bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition
Authors: Chen Lei , Feng Kai-Yan , Cai Yu-Dong , Chou Kuo-Chen , Li Hai-Peng
Published: June 2010

Background

Metabolic pathway is a highly regulated network consisting of many metabolic reactions involving substrates, enzymes, and products, where substrates can be transformed into products with particular catalytic enzymes. Since experimental determination of the network of substrate-enzyme-product triad (whether the substrate can be transformed into the product with a given enzyme) is both time-consuming and expensive, it would be very useful to develop a computational approach for predicting the network of substrate-enzyme-product triads.

Results

A mathematical model for predicting the network of substrate-enzyme-product triads was developed. Meanwhile, a benchmark dataset was constructed that contains 744,192 substrate-enzyme-product triads, of which 14,592 are networking triads, and 729,600 are non-networking triads; i.e., the number of the negative triads was about 50 times the number of the positive triads. The molecular graph was introduced to calculate the similarity between the substrate compounds and between the product compounds, while the functional domain composition was introduced to calculate the similarity between enzyme molecules. The nearest neighbour algorithm was utilized as a prediction engine, in which a novel metric was introduced to measure the "nearness" between triads. To train and test the prediction engine, one tenth of the positive triads and one tenth of the negative triads were randomly picked from the benchmark dataset as the testing samples, while the remaining were used to train the prediction model. It was observed that the overall success rate in predicting the network for the testing samples was 98.71%, with 95.41% success rate for the 1,460 testing networking triads and 98.77% for the 72,960 testing non-networking triads.

Conclusions

It is quite promising and encouraged to use the molecular graph to calculate the similarity between compounds and use the functional domain composition to calculate the similarity between enzymes for studying the substrate-enzyme-product network system. The software is available upon request.
Dietary patterns associated with fall-related fracture in elderly Japanese: a population based prospective study
Authors: Monma Yasutake , Niu Kaijun , Iwasaki Koh , Tomita Naoki , Nakaya Naoki , Hozawa Atsushi , Kuriyama Shinichi , Takayama Shin , Seki Takashi , Takeda Takashi , Yaegashi Nobuo , Ebihara Satoru , Arai Hiroyuki , Nagatomi Ryoichi , Tsuji Ichiro
Published: June 2010

Background

Diet is considered an important factor for bone health, but is composed of a wide variety of foods containing complex combinations of nutrients. Therefore we investigated the relationship between dietary patterns and fall-related fractures in the elderly.

Methods

We designed a population-based prospective survey of 1178 elderly people in Japan in 2002. Dietary intake was assessed with a 75-item food frequency questionnaire (FFQ), from which dietary patterns were created by factor analysis from 27 food groups. The frequency of fall-related fracture was investigated based on insurance claim records from 2002 until 2006. The relationship between the incidence of fall-related fracture and modifiable factors, including dietary patterns, were examined. The Cox proportional hazards regression model was used to examine the relationships between dietary patterns and incidence of fall-related fracture with adjustment for age, gender, Body Mass Index (BMI) and energy intake.

Results

Among 877 participants who agreed to a 4 year follow-up, 28 suffered from a fall-related fracture. Three dietary patterns were identified: mainly vegetable, mainly meat and mainly traditional Japanese. The moderately confirmed (see statistical methods) groups with a Meat pattern showed a reduced risk of fall-related fracture (Hazard ratio = 0.36, 95% CI = 0.13 - 0.94) after adjustment for age, gender, BMI and energy intake. The Vegetable pattern showed a significant risk increase (Hazard ratio = 2.67, 95% CI = 1.03 - 6.90) after adjustment for age, gender and BMI. The Traditional Japanese pattern had no relationship to the risk of fall-related fracture.

Conclusions

The results of this study have the potential to reduce fall-related fracture risk in elderly Japanese. The results should be interpreted in light of the overall low meat intake of the Japanese population.
Inhibition of experimental lung metastasis by systemic lentiviral delivery of kallistatin
Authors: Shiau Ai-Li , Teo Min-Li , Chen Shin-Yao , Wang Chrong-Reen , Hsieh Jeng-Long , Chang Meng-Ya , Chang Chih-Jui , Chao Julie , Chao Lee , Wu Chao-Liang , Lee Che-Hsin
Published: June 2010

Background

Angiogenesis plays an important role in the development and progression of tumors. Kallistatin exerts anti-angiogenic and anti-inflammatory activities that may be effective in inhibiting tumor metastasis. We investigated the antitumor effect of lentivirus-mediated kallistatin gene transfer in a syngeneic murine tumor model.

Methods

Lentiviral vector encoding kallistatin (LV-Kallistatin) was constructed. The expression of kallistatin was verified by enzyme-linked immunosorbent assay (ELISA), and the bioactivity of kallistatin was determined by using cell proliferation, migration, and invasion assays. In addition, antitumor effects of LV-Kallistatin were evaluated by the intravenous injection of virus into tumor-bearing mice.

