Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry

BACKGROUND: Three-dimensional (3D) imaging mass spectrometry (MS) is an analytical chemistry technique for the 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D-imaging MS has unique advantages over existing 3D imaging techniques, offers novel perspectives for understanding the spatial organization of biological processes, and has growing potential to be introduced into routine use in both biology and medicine. Owing to the sheer quantity of data generated, the visualization, analysis, and interpretation of 3D imaging MS data remain a significant challenge. Bioinformatics research in this field is hampered by the lack of publicly available benchmark datasets needed to evaluate and compare algorithms. FINDINGS: High-quality 3D imaging MS datasets from different biological systems at several labs were acquired, supplied with overview images and scripts demonstrating how to read them, and deposited into MetaboLights, an open repository for metabolomics data. 3D imaging MS data were collected from five samples using two types of 3D imaging MS. 3D matrix-assisted laser desorption/ionization imaging (MALDI) MS data were collected from murine pancreas, murine kidney, human oral squamous cell carcinoma, and interacting microbial colonies cultured in Petri dishes. 3D desorption electrospray ionization (DESI) imaging MS data were collected from a human colorectal adenocarcinoma. CONCLUSIONS: With the aim to stimulate computational research in the field of computational 3D imaging MS, selected high-quality 3D imaging MS datasets are provided that could be used by algorithm developers as benchmark datasets

Mixing and chemical ozone loss during and after the Antarctic polar vortex major warming in September 2002

The 3D version of the Chemical Lagrangian Model of the Stratosphere (CLAMS) is used to study the transport of CH4 and 03 in the Antarctic stratosphere between I September and 30 November 2002, that is, over the time period when unprecedented major stratospheric warming in late September split the polar vortex into two parts. The isentropic and cross-isentropic velocities in CLAMS are derived from ECMWF winds and heating/cooling rates calculated with a radiation module. The irreversible part of transport, that is, mixing, is driven by the local horizontal strain and vertical shear rates with mixing parameters deduced from in situ observations.The CH4 distribution after the vortex split shows a completely different behavior above and below 600 K. Above this potential temperature level, until the beginning of November, a significant part of vortex air is transported into the midlatitudes up to 40 degrees S. The lifetime of the vortex remnants formed after the vortex split decreases with the altitude with values of about 3 and 6 weeks at 900 and 700 K, respectively.Despite this enormous dynamical disturbance of the vortex, the intact part between 400 and 600 K that "survived" the major warming was strongly isolated from the extravortex air until the end of November. According to CLAMS simulations, the air masses within this part of the vortex did not experience any significant dilution with the midlatitude air.By transporting ozone in CLAMS as a passive tracer, the chemical ozone loss was estimated from the difference between the observed [Polar Ozone and Aerosol Measurement III (POAM 111) and Halogen Occultation Experiment (HALOE)] and simulated ozone profiles. Starting from I September, up to 2.0 ppmv O-3 around 480 K and about 70 Dobson units between 450 and 550 K were destroyed until the vortex was split. After the major warming, no additional ozone loss can be derived, but in the intact vortex part between 450 and 550 K, the accumulated ozone loss was "frozen in" until the end of November

Migrational Behavior and Seaward Movement of Wild Subyearling Fall Chinook Salmon in the Snake River

Flow augmentation increases flow and decreases temperature in reservoirs in the lower Snake River during the seaward migration of wild subyearling fall chinook salmon Oncorhynchus tshawytscha. A study of the migrational behavior and seaward movement of wild subyearling fall chinook salmon in the Snake River was necessary to help understand the efficacy of flow augmentation. We studied fall chinook salmon in the Snake River during 1992-2001. After analyzing mark-recapture data, we deduced that fall chinook salmon passed through at least four migrational phases, including (1) discontinuous downstream dispersal along the shorelines of the free-flowing river, (2) abrupt and mostly continuous downstream dispersal offshore in the free-flowing river, (3) passive, discontinuous downstream dispersal offshore in the first reservoir encountered en route to the sea, and (4) active and mostly continuous seaward migration. We used ordinary-least-squares multiple regression to test the effects of flow (m3/s), temperature (°C), and three other factors on the rate of seaward movement (km/d) from initial tagging in the free-flowing river to the first dam encountered en route to the sea (period 1) and from passage at this first dam to passage at the next dam downstream (period 2). We found that flow and temperature influenced the rate of seaward movement during period 1 (N = 2,808; flow model R2 = 0.65, P \u3c 0.0001; temperature model R2 = 0.726, P \u3c 0.0001). We failed to find evidence for flow and temperature effects on the rate of seaward movement during period 2, possibly because of limitations on our study. We conclude that flow augmentation increases the rate of seaward movement of fall chinook salmon during period 1, provided that augmentation occurs when the fish have moved offshore in the free-flowing river and are behaviorally disposed to being displaced downstream. The cooling effect of summer flow augmentation likely prevents fish that successfully smolted during period 1 from reverting to parr during period 2, but research is needed to confirm this hypothesis

