LaSER oceanography: Data report number 1, R/V Pelican cruise, July 21-August 1, 1987, CTD and hydrographic data

The LaSER oceanography program is a five year multi-institutional and multi-investigator program titled "Oceanographic Processes on Continental Shelves Influenced by Large Rivers." Funding for this program began in January, 1987. The scientific goals of this program are: a) investigations on a large spatial scale, from the Mississippi River delta to some far field (down-plume) location, to examine biological responses to riverine inputs of dissolved nutrients, suspended sediments, and fresh water; b) investigations on small spatial scales, both horizontally and vertically, in a cross plume direction to examine the role of oceanographic fronts, convergences, and discontinuities in biological production; and c) investigations on small temporal scales, particularly to examine the biological responses to the passage of winter storms. This report summarizes the CTD and hydrographic (bottle) data from the first LaSER oceanography cruise

High Cyanobacterial Abundance in Three Northeastern Gulf of Mexico Estuaries

Aquatic phytoplankton comprise a wide variety of taxa spanning more than 2 orders of magnitude in size, yet studies of estuarine phytoplankton often overlook the picoplankton, particularly chroococcoid cyanobacteria (cf. Synechococcus). Three Gulf of Mexico estuaries (Apalachicola Bay, FL; Pensacola Bay, FL; Weeks Bay, AL) were sampled during summer and fall 2001 to quantify cyanobacterial abundance, to examine how cyanobacterial abundance varied with hydrographic and nutrient distributions, and to estimate the contribution of cyanobacteria to the bulk phytoplankton community. Cyanobacterial abundances in all 3 estuaries were high, averaging 0.59 ± 0.76 X 109 L–1 in Apalachicola Bay, 1.7 ± 1.2 X 109 L–1 in Pensacola Bay and 2.4 ± 1.9 X 109 L–1 in Weeks Bay (mean ± standard deviation). Peak abundances typically occurred in the oligohaline zone (low salinity estuarine zone) during the summer. Freshwater sites had nearly undetectable abundances, and marine sites had abundances several-fold lower than the oligohaline zone. When converted to equivalent chlorophyll a concentrations, cyanobacteria comprised a large fraction of the total phytoplankton biomass, at times approaching 100% in all 3 systems. These observations clearly indicate a cyanobacterial community of estuarine origin that can make up a large proportion of phytoplankton biomass

Comparison of bacterioneuston and bacterioplankton dynamics during a phytoplankton bloom in a fjord mesocosm

The bacterioneuston is the community of Bacteria present in surface microlayers, the thin surface film that forms the interface between aquatic environments and the atmosphere. In this study we compared bacterial cell abundance and bacterial community structure of the bacterioneuston and the bacterioplankton (from the subsurface water column) during a phytoplankton bloom mesocosm experiment. Bacterial cell abundance, determined by flow cytometry, followed a typical bacterioplankton response to a phytoplankton bloom, with Synechococcus and high nucleic acid (HNA) bacterial cell numbers initially falling, probably due to selective protist grazing. Subsequently HNA and low nucleic acid (LNA) bacterial cells increased in abundance but Synechococcus did not. There was no significant difference between bacterioneuston and bacterioplankton cell abundances during the experiment. Conversely, distinct and consistent differences between the bacterioneuston and the bacterioplankton community structure were observed. This was monitored simultaneously by Bacteria 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) and denaturing gradient gel electrophoresis (DGGE). The conserved patterns of community structure observed in all of the mesocosms indicate that the bacterioneuston is distinctive and non-random

Long-term and trans-generational effects of neonatal experience on sheep behaviour

Early life experiences can have profound long-term, and sometimes trans-generational, effects on individual phenotypes. However, there is a relative paucity of knowledge about effects on pain sensitivity, even though these may impact on an individual's health and welfare, particularly in farm animals exposed to painful husbandry procedures. Here, we tested in sheep whether neonatal painful and non-painful challenges can alter pain sensitivity in adult life, and also in the next generation. Ewes exposed to tail-docking or a simulated mild infection (lipopolysaccharide (LPS)) on days 3–4 of life showed higher levels of pain-related behaviour when giving birth as adults compared with control animals. LPS-treated ewes also gave birth to lambs who showed decreased pain sensitivity in standardized tests during days 2–3 of life. Our results demonstrate long-term and trans-generational effects of neonatal experience on pain responses in a commercially important species and suggest that variations in early life management can have important implications for animal health and welfare

Regulation of plasmid-encoded isoprene metabolism in Rhodococcus, a representative of an important link in the global isoprene cycle

Emissions of biogenic volatile organic compounds (VOCs) form an important part of the global carbon cycle, comprising a significant proportion of net ecosystem productivity. They impact atmospheric chemistry and contribute directly and indirectly to greenhouse gases. Isoprene, emitted largely from plants, comprises one third of total VOCs, yet in contrast to methane, which is released in similar quantities, we know little of its biodegradation. Here, we report the genome of an isoprene degrading isolate, Rhodococcus sp. AD45, and, using mutagenesis shows that a plasmid-encoded soluble di-iron centre isoprene monooxygenase (IsoMO) is essential for isoprene metabolism. Using RNA sequencing (RNAseq) to analyse cells exposed to isoprene or epoxyisoprene in a substrate-switch time-course experiment, we show that transcripts from 22 contiguous genes, including those encoding IsoMO, were highly upregulated, becoming among the most abundant in the cell and comprising over 25% of the entire transcriptome. Analysis of gene transcription in the wild type and an IsoMO-disrupted mutant strain showed that epoxyisoprene, or a subsequent product of isoprene metabolism, rather than isoprene itself, was the inducing molecule. We provide a foundation of molecular data for future research on the environmental biological consumption of this important, climate-active compound