Results

The conditioned medium from LV-Kallistatin-treated cells inhibited the migration and proliferation of endothelial cells. Meanwhile, it also reduced the migration and invasion of tumor cells. In the experimental lung metastatic model, tumor-bearing mice receiving LV-Kallistatin had lower tumor nodules and longer survival than those receiving control virus or saline. Moreover, the microvessel densities, the levels of vascular endothelial growth factor (VEGF), tumor necrosis factor (TNF)-α, and nuclear factor κB (NF-κB) transcriptional activity were reduced in the LV-Kallistatin-treated mice.

Conclusion

Results of this study showed that systemic administration of lentiviral vectors encoding kallistatin inhibited the growth of metastatic tumor and prolonged the survival of tumor-bearing mice. These results suggest that gene therapy using lentiviruses carrying the kallistatin gene, which exerts anti-angiogenic and anti-inflammatory activities, represents a promising strategy for the treatment of lung cancer.
Alterations in osteoclast function and phenotype induced by different inhibitors of bone resorption - implications for osteoclast quality
Authors: Neutzsky-Wulff Anita V , Sørensen Mette G , Kocijancic Dino , Leeming Diana J , Dziegiel Morten H , Karsdal Morten A , Henriksen Kim
Published: June 2010

Background

Normal osteoclasts resorb bone by secretion of acid and proteases. Recent studies of patients with loss of function mutations affecting either of these processes have indicated a divergence in osteoclastic phenotypes. These difference in osteoclast phenotypes may directly or indirectly have secondary effects on bone remodeling, a process which is of importance for the pathogenesis of both osteoporosis and osteoarthritis. We treated human osteoclasts with different inhibitors and characterized their resulting function.

Methods

Human CD14 + monocytes were differentiated into mature osteoclasts using RANKL and M-CSF. The osteoclasts were cultured on bone in the presence or absence of various inhibitors: Inhibitors of acidification (bafilomycin A1, diphyllin, ethoxyzolamide), inhibitors of proteolysis (E64, GM6001), or a bisphosphonate (ibandronate). Osteoclast numbers and bone resorption were monitored by measurements of TRACP activity, the release of calcium, CTX-I and ICTP, as well as by counting resorption pits.

Results

All inhibitors of acidification were equally potent with respect to inhibition of both organic and inorganic resorption. In contrast, inhibition of proteolysis by E64 potently reduced organic resorption, but only modestly suppressed inorganic resorption. GM6001 alone did not greatly affect bone resorption. However, when GM6001 and E64 were combined, a complete abrogation of organic bone resorption was observed, without a great effect on inorganic resorption. Ibandronate abrogated both organic and inorganic resorption at all concentrations tested [0.3-100 μM], however, this treatment dramatically reduced TRACP activity.

Conclusions

We present evidence highlighting important differences with respect to osteoclast function, when comparing the different types of osteoclast inhibitors. Each class of osteoclast inhibitors will lead to different alterations in osteoclast quality, which secondarily may lead to different bone qualities.
Smoking decreases the level of circulating CD34+ progenitor cells in young healthy women - a pilot study
Authors: Ludwig Antje , Jochmann Nicoline , Kertesz Andras , Kuhn Claudia , Mueller Simone , Gericke Christine , Baumann Gert , Stangl Karl , Stangl Verena
Published: June 2010

Background

Decreased levels of circulating bone marrow-derived progenitor cells have been associated with risk factors and cardiovascular diseases. Smoking is the most important modifiable risk factor for atherosclerosis in young women. The aim of this pilot study was to assess in healthy premenopausal women without other risk factors for cardiovascular disease the influence of nicotine abuse on the number of circulating progenitor cells in relation to endothelial function.

Methods

The number of endothelial progenitor cells, measured as colony-forming units in a cell-culture assay (EPC-CFU) and the number of circulating CD34 + and CD34 + /CD133 + cells, measured by flow cytometry, was estimated in 32 women at the menstrual phase of the menstrual cycle. In addition, flow-mediated dilation (FMD) was assessed as a marker for vascular function. In a subgroup of these women (n = 20), progenitor cells were also investigated at the mid-follicular and luteal phases of the menstrual cycle.

Results

Compared to non-smokers, the abundance of circulating CD34 + cells was significantly lower in smoking women in the menstrual, mid-luteal, and mid-follicular phases of the menstrual cycle. The number of CD34 + progenitor cells was revealed to have significant positive correlation with FMD in young healthy women, whereas CD34 + /CD133 + progenitor cells and EPC-CFU showed no significant correlation.

Conclusion

The number of CD34 + progenitor cells positively correlates with FMD in young healthy women and is decreased by smoking.
Quantitative analysis of the effect of tubulin isotype expression on sensitivity of cancer cell lines to a set of novel colchicine derivatives
Authors: Tseng Chih-Yuan , Mane Jonathan Y , Winter Philip , Johnson Lorelei , Huzil Torin , Izbicka Elzbieta , Luduena Richard F , Tuszynski Jack A
Published: June 2010

Background

A maximum entropy approach is proposed to predict the cytotoxic effects of a panel of colchicine derivatives in several human cancer cell lines. Data was obtained from cytotoxicity assays performed with 21 drug molecules from the same family of colchicine compounds and correlate these results with independent tubulin isoform expression measurements for several cancer cell lines. The maximum entropy method is then used in conjunction with computed relative binding energy values for each of the drug molecules against tubulin isotypes to which these compounds bind with different affinities.

