of host immunosuppressive regulatory T (Treg) cells. The mouse parasite Heligmosomoides polygyrus can expand the host Treg population by secreting products that activate TGF-β signalling, but the identity of the active molecule is unknown. Here we identify an H. polygyrus TGF-β mimic (Hp-TGM) that replicates the biological and functional properties of TGF-β, including binding to mammalian TGF-β receptors and inducing mouse and human Foxp3+ Treg cells. Hp-TGM has no homology with mammalian TGF-β or other members of the TGF-β family, but is a member of the complement control protein superfamily. Thus, our data indicate that through convergent evolution, the parasite has acquired a protein with cytokine-like function that is able to exploit an endogenous pathway of immunoregulation in the host

Gene expression profile and genomic alterations in colonic tumours induced by 1,2-dimethylhydrazine (DMH) in rats

<p>Abstract</p> <p>Background</p> <p>Azoxymethane (AOM) or 1,2-dimethylhydrazine (DMH)-induced colon carcinogenesis in rats shares many phenotypical similarities with human sporadic colon cancer and is a reliable model for identifying chemopreventive agents. Genetic mutations relevant to human colon cancer have been described in this model, but comprehensive gene expression and genomic analysis have not been reported so far. Therefore, we applied genome-wide technologies to study variations in gene expression and genomic alterations in DMH-induced colon cancer in F344 rats.</p> <p>Methods</p> <p>For gene expression analysis, 9 tumours (TUM) and their paired normal mucosa (NM) were hybridized on 4 × 44K Whole rat arrays (Agilent) and selected genes were validated by semi-quantitative RT-PCR. Functional analysis on microarray data was performed by GenMAPP/MappFinder analysis. Array-comparative genomic hybridization (a-CGH) was performed on 10 paired TUM-NM samples hybridized on Rat genome arrays 2 × 105K (Agilent) and the results were analyzed by CGH Analytics (Agilent).</p> <p>Results</p> <p>Microarray gene expression analysis showed that <it>Defcr4</it>, <it>Igfbp5</it>, <it>Mmp7, Nos2, S100A8 </it>and <it>S100A9 </it>were among the most up-regulated genes in tumours (Fold Change (FC) compared with NM: 183, 48, 39, 38, 36 and 32, respectively), while <it>Slc26a3</it>, <it>Mptx</it>, <it>Retlna </it>and <it>Muc2 </it>were strongly down-regulated (FC: -500; -376, -167, -79, respectively). Functional analysis showed that pathways controlling cell cycle, protein synthesis, matrix metalloproteinases, TNFα/NFkB, and inflammatory responses were up-regulated in tumours, while Krebs cycle, the electron transport chain, and fatty acid beta oxidation were down-regulated. a-CGH analysis showed that four TUM out of ten had one or two chromosomal aberrations. Importantly, one sample showed a deletion on chromosome 18 including <it>Apc</it>.</p> <p>Conclusion</p> <p>The results showed complex gene expression alterations in adenocarcinomas encompassing many altered pathways. While a-CGH analysis showed a low degree of genomic imbalance, it is interesting to note that one of the alterations concerned <it>Apc</it>, a key gene in colorectal carcinogenesis. The fact that many of the molecular alterations described in this study are documented in human colon tumours confirms the relevance of DMH-induced cancers as a powerful tool for the study of colon carcinogenesis and chemoprevention.</p

attract: A Method for Identifying Core Pathways That Define Cellular Phenotypes

attract is a knowledge-driven analytical approach for identifying and annotating the gene-sets that best discriminate between cell phenotypes. attract finds distinguishing patterns within pathways, decomposes pathways into meta-genes representative of these patterns, and then generates synexpression groups of highly correlated genes from the entire transcriptome dataset. attract can be applied to a wide range of biological systems and is freely available as a Bioconductor package and has been incorporated into the MeV software system