25 million years to break a continent : early to middle Miocene rifting and syn-extensional magmatism in the southern Gulf of California

Cenozoic extension in western Mexico has been divided into two episodes separated by the change from convergence to oblique divergence at the plate boundary. The Gulf Extensional Province is thought to have started once subduction ended at ~12.5 Ma whereas early extension is classified as Basin and Range. Mid-Miocene volcanism of the Comondú group has been considered as a subduction-related arc, whereas post ~12.5 Ma volcanism would be extension-related. Our new integration of the continental onshore and offshore geology of the south-east Gulf region, backed by tens of Ar-Ar and U-Pb ages and geochemical studies, document an early-mid Miocene rifting and extension-related bimodal to andesitic magmatism prior to subduction termination. Between ~21 and 11 Ma a system of NNW-SSE high-angle extensional faults rifted the western side of the Sierra Madre Occidental (SMO) ignimbrite plateau. In Nayarit, rhyolitic domes and some basalts were emplaced along this extensional belt at 18-17 Ma. These rocks show strong antecrystic inheritance but an absence of Mesozoic and older xenocrysts, suggesting a genesis in the mid-upper crust triggered by extension-induced basaltic influx. In Sinaloa, large grabens were floored by huge dome complexes at ~21-17 Ma and filled by continental sediments with interlayered basalts dated at 15 Ma. Mid-Miocene volcanism, including the largely volcaniclastic Comondú strata in Baja California, was thus emplaced in rift basins and appears associated to decompression melting rather than subduction. Along the coast, flat-lying basaltic lava flows dated at 11-10 Ma are exposed just above the present sea level. Here crustal thickness is 25-20 Km, almost half that in the core of the SMO, implying significant lithosphere stretching before ~11 Ma. This mafic pulse, with relatively high Ti but still clear Nb-Ta negative spikes, may be related to the detachment of the lower part of the subducted slab, allowing asthenosphere to flow into parts of the mantle previously fluxed by subduction fluids. Very uniform OIB-like lavas appear in late Pliocene and Pleistocene, only 18 m.y. after the onset of rifting and ~9 m.y. after the end of subduction. Our study shows that rifting began much earlier than Late Miocene and progressively overwhelmed subduction in generating magmatism.

Late Oligocene to middle Miocene rifting and syn-extensional magmatism in the southwestern Sierra Madre occidental, Mexico: the beginning of the Gulf of California rift

Although Basin and Range style extension affected several areas of western Mexico since the Late Eocene, extension in the Gulf of California region (the Gulf Extensional Province GEP) is thought to have started as subduction waned and ended at ~14 12.5 Ma. A general consensus also exists in considering the mid Miocene Comondú group as a suprasubduction volcanic arc. Our new integration of the geology of the south east Gulf region, backed by 43 new Ar Ar and U Pb mineral ages and geochemical studies, document a widespread phase of extension in the southern GEP between latest Oligocene and Early Miocene that subsequently focused in the region of the future Gulf in the Middle Miocene. Upper Oligocene to Lower Miocene rocks across the southern Sierra Madre Occidental (SMO)(northern Nayarit and southern Sinaloa) were affected by major ~N S to NNW striking normal faults prior to ~21 Ma. Then, between ~21 and 11 Ma, a system of NNW-SSE high angle extensional faults continued extending the southwestern side of the SMO. Rhyolitic domes, shallow intrusive bodies, and lesser basalts were emplaced along this extensional belt at 20-17 Ma. In northern Sinaloa, large grabens were floored by huge dome complexes at ~21-17 Ma and filled by continental sediments with interlayered basalts dated at 15-14 Ma, a setting and timing very similar to Sonora. Early to Middle Miocene volcanism, including the largely volcaniclastic Comondú strata in Baja California Sur, was thus emplaced in rift basins and was likely associated to decompression melting of upper mantle (inducing crustal partial melting) rather than to fluxing by fluids from the young subducting plate. Along the Nayarit and Sinaloa coast, flatlying basaltic lava flows dated at 11-10 Ma are exposed just above the present sea level. Here, crustal thickness is almost half that in the unextended core of the SMO, implying significant lithosphere stretching before ~11 Ma. Our study shows that rifting began much earlier than Late Miocene and provided a fundamental control on the style and composition of volcanism from at least 30 Ma. We envision a sustained period of lithospheric stretching and magmatism during which the pace and breadth of extension changed at ~20-18 Ma to be narrower and likely more rapid, and again at ~12.5 Ma, when the kinematics of rifting became more oblique.

