bluuebunny/crossref_metadata_2025 huggingface dataset:
Zebrafish IRF1, IRF3, and IRF7 Differentially Regulate IFNΦ1 and IFNΦ3 Expression through Assembly of Homo- or Heteroprotein Complexes
Authors: Feng Hui , Zhang Qi-Min , Zhang Yi-Bing , Li Zhi , Zhang Jun , Xiong Ya-Wei , Wu Min , Gui Jian-Fang
Published: August 2016

In mammals, IFN regulatory factor (IRF)1, IRF3, and IRF7 are three critical transcription factors that are pivotal for cooperative regulation of the type I IFN response. In this study, we explored the relative contribution of zebrafish (Danio rerio) IRF1 (DrIRF1), IRF3 (DrIRF3), and IRF7 (DrIRF7) (DrIRF1/3/7) to zebrafish IFNΦ1 (DrIFNΦ1) and IFNΦ3 (DrIFNΦ3) (DrIFNΦ1/3) activation. Following spring viremia of carp virus infection, DrIFNΦ1/3 and DrIRF1/3/7 transcripts are significantly induced in zebrafish tissues, which correlates with the replication of spring viremia of carp virus. DrIRF1/3/7 selectively bind to the IRF-binding element/IFN-stimulated regulatory element sites of DrIFNΦ1/3 promoters, with the exception that DrIRF3 has no preference for two IRF-binding element/IFN-stimulated regulatory element motifs within the DrIFNΦ3 promoter. Consistently, DrIRF3 alone activates DrIFNΦ1, but not DrIFNΦ3; DrIRF7 predominantly stimulates DrIFNΦ3; and DrIRF1 has similar potential to DrIFNΦ1 and DrIFNΦ3. Strikingly, DrIRF3 facilitates the binding of DrIRF1 and DrIRF7 to both zebrafish IFN promoters, and so does DrIRF7 for the binding of DrIRF1, particularly to the DrIFNΦ3 promoter. These binding properties correlate with differential responses of DrIFNΦ1 and DrIFNΦ3 to the combinatory stimulation of DrIRF1/3/7, depending on their relative amounts. Similar to the dual roles of human IRF3 in regulating IRF7-activated IFNα genes, DrIRF3 exerts dual effects on DrIRF1-mediated DrIFNΦ3 gene expression: an inhibitory effect at lower concentrations and a synergistic effect at higher concentrations. These data provide evidence that fish and mammals have evolved a similar IRF-dependent regulatory mechanism fine-tuning IFN gene activation.
Serum Uric Acid Level in Relation to Severity of the Disease and Mortality of Critically Ill Patients
Authors: Aminiahidashti Hamed , Bozorgi Farzad , Mousavi Seyed Jaber , Sedighi Omid , Gorji Ali Morad Heidari , Rashidian Hale
Published: August 2016

Aim: This study was conducted to evaluate the validity of serum uric acid (UA) in prediction of mortality among patients in the emergency department.

Materials and Methods: This is a prospective cohort study which was conducted during 2014. In this study, 120 critically ill patients who required Intensive Care Unit care services were included. For evaluation of severity of the disease, mortality in emergency department score (MEDS) in the first 24 h of admission, the requirement of using mechanical ventilation, taking vasopressor during the hospitalization time and severity of the disease based on MEDS score were measured. The patients were divided into two groups: Patients with serum UA level lower than 7.3 mg/dl and patients with serum UA level of equal or more than 7.3 mg/dl. For comparison of the mortality rate in groups, Chi-square and fisher exact tests were applied.

Results: In patients, who needed mechanical ventilation, average of serum UA was 7.82 ± 2.82; however, in the patients who did not need mechanical ventilation this amount was 6.16 ± 2.7, a difference was statically significant. We found a statically meaningful difference between serum UA level with requiring mechanical ventilation and the predictive level of UA 6.95 ± 0.73 (F = 8.52; P ≤ 0.004). In the evaluation of MEDS, most patients with serum UA levels lower than 7.3 mg/dl had lower MEDS points (on average 4.6 ± 3.21) in compared to patients with serum UA level higher than 7.3 mg/dl (on average 12 ± 2.99). This difference was found to be statistically significant which indicates the patients whose serum UA was 7.3 mg/dl or higher, were at higher risk of mortality.

Conclusion: The serum UA level in the 1st day of hospitalization of a critically ill patient is not an independent indicative factor in relation to mortality. High level of UA reveals critical status of the patient and requires mechanical ventilation.
Study of Invasive Pneumococcal Infection in Adults with Reference to Penicillin Resistance
Authors: Muley Vrishali Avinash , Ghadage Dnyaneshwari Purushottam , Yadav Gauri Eknath , Bhore Arvind Vamanrao
Published: August 2016

Background: Invasive pneumococcal infections often prove rapidly fatal, even where good medical treatment is readily available. In developed countries, up to 20% of people who contract pneumococcal meningitis die; however, in developing world, mortality is closer to 50%, even among hospitalized patients. The World Health Organization estimated 600,000–800,000 adult deaths each year from pneumococcal pneumonia, meningitis, and sepsis.

Aims: This study aims to estimate isolation rate of invasive pneumococcal infection in adults, to determine the antimicrobial susceptibility profile of Streptococcus pneumoniae. isolates and to study the associated risk factors.

