Evaluating different methods of microarray data normalization

Background  

With the development of DNA hybridization microarray technologies, nowadays it is possible to simultaneously assess the expression levels of thousands to tens of thousands of genes. Quantitative comparison of microarrays uncovers distinct patterns of gene expression, which define different cellular phenotypes or cellular responses to drugs. Due to technical biases, normalization of the intensity levels is a pre-requisite to performing further statistical analyses. Therefore, choosing a suitable approach for normalization can be critical, deserving judicious consideration.     

Factors potentially affecting fertility of lactating dairy cow recipients

Objectives of this study were to evaluate factors that could affect pregnancy rate after embryo transfer (ET) in lactating dairy cow recipients. The trial was conducted at a dairy farm located in Descalvado, SP, Brazil from October 2003 to September 2004. From 1037 cows with CL that were treated with an injection of PGF2alpha, 43.3% were detected in heat; 263 were previously assigned at day of PGF2alpha injection for AI and 186 for ET. Ovulation rate was 85.7% (385/449). Pregnancy rate for cows with CL for AI and embryo transfer recipients were 36.5% (84/230) and 58.7% (91/155) at day 25 and 33.0% (76/230) and 45.8% (71/155) at day 46, respectively. Embryonic loss were 9.5% (8/84) for the AI group and 21.9% (20/91) for the ET group. Average milk production was 31.4 L/day/cow. Average daily milk production from 7 days before PGF2alpha injection to 7 days after ET tended (P < 0.10) to influence pregnancy rate on days 25 and 46. Average daily milk production from the day of embryo transfer to 7 days after influenced embryonic loss (P < 0.05). Cows with higher milk production had lower probability of pregnancy and higher probability of embryonic loss. Cows with higher days in milk had higher probability of pregnancy. Cows with higher rectal body temperature had lower probability of pregnancy and higher probability of embryonic loss. The influence of high milk yield and body temperature on fertility in lactating dairy cow recipients suggests that these effects can occur also after embryo reaches the blastocyst stage.     

Identification of Seroreactive Proteins of Leptospira interrogans Serovar Copenhageni Using a High-Density Protein Microarray Approach

Background

Leptospirosis is a widespread zoonotic disease worldwide. The lack of an adequate laboratory test is a major barrier for diagnosis, especially during the early stages of illness, when antibiotic therapy is most effective. Therefore, there is a critical need for an efficient diagnostic test for this life threatening disease.

Methodology

In order to identify new targets that could be used as diagnostic makers for leptopirosis, we constructed a protein microarray chip comprising 61% of Leptospira interrogans proteome and investigated the IgG response from 274 individuals, including 80 acute-phase, 80 convalescent-phase patients and 114 healthy control subjects from regions with endemic, high endemic, and no endemic transmission of leptospirosis. A nitrocellulose line blot assay was performed to validate the accuracy of the protein microarray results.

Principal findings

We found 16 antigens that can discriminate between acute cases and healthy individuals from a region with high endemic transmission of leptospirosis, and 18 antigens that distinguish convalescent cases. Some of the antigens identified in this study, such as LipL32, the non-identical domains of the Lig proteins, GroEL, and Loa22 are already known to be recognized by sera from human patients, thus serving as proof-of-concept for the serodiagnostic antigen discovery approach. Several novel antigens were identified, including the hypothetical protein LIC10215 which showed good sensitivity and specificity rates for both acute- and convalescent-phase patients.

Conclusions

Our study is the first large-scale evaluation of immunodominant antigens associated with naturally acquired leptospiral infection, and novel as well as known serodiagnostic leptospiral antigens that are recognized by antibodies in the sera of leptospirosis cases were identified. The novel antigens identified here may have potential use in both the development of new tests and the improvement of currently available assays for diagnosing this neglected tropical disease. Further research is needed to assess the utility of these antigens in more deployable diagnostic platforms.     

Cryopreservation of caprine ovarian tissue using dimethylsulphoxide and propanediol

The caprine ovary is a rich source of potentially viable immature oocytes enclosed in preantral follicles (PF). Previous experiments showed that these oocytes can be successfully cryopreserved in ovarian tissue of several species. However, until now, no information about the caprine PF cryopreservation is available in the literature. The aim of the present research was to evaluate the structural and ultrastructural characteristics of caprine PF after treatment and cryopreservation of ovarian tissue with 1.5 and 3 M dimethylsulphoxide (DMSO) and propanediol (PROH). One fragment of ovarian tissue was immediately fixed for histological examination and ultrastructural analysis, after slaughter (control). Four fragments were equilibrated at 20 degrees C/20 min in 1.8 ml of minimum essential medium (MEM) containing 1.5 or 3 M DMSO or PROH for the toxicity test, and the other four fragments were slowly frozen in each cryoprotectant at the concentrations previously described. After toxicity test and freezing/thawing procedures, the ovarian fragments were fixed for histological examination. The results showed that after toxicity test and cryopreservation of ovarian tissue using both cryoprotectants, the percentage of normal PF was less (P < 0.05) as compared with the control group. The present study revealed that the percentage of normal PF after toxicity test and cryopreservation in 1.5 M DSMO was significantly greater (P < 0.05) as compared with results obtained with 3 M DMSO or 1.5 and 3 M PROH. This result was confirmed by transmission electron microscopy, which showed that the PF were preserved in a higher quality state with 1.5 M DMSO. In conclusion, the present study demonstrated that caprine PF can be cryopreserved in ovarian tissue using 1.5 M DMSO.     