Comparison of two suspension control strategies for multi-axle heavy truck

Two simple and effective control strategies for a multi-axle heavy truck, modified skyhook damping (MSD) control and proportional-integration-derivative (PID) control, were implemented into functional virtual prototype (FVP) model and compared in terms of road friendliness and ride comfort. A four-axle heavy truck-road coupling system model was established using FVP technology and validated through a ride comfort test. Then appropriate passive air suspensions were chosen to replace the rear tandem suspensions of the original truck model for preliminary optimization. The mechanical properties and time lag of dampers were taken into account in simulations of MSD and PID semi-active dampers implemented using MATLAB/Simulink. Through co-simulations with Adams and MATLAB, the effects of semi-active MSD and PID control were analyzed and compared, and control parameters which afforded the best comprehensive performance for each control strategy were chosen. Simulation results indicate that compared with the passive air suspension truck, semi-active MSD control improves both ride comfort and road-friendliness markedly, with optimization ratios of RMS vertical acceleration and RMS tyre force ranging from 10.1% to 44.8%. However, semi-active PID control only reduces vertical vibration of the driver’s seat by 11.1%, 11.1% and 10.9% on A, B and C level roads respectively. Both strategies are robust to the variation of road level.

Non-Newtonian natural convection flow along an isothermal horizontal circular cylinder using modified power-law model

Laminar two-dimensional natural convection boundary-layer flow of non-Newtonian fluids along an isothermal horizontal circular cylinder has been studied using a modified power-law viscosity model. In this model, there are no unrealistic limits of zero or infinite viscosity. Therefore, the boundary-layer equations can be solved numerically by using marching order implicit finite difference method with double sweep technique. Numerical results are presented for the case of shear-thinning as well as shear thickening fluids in terms of the fluid velocity and temperature distributions, shear stresses and rate of heat transfer in terms of the local skin-friction and local Nusselt number respectively.

Microorganisms within human follicular fluid : effects on IVF

Our previous study reported microorganisms in human follicular fluid. The objective of this study was to test human follicular fluid for the presence of microorganisms and to correlate these findings with the in vitro fertilization (IVF) outcomes. In this study, 263 paired follicular fluids and vaginal swabs were collected from women undergoing IVF cycles, with various causes for infertility, and were cultured to detect microorganisms. The cause of infertility and the IVF outcomes for each woman were correlated with the microorganisms detected within follicular fluid collected at the time of trans-vaginal oocyte retrieval. Microorganisms isolated from follicular fluids were classified as: (1) ‘colonizers’ if microorganisms were detected within the follicular fluid, but not within the vaginal swab (at the time of oocyte retrieval); or (2) ‘contaminants’ if microorganisms detected in the vagina at the time of oocyte retrieval were also detected within the follicular fluid. The presence of Lactobacillus spp. in ovarian follicular fluids was associated with embryo maturation and transfer. This study revealed microorganisms in follicular fluid itself and that the presence of particular microorganisms has an adverse affect on IVF outcomes as seen by an overall decrease in embryo transfer rates and pregnancy rates in both fertile and infertile women, and live birth rates in women with idiopathic infertility. Follicular fluid microorganisms are a potential cause of adverse pregnancy outcomes in IVF in both infertile women and in fertile women with infertile male partners.

Synthesis of an erodible biomimetic hydrogel for drug delivery using native chemical ligation

