Proper paraffin slide storage is crucial for translational research projects involving immunohistochemistry stains.

The use of paraffin slides and tissue microarrays (TMA) is indispensable for translational research. However, storage of paraffin slides over time has a substantial detrimental effect on the quality and reliability of immunohistochemistry stains. Particularly affected by this issue may be any collaborative efforts where paraffin slides or TMAs are shipped to central laboratories and then 'biobanked' for some time until use. This article summarizes some of the key issues affecting loss of antigenicity on paraffin slides and some simple storage solutions to help maintain high quality immunohistochemistry results when paraffin slides must be stored for a certain time prior to use.

A Missense Change in the ATG4D Gene Links Aberrant Autophagy to a Neurodegenerative Vacuolar Storage Disease.

Inherited neurodegenerative disorders are debilitating diseases that occur across different species. We have performed clinical, pathological and genetic studies to characterize a novel canine neurodegenerative disease present in the Lagotto Romagnolo dog breed. Affected dogs suffer from progressive cerebellar ataxia, sometimes accompanied by episodic nystagmus and behavioral changes. Histological examination revealed unique pathological changes, including profound neuronal cytoplasmic vacuolization in the nervous system, as well as spheroid formation and cytoplasmic aggregation of vacuoles in secretory epithelial tissues and mesenchymal cells. Genetic analyses uncovered a missense change, c.1288G>A; p.A430T, in the autophagy-related ATG4D gene on canine chromosome 20 with a highly significant disease association (p = 3.8 x 10-136) in a cohort of more than 2300 Lagotto Romagnolo dogs. ATG4D encodes a poorly characterized cysteine protease belonging to the macroautophagy pathway. Accordingly, our histological analyses indicated altered autophagic flux in affected tissues. The knockdown of the zebrafish homologue atg4da resulted in a widespread developmental disturbance and neurodegeneration in the central nervous system. Our study describes a previously unknown canine neurological disease with particular pathological features and implicates the ATG4D protein as an important autophagy mediator in neuronal homeostasis. The canine phenotype serves as a model to delineate the disease-causing pathological mechanism(s) and ATG4D function, and can also be used to explore treatment options. Furthermore, our results reveal a novel candidate gene for human neurodegeneration and enable the development of a genetic test for veterinary diagnostic and breeding purposes.

Are carbohydrate storage strategies of trees traceable by early–latewood carbon isotope differences?

Investigations of stable isotopes in early and latewood cellulose offer interesting insights to climate-driven adaptations of trees’ carbon storage strategy during different phenological phases.

Alternative nighttime nutrition regimens in glycogen storage disease type I: a controlled crossover study

BACKGROUND Traditional approaches for nighttime glycemic control in glycogen storage disease type I (GSDI) include continuous tube feeding, or ingestion of uncooked corn starch (CS) at bedtime. A modified corn starch (MCS) has been shown to prolong euglycemia in some patients. The aim of this study was to evaluate whether stable nighttime glucose control can be achieved with other types of slowly digested carbohydrates in adult GSDI patients. METHODS In this cross-over study, nocturnal glucose control and fasting times were assessed with three different nocturnal nutrition regimens in five patients, using continuous glucose monitoring (CGMS) in an outpatient everyday life setting. For each patient, continuous glucose profiles were measured after ingestion of (1) CS, (2) MCS or (3) a pasta meal at bedtime, during 5 to 6 consecutive nights for each regimen. RESULTS Stable nocturnal glucose control was achieved for all patients with a pasta meal, with a mean duration of glycemia >3.5 mmol/l of 7.6 h (range 5.7-10.8), and >4 mmol/l of 7 h (5.2-9.2), similar to CS and MCS. Fasting glucose before breakfast on workdays (after 7.1 ± 0.8 h) was not significantly different between the three interventions (CS 4.1 ± 0.5 mmol/l, MCS 4.6 ± 0.7 mmol/l, pasta 4.3 ± 0.9 mmol/l). During prolonged fasting on weekends, longer duration of normoglycemia was achieved with CS or MCS than with pasta. CONCLUSION Consumption of cooked pasta is a suitable and more palatable alternative to uncooked corn starch to achieve nighttime glucose control in adult patients with GSDI.