Results

We have found by using our analysis thatαβI andαβIII tubulin isoforms are the most important isoforms in establishing predictive response of cancer cell sensitivity to colchicine derivatives. However, sinceαβI tubulin is widely distributed in the human body, targeting it would lead to severe adverse side effects. Consequently, we have identified tubulin isotypeαβIII as the most important molecular target for inhibition of microtubule polymerization and hence cancer cell cytotoxicity. Tubulin isotypesαβI andαβII are concluded to be secondary targets.

Conclusions

The benefit of being able to correlate expression levels of specific tubulin isotypes and the resultant cell death effect is that it will enable us to better understand the origin of drug resistance and hence design optimal structures for the elimination of cancer cells. The conclusion of the study described herein identifies tubulin isotypeαβIII as a target for optimized chemotherapy drug design.
Cellular cholesterol delivery, intracellular processing and utilization for biosynthesis of steroid hormones
Authors: Hu Jie , Zhang Zhonghua , Shen Wen-Jun , Azhar Salman
Published: June 2010

Steroid hormones regulate diverse physiological functions such as reproduction, blood salt balance, maintenance of secondary sexual characteristics, response to stress, neuronal function and various metabolic processes. They are synthesized from cholesterol mainly in the adrenal gland and gonads in response to tissue-specific tropic hormones. These steroidogenic tissues are unique in that they require cholesterol not only for membrane biogenesis, maintenance of membrane fluidity and cell signaling, but also as the starting material for the biosynthesis of steroid hormones. It is not surprising, then, that cells of steroidogenic tissues have evolved with multiple pathways to assure the constant supply of cholesterol needed to maintain optimum steroid synthesis. The cholesterol utilized for steroidogenesis is derived from a combination of sources: 1)de novosynthesis in the endoplasmic reticulum (ER); 2) the mobilization of cholesteryl esters (CEs) stored in lipid droplets through cholesteryl ester hydrolase; 3) plasma lipoprotein-derived CEs obtained by either LDL receptor-mediated endocytic and/or SR-BI-mediated selective uptake; and 4) in some cultured cell systems from plasma membrane-associated free cholesterol. Here, we focus on recent insights into the molecules and cellular processes that mediate the uptake of plasma lipoprotein-derived cholesterol, events connected with the intracellular cholesterol processing and the role of crucial proteins that mediate cholesterol transport to mitochondria for its utilization for steroid hormone production. In particular, we discuss the structure and function of SR-BI, the importance of the selective cholesterol transport pathway in providing cholesterol substrate for steroid biosynthesis and the role of two key proteins, StAR and PBR/TSO in facilitating cholesterol delivery to inner mitochondrial membrane sites, where P450scc (CYP11A) is localized and where the conversion of cholesterol to pregnenolone (the common steroid precursor) takes place.
The val158met Polymorphism of Human Catechol-O-Methyltransferase (COMT) Affects Anterior Cingulate Cortex Activation in Response to Painful Laser Stimulation
Authors: Mobascher Arian , Brinkmeyer Juergen , Thiele Holger , Toliat Mohammad R , Steffens Michael , Warbrick Tracy , Musso Francesco , Wittsack Hans-Joerg , Saleh Andreas , Schnitzler Alfons , Winterer Georg
Published: June 2010

Background:

Pain is a complex experience with sensory, emotional and cognitive aspects. Genetic and environmental factors contribute to pain-related phenotypes such as chronic pain states. Genetic variations in the gene coding for catechol-O-methyltransferase ( COMT) have been suggested to affect clinical and experimental pain-related phenotypes including regional μ-opioid system responses to painful stimulation as measured by ligand-PET (positron emission tomography). The functional val158met single nucleotide polymorphism has been most widely studied. However, apart from its impact on pain-induced opioid release the effect of this genetic variation on cerebral pain processing has not been studied with activation measures such as functional magnetic resonance imaging (fMRI), PET or electroencephalography. In the present fMRI study we therefore sought to investigate the impact of the COMT val158met polymorphism on the blood oxygen level-dependent (BOLD) response to painful laser stimulation.

Results:

57 subjects were studied. We found that subjects homozygous for the met158 allele exhibit a higher BOLD response in the anterior cingulate cortex (ACC), foremost in the mid-cingulate cortex, than carriers of the val158 allele.