Hydrogels are hydrophilic, three dimensional polymers that imbibe large quantities of water while remaining insoluble in aqueous solutions due to chemical or physical cross-linking. The polymers swell in water or biological fluids, immobilizing the bioactive agent, leading to drug release in a well-defined specific manner. Thus the hydrogels’ elastic properties, swellability and biocompatibility make them excellent formulations for drug delivery. Currently, many drug potencies and therapeutic effects are limited or otherwise reduced because of the partial degradation that occurs before the administered drug reaches the desired site of action. On the other hand, sustained release medications release drugs continually, rather than providing relief of symptoms and protection solely when necessary. In fact, it would be much better if drugs could be administered in a manner that precisely matches physiological needs at desired times and at the desired site (site specific targeting). There is therefore an unmet need to develop controlled drug delivery systems especially for delivery of peptide and protein bound drugs. The purpose of this project is to produce hydrogels for structural drug delivery and time-dependent sustained release of drugs (bioactive agents). We use an innovative polymerisation strategy based on native chemical ligation (NCL) to covalently cross-link polymers to form hydrogels. When mixed in aqueous solution, four armed (polyethylene glycol) amine (PEG-4A) end functionalised with thioester and four branched Nterminal cysteine peptide dendrimers spontaneously conjugated to produce biomimetic hydrogels. These hydrogels showed superior resistance to shear stress compared to an equivalent PEG macromonomer system and were shown to be proteolytically degradable with concomitant release of a model payload molecule. This is the first report of a peptide dendrimers/PEG macromonomer approach to hydrogel production and opens up the prospect of facile hydrogel synthesis together with tailored payload release.

Gravity-driven fingering simulations for a thin liquid film flowing down the outside of a vertical cylinder

A numerical study is presented to examine the fingering instability of a gravity-driven thin liquid film flowing down the outer wall of a vertical cylinder. The lubrication approximation is employed to derive an evolution equation for the height of the film, which is dependent on a single parameter, the dimensionless cylinder radius. This equation is identified as a special case of that which describes thin film flow down an inclined plane. Fully three-dimensional simulations of the film depict a fingering pattern at the advancing contact line. We find the number of fingers observed in our simulations to be in excellent agreement with experimental observations and a linear stability analysis reported recently by Smolka & SeGall (Phys Fluids 23, 092103 (2011)). As the radius of the cylinder decreases, the modes of perturbation have an increased growth rate, thus increasing cylinder curvature partially acts to encourage the contact line instability. In direct competition with this behaviour, a decrease in cylinder radius means that fewer fingers are able to form around the circumference of the cylinder. Indeed, for a sufficiently small radius, a transition is observed, at which point the contact line is stable to transverse perturbations of all wavenumbers. In this regime, free surface instabilities lead to the development of wave patterns in the axial direction, and the flow features become perfectly analogous to the two-dimensional flow of a thin film down an inverted plane as studied by Lin & Kondic (Phys Fluids 22, 052105 (2010)). Finally, we simulate the flow of a single drop down the outside of the cylinder. Our results show that for drops with low volume, the cylinder curvature has the effect of increasing drop speed and hence promoting the phenomenon of pearling. On the other hand, drops with much larger volume evolve to form single long rivulets with a similar shape to a finger formed in the aforementioned simulations.

Carbonate cementation in sandstones of the Plover Formation, North West Shelf, W.A

Ancient sandstones include important reservoirs for hydrocarbons (oil and gas), but, in many cases, their ability to serve as reservoirs is heavily constrained by the effects of carbonate cements on porosity and permeability. This study investigated the controls on distribution and abundance of carbonate cements within the Jurassic Plover Formation, Browse Basin, North West Shelf, Australia. Samples were analysed petrographically with point counting of 59 thin sections and mineralogically with x-ray diffraction from two wells within the Torosa Gas Field. Selected samples were also analysed for stable isotopes of O and C. Sandstones are classified into eleven groups. Most abundant are quartzarenites and then calcareous quartzarenites. Lithology ranged between sandstones consisting of mostly quartz with scant or no carbonate in the form of cement or allochems, to sandstones with as much as 40% carbonate. The major sources of carbonate cement in Torosa 1 and Torosa 4 sandstones were found to be early, shallow marine diagenetic processes (including cementation), followed by calcite cementation and recrystallisation of cements and allochems during redistribution by meteoric waters. Blocky and sparry calcite cements, indicative of meteoric environments on the basis of stable isotope values and palaeotemperature assessment, overprinted the initial shallow marine cement phase in all cases and meteoric cements are dominant. Torosa 4 was influenced more by marine settings than Torosa 1, and thus has the greater potential for calcite cement. The relatively low compaction of calcite-cemented sandstones and the stable isotope data suggest deep burial cementation was not a major factor. Insufficient volcanic rock fragments or authigenic clay content infers alteration of feldspars was not a major source of calcite. Very little feldspar is present, altered or otherwise. Hence, increased alkalinity from feldspar dissolution is not a contributing factor in cement formation. Increased alkalinity from bacterial sulphate reduction in organic–rich fine sediments may have driven limited cementation in some samples. The main definable and significant source of diagenetic marine calcite cement originated from original marine cements and the nearby dissolution of biogenic sources (allochems) at relatively shallow depths. Later diagenetic fluids emplaced minor dolomite, but this cement did not greatly affect the reservoir quality in the samples studied.