Dial organic carbon fluctuations in a mangrove tidal creek in Sepetiba bay, Southeast Brazil

The carbon (C) concentration and flux, as dissolved organic carbon (DOC), particulate organic carbon (POC) and macrodetritus (MD), were quantified through 4 tidal cycles in a mangrove tidal creek in Southeastern Brazil. DOC was the major fraction of the total C concentration, accounting for 68 and 61% of the total C concentration during ebb and flood periods respectively. Concentrations of DOC (Ebb = 3.41 +/- 0.57 mgC.L-1 and Flood = 3.55 +/- 0.76 mgC.L-1) and POC (Ebb = 1.73 +/- 0.99 mgC.L-1 and Flood = 1.28 +/- 0.45 mgC.L-1) were relatively similar during the four tidal cycles. Macrodetritus presented a wide variation with concentration peaks probably related to external forces, such as winds, which enrich the ebb flow with leaf litter. DOC and POC fluxes depended primarily on tidal and net water fluxes, whereas MD fluxes were not. The magnitude of the DOC and POC fluxes varied with the area flooded at high tide, but not the MD fluxes. DOC was the major form of carbon export to Sepetiba Bay. During the four tidal cycles, the forest exported a total of 1.2 kg of organic carbon per ha, mostly as DOC (60%), followed by POC (22%) and MD (18%).     

Effect of poly(ADP-ribosyl)ation inhibitors on the genotoxic effects of the boron neutron capture reaction

The boron neutron capture (BNC) reaction results from the interaction of 10B with low-energy thermal neutrons and gives rise to highly damaging lithium and alpha-particles. In this work the genotoxicity caused by the BNC reaction in V79 Chinese hamster cells was evaluated in the presence of poly(ADP-ribosyl)ation inhibitors. Poly(ADP-ribose) polymerase-1 (PARP-1), the most important member of the PARP enzyme family, is considered to be a constitutive factor of the DNA damage surveillance network present in eukaryotic cells, acting through a DNA break sensor function. Inhibition of poly(ADP-ribosyl)ation was achieved with the classical compound 3-aminobenzamide (3-AB), and with two novel and very potent inhibitors, 5-aminoisoquinolinone (5-AIQ) and PJ-34. Dose-response increases in the frequencies of aberrant cells excluding gaps (%ACEG) and chromosomal aberrations excluding gaps per cell (CAEG/cell) were observed for increasing exposures to the BNC reaction. The presence of 3-AB did not increase the %ACEG or CAEG/cell, nor did it change the pattern of the induced chromosomal aberrations. Results with 5-AIQ and PJ-34 were in agreement with the results obtained with 3-AB. We further studied the combined effect of a PARP inhibitor and a DNA-dependent protein kinase (DNA-PK) inhibitors (3-AB and wortmannin, respectively) on the genotoxicity of the BNC reaction, by use of the cytokinesis-block micronucleus assay. DNA-PK is also activated by DNA breaks and binds DNA ends, playing a role of utmost importance in the repair of double-strand breaks. Our results show that the inhibition of poly(ADP-ribosyl)ation does not particularly modify the genotoxicity of the BNC reaction, and that PARP inhibition together with a concomitant inhibition of DNA-PK revealed barely the same sensitizing effect as DNA-PK inhibition per se.     

Inter-rater reliability of physiotherapists using the Action Research Arm Test in chronic stroke

Objectives:The purpose of this study is to establish whether physiotherapists’ ratings are consistent, when using the Action Research Arm Test (ARAT) to score a chronic stroke patient.Methods:This was part of a large project establishing the reliability in chronic stroke. This study used a correlational design comparing the association between physiotherapist scores of the same patient, to establish the ARAT’s inter-rater reliability. The COSMIN checklist was followed to enhance the methodology of the study.Results:Twenty physiotherapists (8 female and 12 male) aged between 25 and 53 years were selected. There were no participant dropouts or withdrawals. The sample size was normally distributed. The physiotherapists appeared representative of the UK physiotherapy population, with the exception of gender. The distribution of scores showed a normal distribution with standard deviation of score of 1.9. The Kendall’s W test showed 0.711 of agreement between the raters. The scores achieved statistical significance showing consistency between physiotherapists’ scores with chronic stroke. Limitations of the study were the use of a small single center convenience sample that may reduce the generalizability of the findings.Conclusions:The ARAT is consistent when scored by physiotherapists in a chronic stroke population. The inter-rater reliability range was (0.70 to 0.90) which is categorized as good.     

α-MSH signalling via melanocortin 5 receptor promotes lipolysis and impairs re-esterification in adipocytes

The melanocortin system has a clear effect on the mobilisation of stored lipids in adipocytes. The aim of the current study was to investigate the role of melanocortin 5 receptor (MC5R) on α-melanocyte-stimulating hormone (α-MSH)-induced lipolysis in 3T3-L1 adipocytes. To this end, MC5R expression was decreased by small interfering RNA (siRNA), which significantly impaired the α-MSH stimulation of lipolysis, as determined by glycerol and nonesterified fatty-acid (NEFA) quantification. The functional role of α-MSH/MC5R on triglyceride (TG) hydrolysis was mediated by hormone-sensitive lipase (HSL), adipose triglyceride lipase (ATGL), perilipin 1 (PLIN1) and acetyl-CoA carboxylase (ACC). Immunofluorescence microscopy revealed that phosphorylated HSL clearly surrounded lipid droplets in α-MSH-stimulated adipocytes, whereas PLIN1 left the immediate periphery of lipids. These observations were lost when the expression of MC5R was suppressed.