Conclusion:

This result is in line with previous studies that reported higher pain sensitivity in homozygous met carriers. It adds to the current literature in suggesting that this behavioral phenotype may be mediated by, or is at least associated with, increased ACC activity. More generally, apart from one report that focused on pain-induced opioid release, this is the first functional neuroimaging study showing an effect of the COMT val158met polymorphism on cerebral pain processing.
Acute reversible inactivation of the bed nucleus of stria terminalis induces antidepressant-like effect in the rat forced swimming test
Authors: Crestani Carlos C , Alves Fernando HF , Correa Fernando MA , Guimarães Francisco S , Joca Sâmia RL
Published: June 2010

Background

The bed nucleus of stria terminalis (BNST) is a limbic forebrain structure involved in hypothalamo-pituitary-adrenal axis regulation and stress adaptation. Inappropriate adaptation to stress is thought to compromise the organism's coping mechanisms, which have been implicated in the neurobiology of depression. However, the studies aimed at investigating BNST involvement in depression pathophysiology have yielded contradictory results. Therefore, the objective of the present study was to investigate the effects of temporary acute inactivation of synaptic transmission in the BNST by local microinjection of cobalt chloride (CoCl2) in rats subjected to the forced swimming test (FST).

Methods

Rats implanted with cannulae aimed at the BNST were submitted to 15 min of forced swimming (pretest). Twenty-four hours later immobility time was registered in a new 5 min forced swimming session (test). Independent groups of rats received bilateral microinjections of CoCl2 (1 mM/100 nL) before or immediately after pretest or before the test session. Additional groups received the same treatment and were submitted to the open field test to control for unspecific effects on locomotor behavior.

Results

CoCl2 injection into the BNST before either the pretest or test sessions reduced immobility in the FST, suggesting an antidepressant-like effect. No significant effect of CoCl2 was observed when it was injected into the BNST immediately after pretest. In addition, no effect of BNST inactivation was observed in the open field test.

Conclusion

These results suggest that acute reversible inactivation of synaptic transmission in the BNST facilitates adaptation to stress and induces antidepressant-like effects.
5th International AIDS Society Conference on HIV Pathogenesis, Treatment and Prevention: summary of key research and implications for policy and practice – Operations research
Authors: Kort Rodney
Published: June 2010

Operations research was added as a fourth scientific track to the pathogenesis conference series at the 5th IAS Conference on HIV Pathogenesis, Treatment and Prevention (IAS 2009) in recognition of the importance of this growing research field and the need for applied research to inform and evaluate the scale up of some key interventions in HIV treatment, care and prevention.

Several studies demonstrated how task shifting and the decentralization of health services can leverage scarce health care resources to support scale‐up efforts. For example, a Ugandan study comparing home‐based and facility‐based antiretroviral therapy (ART) delivery found that both delivered equivalent clinical outcomes, but home‐based delivery resulted in substantial cost savings to patients; and a retrospective cohort analysis of an HIV care programme in Lesotho demonstrated that devolving routine patient management to nurses and trained counsellors resulted in impressive gains in annual enrolment, retention in care and other clinical indicators.

Studies also demonstrated how the use of trained counsellors and public health advisors could effectively expand both clinical and public health capacity in low‐income settings. Studies evaluating the impact of integrating HIV and TB care resulted in improved treatment outcomes in coinfected populations, the development of environmental interventions to reduce TB transmission, and uncovering of the extent of multi‐drug‐resistant and extremely drug‐resistant tuberculosis (MDR‐TB and XDR‐TB) in KwaZulu‐Natal, South Africa.

Some mathematical modelling and cost‐effectiveness studies presented at this meeting addressed interventions to increase retention in care, and strengthened the evidentiary basis for universal voluntary testing and immediate ART on reducing HIV transmission; debate continued about the relative merits of clinical versus laboratory monitoring. Finally, a provocative plenary presentation outlined the shortfalls of current prevention interventions and argued for more cost‐effectiveness analyses to guide the selection of interventions for maximum benefit.

19‐22 July 2009, 5th IAS Conference on HIV Pathogenesis, Treatment and Prevention (IAS 2009), Cape Town, South Africa
Promoting Undergraduate Interest, Preparedness, and Professional Pursuit in the Sciences: An Outcomes Evaluation of the SURE Program at Emory University
Authors: Junge Benjamin , Quiñones Catherine , Kakietek Jakub , Teodorescu Daniel , Marsteller Pat
Published: June 2010

We report on an outcomes assessment of the Summer Undergraduate Research Experience (SURE) Program at Emory University in Atlanta, GA. Using follow-up survey data and academic transcripts, we gauge SURE's impact on levels of interest in, preparedness for, and actual pursuit of graduate study and professional careers in the sciences for the program's first 15 summer cohorts (1990–2004). Our follow-up survey indicated significant increases in all research preparedness skills considered, notably in ability to give a poster research presentation, to discuss research at a graduate school interview, and to apply research ethics principles. About a third of SURE graduates went on to complete a graduate degree >90% considered SURE as important or very important in their academic development. Respondents reported postprogram increases in the level of interest in academic and research careers, and reported high levels of employment in science careers and job satisfaction. Regression analyses of Emory SURE participant transcripts revealed that participants take significantly more science courses as seniors and earn higher grades in those courses than nonparticipants. This trend held after correcting for indicators of prior interest (first-year course work, GPA, and math SAT scores), gender, and minority status. We also report on an external survey completed by SURE participants.
Educating Young Educators: A Pedagogical Internship for Undergraduate Teaching Assistants
Authors: Romm Iyah , Gordon-Messer Susannah , Kosinski-Collins Melissa
Published: June 2010

