One mutation,three phenotypes: novel metabolic insights on MELAS,MIDD and myopathy caused by the m.3243A > G mutation

Metabolomics - Studies investigating crop resistance to abiotic and biotic stress have largely focused on plant responses to singular forms of stress and individual biochemical pathways that only...     

Disclosure of a putative biosignature for respiratory chain disorders through a metabolomics approach

The diagnosis of respiratory chain deficiencies (RCDs) is complicated and the need for a diagnostic biomarker or biosignature has been widely expressed. In this study, the metabolic profile of a selected group of 29 RCD patients, with a predominantly muscle disease phenotype, and 22 controls were investigated using targeted and untargeted analyses of three sub-sections of the human metabolome, including urinary organic acids and amino acids [measured by gas chromatography–mass spectrometry (GC–MS)], as well as acylcarnitines (measured by electrospray ionization tandem MS). Although MS technologies are highly sensitive and selective, they are restrictive by being applied only to sub-sections of the metabolome; an untargeted nuclear magnetic resonance (NMR) spectroscopy approach was therefore also included. After data reduction and pre-treatment, a biosignature comprising six organic acids (lactic, succinic, 2-hydroxyglutaric, 3-hydroxyisobutyric, 3-hydroxyisovaleric and 3-hydroxy-3-methylglutaric acids), six amino acids (alanine, glycine, glutamic acid, serine, tyrosine and α-aminoadipic acid) and creatine, was constructed from uni- and multivariate statistical analyses and verified by cross-validation. The results presented here provide the first proof-of-concept that the metabolomics approach is capable of defining a biosignature for RCDs. We postulate that the composite of organic acids ≈ amino acids > creatine > betaine > carnitines represents the basic biosignature for RCDs. Validated through a prospective study, this could offer an improved ability to assign individual patients to a group with defined RCD characteristics and improve case selection for biopsy procedures, especially in infants and children.     

Standardising Home Range Studies for Improved Management of the Critically Endangered Black Rhinoceros

Comparisons of recent estimations of home range sizes for the critically endangered black rhinoceros in Hluhluwe-iMfolozi Park (HiP), South Africa, with historical estimates led reports of a substantial (54%) increase, attributed to over-stocking and habitat deterioration that has far-reaching implications for rhino conservation. Other reports, however, suggest the increase is more likely an artefact caused by applying various home range estimators to non-standardised datasets. We collected 1939 locations of 25 black rhino over six years (2004–2009) to estimate annual home ranges and evaluate the hypothesis that they have increased in size. A minimum of 30 and 25 locations were required for accurate 95% MCP estimation of home range of adult rhinos, during the dry and wet seasons respectively. Forty and 55 locations were required for adult female and male annual MCP home ranges, respectively, and 30 locations were necessary for estimating 90% bivariate kernel home ranges accurately. Average annual 95% bivariate kernel home ranges were 20.4 ± 1.2 km², 53 ±1.9% larger than 95% MCP ranges (9.8 km² ± 0.9). When home range techniques used during the late-1960s in HiP were applied to our dataset, estimates were similar, indicating that ranges have not changed substantially in 50 years. Inaccurate, non-standardised, home range estimates and their comparison have the potential to mislead black rhino population management. We recommend that more care be taken to collect adequate numbers of rhino locations within standardized time periods (i.e., season or year) and that the comparison of home ranges estimated using dissimilar procedures be avoided. Home range studies of black rhino have been data deficient and procedurally inconsistent. Standardisation of methods is required.     

Naturally occurring fragments from two distinct regions of the prostatic acid phosphatase form amyloidogenic enhancers of HIV infection

Semen is the major vector for HIV-1 transmission. We previously isolated C-proximal fragments of the prostatic acid phosphatase (PAP) from semen which formed amyloid fibrils that potently enhanced HIV infection. Here, we used the same methodology and identified another amyloidogenic peptide. Surprisingly, this peptide is derived from an N-proximal fragment of PAP (PAP85-120) and forms, similar to the C-proximal fragments, positively charged fibrillar structures that increase virion attachment to cells. Our results provide a first example for amyloid formation by fragments of distinct regions of the same precursor and further emphasize the possible importance of amyloidogenic peptides in HIV transmission.     

