Assessing Mitochondrial DNA Variation and Copy Number in Lymphocytes of ~2,000 Sardinians Using Tailored Sequencing Analysis Tools

DNA sequencing identifies common and rare genetic variants for association studies, but studies typically focus on variants in nuclear DNA and ignore the mitochondrial genome. In fact, analyzing variants in mitochondrial DNA (mtDNA) sequences presents special problems, which we resolve here with a general solution for the analysis of mtDNA in next-generation sequencing studies. The new program package comprises 1) an algorithm designed to identify mtDNA variants (i.e., homoplasmies and heteroplasmies), incorporating sequencing error rates at each base in a likelihood calculation and allowing allele fractions at a variant site to differ across individuals; and 2) an estimation of mtDNA copy number in a cell directly from whole-genome sequencing data. We also apply the methods to DNA sequence from lymphocytes of ~2,000 SardiNIA Project participants. As expected, mothers and offspring share all homoplasmies but a lesser proportion of heteroplasmies. Both homoplasmies and heteroplasmies show 5-fold higher transition/transversion ratios than variants in nuclear DNA. Also, heteroplasmy increases with age, though on average only ~1 heteroplasmy reaches the 4% level between ages 20 and 90. In addition, we find that mtDNA copy number averages ~110 copies/lymphocyte and is ~54% heritable, implying substantial genetic regulation of the level of mtDNA. Copy numbers also decrease modestly but significantly with age, and females on average have significantly more copies than males. The mtDNA copy numbers are significantly associated with waist circumference (p-value = 0.0031) and waist-hip ratio (p-value = 2.4×10^-5), but not with body mass index, indicating an association with central fat distribution. To our knowledge, this is the largest population analysis to date of mtDNA dynamics, revealing the age-imposed increase in heteroplasmy, the relatively high heritability of copy number, and the association of copy number with metabolic traits.     

The effects of ATP and sodium chloride on the cytochrome c-cardiolipin interaction: the contrasting behavior of the horse heart and yeast proteins

In cells a portion of cytochrome c (cyt c) (15–20%) is tightly bound to cardiolipin (CL), one of the phospholipids constituting the mitochondrial membrane. The CL-bound protein, which has nonnative tertiary structure, altered heme pocket, and disrupted Fe(III)-M80 axial bond, is thought to play a role in the apoptotic process. This has attracted considerable interest in order to clarify the mechanisms governing the cyt c–CL interaction. Herein we have investigated the binding reaction of CL with the c-type cytochromes from horse heart and yeast. Although the two proteins possess a similar tertiary architecture, yeast cyt c displays lower stability and, contrary to the equine protein, it does not bind ATP and lacks pro-apoptotic activity. The study has been performed in the absence and in the presence of ATP and NaCl, two compounds that influence the (horse cyt c)-CL binding process and, thus, the pro-apoptotic activity of the protein. The two proteins behave differently: while CL interaction with horse cyt c is strongly influenced by the two effectors, no effect is observed for yeast cyt c. It is noteworthy that NaCl induces dissociation of the (horse cyt c)–CL complex but has no influence on that of yeast cyt c. The differences found for the two proteins highlight that specific structural factors, such as the different local structure conformation of the regions involved in the interactions with either CL or ATP, can significantly affect the behavior of cyt c in its reaction with liposomes and the subsequent pro-apoptotic action of the protein.     

Computational, spectroscopic, and resonant mirror biosensor analysis of the interaction of adrenodoxin with native and tryptophan-modified NADPH-adrenodoxin reductase

In steroid hydroxylation system in adrenal cortex mitochondria, NADPH-adrenodoxin reductase (AR) and adrenodoxin (Adx) form a short electron-transport chain that transfers electrons from NADPH to cytochromes P-450 through FAD in AR and [2Fe-2S] cluster in Adx. The formation of [AR/Adx] complex is essential for the electron transfer mechanism in which previous studies suggested that AR tryptophan (Trp) residue(s) might be implicated. In this study, we modified AR Trps by N-bromosuccinimide (NBS) and studied AR binding to Adx by a resonant mirror biosensor. Chemical modification of tryptophans caused inhibition of electron transport. The modified protein (AR*) retained the native secondary structure but showed a lower affinity towards Adx with respect to AR. Activity measurements and fluorescence data indicated that one Trp residue of AR may be involved in the electron transferring activity of the protein. Computational analysis of AR and [AR/Adx] complex structures suggested that Trp193 and Trp420 are the residues with the highest probability to undergo NBS-modification. In particular, the modification of Trp420 hampers the correct reorientation of AR* molecule necessary to form the native [AR/Adx] complex that is catalytically essential for electron transfer from FAD in AR to [2Fe-2S] cluster in Adx. The data support an incorrect assembly of [AR*/Adx] complex as the cause of electron transport inhibition.     