Measuring mechanical properties of tendon in vivo

Introduction: Understanding the mechanical properties of tendon is an important step to guiding the process of improving athletic performance, predicting injury and treating tendinopathies. The speed of sound in a medium is governed by the bulk modulus and density for fluids and isotropic materials. However, for tendon,which is a structural composite of fluid and collagen, there is some anisotropy requiring an adjustment for Poisson’s ratio. In this paper, these relationships are explored and modelled using data collected, in vivo, on human Achilles tendon. Estimates for elastic modulus and hysteresis based on speed of sound data are then compared against published values from in vitro mechanical tests. Methods: Measurements using clinical ultrasound imaging, inverse dynamics and acoustic transmission techniques were used to determine dimensions, loading conditions and longitudinal speed of sound for the Achilles tendon during a series of isometric plantar flexion exercises against body weight. Upper and lower bounds for speed of sound versus tensile stress in the tendon were then modelled and estimates derived for elastic modulus and hysteresis. Results: Axial speed of sound varied between 1850 to 2090 m.s−1 with a non-linear, asymptotic dependency on the level of tensile stress in the tendon 5–35 MPa. Estimates derived for the elastic modulus ranged between 1–2 GPa. Hysteresis derived from models of the stress-strain relationship, ranged from 3–11%. These values agree closely with those previously reported from direct measurements obtained via in vitro mechanical tensile tests on major weight bearing tendons. Discussion: There is sufficiently good agreement between these indirect (speed of sound derived) and direct (mechanical tensile test derived) measures of tendon mechanical properties to validate the use of this non-invasive acoustic transmission technique. This non-invasive method is suitable for monitoring changes in tendon properties as predictors of athletic performance, injury or therapeutic progression.

Ultra-trace detection of diagnostically important biomarkers using functionalised-Surface Enhanced Raman Spectroscopy (SERS)

Here we report an ultrasensitive method for detecting bio-active compounds in biological samples by means of functionalised nanoparticles interrogated by surface enhanced Raman spectroscopy (SERS). This method is applicable to the recovery and detection of many diagnostically important peptidyl analytes such as insulin, human growth hormone, growth factors (IGFs) and erythropoietin (EPO), as well as many small molecule analytes and metabolites. Our method, developed to detect EPO, demonstrates its utility in a complex yet well defined biological system. Recombinant human EPO (rhEPO) and EPO analogues have successfully been used to treat anaemia in end-stage renal failure, chronic disorders and infections, cancer and AIDS. Current methods for EPO testing are lengthy, laborious and relatively insensitive to low concentrations. In our rapid screening methodology, gold nanoparticles were functionalised with anti-EPO antibodies to provide very high selectivity towards the EPO protein in urine. These “smart sensor” nanoparticles interact with and trap EPO. Subsequent SERS screening allows for the detection and quantisation of ultra trace amounts (<<10-15 M) of EPO in urine samples with minimal sample preparation. We present data showing that the SERS spectrum differentiates between human endogenous EPO and rhEPO in unpurified urine, and potentially distinguishes between purified EPO isoforms. The elimination of sample preparation and direct screening in biological fluids significantly reduces the time required by current methods. Antibody recognition against a variety of biological targets and the availability of portable commercial SERS analysers for rapid onsite testing suggest broad diagnostic applicability in a flexible analytical platform.

Does preoperative oral carbohydrate reduce hospital stay?

Background Carbohydrate-rich fluids are used to improve postoperative recovery but the effectiveness of the product for reducing length of hospital stay is uncertain. Objective To assess the effectiveness of preoperative loading with carbohydrates on postoperative outcomes. Participants Forty six patients booked for elective colorectal surgery. Methods Participants were allocated to a Carbohydrate-rich fluid group or Usual Care group during their pre-admission clinic visit. The primary outcome was ‘Time to readiness for discharge’. Results Patients in the control group spent on average 4.3 days (95% confidence interval 3.2 to 5.7) and the Carbohydrate-rich fluid group spent 4.1 days (95% confidence interval 3.2 to 5.4) until the primary outcome was met (p=0.824). Conclusion The safety of preoperative high carbohydrate fluids is supported but we were unable to confirm or refute the benefit of CHO for shorter hospital stay following elective colorectal surgery.