Pigment data set from the SeaWiFS Bio-optical Archive and Storage System (1961-1996)

The oceans play a critical role in the Earth's climate, but unfortunately, the extent of this role is only partially understood. One major obstacle is the difficulty associated with making high-quality, globally distributed observations, a feat that is nearly impossible using only ships and other ocean-based platforms. The data collected by satellite-borne ocean color instruments, however, provide environmental scientists a synoptic look at the productivity and variability of the Earth's oceans and atmosphere, respectively, on high-resolution temporal and spatial scales. Three such instruments, the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) onboard ORBIMAGE's OrbView-2 satellite, and two Moderate Resolution Imaging Spectroradiometers (MODIS) onboard the National Aeronautic and Space Administration's (NASA) Terra and Aqua satellites, have been in continuous operation since September 1997, February 2000, and June 2002, respectively. To facilitate the assembly of a suitably accurate data set for climate research, members of the NASA Sensor Intercomparison and Merger for Biological and Interdisciplinary Oceanic Studies (SIMBIOS) Project and SeaWiFS Project Offices devote significant attention to the calibration and validation of these and other ocean color instruments. This article briefly presents results from the SIMBIOS and SeaWiFS Project Office's (SSPO) satellite ocean color validation activities and describes the SeaWiFS Bio-optical Archive and Storage System (SeaBASS), a state-of-the-art system for archiving, cataloging, and distributing the in situ data used in these activities.

Soil, snow, weather, and sub-surface storage data from a mountain catchment in the rain-snow transition zone

A comprehensive hydroclimatic data set is presented for the 2011 water year to improve understanding of hydrologic processes in the rain-snow transition zone. This type of dataset is extremely rare in scientific literature because of the quality and quantity of soil depth, soil texture, soil moisture, and soil temperature data. Standard meteorological and snow cover data for the entire 2011 water year are included, which include several rain-on-snow events. Surface soil textures and soil depths from 57 points are presented as well as soil texture profiles from 14 points. Meteorological data include continuous hourly shielded, unshielded, and wind corrected precipitation, wind speed, air temperature, relative humidity, dew point temperature, and incoming solar and thermal radiation data. Sub-surface data included are hourly soil moisture data from multiple depths from 7 soil profiles within the catchment, and soil temperatures from multiple depths from 2 soil profiles. Hydrologic response data include hourly stream discharge from the catchment outlet weir, continuous snow depths from one location, intermittent snow depths from 5 locations, and snow depth and density data from ten weekly snow surveys. Though it represents only a single water year, the presentation of both above and below ground hydrologic condition makes it one of the most detailed and complete hydro-climatic datasets from the climatically sensitive rain-snow transition zone for a wide range of modeling and descriptive studies.

Oxygen contents, sulfate concentrations, and changes of IPLs under different storage conditions of samples from ODP Leg 204 and IODP Expedition 311

We have studied the effects of slow infiltration of oxygen on microbial communities in refrigerated legacy samples from ocean drilling expeditions. Storage was in heat-sealed, laminated foil bags with a N2 headspace for geomicrobiological studies. Analysis of microbial lipids suggests that Bacteria were barely detectable in situ but increased remarkably during storage. Detailed molecular examination of a methane-rich sediment horizon showed that refrigeration triggered selective growth of ANME-2 archaea and a drastic change in the bacterial community. Subsequent enrichment targeting methanogens yielded exclusively methylotrophs, which were probably selected for by high sulfate levels caused by oxidation of reduced sulfur species. We provide recommendations for sample storage in future ocean drilling expeditions.

