Common dynamics of globin family proteins

The recently discovered new members of the globin family, neurogobin and cytoglobin, are the object of sustained structural and functional studies aimed at understanding their physiological role and elucidating the impact of their bis-his heme hexacoordination. However, no studies have yet considered the dynamics of this protein family, an essential link between structure and function. In this communication, we present normal mode analysis results for neuroglobin, cytoglobin, hemoglobin and myoglobin to provide exploratory insights into globin characteristic motions. Our results show a clear correlation in the protein dynamics of this family. All four globins exhibit a high degree of correlated displacements involving residues in the C, E and F helices and link regions. They suggest that these motions play an important role in the reversible oxygen binding function of these proteins. Further, our results may help rationalize some functional features of the 6c-globins in that they alone exhibit correlated displacements of the G-helix region.     

New clinically relevant,orthotopic mouse models of human chondrosarcoma with spontaneous metastasis

Background  

Chondrosarcoma responds poorly to adjuvant therapy and new, clinically relevant animal models are required to test targeted therapy.     

Growth characteristics of Sanguinaria canadensis L. Cell suspensions and immobilized cultures for production of benzophenanthridine alkaloids

Summary Sanguinaria canadensis L. plants were harvested from a local forest and calli were initiated from leaf explants. The production of benzophenanthridine alkaloids (i.e. sanguinarine, sanguilutine, sanguirubine, chelerythrine, chelilutine and chelirubine) by S. canadensis cell grown in modified B5 and IM2 media was compared to the alkaloid content of rhizomes. Sanguinarine accounted for approximately 80% of the total alkaloid content of cultured cells (1.3%,g g^–1) while sanguinarine and sanguirubine accounted for 70% of rhizome alkaloids (9.0%, g g^–1). Sanguinarine, chelirubine and chererythrine were the only known alkaloids detected in cultured S. canadensis cells. Maximum alkaloid production of cultures performed using B5 medium, containing half the original nitrate concentration, was observed following extracellular nitrate and sugar depletion. The scale-up of this culture was successfully performed in a 2-1 immobilization bioreactor. The consumption of sugar and nitrate as well as the oxygen (OTR) and carbon dioxide (CTR) transfer rates of the immobilized cell culture were monitored for 15 days. The maximum sugar and nitrate consumption rates were 1.8 g l^–1 per day and 2.3 mm per day respectively. The maximum OTR and CTR of the immobilized cell culture were 0.8 mmol O₂ l^–1 h^–1 and 0.95 mmol CO₂ l^–1 h^–1 respectively. The sanguinarine yield of this culture reached 1.0% based on biomass dry weight (g g^–1 dw) by day 15.     

Fumarylacetoacetase measurement as a mass-screening procedure for hereditary tyrosinemia type I.

Fluorometric quantitative tyrosine determination on dried-blood spots is the primary neonatal screening test used for tyrosinemia type I (HT) in the province of Quebec. Succinylacetone determination on these same spots is used as the complementary test when the tyrosine level is higher than a given threshold. This procedure has proved to be less discriminant over the past few years because of changes in newborn feeding and because of early discharge of newborns from the nursery. We have developed an enzyme-linked immunosorbent assay (ELISA) to measure the deficient enzyme in HT in dried-blood spots. Fumarylacetoacetase (FAH) (E.C.3.7.1.2) was measured retrospectively by an ELISA on 25 dried-blood samples from proven patients with HT and prospectively in 72,000 specimens received in the neonatal screening program. In this pilot project, FAH was measured first, and, if necessary, succinylacetone was determined as the complementary test. All 25 samples from proven patients and specimens from four other patients detected in the pilot study have shown almost complete absence of FAH in dried-blood samples. At a cutoff level of 12.5% of normal adult blood spotted on the same type of paper, only 30 other cases disclosed FAH levels low enough to warrant succinylacetone measurement but had no detectable succinylacetone. The false-positive rate is thus 1:2,400 with this primary ELISA. However, blood transfusion in newborns prior to blood collection on filter paper may yield false-negative tests, since FAH is present in erythrocytes of normal donors.(ABSTRACT TRUNCATED AT 250 WORDS)     

Low production of reactive oxygen species in granulocytes is associated with organ damage in systemic lupus erythematosus

Introduction

Polymorphonuclear leukocytes (PMN) are main effector cells in the acute immune response. While the specific role of PMN in systemic lupus erythematosus (SLE) and autoimmunity is still unclear, their importance in chronic inflammation is gaining more attention. Here we investigate aspects of function, bone marrow release and activation of PMN in patients with SLE.