Soluble TNF-like cytokine (TL1A) production by immune complexes stimulated monocytes in rheumatoid arthritis

TNF-like cytokine (TL1A) is a newly identified member of the TNF superfamily of ligands that is important for T cell costimulation and Th1 polarization. However, despite increasing information about its functions, very little is known about expression of TL1A in normal or pathological states. In this study, we report that mononuclear phagocytes appear to be a major source of TL1A in rheumatoid arthritis (RA), as revealed by their strong TL1A expression in either synovial fluids or synovial tissue of rheumatoid factor (RF)-seropositive RA patients, but not RF-/RA patients. Accordingly, in vitro experiments revealed that human monocytes express and release significant amounts of soluble TL1A when stimulated with insoluble immune complexes (IC), polyethylene glycol precipitates from the serum of RF+/RA patients, or with insoluble ICs purified from RA synovial fluids. Monocyte-derived soluble TL1A was biologically active as determined by its capacity to induce apoptosis of the human erythroleukemic cell line TF-1, as well as to cooperate with IL-12 and IL-18 in inducing the production of IFN-gamma by CD4(+) T cells. Because RA is a chronic inflammatory disease with autoimmune etiology, in which ICs, autoantibodies (including RF), and various cytokines contribute to its pathology, our data suggest that TL1A could be involved in its pathogenesis and contribute to the severity of RA disease that is typical of RF+/RA patients.     

Diiron and diruthenium aminocarbyne complexes containing pseudohalides: stereochemistry and reactivity

Acetonitrile is easily displaced from [Fe₂{μ-CN(Me)(R)}(μ-CO)(CO)(MeCN)(Cp)₂][SO₃CF₃] (R = 2,6-Me₂C₆H₃ (Xyl) (1a); Me (1b)) upon stirring in THF at room temperature in the presence of [NBu₄][SCN]. The resulting complexes trans-[Fe₂{μ-CN(Me)(R)}(μ-CO)(CO)(NCS)(Cp)₂] (R = Xyl (trans-2a); Me (trans-2b)) are completely isomerised to cis-[Fe₂{μ-CN(Me)(R)}(μ-CO)(CO)(NCS)(Cp)₂] (R = Xyl (cis-2a); Me (cis-2b)) when heated at reflux temperature. Similarly, the complexes cis-[M₂{μ-CN(Me)(R)}(μ-CO)(CO)(NCO)(Cp)₂] (M = Fe, R = Me (4a); M = Ru, R = Xyl (4b); M = Ru, R = Me (4c)) and cis-[M₂{μ-CN(Me)(R)}(μ-CO)(CO)(N₃)(Cp)₂] (M = Fe, R = Xyl (5a); M = Fe, R = Me (5b); M = Ru, R = Xyl (5c)) can be obtained by heating at reflux temperature a THF solution of [M₂{μ-CN(Me)(R)}(μ-CO)(CO)(MeCN)(Cp)₂][SO₃CF₃] (M = Fe, R = Xyl (1a); M = Fe, Me (1b); M = Ru, R = Xyl (1c); M = Ru, R = Me (1d)) in the presence of NaNCO and NaN₃, respectively. The reactions of 5 with MeO₂CCCCO₂Me, HCCCO₂Me and (NC)(H)CC(H)(CN) afford the triazolato complexes [M₂{μ-CN(Me)(R)}(μ-CO)(CO){N₃C₂(CO₂Me)₂}(Cp)₂] (M = Fe, R = Xyl (6a); M = Fe, R = Me (6b); M = Ru, R = Xyl (6c)), [M₂{μ-CN(Me)(R)}(μ- CO)(CO){N₃C₂(H)(CO₂Me)}(Cp)₂] (M = Fe, R = Me (7a); M = Ru, R = Xyl (7b)) and [Fe₂{μ-CN(Me)(Xyl)}(μ-CO)(CO){N₃C₂(H)(CN)}(Cp)₂] (8), respectively. The asymmetrically substituted triazolato complexes 7-8 are obtained as mixtures of N(1) and N(2) bonded isomers, whereas 6 exists only in the N(2) form. Methylation of 6-8 results in the formation of the triazole complexes [Fe₂{μ-CN(Me)(Xyl)}(μ-CO)(CO){N₃(Me)C₂(CO₂Me)₂}(Cp)₂][CF₃SO₃] (9), [M₂{μ-CN(Me)(R)}(μ-CO)(CO){N₃(Me)C₂(H)(CO₂Me)}(Cp)₂][CF₃SO₃] (M = Fe, R = Me (10a); M = Ru, R = Xyl (10b)) and [Fe₂{μ-CN(Me)(Xyl)}(μ-CO)(CO){N₃(Me)C₂(H)(CN)}(Cp)₂][CF₃SO₃], 11. The crystal structures of trans-2b, 4b · CH₂Cl₂, 5a, 6b · 0.5CH₂Cl₂ and 8 · CH₂Cl₂ have been determined.     