Although undergraduates have long held a role as teaching assistants for introductory science courses at liberal arts colleges and universities, educational institutions often do not provide these students with opportunities to explore science teaching and pedagogy. At Brandeis University, we designed an internship course to help increase the motivation, understanding, and knowledge of teaching pedagogy for undergraduate teaching assistants that is offered concurrently with their teaching responsibilities. Weekly sessions with faculty mentors are guided by readings in current science education literature, and throughout the semester students are asked to develop new course material based on the pedagogical frameworks discussed. To evaluate the effectiveness of this course, we surveyed students at the close of the semester. We found an overall increase in student confidence levels with regard to teaching and better awareness of the difficulties faced in science education. All students who participated in the course expressed interest in participating in future educational internships. We believe that the Educating Young Educators internship has the potential to be a catalyst for personal and professional growth from a novice into an informed young educator.
Neonatal Informatics—Dream of a Paperless NICU: Part Five: Putting “IT” All Together
Authors: Drummond Willa H.
Published: June 2010

The promise of computer-assisted neonatal intensive care unit (NICU) medical management is an intellectually global challenge. In early 2009, President Obama presented a “carrot and stick” plan to accelerate use of electronic health records. Financial incentives are offered to early adopters who meaningfully use certified systems; penalties begin in 2015 for those who do not.

NICU critical care environments are extremely difficult to computerize because clinical data are time-dependent and highly variable, use repeated measures of many different elements, and run in real-time. Effective clinical computerization requires translation of complex human thinking models into software bits and bytes. All efforts require a logical, stepwise approach to designing effective databases and systems, and no existing system is currently adequate. Creating meaningful computerization for a busy NICU remains an ongoing challenge.

On a daily basis, bedside visit and other care-related notes that outline the patient's condition, medications, treatments, nutrition, new problems, care being provided, plans, and family updates must be generated by physicians or neonatal nurse practitioners (NNPs). Clinical data management in NICUs is currently a “mixed model.” Real-time information management by typing is extremely difficult for hands-on critical caregivers, both in paper records and in computer systems. Workarounds involving paper remain the most common current practice in many institutions (including the scrub pants’ notational workaround).

Medicolegal and service billing rules require documentation, and hundreds of different approaches are used, none of which is “certified.” Vendors’ old databases and newer databases designed by nonengineering individuals for clinical documentation tend to have significant technical problems that limit usability. In the future, good database design using modern techniques and technology should improve the situation. Direct download from devices and laboratories to local real-time systems is on the horizon, as is voice recognition for neonatal applications.

However, for this year and through 2011, NICUs are not on the radar. Industry and political focus remains on administrative and population “quality management” functionality, now known as “meaningful use.” Emerging drafts of criteria for 2011 incentive payments formally excluded all hospitalists and infants younger than age 2 years from eligibility. Head circumference, respiratory rate, and temperature are not official parts of the vital signs specifications criteria for testing. The dream of a paperless NICU remains only a dream.
Skeletal Dysplasias in the Newborn: Diagnostic Evaluation and Developmental Genetics
Authors: Swarr Daniel T. , Sutton V. Reid
Published: June 2010

Many of the genetic disorders of skeletal development lead to significant morbidity and mortality in utero or in the early neonatal period. Due to the large number and heterogeneous nature of these disorders, their diagnosis and management can be overwhelming. A basic knowledge of skeletal development and a structured, comprehensive approach to the history, physical examination, and interpretation of radiographic studies are crucial. Understanding the power and limitations of prenatal diagnostic technology and genetic testing is essential for accurate counseling and judicious use of resources. Finally, familiarity with individual disorders and online resources aids the neonatologist in coordinating the complex, multidisciplinary care that these infants demand in the neonatal intensive care unit (NICU) and after hospital discharge.
Pharmacology Review
Authors: Marro Peter J. , Delivoria-Papadopoulos Maria
Published: June 2010

Although the evidence supporting the efficacy of neuroprotective treatments for hypoxic-ischemic injury in human newborns is limited, efforts to develop effective treatments continue in laboratory studies. In this article, we review some of the treatments that have found their way from the laboratory to clinical studies in newborns. Specifically, the evidence for use of magnesium sulfate, allopurinol, opioids, and hypothermia as possible treatments of hypoxic-ischemic encephalopathy are discussed.
Athletic Participation by Children and Adolescents Who Have Systemic Hypertension
Authors: Demorest Rebecca A. , Washington Reginald L. ,   Council on Sports Medicine and Fitness
Published: June 2010

This Policy Statement was retired November 2017.