Methods

The following PMN functions and subsets were evaluated using flow cytometry; (a) production of reactive oxygen species (ROS) after ex vivo stimulation with phorbol 12-myristate 13-acetate (PMA) or Escherichia coli (E. coli); (b) capacity to phagocytose antibody-coated necrotic cell material; (c) PMN recently released from bone marrow, defined as percentage of CD10⁻D16^low in peripheral blood, and (d) PMN activation markers; CD11b, CD62L and C5aR.

Results

SLE patients (n = 92) showed lower ROS production compared with healthy controls (n = 38) after activation ex vivo. The ROS production was not associated with corticosteroid dose or other immunotherapies. PMA induced ROS production was significantly reduced in patients with severe disease. In contrast, neither ROS levels after E. coli activation, nor the capacity to phagocytose were associated with disease severity. This suggests that decreased ROS production after PMA activation is a sign of changed PMN behaviour rather than generally impaired functions. The CD10⁻CD16^low phenotype constitute 2% of PMN in peripheral blood of SLE patients compared with 6.4% in controls, indicating a decreased release of PMN from the bone marrow in SLE. A decreased expression of C5aR on PMN was observed in SLE patients, pointing towards in vivo activation.

Conclusions

Our results indicate that PMN from SLE patients have altered function, are partly activated and are released abnormally from bone marrow. The association between low ROS formation in PMN and disease severity is consistent with findings in other autoimmune diseases and might be considered as a risk factor.     

Molecular evolution of the ZFY and ZNF6 gene families

Members of the ZFY and ZNF6 gene families have been cloned from species representing different taxa and different modes of sex determination. Comparisons of these genes show the ZFY-like and ZNF6 sequences to be strongly conserved across marsupials, birds, and lepidosaurians. Sequence analyzed by neighbor-joining indicated that both gene families are monophyletic with a high bootstrap value. Pairing of sequences from males and females of nonmammalian species showed there to be no significant difference between male and female sequences from a single species, consistent with autosomal locations. The molecular distances between murine Zfy-1, Zfy-2, and other ZFY-like sequences suggested that Zfy genes have undergone a period of rapid evolutionary change not seen in human ZFY.      

Effect of drift sampler exposure time and net mesh size on invertebrate drift density in the Njoro River,Kenya

Although invertebrate drift is an important ecological process in lotic ecosystems, very little is known about it in Kenyan rivers. The primary aim of this study was to investigate the effect of driftnet mesh size and exposure duration on drift density in 2017. Drift samples were dominated by Chironomidae, Baetidae, Simuliidae, Caenidae and Culicidae. The 100 µm mesh driftnet had the highest mean invertebrate density, followed by the 250 µm and 500 µm nets. Invertebrate drift densities decreased with increased exposure time. This study demonstrates that sampler mesh size and exposure time should be taken into account when characterising invertebrate drift in streams. Future studies should consider sampling different biotopes and during different seasons.     

Perspectives of clinician and biomedical scientists on interdisciplinary health research

Background

Interdisciplinary health research is a priority of many funding agencies. We surveyed clinician and biomedical scientists about their views on the value and funding of interdisciplinary health research.

Methods

We conducted semistructured interviews with 31 biomedical and 30 clinician scientists. The scientists were selected from the 2000–2006 membership lists of peer-review committees of the Canadian Institutes of Health Research. We investigated respondents’ perspectives on the assumption that collaboration across disciplines adds value to health research. We also investigated their perspectives on funding agencies’ growing support of interdisciplinary research.

Results

The 61 respondents expressed a wide variety of perspectives on the value of interdisciplinary health research, ranging from full agreement (22) to complete disagreement (11) that it adds value; many presented qualified viewpoints (28). More than one-quarter viewed funding agencies’ growing support of interdisciplinary research as appropriate. Most (44) felt that the level of support was unwarranted. Arguments included the belief that current support leads to the creation of artificial teams and that a top-down process of imposing interdisciplinary structures on teams constrains scientists’ freedom. On both issues we found contrasting trends between the clinician and the biomedical scientists.

