Evaluation of methods for the extraction and purification of DNA from the human microbiome

Background

DNA extraction is an essential step in all cultivation-independent approaches to characterize microbial diversity, including that associated with the human body. A fundamental challenge in using these approaches has been to isolate DNA that is representative of the microbial community sampled.

Methodology/Principal Findings

In this study, we statistically evaluated six commonly used DNA extraction procedures using eleven human-associated bacterial species and a mock community that contained equal numbers of those eleven species. These methods were compared on the basis of DNA yield, DNA shearing, reproducibility, and most importantly representation of microbial diversity. The analysis of 16S rRNA gene sequences from a mock community showed that the observed species abundances were significantly different from the expected species abundances for all six DNA extraction methods used.

Conclusions/Significance

Protocols that included bead beating and/or mutanolysin produced significantly better bacterial community structure representation than methods without both of them. The reproducibility of all six methods was similar, and results from different experimenters and different times were in good agreement. Based on the evaluations done it appears that DNA extraction procedures for bacterial community analysis of human associated samples should include bead beating and/or mutanolysin to effectively lyse cells.     

Differential Tumorigenic Potential and Matriptase Activation between PDGF B versus PDGF D in Prostate Cancer

The platelet-derived growth factors (PDGF A, B, C, and D) and their receptors (α-PDGFR and β-PDGFR) play an indispensible role in physiologic and pathologic conditions, including tumorigenesis. The transformative β-PDGFR is overexpressed and activated during prostate cancer progression, but the identification and functional significance of its complementary ligand have not been elucidated. This study examined potential oncogenic functions of β-PDGFR ligands PDGF B and PDGF D, using nonmalignant prostate epithelial cells engineered to overexpress these ligands. In our models, PDGF D induced cell migration and invasion more effectively than PDGF B in vitro. Importantly, PDGF D supported prostate epithelial cell tumorigenesis in vivo and showed increased tumor angiogenesis compared with PDGF B. Autocrine signaling analysis of the mitogen-activated protein kinase and phosphoinositide 3-kinase pathways found PDGF D-specific activation of the c-jun-NH(2)-kinase (JNK) signaling cascade. Using short hairpin RNA and pharmacologic inhibitors, we showed that PDGFD-mediated phenotypic transformation is β-PDGFR and JNK dependent. Importantly, we made a novel finding of PDGF D-specific increase in the shedding and activation of the serine protease matriptase in prostate epithelial cells. Our study, for the first time to our knowledge, showed ligand-specific β-PDGFR signaling as well as PDGF D-specific regulation of matriptase activity and its spatial distribution through shedding. Taken together with our previous finding that matriptase is a proteolytic activator of PDGF D, this study provides a molecular insight into signal amplification of the proteolytic network and PDGF signaling loop during cancer progression. Mol Cancer Res; 10(8); 1087-97. ?2012 AACR.     

RANTES gene polymorphisms (-403G>A and -28C>G) associated with hepatitis B virus infection in a Saudi population

Besides the host immune response, genetic and environmental factors play crucial roles in the manifestation of hepatitis B virus (HBV) infection. "Regulated on activation normal T-cell expressed and secreted" factor (RANTES) plays a vital role in CD4(+), CD8(+) T-lymphocyte and dendritic cell activation and proliferation in inflammation. Single nucleotide polymorphisms (SNPs) in the RANTES gene are associated with several viral and non-viral diseases. Association studies have invariably indicated a lack of association between RANTES gene SNPs and HBV infection in ethnic populations, even though RANTES gene SNPs exhibit distinct ethnic distributions. Despite the high prevalence of HBV infections in Saudi Arabia, no studies have been made concerning a possible relationship between RANTES gene polymorphisms and susceptibility to and progression of HBV infection. We examined -403G>A and -28C>G RANTES gene variants in 473 healthy controls and 484 HBV patients in ethnic Saudi populations. Significant differences were found in the genotype and allele distributions of the SNPs between the controls and the HBV patients. Both SNPs were significantly linked to viral clearance in these subjects. Our data demonstrate for the first time in a Saudi population, a relationship between the RANTES gene polymorphisms and the clinical course of HBV infection and underscore the importance of evaluating the genetic background of the affected individual to determine how it may affect disease progression.     

Sounding out pests: the potential of hydroacoustics as a surveillance and compliance tool in aquatic biosecurity

Shipping is the main method for goods transportation, accounting for approximately 60% of all global trade. Biofouling of these shipping vessels is a critical pathway for the introduction of non-indigenous species (NIS) across the world’s oceans. In order to reduce the likelihood of NIS introductions, appropriate biosecurity mechanism need to be in place, including maintaining high standards in vessel hygiene, such as zero secondary biofouling. Development of methodologies that can accurately quantify vessel biofouling without impeding maritime operations, while simultaneously providing effective biosecurity for the marine environment and resources, and mitigation of introduced marine pests would be highly advantageous. This study tests such a methodology. We conduct a proof-of-concept study that uses hydroacoustics to quantify the biofouling on a vessel’s hull, using surrogates for a vessel hull and biofouling. Based on a simple off-the-shelf single beam echosounder, the method was able to visually detect and quantify various biofouling mimics (ranging in height from 10 to 200 mm in height) at a slow tow speed (0.5 m/s). The efficacy of the hydroacoustic method was influenced by the movement of the echosounder, with the discriminating capability reduced to the detection of only larger mimics as the speed of movement increased. With further development, the use of hydroacoustics could become a viable biosecurity surveillance option for the mitigation of introduced marine pest incursions.     