Children and adolescents who have hypertension may be at risk for complications when exercise causes their blood pressure to rise even higher. The purpose of this statement is to update recommendations concerning the athletic participation of individuals with hypertension, including special populations such as those with spinal cord injuries or obesity, by using the guidelines from “The 36th Bethesda Conference: Eligibility Recommendations for Competitive Athletes with Cardiovascular Abnormalities”; “The Fourth Report on the Diagnosis, Evaluation, and Treatment of High Blood Pressure in Children and Adolescents”; and “The Seventh Report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure.”
Production of Gulf Killifish in the Black Belt Region of Alabama Using Saline Groundwater
Authors: Phelps Ronald P , Daniels William H , Sansing Nelson R , Brown Travis W
Published: June 2010

The Gulf killifish Fundulus grandis, commonly called the bull minnow, mudminnow, or cacahoe, is a popular live bait along the Gulf of Mexico coast in the United States. Although culture techniques for Gulf killifish have been established for more than 30 years, this species is not commonly produced. Suitable coastal areas are thought to be one of the limitations. Low-salinity groundwater occurs in much of the United States, including portions of the Alabama Black Belt region; however, the relative abundance of minerals in the water varies. Spawning success was compared among Gulf killifish held in saline groundwater (salinity = 4.2–11.1‰) from four inland sites and in 5‰ synthetic seawater. Gulf killifish production (fry to subadult) was compared between two sites of similar salinity but with different mineral profiles (site A had 4.0‰ salinity and received water from a fertilized source pond; site B had 3.2‰ salinity and received water with no fertilizer additions); initial stocking densities in 1.15-m2 outdoor tanks were 25, 50, and 100 fry/m2. Gulf killifish spawned successfully under all conditions tested. Mean (±SD) fry production of 1.7 ± 0.88 fry/g of female was obtained. The yields and mean weights obtained differed by site and stocking density. After 104 d of production, the highest yield was 133.3 ± 40.4 g/m2 (1,333 ± 404 kg/ha) at site A for fish stocked at 100 fry/m2. The yield at site B for fish at the same stocking density was 62.6 ± 18.8 g/m2. Market-sized fish (total length ≥ 6.35 cm; weight = 3.3 g) were obtained at site A for the stocking density of 25 fry/m2, but market-sized fish were not obtained for any stocking density at site B. Although the mineral profiles differ between saline groundwater and natural seawater, saline groundwater is suitable for the reproduction and growth of this species. Egg production and fish growth were similar to levels expected for Gulf killifish culture in brackish-water ponds along the Gulf of Mexico coast.
The Effects of Proliferative Gill Disease on the Blood Physiology of Channel Catfish, Blue Catfish, and Channel Catfish × Blue Catfish Hybrid Fingerlings
Authors: Beecham Rachel V , Griffin Matt J , LaBarre Susan B , Wise David , Mauel Michael , Pote Linda M W , Minchew C Douglas
Published: June 2010

This study was conducted to gain a better understanding of the effect of exposure to the myxozoan Henneguya ictaluri (the agent of proliferative gill disease [PGD]) on host physiology by measuring the variation in selected blood characteristics in three differently affected host taxa (channel catfish Ictalurus punctatus, blue catfish I. furcatus, and blue catfish × channel catfish hybrid fingerlings). Forty-five fish of each host taxon were exposed to PGD, and 10 fish of each host taxon were sampled at 24, 96, and 168 h. Fish were weighed, blood was collected and analyzed for a suite of physiological variables, and wet mount preparations of gill clips were examined grossly for the presence of cartilage breaks. The results of this study are consistent with the current knowledge regarding H. ictaluri infections in blue catfish, channel catfish, and blue catfish × channel catfish hybrids. Chondrocytic lysis was observed in channel catfish and hybrid catfish at 96 and 168 h but was not observed in blue catfish. There was an observed reduction in oxygen partial pressure (pO2) and an increase in carbon dioxide partial pressure (pCO2) at 96 h in the blood of channel catfish and hybrid catfish, but these changes were not exhibited by blue catfish. For all species, pH decreased as lactate concentrations increased. The lack of physiological changes and the absence of H. ictaluri sporozoites and DNA in gill tissue lead us to speculate that H. ictaluri is unable to establish infection in blue catfish. Current research investigating the mechanisms of infection and portals of parasite entry into blue catfish, channel catfish, and blue catfish × channel catfish hybrids is underway to better elucidate the defenses employed by blue catfish against H. ictaluri.
Limiting and Optimal Temperatures for the Northern Atlantic Population of Black Sea Bass
Authors: Sullivan M L , Tomasso J R
Published: June 2010

Northern-stock black sea bass Centropristis striata demonstrated upper and lower median lethal temperatures of 33.6°C and 2.7°C, respectively, when temperatures were increased or decreased at a rate of approximately 0.5°C per day. The temperature for optimal growth was 25.6°C. This work, along with information in the literature, indicates that thermal tolerances and preferences do not differ greatly between the northern and southern stocks of black sea bass.
Effect of Potassium Permanganate Treatments on New Zealand Mud Snail Behavior and Survival and Rainbow Trout Growth and Condition
Authors: Oplinger Randall W , Wagner Eric J
Published: June 2010