Movement and spawner distribution of hatchery fall Chinook salmon adults acclimated and released as yearlings at three locations in the Snake River basin

As part of the supplementation program for fall Chinook salmon Oncorhynchus tshawytscha in the Snake River basin, yearlings from Lyons Ferry Hatchery were released at acclimation facilities stationed along the lower Clearwater River and the lower and upper reaches of the Snake River. The distance required for migration out of the release reach was greatest for juveniles released in the lower Clearwater River. The distance required for migration out of the release river was greatest for juveniles released in the upper Snake River. We captured and radio-tagged returning adults at Lower Granite Dam (the last dam encountered prior to entering the release reaches), monitored adult movements, and assessed the performance of acclimation facilities in terms of their ability to distribute adults to their corresponding release reaches. Adults from the lower Clearwater River acclimation group had the lowest frequency of movement, the most restricted spatial movement, and the highest observed rate of spawning in the intended reach. The upper Snake River acclimation facility distributed spawners to the intended river at the highest rate observed. Though differences in water flow and temperature during immigration were possible explanations for these findings, acclimation facility location provided the most plausible explanation. We conclude that acclimation facility location can affect prespawning movement and the spawning distribution of hatchery fall Chinook salmon in the Snake River basin

Early life history attributes and run composition of PIT-tagged wild subyearling Chinook salmon recaptured after migrating downstream past Lower Granite Dam

Seaward migration timing of Snake River fall chinook salmon (Oncorhynchus tshawytscha) smolts is indexed using subyearling chinook salmon passage data collected at Lower Granite Dam. However, not all of the subyearlings are fall chinook salmon. For six years, we recaptured wild subyearling chinook salmon smolts, which had been previously PIT tagged in the Snake River, to genetically determine if the fish were offspring of spring and summer (hereafter, spring/summer), or fall chinook salmon. Springfall chinook salmon comprised over 10% of the samples of recaptured smolts in five of six years. For these five years, we used discriminant analysis to determine run membership of PIT-tagged smolts that were not recaptured (i.e., not sampled for genetic identification). Accuracy of the discriminant analysis models, based on genetically identified smolts, varied between 75 and 85%. After using discriminant analysis to classify run membership for each PIT-tagged smolt that was not genetically identified, we compared early life history attributes between fall and spring/summer chinook salmon and calculated annual run composition. The life history attributes we studied overlapped, but spring/summer chinook salmon reared along the shoreline of the free-flowing Snake River earlier, were larger, and began seaward migration earlier than fall chinook salmon. Spring/summer chinook salmon made up from 15.1 to 44.4% of the tagged subyearling smolts that were detected passing Lower Granite Dam. As a result, the presence of spring/summer chinook salmon makes migration timing for the fall chinook salmon seem earlier and more protracted than is the case. If wild subyearling spring/summer chinook salmon smolts are not considered, fall chinook salmon abundance at Lower Granite Dam will be overestimated

A Ca2+-sensor switch for tolerance to elevated salt stress in Arabidopsis

Summary Excessive Na+ in soils inhibits plant growth. Here, we report that Na+ stress triggers primary calcium signals specifically in a cell group within the root differentiation zone, thus forming a “sodium-sensing niche” in Arabidopsis. The amplitude of this primary calcium signal and the speed of the resulting Ca2+ wave dose-dependently increase with rising Na+ concentrations, thus providing quantitative information about the stress intensity encountered. We also delineate a Ca2+-sensing mechanism that measures the stress intensity in order to mount appropriate salt detoxification responses. This is mediated by a Ca2+-sensor-switch mechanism, in which the sensors SOS3/CBL4 and CBL8 are activated by distinct Ca2+-signal amplitudes. Although the SOS3/CBL4-SOS2/CIPK24-SOS1 axis confers basal salt tolerance, the CBL8-SOS2/CIPK24-SOS1 module becomes additionally activated only in response to severe salt stress. Thus, Ca2+-mediated translation of Na+ stress intensity into SOS1 Na+/H+ antiporter activity facilitates fine tuning of the sodium extrusion capacity for optimized salt-stress tolerance