Materials and Methods: A total of 120 patients with suspected invasive infection such as meningitis, septicemia, and pleural effusion, were included in the study. Various clinical specimens such as pus, cerebrospinal fluid, and other sterile body fluids were processed for isolation and identification of S. pneumoniae. Kirby–Bauer disc diffusion method was performed to determine the antimicrobial susceptibility profile. Minimum inhibitory concentration test was performed to determine the penicillin resistance.

Results: Of 120 patients, 40 (33.33%) cases were proven by culture to have an invasive pneumococcal infection. The most common clinical condition observed was meningitis followed by pneumonia with pleural effusion and sepsis. Pneumococcal isolates exhibited 40% resistance to cotrimoxazole and 12.73% to chloramphenicol. Two meningeal isolates exhibited penicillin resistance. Comorbidities observed in 21 (52.5%) cases were mainly Diabetes mellitus, smoking, and alcoholism.

Conclusions: Invasive pneumococcal infection has poor prognosis and penicillin‑resistant strains have become increasingly common. This study emphasizes the importance of judicious use of antibiotics, especially to refrain their use in mild self-limiting upper respiratory infections.
Unusual Presentation of Multibacillary Nodular Leprosy
Authors: Raut Shweta , Kanade Swapna , Nataraj Gita , Mehta Preeti
Published: August 2016

Despite India achieving the goal of elimination of leprosy as a public health problem, leprosy is still being transmitted in India. However, due to decreased clinical suspicion of leprosy and atypical case presentations, such cases may be not be diagnosed. We present a case report of an unusual presentation of multibacillary leprosy which presented as nodular lesions. This case report indicates that atypical presentations of leprosy may be missed out by primary care physicians.
Urine Albumin Excretion as a Marker of Acute Glycemic Changes in Isolated Postprandial Hyperglycemia
Authors: Shilpasree Alagilawada S , Patil Vidya S , Patil Vijayetha P , Ingleshwar Deepti G
Published: August 2016

Introduction: Postprandial hyperglycemia is a major risk factor for the development of cardiovascular diseases (CVDs), and Most of the times it occurs in patients with normal glycemic control diagnosed by fasting blood glucose (FBG) and glycated hemoglobin levels. Urine albumin excretion (UAE) is an independent predictor of CVD risk.

Aim: To estimate UAE in isolated postprandial hyperglycemia (IPPHG) patients and to assess the relationship of UAE with FBG and postprandial blood glucose (PPBG) levels.

Settings and Design: A cross-sectional study was carried out in 318 patients with Type II diabetes in the age group 30–60 years for 6 months.

Materials and Methods: Patients were divided into five groups based on their FBG and PPBG values. UAE and lipid profile were measured in all the groups.

Statistical Analysis: UAE and lipid profile in different groups were compared using ANOVA. Regression analysis was used to predict the variation of UAE with FBG, PPBG, and total cholesterol (TC).

Results: Patients with IPPHG had significantly higher albumin excretion compared to normoglycemia (NG) group [P < 0.0001]. In impaired glucose tolerance and isolated fasting hyperglycemia groups, it did not differ significantly from NG group [P = 0.206 and P = 0.173]. Lipid profile did not show any significant difference between the groups. On regression analysis, PPBG but not FBG or TC correlated positively with UAE.

Conclusion: UAE is easy, less expensive, and Widely available method done on spot urine samples which predicts the acute glycemic changes and increased risk of developing CVDs in patients with IPPHG.
Study of the Stability of Various Biochemical Analytes in Samples Stored at Different Predefined Storage Conditions at an Accredited Laboratory of India
Authors: Kachhawa Kamal , Kachhawa Poonam , Varma Meena , Behera Rasmirekha , Agrawal Divya , Kumar Sanjay
Published: August 2016

Background: Storage of serum and other blood products is often necessary in laboratories because of technical issues or to preserve samples for subsequent research purposes. The aim of this study was to determine whether the stability of biochemical analytes is affected by storage conditions.

Materials and Methods: A total of 17 biochemical analytes in the sera of ten patients were examined following storage. Subsequent to determining the baseline measurements, the serum of each patient was aliquoted and stored at −20°C for 7, 15, and 30 days and then analyzed for stability. The results were compared with the initial analysis measurements obtained from fresh samples. Mean changes compared to baseline (T0) concentrations were evaluated both statistically and clinically.

Results: Our results show that sodium, potassium, urea, creatinine, uric acid, total calcium, phosphorus, direct bilirubin, total bilirubin, aspartate aminotransferase, alanine aminotransferase, alkaline phosphatase, total protein, albumin, cholesterol, and triglyceride levels were stable under all conditions. Serum amylase was the only analyte demonstrating instability following prolonged storage; amylase levels changed significantly (both statistically and clinically) at 7, 15, and 30 days (P < 0.05).

Conclusion: Most common biochemical analytes, except for amylase, showed adequate stability in serum following 30 days of storage at −20°C. Serum amylase analysis should be conducted on the same day that the sample is received in the laboratory.
A Comparative Analysis of Polymerase Chain Reaction and Direct Fluorescent Antibody Test for Diagnosis of Genital Herpes
Authors: Patwardhan Vrushali , Bhalla Preena , Rawat Deepti , Garg Vijay Kumar , Sardana Kabir , Sethi Sumit
Published: August 2016

Objective: To compare laboratory tests that can simultaneously detect and type herpes simplex virus (HSV) directly from the genital ulcer specimens in clinically suspected cases of genital herpes.