The New Zealand mud snail (NZMS) Potamopyrgus antipodarum, a nonnative species recently introduced into North America, has been shown to negatively influence ecosystem function. Methods to control or eliminate NZMS are needed. Twenty-four-hour treatments with 2 mg of potassium permanganate (KMnO4) per liter of water were evaluated against NZMS held for 24 h in artificial stream sections that contained refuge areas. The snails did not seek refuge when placed into an area that contained KMnO4 and also had neutral preference when provided the opportunity to select between artificial stream sections with and without KMnO4. In a separate series of experiments, NZMS and rainbow trout Oncorhynchus mykiss were placed into hatchery raceway sections that were treated with a 2-mg/L KMnO4 solution for 2 h/d over a period of 14 consecutive days. Mortality of NZMS and rainbow trout was not elevated in these raceways relative to nontreated control raceways. There was evidence, however, that the presence of the KMnO4 depressed fish growth (i.e., Fulton's condition factor). The KMnO4 treatment did not cause significant gill damage in rainbow trout. Our results show that KMnO4 at 2 mg/L is not effective in controlling or eliminating NZMS populations.
Golden Shiner Egg Production during a Spawning Season
Authors: Clemment Troy , Stone Nathan
Published: June 2010

This study determined the number of eggs produced daily by golden shiners Notemigonus crysoleucas during a 111-d spawning season and the relationship of egg production to water temperature. On March 15, 2000, four 5.9-m2, plastic-lined pools were each stocked with fifty 1-year-old golden shiners. Mean (±SD) individual weight of fish at stocking was 9.2 ± 3.7 g. During March 16 through July 4, the spawning substrate in each pool was collected daily and replaced with clean substrate. Eggs were removed from mats in a 1.5% sodium sulfite bath, and the total volume of eggs from each pool was recorded. The mean number of eggs per unit volume (based on twenty-seven 2-mL samples) was 704 ± 109 eggs/mL. Approximately 2.75 million eggs were produced by no more than 200 brooders (∼2.4-kg total mass) over 111 d. Egg production was greatest during the month of May (average = 14,339 eggs·kg−1·d−1). The number of eggs collected daily showed a significant positive correlation with water temperature (P < 0.05) up to 22°C and then declined with further increases in water temperature.
Comparison of Percent Hatch and Fungal Infestation in Channel Catfish Eggs after Copper Sulfate, Diquat Bromide, Formalin, and Hydrogen Peroxide Treatment
Authors: Mitchell Andrew J , Straus David L , Farmer Bradley , Carter Ray
Published: June 2010

Reduced survival of fish eggs is often a result of infestation with fungi Saprolegnia spp. However, timely chemical treatments often limit these infestations and increase survival. The effect of copper sulfate pentahydrate (CSP; 10 mg of CSP/L of water), diquat bromide (25 mg of diquat cation/L), formalin (433 mg/L), and hydrogen peroxide (H2O2; 250 mg/L) on percent hatch and fungal infestation in eggs of channel catfish Ictalurus punctatus was compared in two identical trials (five replicates for each chemical treatment per trial). The percent hatch in all chemical treatments was significantly better than percent hatch of the controls. The amount of fungal coverage on egg masses treated with CSP, formalin, and H2O2 was significantly less than that observed on the controls. Although not statistically different from the other treatments, H2O2 at 250 mg/L exhibited the highest average percent hatch (64%; control hatch = 34%), the lowest fungal coverage (1.5 cm; control coverage = 7.2 cm), and the lowest occurrence of fungi (50%; control occurrence = 100%) among the treatments.
Effect of Pond Size on Striped Bass Growth and Survival in Brackish Water
Authors: Matlock Gary C
Published: June 2010

The effect of pond size on survival and growth of fingerling striped bass Morone saxatilis in brackish-water (5–10‰) ponds may be important in designing striped bass production facilities. Seven-day-old fry were stocked at densities of 248,000–317,000 fish/ha into 13 ponds (0.2–1.6 ha), and surviving fish were harvested about 1 month later. Pond size did not affect striped bass survival, growth, or production. Mean (±SE) survival over the rearing period was 36.4 ± 5.6%. Mean total length (TL) was 34.2 ± 0.9 mm. Mean production was 1.40 ± 0.17 kg·ha−1·d−1. Large ponds (at least 1.6 ha) are preferable over smaller ponds for producing 34-mm-TL striped bass fingerlings in brackish-water ponds because of the lower cost of construction and maintenance and the reduced land and water use.
Spatial congruency of benthic diatom, invertebrate, macrophyte, and fish assemblages in European streams
Authors: Johnson Richard K. , Hering Daniel
Published: June 2010