The ectodomain shedding of E-cadherin by ADAM15 supports ErbB receptor activation

The zinc-dependent disintegrin metalloproteinases (a disintegrin and metalloproteinases (ADAMs) have been implicated in several disease processes, including human cancer. Previously, we demonstrated that the expression of a catalytically active member of the ADAM family, ADAM15, is associated with the progression of prostate and breast cancer. The accumulation of the soluble ectodomain of E-cadherin in human serum has also been associated with the progression of prostate and breast cancer and is thought to be mediated by metalloproteinase shedding. Utilizing two complementary models, overexpression and stable short hairpin RNA-mediated knockdown of ADAM15 in breast cancer cells, we demonstrated that ADAM15 cleaves E-cadherin in response to growth factor deprivation. We also demonstrated that the extracellular shedding of E-cadherin was abrogated by a metalloproteinase inhibitor and through the introduction of a catalytically inactive mutation in ADAM15. We have made the novel observation that this soluble E-cadherin fragment was found in complex with the HER2 and HER3 receptors in breast cancer cells. These interactions appeared to stabilize HER2 heterodimerization with HER3 and induced receptor activation and signaling through the Erk pathway, supporting both cell migration and proliferation. In this study, we provide evidence that ADAM15 catalyzes the cleavage of E-cadherin to generate a soluble fragment that in turn binds to and stimulates ErbB receptor signaling.     

Investigating copper-regulated protein expression in Menkes fibroblasts using antibody microarrays

Neurodegenerative illnesses are characterized by aberrant metabolism of biometals such as copper (Cu), zinc (Zn) and iron (Fe). However, little is known about the metabolic effects associated with altered metal homeostasis. In this study, we used an in vitro model of altered Cu homeostasis to investigate how Cu regulates cellular protein expression. Human fibroblasts containing a natural deletion mutation of the Menkes (MNK) ATP7A Cu transporter (MNK deleted) were compared to fibroblasts overexpressing ATP7A (MNK transfected). Cultures of MNK-transfected (Low-Cu) cells exhibited 95% less intracellular Cu than MNK-deleted (High-Cu) cells. Comparative proteomic analysis of the two cell-lines was performed using antibody microarrays, and significant differential protein expression was observed between Low-Cu and High-Cu cell-lines. Western blot analysis confirmed the altered protein expression of Ku80, nexilin, L-caldesmon, MAP4, Inhibitor 2 and DNA topoisomerase I. The top 50 altered proteins were analysed using the software program Pathway Studio (Ariadne Genomics) and revealed a significant over-representation of proteins involved in DNA repair and maintenance. Further analysis confirmed that expression of the DNA repair protein Ku80 was dependent on cellular Cu homeostasis and that Low-Cu levels in fibroblasts resulted in elevated susceptibility to DNA oxidation.     

Advances in the use of terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA genes to characterize microbial communities

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a popular high-throughput fingerprinting technique used to monitor changes in the structure and composition of microbial communities. This approach is widely used because it offers a compromise between the information gained and labor intensity. In this review, we discuss the progress made in T-RFLP analysis of 16S rRNA genes and functional genes over the last 10 years and evaluate the performance of this technique when used in conjunction with different statistical methods. Web-based tools designed to perform virtual polymerase chain reaction and restriction enzyme digests greatly facilitate the choice of primers and restriction enzymes for T-RFLP analysis. Significant improvements have also been made in the statistical analysis of T-RFLP profiles such as the introduction of objective procedures to distinguish between signal and noise, the alignment of T-RFLP peaks between profiles, and the use of multivariate statistical methods to detect changes in the structure and composition of microbial communities due to spatial and temporal variation or treatment effects. The progress made in T-RFLP analysis of 16S rRNA and genes allows researchers to make methodological and statistical choices appropriate for the hypotheses of their studies.     

Role of tumor necrosis factor-alpha and the modulating effect of the caspases in rat corpus luteum apoptosis

Tumor necrosis factor-alpha (TNFalpha) is a pleiotropic cytokine that has been implicated in apoptosis of many cell systems. However, the signal transduction of TNFalpha during the structural and functional regression of the corpus luteum (CL) is largely unknown. In this study, we investigate the role of TNFalpha in rat CL apoptosis and the involvement of monocyte chemoattractant protein-1 (MCP-1) and the modulating effect of the caspases in this process. An in vivo study of CL during pregnancy and postpartum using immunohistochemistry and Western blot analysis indicated that increases in TNFalpha correspond with luteal apoptosis approaching term (Day 22) and at postpartum (Day 3). CL apoptosis was further investigated using a whole-CL culture model of tropic withdrawal. An increase was observed in both low molecular weight (MW) DNA fragmentation and TUNEL staining from 0 h to 8 h in culture. CL apoptosis in vitro was associated with increased protein expression of both TNFalpha and MCP-1 as measured by immunohistochemistry and Western blot analysis. Using a whole-CL culture model, apoptosis was induced in vitro by TNFalpha as demonstrated by a dose-dependent increase in DNA fragmentation. Treatment of luteal cells with TNFalpha and both specific caspase inhibitors (Z-DEVD-FMK, Z-VEID-FMK, Z-IETD-FMK) or a general caspase inhibitor (Boc-D-FMK) prevented the effect of TNFalpha. CL regression involves the apoptotic deletion of luteal cells; the results of this study suggest that TNFalpha is possibly involved in this process. The observed increases in MCP-1 expression suggest the coordination of TNFalpha expression with the infiltration and activation of macrophages. Furthermore, the results demonstrate the importance of the caspases in the TNFalpha signal transduction pathway and suggest a hierarchy within the caspase family.