Strategies for improved disease resistance in micro-propagated bananas

Bananas (Musa sp) are one of the most important food crops in the world and provide a staple food and source of income in many households especially in Africa. Diseases are a major constraint to production with bunchy top, caused by Banana bunchy top virus (BBTV) generally considered the most important virus disease of bananas worldwide. Of the fungal diseases, Fusarium wilt, caused by the Fusarium oxysporum f.sp cubense (Foc), and black Sigatoka, caused by Mycosphaerella fijiensis, are arguably two of the most important and cause significant yield losses. The low fertility of commercially important banana cultivars has hampered efforts to generate disease resistance using conventional breeding. Possible alternative strategies to generate or increase disease resistance are through genetic engineering or by manipulation of the innate plant defence mechanisms, namely systemic acquired resistance (SAR). The first research component of this thesis describes attempts to generate BBTV-resistant banana plants using a genetic modification approach. The second research component of the thesis focused on the identification of a potential marker gene associated with SAR in banana plants and a comparison of the expression levels of the marker gene in response to biotic and abiotic stresses, and chemical inducers. Previous research at QUT CTCB showed that replication of BBTV DNA components in banana embryogenic cell suspensions (ECS) was abolished following co-bombardment with 1.1mers of mutated BBTV DNA-R. BBTV DNA-R encodes the master replication protein (Rep) and is the only viral protein essential for BBTV replication. In this study, ECS of banana were stably transformed with the same constructs, each containing a different mutation in BBTV DNA-R, namely H41G, Y79F and K187M, to examine the effect on virus replication in stably transformed plants. Cells were also transformed with a construct containing a native BBTV Rep. A total of 16, 16, 11 and five lines of stably transformed banana plants containing the Y79F, H41G, K187M and native Rep constructs, respectively, were generated. Of these, up to nine replicates from Y79F lines, four H41G lines, seven K187M lines and three native Rep lines were inoculated with BBTV by exposure to viruliferous aphids in two separate experiments. At least one replicate from each of the nine Y79F lines developed typical bunchy top symptoms and all tested positive for BBTV using PCR. Of the four H41G lines tested, at least one replicate from three of the lines showed symptoms of bunchy top and tested positive using PCR. However, none of the five replicates of one H41G line (H41G-3) developed symptoms of bunchy top and none of the plants tested positive for BBTV using PCR. Of the seven K187M lines, at least one replicate of all lines except one (K187M-1) developed symptoms of bunchy top and tested positive for BBTV. Importantly, none of the four replicates of line K187M-1 showed symptoms or tested positive for BBTV. At least one replicate from each of the three native Rep lines developed symptoms and tested positive for BBTV. The H41G-3 and K187M-1 lines possibly represent the first transgenic banana plants generated using a mutated Rep strategy. The second research component of this thesis focused on the identification of SAR-associated genes in banana and their expression levels in response to biotic and abiotic stresses and chemical inducers. The impetus for this research was the observation that tissue-cultured (TC) banana plants were more susceptible to Fusarium wilt disease (and possibly bunchy top disease) than plants grown from field-derived suckers, possibly due to decreased levels of SAR gene expression in the former. In this study, the pathogenesis-related protein 1 (PR-1) gene was identified as a potential marker for SAR gene expression in banana. A quantitative real-time PCR assay was developed and optimised in order to determine the expression of PR-1, with polyubiquitin (Ubi-1) found to be the most suitable reference gene to enable relative quantification. The levels of PR-1 expression were subsequently compared in Lady Finger and Cavendish (cv. Williams) banana plants grown under three different environmental conditions, namely in the field, the glass house and in tissue-culture. PR-1 was shown to be expressed in both cultivars growing under different conditions. While PR-1 expression was highest in the field grown bananas and lowest in the TC bananas in Lady Finger cultivar, this was not the case in the Cavendish cultivar with glass house plants exhibiting the lowest PR-1 expression compared with tissue culture and field grown plants. The important outcomes of this work were the establishment of a qPCR-based assay to monitor PR-1 expression levels in banana and a preliminary assessment of the baseline PR-1 expression levels in two banana cultivars under three different growing conditions. After establishing the baseline PR-1 expression levels in Cavendish bananas, a study was done to determine whether PR-1 levels could be increased in these plants by exposure to known banana pathogens and non-pathogens, and a known chemical inducer of SAR. Cavendish banana plants were exposed to pathogenic Foc subtropical race 4 (FocSR4) and non-pathogenic Foc race 1 (Foc1), as well as two putative inducers of resistance, Fusarium lycopersici (Fol) and the chemical, acibenzolar-S-methyl (BION®). Tissue culture bananas were acclimatised under either glass house (TCS) or field (TCH) conditions and treatments were carried out in a randomised complete block design. PR-1 expression was determined using qPCR for both TCS and TCH samples for the period 12-72h post-exposure. Treatment of TCH plants using Foc1 and FocSR4 resulted in 120 and 80 times higher PR-1 expression than baseline levels, respectively. For TCS plants treated with Foc1, PR-1 expression was 30 times higher than baseline levels at 12h post-exposure, while TCS plants treated with FocSR4 showed the highest PR-1 expression (20 times higher than baseline levels) at 72h post-exposure. Interestingly, when TCS plants were treated with Fol there was a marked increase of PR-1 expression at 12 h and 48 h following treatment which was 4 and 8 times higher than the levels observed when TCS plants were treated with Foc1 and FocSR4, respectively. In contrast, when TCH plants were treated with Fol only a slight increase in PR-1 expression was observed at 12 h, which eventually returned to baseline levels. Exposure of both TCS and TCH plants to BION® resulted in no effect on PR-1 expression levels at any time-point. The major outcome of the SAR study was that the glass house acclimatised tissue culture bananas exhibited lower PR-1 gene expression compared to field acclimatised tissue culture plants and the identification of Fol as a good candidate for SAR induction in banana plants exhibiting low PR-1 levels. A number of outcomes that foster understanding of both pathogen-derived and plant innate resistance strategies in order to potentially improve banana resistance to diseases were explored in this study and include identification of potential inducers of systemic acquired resistance and a promising mutated Rep approach for BBTV resistance. The work presented in this thesis is the first report on the generation of potential BBTV resistant bananas using the mutated Rep approach. In addition, this is the first report on the status of SAR in banana grown under different conditions of exposure to the biotic and abiotic environment. Further, a robust qPCR assay for the study of gene expression using banana leaf samples was developed and a potential inducer of SAR in tissue culture bananas identified which could be harnessed to increase resistance in tissue culture bananas.