Understanding patterns in taxonomic congruency and the importance of environmental variables as drivers of these patterns is a prerequisite for analyzing changes in regional species pools. Here we evaluated the spatial correspondence of benthic diatoms, invertebrates, macrophytes, and fish assemblages in minimally disturbed lowland (n = 38) and mountain (n = 32) streams and, using constrained ordination and variance decomposition, determined how environmental and biological variables related to these patterns. Using different measures of diversity, abundance, and community composition, principal components analysis failed to reveal a single gradient in lowland and mountain streams. This was due to differences in the relationships between individual diversity measures and environmental variables characterizing habitat diversity (number of debris dams, silt and cobble substratum) in lowland streams, and catchment area and oxygen saturation in mountain streams. Despite the low spatial coherence of individual measures, integral multivariate analyses of community structure revealed coherent patterns between taxonomic groups. From 31.0% to 47.7% of the variance in diversity of fish, invertebrate, and macrophyte assemblages in mountain streams and from 11.9% to 33.7% of the variance in diversity in lowland streams were explained by one or more of the remaining three groups. Partial redundancy analyses showed that composition of other taxonomic groups was generally a better predictor of assemblage diversity than interactions with environmental variables, lending support to the importance of species interactions for spatial coherence. Finally, although we found little support for a single biodiversity gradient, correlations between fish diversity and macrophyte and invertebrate diversity in mountain streams and between macrophyte diversity and invertebrate and diatom diversity in lowland streams suggest that these two groups (i.e., fish in mountain and macrophytes in lowland streams) may function as surrogate indicators for the diversity of other taxonomic groups.
Cropland carbon fluxes in the United States: increasing geospatial resolution of inventory‐based carbon accounting
Authors: West Tristram O. , Brandt Craig C. , Baskaran Latha M. , Hellwinckel Chad M. , Mueller Richard , Bernacchi Carl J. , Bandaru Varaprasad , Yang Bai , Wilson Bradly S. , Marland Gregg , Nelson Richard G. , Ugarte Daniel G. De La Torre , Post Wilfred M.
Published: June 2010

Net annual soil carbon change, fossil fuel emissions from cropland production, and cropland net primary production were estimated and spatially distributed using land cover defined by NASA's moderate resolution imaging spectroradiometer (MODIS) and by the USDA National Agricultural Statistics Service (NASS) cropland data layer (CDL). Spatially resolved estimates of net ecosystem exchange (NEE) and net ecosystem carbon balance (NECB) were developed. The purpose of generating spatial estimates of carbon fluxes, and the primary objective of this research, was to develop a method of carbon accounting that is consistent from field to national scales. NEE represents net on‐site vertical fluxes of carbon. NECB represents all on‐site and off‐site carbon fluxes associated with crop production. Estimates of cropland NEE using moderate resolution (∼1 km2) land cover data were generated for the conterminous United States and compared with higher resolution (30‐m) estimates of NEE and with direct measurements of CO2 flux from croplands in Illinois and Nebraska, USA. Estimates of NEE using the CDL (30‐m resolution) had a higher correlation with eddy covariance flux tower estimates compared with estimates of NEE using MODIS. Estimates of NECB are primarily driven by net soil carbon change, fossil fuel emissions associated with crop production, and CO2 emissions from the application of agricultural lime. NEE and NECB for U.S. croplands were −274 and 7 Tg C/yr for 2004, respectively. Use of moderate‐ to high‐resolution satellite‐based land cover data enables improved estimates of cropland carbon dynamics.
An empirical probability model of detecting species at low densities
Authors: Delaney David G. , Leung Brian
Published: June 2010

False negatives, not detecting things that are actually present, are an important but understudied problem. False negatives are the result of our inability to perfectly detect species, especially those at low density such as endangered species or newly arriving introduced species. They reduce our ability to interpret presence–absence survey data and make sound management decisions (e.g., rapid response). To reduce the probability of false negatives, we need to compare the efficacy and sensitivity of different sampling approaches and quantify an unbiased estimate of the probability of detection. We conducted field experiments in the intertidal zone of New England and New York to test the sensitivity of two sampling approaches (quadrat vs. total area search, TAS), given different target characteristics (mobile vs. sessile). Using logistic regression we built detection curves for each sampling approach that related the sampling intensity and the density of targets to the probability of detection. The TAS approach reduced the probability of false negatives and detected targets faster than the quadrat approach. Mobility of targets increased the time to detection but did not affect detection success. Finally, we interpreted two years of presence–absence data on the distribution of the Asian shore crab (Hemigrapsus sanguineus) in New England and New York, using our probability model for false negatives. The type of experimental approach in this paper can help to reduce false negatives and increase our ability to detect species at low densities by refining sampling approaches, which can guide conservation strategies and management decisions in various areas of ecology such as conservation biology and invasion ecology.
Management of infectious wildlife diseases: bridging conventional and bioeconomic approaches
Authors: Fenichel Eli P. , Horan Richard D. , Hickling Graham J.
Published: June 2010

The primary goal of disease ecology is to understand disease systems and then use this information to inform management. The purpose of this paper is to show that conventional disease ecology models are limited in their ability to inform management of systems that are already infected, and to show how such models can be integrated with economic decision models to improve upon management recommendations. Management strategies based solely on disease ecology entail managing infected host populations or reservoir populations below a threshold value based on R0, the basic reproductive ratio of the pathogen, or a multiple‐host version of this metric. These metrics measure a pathogen's ability to invade uninfected systems and do not account for postinfection dynamics. Once a pathogen has invaded a population, alternative management criteria are needed. Bioeconomic modeling offers a useful alternative approach to developing management criteria and facilitates the consideration of ecological–economic trade‐offs so that diseases are managed in a cost‐effective manner. The threshold concept takes on a more profound role under a bioeconomic paradigm: rather than unilaterally determining disease control choices, thresholds inform control choices and are influenced by them.