Cell Survival and Polarity of Drosophila Follicle Cells Require the Activity of Ecdysone Receptor B1 Isoform

Proper assembly and maintenance of epithelia are critical for normal development and homeostasis. Here, using the Drosophila ovary as a model, we identify a role for the B1 isoform of the ecdysone receptor (EcR-B1) in this process. We performed a reverse genetic analysis of EcR-B1 function during oogenesis and demonstrate that silencing of this receptor isoform causes loss of integrity and multilayering of the follicular epithelium. We show that multilayered follicle cells lack proper cell polarity with altered distribution of apical and basolateral cell polarity markers including atypical-protein kinase C (aPKC), Discs-large (Dlg), and Scribble (Scrib) and aberrant accumulation of adherens junctions and F-actin cytoskeleton. We find that the EcR-B1 isoform is required for proper follicle cell polarity both during early stages of oogenesis, when follicle cells undergo the mitotic cell cycle, and at midoogenesis when these cells stop dividing and undergo several endocycles. In addition, we show that the EcR-B1 isoform is required during early oogenesis for follicle cell survival and that disruption of its function causes apoptotic cell death induced by caspase.     

Effects induced by mono- and divalent cations on protein regions responsible for thermal adaptation in β-glycosidase from<Emphasis Type="Italic"> Sulfolobus solfataricus</Emphasis>

The perturbation induced by mono- and divalent cations on the thermophilicity and thermostability of Solfolobus solfataricus -glycosidase, a hyperthermophilic tetrameric enzyme, has been investigated by spectroscopic and computational simulation methods to ascertain the Hofmeister effects on two strategic protein regions identified previously. Specifically, (1) an extra segment (83–124), present only in the sequence of hyperthermophilic glycosidases and recognized as an important thermostability determinant for the enzyme structure; and (2) a restricted area of the subunit interface responsible for the quaternary structure maintenance. Mono- and divalent cations inhibit to a different extent the -glycosidase activity, whose kinetic constants show an apparent competitive inhibition of the catalytic process that reflects the Hofmeister order. The thermostability is also affected by the nature and charge of the cations, reaching maximal effects for the case of Mg²⁺. Fourier transform infrared spectroscopy has revealed very small changes in the protein secondary structure in the presence of the investigated cations at 20 °C, while large effects on the protein melting temperatures are observed. Computational analysis of the enzyme structure has identified negative patches on the accessible surface of the two identified regions. Following the Hofmeister series, cations weaken the existing electrostatic network that links the extra segment to the remaining protein matrix. In particular, the perturbing action of cations could involve the ionic pair interactions E107–R245 and E109–R185, thus leading to a local destructuring of the extra segment as a possible starting event for thermal destabilization. A detailed investigation of the electrostatic network at the A–C intermolecular interface of Sgly after energy minimization suggests that cations could cause a strong attenuation of the ion pair interactions E474–K72 and D473–R402, with consequent partial dissociation of the tetrameric structure.Abbreviations Amide I amide I band in a ²H₂O medium - EM energy minimization - ONPG o-nitrophenyl--d-galactopyranoside - Sgly Escherichia coli expressed Sulfolobus solfataricus -glycosidase     