Alarmins in frozen shoulder: a molecular association between inflammation and pain

Background: The pathophysiological mechanisms behind proliferation of fibroblasts and deposition of dense collagen matrix in idiopathic frozen shoulder remain unclear. Alarmins (also known as danger signals) are endogenous molecules that are released into the extracellular milieu after infection or tissue injury and that signal cell and tissue damage. Purpose: To investigate whether the presence of alarmins is higher in patients with idiopathic frozen shoulder than in control subjects. Study Design: Controlled laboratory study. Methods: Shoulder capsule samples were collected from 10 patients with idiopathic frozen shoulder and 10 patients with unstable shoulders (control). The samples were stained with hematoxylin and eosin (H&E) and analyzed by immunohistochemistry using antibodies against alarmin molecules including high-mobility group protein B1 (HMGB1), interleukin 33, S100A8, S100A9, and the peripheral nerve marker PGP9.5. Immunoreactivities were rated in a blinded fashion from “none” to “strong.” Immunohistochemical distribution within the capsule was noted. Before surgery, patient-ranked pain frequency, severity, stiffness, and the range of passive shoulder motion were recorded and statistically analyzed. Results: Compared with control patients, patients with frozen shoulder had greater frequency and severity of self-reported pain (P = .02) and more restricted range of motion in all planes (P < .05). H&E-stained capsular tissue from frozen shoulder showed fibroblastic hypercellularity and increased subsynovial vascularity. Immunoreactivity of alarmins was significantly stronger in frozen shoulder capsules compared with control capsules (P < .05). Furthermore, the expression of the alarmin molecule HMGB1 significantly correlated (r > 0.9, P < .05) with the severity of patient-reported pain. Conclusion: This study demonstrates a potential role for key molecular danger signals in frozen shoulder and suggests an association between the expression of danger molecules and the pain experienced by patients

Benthic Nutrient Flux in a Small Estuary in Northwestern Florida (USA)

Benthic nutrient fluxes of ammonium (NH4+), nitrite/nitrate (NO2- + NO3-), phosphate (PO4-3), and dissolved silica (DSi) were measured in Escambia Bay, an estuary within the larger Pensacola Bay system of northwestern Florida (USA). Our study occurred during a severe drought which reduced riverine inputs to Escambia Bay. Laboratory incubations of field-collected cores were conducted on 8 dates between June and October 2000 to estimate nutrient flux, and cores were collected from locations exhibiting a range of sediment organic matter content. NH4+ flux ranged from – 48.1 to 110.4 μmol m-2 h-1, but the mean flux was 14.6 μmol m-2 h-1. Dissolved silica (DSi) fluxes were also variable (-109. 3 to 145.3 μmol m-2 h-1), but the mean net flux (9.3 μmol m-2 h-1) was from the sediment to the water column. Bay sediment fluxes for NO2-+ NO3- and PO4-3 were less variable during this period (– 7.93 to 28.73 and – 1.74 to 3.29 μmol m-2 h-1 for NO2-+ NO3- and PO4-3, respectively). Low NH4+ fluxes were similar to published estimates from lagoonal Gulf of Mexico (GOM) estuaries, possibly due to the reduced freshwater input. Diminished regeneration of phosphate relative to inorganic nitrogen observed during the study period was consistent with previous research in Pensacola Bay suggesting phytoplankton phosphorus limitation. Finally, the estimated residence time of Escambia Bay and the mean turnover times for NH4+ and NO2-+ NO3- suggested that benthic flux significantly influenced nitrogen concentrations in overlying water

Human cytomegalovirus: taking the strain

In celebrating the 60th anniversary of the first isolation of human cytomegalovirus (HCMV), we reflect on the merits and limitations of the viral strains currently being used to develop urgently needed treatments. HCMV research has been dependent for decades on the high-passage strains AD169 and Towne, heavily exploiting their capacity to replicate efficiently in fibroblasts. However, the genetic integrity of these strains is so severely compromised that great caution needs to be exercised when considering their past and future use. It is now evident that wild-type HCMV strains are not readily propagated in vitro. HCMV mutants are rapidly selected during isolation in fibroblasts, reproducibly affecting gene RL13, the UL128 locus (which includes genes UL128, UL130 and UL131A) and often the UL/b′ region. As a result, the virus becomes less cell associated, altered in tropism and less pathogenic. This problem is not restricted to high-passage strains, as even low-passage strains can harbour biologically significant mutations. Cloning and manipulation of the HCMV genome as a bacterial artificial chromosome (BAC) offers a means of working with stable, genetically defined strains. To this end, the low-passage strain Merlin genome was cloned as a BAC and sequentially repaired to match the viral sequence in the original clinical sample from which Merlin was derived. Restoration of UL128L to wild type was detrimental to growth in fibroblasts, whereas restoration of RL13 impaired growth in all cell types tested. Stable propagation of phenotypically wild-type virus could be achieved only by placing both regions under conditional expression. In addition to the development of these tools, the Merlin transcriptome and proteome have been characterized in unparalleled detail. Although Merlin may be representative of the clinical agent, high-throughput whole-genome deep sequencing studies have highlighted the remarkable high level of interstrain variation present in circulating virus. There is a need to develop systems capable of addressing the significance of this diversity, free from the confounding effects of genetic changes associated with in vitro adaptation. The generation of a set of BAC clones, each containing the genome of a different HCMV strain repaired to match the sequence in the clinical sample, would provide a pathway to address the biological and clinical effects of natural variation in wild-type HCMV