Utilizing Nonequilibrium Isotope Enrichments to Dramatically Increase Turnover Measurement Ranges in Single Biopsy Samples from Humans.

The synthesis of new proteins and the degradation of old proteins in vivo can be quantified in serial samples using metabolic isotope labeling to measure turnover. Because serial biopsies in humans are impractical, we set out to develop a method to calculate the turnover rates of proteins from single human biopsies. This method involved a new metabolic labeling approach and adjustments to the calculations used in previous work to calculate protein turnover. We demonstrate that using a nonequilibrium isotope enrichment strategy avoids the time dependent bias caused by variable lag in label delivery to different tissues observed in traditional metabolic labeling methods. Turnover rates are consistent for the same subject in biopsies from different labeling periods, and turnover rates calculated in this study are consistent with previously reported values. We also demonstrate that by measuring protein turnover we can determine where proteins are synthesized. In human subjects a significant difference in turnover rates differentiated proteins synthesized in the salivary glands versus those imported from the serum. We also provide a data analysis tool, DeuteRater-H, to calculate protein turnover using this nonequilibrium metabolic 2H2O method.

Multi-parametric MRI of kidney disease progression for autosomal recessive polycystic kidney disease: mouse model and initial patient results.

BACKGROUND: Autosomal recessive polycystic kidney disease (ARPKD) is a rare but potentially lethal genetic disorder typically characterized by diffuse renal microcysts. Clinical trials for patients with ARPKD are not currently possible due to the absence of sensitive measures of ARPKD kidney disease progression and/or therapeutic efficacy. METHODS: In this study, animal and human magnetic resonance imaging (MRI) scanners were used to obtain quantitative kidney T1 and T2 relaxation time maps for both excised kidneys from bpk and wild-type (WT) mice as well as for a pediatric patient with ARPKD and a healthy adult volunteer. RESULTS: Mean kidney T1 and T2 relaxation times showed significant increases with age (p < 0.05) as well as significant increases in comparison to WT mice (p < 2 × 10-10). Significant or nearly significant linear correlations were observed for mean kidney T1 (p = 0.030) and T2 (p = 0.054) as a function of total kidney volume, respectively. Initial magnetic resonance fingerprinting assessments in a patient with ARPKD showed visible increases in both kidney T1 and T2 in comparison to the healthy volunteer. CONCLUSIONS: These preclinical and initial clinical MRI studies suggest that renal T1 and T2 relaxometry may provide an additional outcome measure to assess cystic kidney disease progression in patients with ARPKD. IMPACT: A major roadblock for implementing clinical trials in patients with ARPKD is the absence of sensitive measures of ARPKD kidney disease progression and/or therapeutic efficacy. A clinical need exists to develop a safe and sensitive measure for kidney disease progression, and eventually therapeutic efficacy, for patients with ARPKD. Mean kidney T1 and T2 MRI relaxation times showed significant increases with age (p < 0.05) as well as significant increases in comparison to WT mice (p < 2 ×10-10), indicating that T1 and T2 may provide sensitive assessments of cystic changes associated with progressive ARPKD kidney disease. This preclinical and initial clinical study suggests that MRI-based kidney T1 and T2 mapping could be used as a non-invasive assessment of ARPKD kidney disease progression. These non-invasive, quantitative MRI techniques could eventually be used as an outcome measure for clinical trials evaluating novel therapeutics aimed at limiting or preventing ARPKD kidney disease progression.

Social deprivation modifies the association between incident foot ulceration and mortality in type 1 and type 2 diabetes: a longitudinal study of a primary-care cohort.

AIMS/HYPOTHESIS: The aim of this study was to determine whether social deprivation in the presence of diabetes is an independent predictor of developing a foot ulcer and separately of mortality. METHODS: This was a primary-care-based retrospective analysis of 13,955 adults with type 1 (n = 1370) or type 2 (n = 12,585) diabetes after a median follow-up of 10.5 years. Demographic characteristics, indices of social deprivation and clinical variables were assessed at baseline. The primary outcomes were new foot ulceration (in those without a previous history of foot ulcers) and all-cause mortality. Cox proportional hazard models were used to describe the associations among foot ulceration, social deprivation and mortality. RESULTS: The mean age of the population was 69.4 (range: 16-89) years. The incidence of foot ulceration was greater in individuals with type 2 (8.6%) compared with type 1 diabetes (4.8%). Occurrence was similar by sex, but increased with age and deprivation index. Individuals in the highest quintile of deprivation were 77% more likely to develop a foot ulcer compared with those in the lowest quintile (OR 1.77 [95% CI 1.45, 2.14], p < 0.0001). Overall, 2946 (21.1%) deaths were recorded. Compared with individuals without a foot ulcer, the development of a foot ulcer was associated with a higher age- and sex-adjusted mortality rate (25.9% vs 14.0%), and a 72% (HR 1.72 [95% CI 1.56, 1.90], p < 0.001) increased risk of mortality in those with type 2 diabetes. Risk of death increased by 14% per quintile of deprivation in a univariable analysis (HR 1.14 [95% CI 1.10, 1.17]). In multivariable Cox regression analyses, there was a 48% increased risk of mortality in individuals with a foot ulcer (HR 1.48 [95% CI 1.33, 1.66]) independent of the Townsend index score (HR 1.13 [95% CI 1.10, 1.17], per quintile), baseline age, sex, diabetes type, smoking status, hypertension, statin use, ß-blocker use, metformin use, HbA1c levels and insulin use. CONCLUSIONS/INTERPRETATION: This study confirms the high mortality rate in individuals with diabetes-related foot ulcers. In addition, socioeconomic disadvantage was found to be an independent effect modifier, contributing to an increased burden of mortality in people with diabetes who develop foot ulceration. In light of this, and as diabetes service configurations are orientated for the next 5-10 years, modelling of foot ulceration risk needs to take socioeconomic disadvantage into account.