Materials and Methods: A study was conducted over 10 months and 44 adult male and female patients clinically suspected with genital herpes were recruited. Genital ulcer swab specimens were subjected to glycoprotein-G gene-based conventional polymerase chain reaction (PCR) and commercially available direct fluorescent antibody (DFA) test and the results were compared.

Results: PCR for HSV was positive in 82% (36/44) cases. DFA was positive in 68.2% (30/44) cases. There was 100% agreement between HSV types detected by DFA and PCR. The strength of agreement between the results was better in primary genital herpes than recurrent cases.

Conclusion: PCR was found to be better in the detection of HSV in recurrent genital herpes patients. It is a better modality, especially when genital herpes clinically presents with ulcerative or crusted lesions, and is also a cheaper alternative as compared to DFA.
Genetic Association of HLA-A*26, -A*31, and -B*51 with Behcet's Disease in Saudi Patients
Authors: Al-Okaily Fahda , Al-Rashidi Seham , Al-Balawi Maysoon , Mustafa MD. , Arfin Misbahul , Al-Asmari Abdulrahman
Published: August 2016

Background

HLA-B*51 has been universally associated with Behcet's disease (BD) susceptibility, while different alleles of HLA-A have also been identified as independent BD susceptibility loci in various ethnic populations. The objective of this study was to investigate associations of HLA-A and - B alleles with BD in Saudi patients.

Materials and Methods

Genotyping for HLA-A and HLA-B was performed using HLA genotyping kit (Lab type(R) SSO) in 120 Saudi subjects, including 60 BD patients and 60 matched healthy controls.

Results

Our results revealed that frequencies of HLA-A*26, -A*31, and - B*51 were significantly higher in BD patients than in controls, suggesting that HLA-A*26, -A*31, and - B*51 are associated with BD. The frequency of HLA-B*15 was significantly lower in BD patients than in controls. Stratification of genotyping results into active and nonactive forms of BD revealed that the frequency of HLA-A*31 was significantly higher in the nonactive form than in the active form of BD, while there was no significant difference in the distribution of other alleles between the two forms of BD.

Conclusion

This study suggests that HLA-A*26, -A*31, and - B*51 are associated with susceptibility risk to BD, while HLA-B*15 may be protective in Saudi patients. However, larger scale studies are needed to confirm these findings.
PATTERNS OF MARSH FORAMINIFERA, GALVESTON BAY, TEXAS
Authors: Phleger Fred B.
Published: August 2016

Populations of living Foraminifera were studied from six areas of marine marsh in Galveston Bay. The general marsh foraminiferal assemblage is an Ammotium salsum‐Miliammina fusca one, with common Ammonia beccarii, Arenoparrella mexicana, and Trochammina inflata, and also containing Ammoastuta inepta, Elphidium spp., Tiphotrocha comprimata, and Trochammina macrescens in somewhat smaller frequencies.

The following marsh environments have distinctive assemblages of Foraminifera: 1) channel or bay bordering a marsh, 2) fringing Spartina zone, 3) Salicornia berm, 4) inner Spartina zone, 5) inner Salicornia zone, 6) lagoon barrier marsh, 7) “more saline” marsh, and 8) “less saline” marsh. Living populations are very small to very large, living‐total population rates are large and deposition rates are high.

Extreme range of environmental conditions limits the variety of marsh Foraminifera. Knowledge of the environment is inadequate to explain distributions within the marsh.
CHARACTERISTICS OF A MARINE NITRIFYING BACTERIUM, NITROSOCYSTIS OCEANUS SP. N.1
Authors: Watson Stanley W.
Published: August 2016

A new species of an ammonia‐oxidizing bacterium, Nitrosocystis oceanus, is described. This is the first nitrifying bacterium ever isolated from open ocean waters and the first species of the genus Nitrosocystis observed in over 30‐years. The cells are gram negative, spherical to ellipsoidal, 1.8–2.2 µ in diameter, and occur as single cells, diploids, and occasionally as tetrads. Cells at times formed cysts and zoogloea. The most consistent and outstanding generic characteristic is the ultrastructure of the cells. Cells of this genus have a cytomembrane organelle composed of a series of flattened vesicles that transverse and bisect the cell; while cells of Nitrosomonas sp. lack this complex membranous organelle, they do have one to two concentric membranes at the periphery of the cell adjacent to the plasma membrane. Nitrosocystis oceanus is an obligate autotroph using only ammonia as an energy source and carbon dioxide as a carbon source. This bacterium grows optimally at 30C and in ammonia concentrations of 5 × 108 – 2.4 × 105 µg‐at. NH3‐N/liter. It is an obligate halophile, requiring natural seawater for growth, and it lyses when suspended in distilled water. Growing optimally in continuous cultures, individual cells produced 2 × 10‐6 µM of NO2– per day. Nitrosocystis oceunus was cultured repeatedly from offshore waters of the western North and South Atlantic Ocean since 1959. It is estimated that the standing crop of these organisms is less than one bacterium per ml. This number of bacteria in the upper 100 m of tropical waters would produce approximately 0.07 µg‐at. NO2–‐N liter−1 year−1.
SOME FEATURES OF SALINE LAKES IN CENTRAL WASHINGTON1
Authors: Edmondson W. T. , Anderson George C.
Published: August 2016

The central part of the State of Washington has an arid climate and contains a number of saline lakes. Several are meromictic and show a variety of vertical gradients of salinity and temperature.