Seminal Plasma and Semen Amyloids Enhance Cytomegalovirus Infection in Cell Culture

Among the modes of transmission available to the cytomegalovirus (CMV) is sexual transmission, primarily via semen. Both male-to-female (M-F) and male-to-male (M-M) sexual transmission significantly contribute toward the spread of CMV infections in the global population. Semen plays an important role in carrying the viral particle that invades the vaginal or rectal mucosa, thereby initiating viral replication. Both semen and seminal plasma (SP) can enhance HIV-1 infection in cell culture, and two amyloid fibrils, semen-derived enhancer of viral infection (SEVI) and amyloids derived from the semenogelins (SEM amyloids), have been identified as seminal factors sufficient to enhance HIV-1 infection (J. Munch et al., Cell 131:1059–1071, 2007; N. R. Roan et al., Cell Host Microbe 10:541–550, 2011; F. Arnold et al., J. Virol. 86:1244–1249, 2012). Whether SP, SEVI, or SEM amyloids can enhance other viral infections has not been extensively examined. In this study, we found that SP, SEVI, and SEM amyloids strongly enhance both human CMV (HCMV) and murine CMV infection in cell culture. SEVI and SEM amyloids increased infection rates by >10-fold, as determined by both flow cytometry and fluorescence microscopy. Viral replication was increased by 50- to 100-fold. Moreover, viral growth curve assays showed that SP, SEVI, and SEM amyloids sped up the kinetics of CMV replication such that the virus reached its replicative peak more quickly. Finally, we discovered that SEM amyloids and SEVI counteracted the effect of anti-gH in protecting against CMV infection. Collectively, the data suggest that semen enhances CMV infection through interactions between semen amyloid fibrils and viral particles, and these interactions may prevent HCMV from being neutralized by anti-gH antibody.     

Miniaturized <Superscript>1</Superscript>H-NMR method for analyzing limited-quantity samples applied to a mouse model of Leigh disease

Introduction

The analysis of limited-quantity samples remains a challenge associated with mouse models, especially for multi-platform metabolomics studies. Although inherently insensitive, the highly specific characteristics of nuclear magnetic resonance (NMR) spectroscopy make it an advantageous platform for global metabolite profiling, particularly in mitochondrial disease research.

Objectives

Show method equivalency between a well-established standard operating protocol (SOP) and our novel miniaturized ¹H-NMR method.

Method

The miniaturized method was performed in a 2 mm NMR tube on a standard 500 MHz NMR spectrometer with a 5 mm triple-resonance inverse TXI probe at room temperature.

Results

Firstly, using synthetic urine spiked with low (50 µM), medium (250 µM) and high (500 µM) levels (n?=?10) of nine standards, both the SOP and miniaturized method were shown to have acceptable precision (CV?<?15%), relative accuracy (80–120%), and linearity (R²?>?0.95), except for taurine. Furthermore, statistical equivalence was shown using the two one-sided test. Secondly, pooled mouse quadriceps muscle extract was used to further confirm method equivalence (n?=?3), as well as explore the analytical dynamics of this novel approach by analyzing more-concentrated versions of samples (up to 10× concentration) to expand identification of metabolites qualitatively, with quantitative linearity. Lastly, we demonstrate the new technique’s application in a pilot metabolomics study using minute soleus muscle tissue from a mouse model of Leigh syndrome using Ndufs4 KO mice.

Conclusion

We demonstrate method equivalency, supporting our novel miniaturized ¹H-NMR method as a financially feasible alternative to cryoprobe technology—for limited-quantity biological samples in metabolomics studies that requires a volume one-tenth of the SOP.

     

Research Design and the Politics of Abstraction: Unpacking the Environmentality of Scientific Practice in Socioecological Assessments

Scientific assessments of socio-ecological systems are becoming mainstays in guiding policymaking and other interventions in response to global environmental change. The environmentality literature emphasizes the institutional architecture of emergent science-policy regimes and how scientific research is used in political settings, creating new modes of governance and subjectivities. However, there has been relatively little attention to domain-level socio-ecological assessments as socially produced technologies where specific scientific choices are mechanisms connecting governance architecture and popular subjectivities.Combining empirical case study and literature review, assessment technologies are analyzed in three domains: vulnerability assessment, ecosystem services assessment, life-cycle assessment. Using conceptualization, operationalization, and institutionalization as analytical lenses, the cases illustrate ways that scientific choices simplify complex socio-ecological relationships with implications for both governance practices and subjectivities. Furthermore, findings explore the possibility for assessments to be more inclusive of diverse social values and practices, enabling more empowering subjectivities.