Benthic foraminiferal denitrification rates and nitrate storage

The discovery that foraminifera are able to use nitrate instead of oxygen as energy source for their metabolism has challenged our understanding of nitrogen cycling in the ocean. It was evident before that only prokaryotes and fungi are able to denitrify. Rate estimates of foraminiferal denitrification were very sparse on a regional scale. Here, we present estimates of benthic foraminiferal denitrification rates from six stations at intermediate water depths in and below the Peruvian oxygen minimum zone (OMZ). Foraminiferal denitrification rates were calculated from abundance and assemblage composition of the total living fauna in both, surface and subsurface sediments, as well as from individual species specific denitrification rates. A comparison with total benthic denitrification rates as inferred by biogeochemical models revealed that benthic foraminifera account for the total denitrification on the shelf between 80 and 250 m water depth. They are still important denitrifiers in the centre of the OMZ around 320 m (29-56% of the benthic denitrification) but play only a minor role at the lower OMZ boundary and below the OMZ between 465 and 700 m (3-7% of total benthic denitrification). Furthermore, foraminiferal denitrification was compared to the total benthic nitrate loss measured during benthic chamber experiments. Foraminiferal denitrification contributes 1 to 50% to the total nitrate loss across a depth transect from 80 to 700 m, respectively. Flux rate estimates ranged from 0.01 to 1.3 mmol m?2 d?1. Furthermore we show that the amount of nitrate stored in living benthic foraminifera (3 to 705 µmol L?1) can be higher by three orders of magnitude as compared to the ambient pore waters in near surface sediments sustaining an important nitrate reservoir in Peruvian OMZ sediments. The substantial contribution of foraminiferal nitrate respiration to total benthic nitrate loss at the Peruvian margin, which is one of the main nitrate sink regions in the world oceans, underpins the importance of previously underestimated role of benthic foraminifera in global biochemical cycles.

Shifts in the microbial community structure in different temperatures during sample storage from IODP Hole 325-M0058A

The objective of this study was to determine shifts in the microbial community structure and potential function based on standard Integrated Ocean Drilling Program (IODP) storage procedures for sediment cores. Standard long-term storage protocols maintain sediment temperature at 4°C for mineralogy, geochemical, and/or geotechnical analysis whereas standard microbiological sampling immediately preserves sediments at -80°C. Storage at 4°C does not take into account populations may remain active over geologic time scales at temperatures similar to storage conditions. Identification of active populations within the stored core would suggest geochemical and geophysical conditions within the core change over time. To test this potential, the metabolically active fraction of the total microbial community was characterized from IODP Expedition 325 Great Barrier Reef sediment cores prior to and following a 3-month storage period. Total RNA was extracted from complementary 2, 20, and 40 m below sea floor sediment samples, reverse transcribed to complementary DNA and then sequenced using 454 FLX sequencing technology, yielding over 14,800 sequences from the six samples. Interestingly, 97.3% of the sequences detected were associated with lineages that changed in detection frequency during the storage period including key biogeochemically relevant lineages associated with nitrogen, iron, and sulfur cycling. These lineages have the potential to permanently alter the physical and chemical characteristics of the sediment promoting misleading conclusions about the in situ biogeochemical environment. In addition, the detection of new lineages after storage increases the potential for a wider range of viable lineages within the subsurface that may be underestimated during standard community characterizations.

(Table 1) Water storage changes of the 33 world's largest river basins between 2002-2009

Global change in land water storage and its effect on sea level is estimated over a 7-year time span (August 2002 to July 2009) using space gravimetry data from GRACE. The 33 World largest river basins are considered. We focus on the year-to-year variability and construct a total land water storage time series that we further express in equivalent sea level time series. The short-term trend in total water storage adjusted over this 7-year time span is positive and amounts to 80.6 ± 15.7 km**3/yr (net water storage excess). Most of the positive contribution arises from the Amazon and Siberian basins (Lena and Yenisei), followed by the Zambezi, Orinoco and Ob basins. The largest negative contributions (water deficit) come from the Mississippi, Ganges, Brahmaputra, Aral, Euphrates, Indus and Parana. Expressed in terms of equivalent sea level, total water volume change over 2002-2009 leads to a small negative contribution to sea level of -0.22 ± 0.05 mm/yr. The time series for each basin clearly show that year-to-year variability dominates so that the value estimated in this study cannot be considered as representative of a long-term trend. We also compare the interannual variability of total land water storage (removing the mean trend over the studied time span) with interannual variability in sea level (corrected for thermal expansion). A correlation of ~0.6 is found. Phasing, in particular, is correct. Thus, at least part of the interannual variability of the global mean sea level can be attributed to land water storage fluctuations.