The mixolimnion of Soap Lake has been diluted by increased entry of freshwater from 39.4 g/liter in 1946 to 18.0 in 1964 while the monimolimnion has been maintained at more than 130 g/liter. The stability of the chemocline was studied by an injection of radioactive rubidium. The radioactivity spread laterally in all directions, mostly in a layer less than 2 m thick, to a maximum observed mean radius of 53 m in 13 days. The corresponding eddy diffusion coefficient is 3.2 cm2/sec.
COMPARATIVE ENERGETICS OF A POLLUTED STREAM
Authors: King Darrell L. , Ball Robert C.
Published: August 2016

An attempt was made to relate changes in production to variation in stream ecology within a 48.3 km section of a polluted warm‐water stream. Energy budgets were constructed for the entire river and for five different ecological zones. The greatest variations were associated with industrial and domestic pollution and the inflow of inorganic sediment from an area of highway construction. Net yield of various aquatic invertebrates was determined from changes in population size between sampling periods. Average net yields for the summer of 1961 were 17 cal m−2 day−1 for the herbivorous aquatic insects, and 13 cal m−2 day−1 for the tubificid worms. Photosynthetic efficiency was estimated to be 0.045% of the solar energy available at the surface of the stream.
PHOSPHATE ABSORPTION IN EELGRASS1
Authors: McRoy C. Peter , Barsdate Robert J.
Published: August 2016

The absorption of phosphate by eelgrass (Zostera marina L.) was studied using 32P in a partitioned container where leaves were separated from roots and rhizomes. Absorption, which was greatest in the light, occurred through both leaves and roots, and the absorbed phosphorus was transported rapidly to all parts of the plant. It therefore appears that eelgrass can use phosphate from sediments and from water. Phosphate removed from solution by the roots and rhizomes was returned in part to the surrounding water through the leaves, suggesting that in nature seagrass may act either as a sink or as a source for dissolved phosphorus in estuarine waters.
The predatory behavior of Mesocyclops edax: Predator preferences, prey defenses, and starvation‐induced changes1
Authors: Williamson Craig E.
Published: August 2016

The predatory behavior of field‐collected Mesocyclops edax on four different kinds of prey was compared under similar and different predator starvation regimes. Unstarved Mesocyclops did not consume either the ciliate Rhabdostyla or the cladoceran Bosmina. Increasing starvation in the predator increased the probability of ingestion after encounter for both of these prey. The rotifer Asplanchna and the nauplii of the copepod Diaptomus were consumed by starved and unstarved Mesocyclops. The probability of ingestion after encounter increased with increasing predator starvation for Asplanchna, hut not for nauplii. Both behavioral and morphological characteristics of the prey were important in regulating the predator’s ability to capture and ingest the prey and in determining the time and energy which the predator had to invest to receive its nutritional rewards.
Elemental and isotopic characterization of dissolved and particulate organic matter in a unique California upwelling system: Importance of size and composition in the export of labile material
Authors: Walker B. D. , McCarthy M. D.
Published: August 2016

We report the interseasonal variation in bulk elemental and stable isotopic (δ13C, δ15N) composition of dissolved and particulate organic matter (DOM, POM) during a high‐resolution time series (2007–2009) on the Big Sur coast. In addition to interseasonal variations, we explore the relationships between physical size and reactivity (i.e., composition) of exportable organic matter (OM) pools, and characterize the elemental and isotopic composition of size‐fractionated POM and DOM pools within this potentially high‐nutrient, low‐chlorophyll (HNLC) California upwelling region. Average POM concentrations were low (< 5.2 µmol C L−1 and < 0.7 µmol N L−1), and all OM pools had low C : N ratios (DOM average = 15.0 and POM < 7.8)—indicating that this upwelling center may represent an important source of N‐rich material to offshore environments. Seasonal “excess” dissolved organic carbon (DOC) production was significant (~ 30–80 µmol L−1 DOC); however, dissolved organic nitrogen (DON) production and cycling was largely decoupled from both DOC and physical processes. Overall, our results are consistent with this region representing an “HNLC upwelling system.” The distinct bulk elemental and isotopic OM composition and seasonality vs. that of high‐productivity upwelling regions highlights the need to better understand the biogeochemical diversity of upwelling systems. Finally, we observed a quantifiable size–composition relationship across both POM and DOM size classes, perhaps representing a powerful new tool for modeling N vs. C fluxes in ocean biogeochemical cycles.
Zooplankton fecal pellet flux in the abyssal northeast Pacific: A 15 year time‐series study
Authors: Wilson S. E. , Ruhl H. A. , Smith, Jr. K. L.
Published: August 2016