Olive flowering trends in a large Mediterranean area (Italy and Spain)

The aim of this study was to investigate the main climatic and biological trends related to olive flowering in central-southern Italy compared to those in Andalusia, Spain. Results since 1982 were compared for the two long-series monitoring areas of Cordoba and Perugia, and since 1992–1999 for the short-series areas. The relationship between climatic trends and the biological response of the olive, a widespread culture in the Mediterranean basin, were investigated. An aerobiological method involving capturing pollen released into the atmosphere was utilised as a bioindicator of flowering phenology. The study results confirm the strong relationship between flowering periods and spring temperature trends for the olive. Temperature during March, April and May was the parameter most related to flowering date in the study areas, particularly in Italy. In some cases we found a significant correlation between flowering and past autumn temperatures, probably due to their effect on floral bud dormancy induction, but this phenomenon appeared to be of minor importance in the studied areas. The phenological trend results show the continuous advance of flowering dates to the late 1990s, followed by a relatively stationary time series related to a short-term temperature fluctuation in the Mediterranean area. This latter period probably represents a mesoscale event forced by a macroscale event—the North Atlantic Oscillation. The results reveal that the trend towards increased temperatures, and the consequent flowering advance of some species, indicated some years ago is nowadays not as clear as was expected and should be confirmed over the next few years in the Mediterranean areas under investigation.     

Metabolic engineering of Pseudomonas fluorescens for the production of vanillin from ferulic acid

Vanillin is one of the most important flavors in the food industry and there is great interest in its production through biotechnological processes starting from natural substrates such as ferulic acid. Among bacteria, recombinant Escherichia coli strains are the most efficient vanillin producers, whereas Pseudomonas spp. strains, although possessing a broader metabolic versatility, rapidly metabolize various phenolic compounds including vanillin. In order to develop a robust Pseudomonas strain that can produce vanillin in high yields and at high productivity, the vanillin dehydrogenase (vdh)-encoding gene of Pseudomonas fluorescens BF13 strain was inactivated via targeted mutagenesis. The results demonstrated that engineered derivatives of strain BF13 accumulate vanillin if inactivation of vdh is associated with concurrent expression of structural genes for feruloyl-CoA synthetase (fcs) and hydratase/aldolase (ech) from a low-copy plasmid. The conversion of ferulic acid to vanillin was enhanced by optimization of growth conditions, growth phase and parameters of the bioconversion process. The developed strain produced up to 8.41 mM vanillin, which is the highest final titer of vanillin produced by a Pseudomonas strain to date and opens new perspectives in the use of bacterial biocatalysts for biotechnological production of vanillin from agro-industrial wastes which contain ferulic acid.     

Dynamic root growth and architecture responses to limiting nutrient availability: linking physiological models and experimentation

In recent years the study of root phenotypic plasticity in response to sub-optimal environmental factors and the genetic control of these responses have received renewed attention. As a path to increased productivity, in particular for low fertility soils, several applied research projects worldwide target the improvement of crop root traits both in plant breeding and biotechnology contexts. To assist these tasks and address the challenge of optimizing root growth and architecture for enhanced mineral resource use, the development of realistic simulation models is of great importance. We review this research field from a modeling perspective focusing particularly on nutrient acquisition strategies for crop production on low nitrogen and low phosphorous soils. Soil heterogeneity and the dynamics of nutrient availability in the soil pose a challenging environment in which plants have to forage efficiently for nutrients in order to maintain their internal nutrient homeostasis throughout their life cycle. Mathematical models assist in understanding plant growth strategies and associated root phenes that have potential to be tested and introduced in physiological breeding programs. At the same time, we stress that it is necessary to carefully consider model assumptions and development from a whole plant-resource allocation perspective and to introduce or refine modules simulating explicitly root growth and architecture dynamics through ontogeny with reference to key factors that constrain root growth. In this view it is important to understand negative feedbacks such as plant–plant competition. We conclude by briefly touching on available and developing technologies for quantitative root phenotyping from lab to field, from quantification of partial root profiles in the field to 3D reconstruction of whole root systems. Finally, we discuss how these approaches can and should be tightly linked to modeling to explore the root phenome.