Late Oligocene to Middle Miocene rifting and synextensional magmatism in the southwestern Sierra Madre Occidental, Mexico : the beginning of the Gulf of California rift

Although Basin and Range–style extension affected large areas of western Mexico after the Late Eocene, most consider that extension in the Gulf of California region began as subduction waned and ended ca. 14–12.5 Ma. A general consensus also exists in considering Early and Middle Miocene volcanism of the Sierra Madre Occidental and Comondú Group as subduction related, whereas volcanism after ca. 12.5 Ma is extension related. Here we present a new regional geologic study of the eastern Gulf of California margin in the states of Nayarit and Sinaloa, Mexico, backed by 43 new Ar-Ar and U-Pb mineral ages, and geochemical data that document an earlier widespread phase of extension. This extension across the southern and central Gulf Extensional Province began between Late Oligocene and Early Miocene time, but was focused in the region of the future Gulf of California in the Middle Miocene. Late Oligocene to Early Miocene rocks across northern Nayarit and southern Sinaloa were affected by major approximately north-south– to north-northwest– striking normal faults prior to ca. 21 Ma. Between ca. 21 and 11 Ma, a system of north-northwest–south-southeast high angle extensional faults continued extending the southwestern side of the Sierra Madre Occidental. Rhyolitic domes, shallow intrusive bodies, and lesser basalts were emplaced along this extensional belt at 20–17 Ma. Rhyolitic rocks, in particular the domes and lavas, often show strong antecrystic inheritance but only a few Mesozoic or older xenocrysts, suggesting silicic magma generation in the mid-upper crust triggered by an extension induced basaltic infl ux. In northern Sinaloa, large grabens were occupied by huge volcanic dome complexes ca. 21–17 Ma and filled by continental sediments with interlayered basalts dated as 15–14 Ma, a stratigraphy and timing very similar to those found in central Sonora (northeastern Gulf of California margin). Early to Middle Miocene volcanism occurred thus in rift basins, and was likely associated with decompression melting of upper mantle (inducing crustal partial melting) rather than with fluxing by fluids from the young and slow subducting microplates. Along the eastern side of the Gulf of California coast, from Farallón de San Ignacio island offshore Los Mochis, Sinaloa, to San Blas, Nayarit, a strike distance of >700 km, flat lying basaltic lavas dated as ca. 11.5–10 Ma are exposed just above the present sea level. Here crustal thickness is almost half that in the unextended core of the adjacent Sierra Madre Occidental, implying signifi cant lithosphere stretching before ca. 11 Ma. This mafic pulse, with subdued Nb-Ta negative spikes, may be related to the detachment of the lower part of the subducted slab, allowing an upward asthenospheric flow into an upper mantle previously modified by fluid fluxes related to past subduction. Widespread eruption of very uniform oceanic island basalt–like lavas occurred by the late Pliocene and Pleistocene, only 20 m.y. after the onset of rifting and ~9 m.y. after the end of subduction, implying that preexisting subduction-modified mantle had now become isolated from melt source regions. Our study shows that rifting across the southern-central Gulf Extensional Province began much earlier than the Late Miocene and provided a fundamental control on the style and composition of volcanism from at least 30 Ma. We envision a sustained period of lithospheric stretching and magmatism during which the pace and breadth of extension changed ca. 20–18 Ma to be narrower, and again after ca. 12.5 Ma, when the kinematics of rifting became more oblique.