Interpretation

Despite having some positive views about the value of interdisciplinary research, scientists, especially biomedical scientists, expressed reservations about the growing support of interdisciplinary research.Collaboration between health disciplines is a new priority of research institutions and funding agencies. Many of these agencies have undergone restructuring and have developed programs specifically to intensify interdisciplinary research. In 2007, the US National Institutes of Health created 9 interdisciplinary research consortia “as a means of integrating aspects of different disciplines to address health challenges that have been resistant to traditional research approaches.”¹ In 2000, the Canadian Institutes of Health Research (CIHR) was established with an express mandate “to forge a health research agenda across disciplines, sectors, and regions that embraces scientific opportunity and reflects the emerging health needs of Canadians, the evolution of the health care system and the information needs of health policy decision-makers.”²This change in priority has been attributed to 3 main factors: the need to answer complex health problems, the need to explore questions that are not confined to a single discipline and the need to provide effective solutions to societal problems.^3,4 Although the arguments advocating for interdisciplinary health research have evoked many kinds of promises, scientists undertaking collaborative research can also face many challenges. The past 10 years have seen a growing body of literature examining the impediments and facilitators to interdisciplinary collaboration.^3,5–14Despite this growing interest, little is known about scientists’ opinions on the prevalent assumption that working across disciplines adds value to health research. Moreover, little consideration has been given to how scientists perceive the growing support of interdisciplinary research by funding agencies. In a survey commissioned by the CIHR, 36% of funded researchers indicated that their collaboration across disciplines had increased as a result of the agency’s establishment.¹⁵ Whether this shift reflects researchers’ scientific interests or their attempts to secure funding by appealing to the agency’s policy of promoting interdisciplinary research is unknown.As part of a broad research program investigating the integration of social science in health research,¹⁶ we conducted this study to examine to what extent, and why, biomedical and clinician scientists are for or against the promotion of interdisciplinary research. We targeted these types of scientists because they were predominantly affected by the move toward interdisciplinary research that occurred after the creation of the CIHR.     

Cowpea N rhizodeposition and its below-ground transfer to a co-existing and to a subsequent millet crop on a sandy soil of the Sudano-Sahelian eco-zone

Nitrogen (N) rhizodeposition by cowpea (Vigna unguiculata (L.) Walp) is potentially a large N source in cropping systems of Sub-Saharan Africa. A field experiment was conducted to measure cowpea N rhizodeposition under the conditions of the Sudano-Sahelian zone using direct ¹⁵N labelling techniques to trace the amount of deposition and its transfer to associated and subsequent crops. Half of the total cowpea crop N was located below-ground at plant maturity, which exceeded 20 kg?N ha^?1 when intercropped with millet. Only 15% of the below-ground cowpea N was recovered in roots, while 85% was found in the rhizodeposited pools. The experiment demonstrated that direct below-ground N transfer occurred from cowpea to millet in intercrop at a rate of 2 kg?N ha^?1 over the growing season. Forty percent of the 25 kg below-ground N that the cowpea crop left at harvest were identifiable in the top 0.30 m soil in the beginning of the next planting season 7 months later; a pool still present at the end of that second season. Thus, the subsequent crop of millet (Pennisetum glaucum (L.) R. Br.) only recovered 2.5 kg?N ha^?1 from the below-ground cowpea pre-crop N during this growth season. The role and potential of cowpea as N provider has been underestimated in the past by ignoring the large proportion of N contained in its rhizodeposits. However, information is needed to determine how losses of the rhizodeposited N can be minimized to fully harness the potential of cowpea as N provider in agro-ecosystems of the region.     

Extent and consistency of linkage disequilibrium and identification of DNA markers for production and egg quality traits in commercial layer chicken populations

Background

The genome sequence and a high-density SNP map are now available for the chicken and can be used to identify genetic markers for use in marker-assisted selection (MAS). Effective MAS requires high linkage disequilibrium (LD) between markers and quantitative trait loci (QTL), and sustained marker-QTL LD over generations. This study used data from a 3,000 SNP panel to assess the level and consistency of LD between single nucleotide polymorphisms (SNPs) over consecutive years in two egg-layer chicken lines, and analyzed one line by two methods (SNP-wise association and genome-wise Bayesian analysis) to identify markers associated with egg-quality and egg-production phenotypes.

Results

The LD between markers pairs was high at short distances (r² > 0.2 at < 2 Mb) and remained high after one generation (correlations of 0.80 to 0.92 at < 5 Mb) in both lines. Single- and 3-SNP regression analyses using a mixed model with SNP as fixed effect resulted in 159 and 76 significant tests (P < 0.01), respectively, across 12 traits. A Bayesian analysis called BayesB, that fits all SNPs simultaneously as random effects and uses model averaging procedures, identified 33 SNPs that were included in the model >20% of the time (φ > 0.2) and an additional ten 3-SNP windows that had a sum of φ greater than 0.35. Generally, SNPs included in the Bayesian model also had a small P-value in the 1-SNP analyses.

Conclusion

High LD correlations between markers at short distances across two generations indicate that such markers will retain high LD with linked QTL and be effective for MAS. The different association analysis methods used provided consistent results. Multiple single SNPs and 3-SNP windows were significantly associated with egg-related traits, providing genomic positions of QTL that can be useful for both MAS and to identify causal mutations.