Sinking particulate material collected in sequencing sediment traps moored at 3500 m depth (600 m above bottom) from 1993 to 2008 at the abyssal time‐series Sta. M in the northeast Pacific was analyzed via microscopy and digital imaging. Intact zooplankton fecal pellets were quantified and size, shape, and carbon content were measured. The most common identifiable fecal pellets were from larvaceans, which feed on small particles. Other abundant fecal pellets were likely produced by large copepods and euphausiids. The proportion of identifiable fecal pellet carbon to total particulate organic carbon (POC) flux varied and ranged from 3.3% to 47.7%. Fecal pellet flux and fecal pellet‐derived carbon flux was lowest in February, and highest in May, August, and November samples. The proportion of total POC in identifiable fecal pellets was negatively correlated to overall POC flux and to indicators of climate variability. The North Pacific Gyre Oscillation and Northern Oscillation Index climate indices were negatively correlated to the dominance of fecal pellets in POC flux, with changes in fecal pellet fluxes temporally lagging climate‐related changes by about 3 and 5 months, respectively. Variations in zooplankton distribution and abundance affect biogeochemical cycling to abyssal depths, further demonstrating how a changing climate may affect deep‐sea ecology. The dominance of zooplankton fecal pellets can shift proportionally, providing new insight into the processes controlling marine carbon sequestration in the deep sea.
Assessment of light absorption within highly scattering bottom sea ice from under‐ice light measurements: Implications for Arctic ice algae primary production
Authors: Ehn Jens K. , Mundy C. J.
Published: August 2016

Primary production estimates of ice algae within the bottommost layers of the Arctic ice cover are commonly derived using irradiance measurements taken immediately below the solid ice bottom. However, radiation absorbed by ice algae is significantly affected by the high‐scattering sea ice environment they are embedded within because scattering increases the pathlength traveled by photons and therefore the probability of photon encounters with algal cells. Failing to account for this enhanced absorption may considerably affect estimates of the timing and magnitude of ice algal production. To demonstrate the effect of scattering and attenuation, multipliers for absorption amplification (Φ) and layer average opacity (χ) were derived from observations of chlorophyll a concentration and the vertical attenuation coefficient over the bottom 2.5 cm of landfast sea ice. Φ reached values over 19 at low chlorophyll a, but became < 2 at high biomass levels, whereas χ became larger as biomass levels increased. Using Φ to construct an apparent photosynthesis vs. irradiance relationship showed that light limitation is greatly reduced relative to the case where scattering is not considered. This highlights an important interaction not previously noted for ice algal production in their high‐scattering environment. Knowledge of this absorption amplification can help explain ice algal phenology during the spring bloom and will improve ice algal production estimates and model parameterizations.
The extent that natural lakes in the United States of America have been changed by cultural eutrophication
Authors: Bachmann Roger W. , Hoyer Mark V. , Canfield, Jr. Daniel E.
Published: August 2016

We used paleolimnological data for 240 lakes from the U.S. Environmental Protection Agency's (USEPA) 2007 National Lakes Assessment to estimate the extent that natural lakes in the coterminous United States have been changed by anthropogenic activities. In order to detect cultural eutrophication, we analyzed data on diatom‐inferred concentrations of total nitrogen (TN), total phosphorus (TP), specific conductance (SC), and pH as determined from lake sediments from the tops and bottoms of sediment cores from 240 natural lakes where the bottom of the core was judged to represent conditions prior to European settlement. We found no statistically significant increases in the average concentrations of TN, while TP decreased by 14% in this population of lakes since the time of European settlement. We also analyzed data from 48 reference lakes used by the USEPA to determine the relative condition of the sample lakes. Paired t‐tests showed the TN concentrations were not significantly different between the two time periods (p > 5%), while the average TP concentrations had significantly decreased by 26% since presettlement times (p < 5%). There were statistically significant increases in SC (17%) and pH (0.05 pH units). There were no statistically significant differences between the changes in TP, TN, SC, and pH in the 240 sample lakes and the changes in the 48 reference lakes. The proportions of lakes categorized as oligotrophic, mesotrophic, eutrophic, and hypereutrophic for the presettlement time period were not significantly different from the proportions found in 2007.
A spatiotemporal investigation of varved sediments highlights the dynamics of hypolimnetic hypoxia in a large hard‐water lake over the last 150 years
Authors: Jenny Jean-Philippe , Arnaud Fabien , Dorioz Jean-Marcel , Covex Charline Giguet , Frossard Victor , Sabatier Pierre , Millet Laurent , Reyss Jean-Louis , Tachikawa Kazuyo , Bard Edouard , Pignol Cécile , Soufi Fayçal , Romeyer Olivier , Perga Marie-Elodie
Published: August 2016

The spatiotemporal distribution of biochemical varves spanning the last 150 yr was investigated using 40 cores collected over a depth gradient in a large subalpine lake—Lake Bourget—in the French Alps. Four‐dimensional sedimentological, biological, and geochemical analyses show that varve preservation can be used as a reliable proxy to reconstruct annual‐to‐decadal oscillations of hypoxia in large lakes. The volume of hypoxic waters was calculated by integrating the volume between the lake bottom and the depth of the shallowest varve‐bearing core for each year. Although Lake Bourget bottom waters have been oxic over the last 9000 yr, severe hypoxia has occurred only since 1933 ± 1. The volume of hypoxic waters showed, thereafter, a succession of pronounced fluctuations, leading to an increase of 8% of the total lake volume in the 1960s, a decline in the 1980s, and a second, ongoing increase since 1990. Whereas the initial onset of persistent hypoxic conditions could be attributed to eutrophication due to nutrient‐rich inputs from sewage water and/or diffuse contamination, the later fluctuations were also driven by climatic factors, i.e., flooding, rising air temperatures, and phosphorus‐independent changes in primary production. Hence, cumulative effects related to global warming seem to have driven hypolimnetic hypoxic conditions since equilibrium was initially disrupted due to a drastic shift in the trophic state.
Evidence for active vertical migration by two dinoflagellates experiencing iron, nitrogen, and phosphorus limitation
Authors: Peacock Melissa B. , Kudela Raphael M.
Published: August 2016