TUNEL analysis of DNA fragmentation in mouse unfertilized oocytes : the effect of microorganisms within human follicular fluid collected during IVF cycles

Recently we reported the presence of bacteria within follicular fluid. Previous studies have reported that DNA fragmentation in human spermatozoa after in vivo or in vitro incubation with bacteria results in early embryo demise and a reduced rate of ongoing pregnancy, but the effect of bacteria on oocytes is unknown. This study examined the DNA within mouse oocytes after 12 hours’ incubation within human follicular fluids (n = 5), which were collected from women undergoing in vitro fertilization (IVF) treatment. Each follicular fluid sample was cultured to detect the presence of bacteria. Terminal deoxynucleotidyl transferase mediated dUTP nick-end labeling (TUNEL) was used to label DNA fragmentation in ovulated, non-fertilized mouse oocytes following in vitro incubation in human follicular fluid. The bacteria Streptococcus anginosus and Peptoniphilus spp., Lactobacillus gasseri (low-dose), L. gasseri (high-dose), Enterococcus faecalis, or Propionibacterium acnes were detected within the follicular fluids. The most severe DNA fragmentation was observed in oocytes incubated in the follicular fluids containing P. acnes or L. gasseri (high-dose). No DNA fragmentation was observed in the mouse oocytes incubated in the follicular fluid containing low-dose L. gasseri or E. faecalis. Low human oocyte fertilization rates (<29%) were associated with extensive fragmentation in mouse oocytes (80–100%). Bacteria colonizing human follicular fluid in vivo may cause DNA fragmentation in mouse oocytes following 12 h of in vitro incubation. Follicular fluid bacteria may result in poor quality oocytes and/or embryos, leading to poor IVF outcomes.

Spectroscopic correlation analysis of NMR-based metabonomics in exercise science

Spectroscopic studies of complex clinical fluids have led to the application of a more holistic approach to their chemical analysis becoming more popular and widely employed. The efficient and effective interpretation of multidimensional spectroscopic data relies on many chemometric techniques and one such group of tools is represented by so-called correlation analysis methods. Typical of these techniques are two-dimensional correlation analysis and statistical total correlation spectroscopy (STOCSY). Whilst the former has largely been applied to optical spectroscopic analysis, STOCSY was developed and has been applied almost exclusively to NMR metabonomic studies. Using a 1H NMR study of human blood plasma, from subjects recovering from exhaustive exercise trials, the basic concepts and applications of these techniques are examined. Typical information from their application to NMR-based metabonomics is presented and their value in aiding interpretation of NMR data obtained from biological systems is illustrated. Major energy metabolites are identified in the NMR spectra and the dynamics of their appearance and removal from plasma during exercise recovery are illustrated and discussed. The complementary nature of two-dimensional correlation analysis and statistical total correlation spectroscopy are highlighted.