Vertical migration and subsequent assimilation of iron (Fe) and nitrate at depth by the dinoflagellates Akashiwo sanguinea and Prorocentrum micans were investigated using laboratory vertically stratified water columns. Active migration was observed in four separate experiments with varying degrees of nitrogen (N), phosphorus, and Fe stress. Stable isotopes of Fe (57Fe‐FeCl3) and N (15N‐NaNO3) were assimilated from the bottom 0.4 m of the column during migration, with significant enrichment of particulate samples collected from the surface compared to the initial A. sanguinea culture or natural water from Monterey Bay containing P. micans. In all four experiments, there was significant drawdown of nitrate from the column, with depth‐integrated drawdown of greater than 50 mmol m−2 in the P. micans experiment over 72 h. These experiments provide evidence for dinoflagellate assimilation of N and Fe at depth. Harmful algal blooms of vertically migrating dinoflagellates such as A. sanguinea and P. micans are often associated with macro‐ and micronutrient depletion in surface waters; assimilation of iron as well as macronutrients at depth could be an important ecological advantage in environments where light and nutrients are spatially separated.
The quantitative filter technique for measuring phytoplankton absorption: Interference by MAAs in the UV waveband
Authors: Laurion Isabelle , Blouin Frédérick , Roy Suzanne
Published: August 2016

The absorption of suspended particulate material is commonly estimated with the filter pad technique, which requires a correction for pathlength amplification. The pathlength amplification factor (β) varies among different studies and phytoplankton species or communities. It remains the largest source of uncertainty in estimated absorption coefficients. Recently, several empirical models estimating this correction were developed but mostly for visible range. In this study, β was calculated empirically from the ratio of filtered to suspension absorption between 280 and 850 nm for cultures of two dinoflagellates and one diatom. Results show that in the visible waveband, β values are relatively constant and fall within the published range (averages between 2.4 and 2.8). These values remain flat over the UV waveband for the diatom tested. However, below 400 nm, the presence of mycosporine‐like amino acids (MAAs) strongly influences the absorbance measurements. For the dinoflagellates studied, the ultraviolet (UV) absorbance measured on frozen filters (stored in liquid nitrogen) reveals a large peak (Sosik 1999) caused by high concentrations of MAAs, which is much smaller on absorbance scans of suspended cells. This amplified UV peak adds to the true amplification effect caused by the extended pathlength of light in filter pads. This artifact, caused by the extracellular release of the water‐soluble MAAs during freezing, also was observed to a lower degree with measurements performed on fresh filters (immediate scanning), precluding the use of this method to estimate UV absorption in the species tested.
Ethanol: a better preservation technique for Daphnia
Authors: Black A. Ross , Dodson Stanley I.
Published: August 2016

A 4% formalin‐40% sucrose solution has been used by limnologists for three decades as the preferred freshwater zooplankton preservative because it kills and fixes cladocera (Branchiopoda) with relatively little distortion. Because of the increasing evidence of health hazards related to formalin, we sought an alternative, safer preservative that satisfies the need for low distortion. Our results suggest the ethanol preservative methods (70% and 95% treatments) are as good or better as using 4% sugar formalin to fix and store samples. Our results indicate the best method is to fix samples in 95% EtOH followed by storage in 70% EtOH. This technique gave us the least frequent distortion, the highest average number of eggs per female, and the fewest embryos lost from the brood chamber. None of the techniques appeared to have positive or negative effects on body length. Using hot water to fix animals before storage is not recommended.
Analysis of dissolved noble gases in the porewater of lacustrine sediments
Authors: Brennwald Matthias S. , Hofer Markus , Peeters Frank , Aeschbach‐Hertig Werner , Strassmann Kuno , Kipfer Rolf , Imboden Dieter M.
Published: August 2016

Here we present a new method for the sampling and quantitative extraction of dissolved He, Ne, Ar, Kr, and Xe from lake sediment samples leading to determinations of porewater noble gas concentration profiles and the isotopic ratios 3He/4He, 20Ne/22Ne, and 40Ar/36Ar. Bulk sediment is transferred from a sediment core into standard Cu sample tubes without exposure to the atmosphere or other gas reservoirs. The noble gases are then extracted from the porewater by degassing the sediment in an evacuated extraction vessel and analyzed following standard mass spectrometric procedures. In tests of the new method using 0.8 to 1.4 m long sediment cores from two Swiss lakes, analytical uncertainties were only slightly greater than those of standard water samples. The majority of porewater noble gas concentrations and isotopic ratios were found to correspond closely to those measured in the overlying lake water. Because these values reflect water temperature and salinity during atmospheric equilibration at the lake surface, historical conditions are expected to be archived further downcore in the sediment porewater. This method therefore has great potential for paleolimnological reconstructions. The formation of methane bubbles in anoxic sediment layers is one process that may alter gas distributions. However because the lighter noble gases are most sensitive to degassing effects, noble gas data can be used to detect this process. In addition, noble gas data can yield information on the transport processes occurring in the sediment pore space and on the input of water or gas to the sediment from external sources.
Application of the isotope pairing technique in sediments where anammox and denitrification coexist
Authors: Risgaard‐Petersen Nils , Nielsen Lars Peter , Rysgaard Søren , Dalsgaard Tage , Meyer Rikke Louise
Published: August 2016

The isotope pairing technique (IPT) is a well‐established 15N method for estimation of denitrification. Presence of anammox, the anaerobic oxidation of NH4+ to N2 with NO2− results in violation of central assumptions on which the IPT is built. It is shown that anammox activity causes overestimation of the N2 production calculated by the IPT. However, experiments with different additions of 15NO3− will reveal the problems posed by anammox. Two alternative calculation procedures are presented, which enable a more accurate quantification of anammox and denitrification activity in sediments where the processes coexist. One procedure is based on measurements of 15N‐N2 production in 15NOx−‐amended intact sediment cores and data addressing the contribution of anammox to total N2 production estimated from slurry incubations. The other procedure is based on measurements of 15N2 production in at least two parallel series of sediment cores incubated with different 15NOx− additions. The calculation procedure presented is used on field data from four studies where the IPT was used and the potential anammox rate measured. The IPT overestimated total 14N‐N2 production rates by 0%, 2.5%, 31%, and 82% relative to the revised estimates from the 4 different sites, where anammox accounted for 0%, 6%, 18%, and 69.8%, respectively, of N2 production. The overestimation of true denitrification was, however, up to several hundred percent. Our analysis suggests however that the IPT does not seriously overestimate N2 production in estuarine sediments because anammox accounts for <6% of N2 production in such sediments, according to present knowledge.
A new method for the quantitative separation of diatom frustules from lake sediments
Authors: Rings Andreas , Lücke Andreas , Schleser Gerhard H.
Published: August 2016

Achieving a purified fraction of diatom frustules from soft sediment samples is an essential requirement for using their biogenic silica as a carrier of paleolimnological and paleoenvironmental information. Because diatom frustules behave hydrodynamically unlike most mineral grains, these types of particles can theoretically be separated in liquids. Based on this principle, a new method has been developed, which employs split‐flow thin fractionation (SPLITT) as a tool for separating diatom frustules from other sedimentary particles. The SPLITT channel selected for this study had a length of 20 cm, a breadth of 4 cm, and a height of 371 µm. For optimum results, samples were pretreated, e.g., suspended and wet‐sieved prior to any processing with the SPLITT cell. The sample concentrations used in the fractionation process were below 0.1% (w/v) to minimize particle‐particle interaction, which affects the quality of the separation. The advantages of SPLITT fractionation over other tested methods are good reproducibility, high throughput by continuous flow, minimum losses of frustules, and minimum contamination of the diatom fraction by minerals or sponge spicules. Separation results from representative sediment samples of different origin, age, and compaction as well as various organic (0.5% to 10% total organic carbon) and biogenic opal contents (1% to 20% biogenic silica) are presented and discussed. They demonstrate that the developed separation technique yields highly purified and, within the processing tolerances, quantitative samples of diatom frustules from bulk lacustrine sediments.
Application of a Fast Isoprene Sensor (FIS) for measuring isoprene production from marine samples
Authors: Exton Dan A. , Smith David J. , McGenity Terry J. , Steinke Michael , Hills Alan J. , Suggett David J.
Published: August 2016

Research into isoprene production from marine sources traditionally relies on gas chromatography techniques which are labor intensive, provide a slow sample turnover, and require significant method training. An alternative method is the use of a Fast Isoprene Sensor (FIS), a chemiluminescence‐based approach that provides real time isoprene analysis, but is relatively simple to run and also portable. Until now, the FIS has been used in terrestrial but not aquatic isoprene studies. Due to the added difficulties with marine compared with terrestrial sampling, particularly potential interference from dimethyl sulfide (DMS), we have developed a new protocol that allows accurate and reliable data to be obtained from FIS analysis. The detection limit of our modified system to standard gas was 0.02 nM (0.5 ppbv), while minimum isoprene production detected by the FIS was 0.59 nmol h−1 (for Thalassiosira weissflogii). We also compared our FIS‐based approach with GC analysis of isoprene emission from marine samples of micro‐ and macro‐algae, and demonstrated a strong similarity (r2 = 0.910, slope = 1.003). The ability to use FIS analysis with marine samples will significantly broaden the scope of isoprene research in marine environments, permitting remote field work, and allow previously unanswered questions to be addressed.
An assessment of the accuracy and precision of water quality parameters retrieved with the Matrix Inversion Method.
Authors: Campbell Glenn , Phinn Stuart R.
Published: August 2016

There is an increasing demand for quantitative inland water quality observations from satellites. One approach to estimate water quality constituent (chlorophyll and other pigments, total suspended material, and colored dissolved organic matter) concentrations from remote sensing radiance measured over inland waters is to apply a Matrix Inversion Method (MIM). Using the Hydrolight® radiative transfer model and typical water quality constituent concentrations from subtropical Wivenhoe Dam, Australia, this article demonstrates that significant improvements in the accuracy and precision of retrieved water quality constituent values can be obtained by using semianalytically estimated values for the proportionality factor that are calculated separately for each spectral band of the MERIS sensor. Furthermore, it shows that overdetermined systems of equations can be used to mitigate the effect of unknown and endemic sources of error in the remote sensing system. The residuals left after the inversion of the reflectance spectrum can also be used to assign a reliability measure to the retrievals of total suspended material (TSM) and colored dissolved organic matter (CDOM), but not for chlorophyll a. The results of this study may be used to improve algorithms for the remote sensing of water quality for freshwater impoundments.
Counting and measuring epibenthic organisms from digital photographs: A semiautomated approach
Authors: Beuchel Frank , Primicerio Raul , Lønne Ole Jørgen , Gulliksen Bjørn , Birkely Sten‐Richard
Published: August 2016

Benthic rocky bottom studies often investigate community structure and function where estimates of percentage cover and abundance of epibenthic organisms are required. Nondestructive photographic methods have the advantage of preserving benthic communities for repeated sampling. There is a need to accelerate image processing to make sample analysis more cost efficient and to make the data available in a timely manner. A semiautomated procedure to estimate epibenthic cover and abundance using Adobe Photoshop and the image analysis plug‐in Fovea Pro was developed to meet this need. The method improves upon previous techniques by using color‐based automated selection tools and a species‐coding system. The technique required some manual processing because some species were less suitable for color recognition and the photographs were of inconsistent quality. The semiautomated selection of colony‐forming organisms was validated by comparing it to a strictly manual approach using a data set from Balsfjord/northern Norway. Constrained ordination and Procrustes analyses showed that the automatic and manual methods were equally effective at documenting variation in the species/abundance data along the driving ecological gradient of depth. The minor deviations in species abundance estimation between the two methods (mostly <20%) were unrelated to the depth gradient and thus had negligible influence on the main ecological conclusions of the study. The semiautomated method is up to four times faster than the manual approach, has clear advantages over former benthic image analysis methods, and is well suited for detection of systematic biological patterns like ecological gradients.
A comparative study of methods for surface area and three‐dimensional shape measurement of coral skeletons
Authors: Veal C. J. , Holmes G. , Nunez M. , Hoegh‐Guldberg O. , Osborn J.
Published: August 2016

The three‐dimensional morphology and surface area of organisms such as reef‐building corals is central to their biology. Consequently, being able to detect and measure this aspect of corals is critical to understanding their interactions with the surrounding environment. This study explores six different methods of three‐dimensional shape and surface area measurements using the range of morphology associated with the Scleractinian corals: Goniopora tenuidens, Acropora intermedia, and Porites cylindrica. Wax dipping; foil wrapping; multi‐station convergent photogrammetry that used the naturally occurring optical texture for conjugate point matching; stereo photogrammetry that used projected light to provide optical texture; a handheld laser scanner that employed two cameras and a structured light source; and X‐ray computer tomography (CT) scanning were applied to each coral skeleton to determine the spatial resolution of surface detection as well as the accuracy of surface area estimate of each method. Compared with X‐ray CT, wax dipping provided the best estimate of the surface area of coral skeletons that had external corallites, regardless of morphological complexity. Foil wrapping consistently showed a large degree of error on all coral morphologies. The photogrammetry and laserscanning solutions were effective only on corals with simple morphologies. The two techniques that used projected lighting were both subject to skeletal light scattering, caused by both gross morphology and meso‐coral architecture and which degraded signal triangulation, but otherwise provided solutions with good spatial resolution. X‐ray CT scanning provided the highest resolution surface area estimates, detecting surface features smaller than 1000 µm2.
Isotopic composition of carbon dioxide lost by evasion from surface water to the atmosphere: Methodological comparison of a direct and indirect approach
Authors: Billett Michael F. , Garnett Mark H.
Published: August 2016

The age and source of CO2 released from water surfaces to the atmosphere provides significant insight into the processes that control this important flux in key areas of the biosphere, such as peatlands and tropical river systems. Two approaches currently exist that enable the isotopic composition of CO2 lost by evasion (degassing) to be either measured or estimated. 13C‐CO2 and 14C‐CO2 can be measured directly using a molecular sieve trapping system attached to a floating chamber, or indirectly by calculation from DIC. We present a comparison of the two methods from samples collected from low‐productivity UK peatland streams supersaturated in CO2. On six occasions, samples of evaded CO2 were collected above the water surface for the determination of δ13C and 14C. Simultaneously, samples of streamwater were collected for the determination of the isotopic composition of DIC. Our results suggest that whereas on some occasions the radiocarbon ages of evaded CO2 and DIC were similar, on others the measured 14C‐DIC age was significantly older. Differences were also observed between the directly measured and calculated δ13C‐CO2 values. We critically evaluate both methods, highlight the importance of making the appropriate isotopic corrections for evasion CO2, and conclude that care needs to be taken in applying the indirect approach, as some of the inherent assumptions associated with equilibrium conditions used in the underlying calculation may not hold in certain aquatic systems.