Regularly incremented phase encoding - MR fingerprinting (RIPE-MRF) for enhanced motion artifact suppression in preclinical cartesian MR fingerprinting.

PURPOSE: The regularly incremented phase encoding-magnetic resonance fingerprinting (RIPE-MRF) method is introduced to limit the sensitivity of preclinical MRF assessments to pulsatile and respiratory motion artifacts. METHODS: As compared to previously reported standard Cartesian-MRF methods (SC-MRF), the proposed RIPE-MRF method uses a modified Cartesian trajectory that varies the acquired phase-encoding line within each dynamic MRF dataset. Phantoms and mice were scanned without gating or triggering on a 7T preclinical MRI scanner using the RIPE-MRF and SC-MRF methods. In vitro phantom longitudinal relaxation time (T1 ) and transverse relaxation time (T2 ) measurements, as well as in vivo liver assessments of artifact-to-noise ratio (ANR) and MRF-based T1 and T2 mean and standard deviation, were compared between the two methods (n = 5). RESULTS: RIPE-MRF showed significant ANR reductions in regions of pulsatility (P < 0.005) and respiratory motion (P < 0.0005). RIPE-MRF also exhibited improved precision in T1 and T2 measurements in comparison to the SC-MRF method (P < 0.05). The RIPE-MRF and SC-MRF methods displayed similar mean T1 and T2 estimates (difference in mean values < 10%). CONCLUSION: These results show that the RIPE-MRF method can provide effective motion artifact suppression with minimal impact on T1 and T2 accuracy for in vivo small animal MRI studies. Magn Reson Med 79:2176-2182, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

Fast magnetic resonance fingerprinting for dynamic contrast-enhanced studies in mice.

PURPOSE: The goal of this study was to develop a fast MR fingerprinting (MRF) method for simultaneous T1 and T2 mapping in DCE-MRI studies in mice. METHODS: The MRF sequences based on balanced SSFP and fast imaging with steady-state precession were implemented and evaluated on a 7T preclinical scanner. The readout used a zeroth-moment-compensated variable-density spiral trajectory that fully sampled the entire k-space and the inner 10 × 10 k-space with 48 and 4 interleaves, respectively. In vitro and in vivo studies of mouse brain were performed to evaluate the accuracy of MRF measurements with both fully sampled and undersampled data. The application of MRF to dynamic T1 and T2 mapping in DCE-MRI studies were demonstrated in a mouse model of heterotopic glioblastoma using gadolinium-based and dysprosium-based contrast agents. RESULTS: The T1 and T2 measurements in phantom showed strong agreement between the MRF and the conventional methods. The MRF with spiral encoding allowed up to 8-fold undersampling without loss of measurement accuracy. This enabled simultaneous T1 and T2 mapping with 2-minute temporal resolution in DCE-MRI studies. CONCLUSION: Magnetic resonance fingerprinting provides the opportunity for dynamic quantification of contrast agent distribution in preclinical tumor models on high-field MRI scanners.

Quantitative magnetic resonance imaging assessments of autosomal recessive polycystic kidney disease progression and response to therapy in an animal model.

BackgroundAutosomal recessive polycystic kidney disease (ARPKD) is associated with significant mortality and morbidity, and currently, there are no disease-specific treatments available for ARPKD patients. One major limitation in establishing new therapies for ARPKD is a lack of sensitive measures of kidney disease progression. Magnetic resonance imaging (MRI) can provide multiple quantitative assessments of the disease.MethodsWe applied quantitative image analysis of high-resolution (noncontrast) T2-weighted MRI techniques to study cystic kidney disease progression and response to therapy in the PCK rat model of ARPKD.ResultsSerial imaging over a 2-month period demonstrated that renal cystic burden (RCB, %)=[total cyst volume (TCV)/total kidney volume (TKV) × 100], TCV, and, to a lesser extent, TKV detected cystic kidney disease progression, as well as the therapeutic effect of octreotide, a clinically available medication shown previously to slow both kidney and liver disease progression in this model. All three MRI measures correlated significantly with histologic measures of renal cystic area, although the correlation of RCB and TCV was stronger than that of TKV.ConclusionThese preclinical MRI results provide a basis for applying these quantitative MRI techniques in clinical studies, to stage and measure progression in human ARPKD kidney disease.

Invader or resident? Ancient-DNA reveals rapid species turnover in New Zealand little penguins.

The expansion of humans into previously unoccupied parts of the globe is thought to have driven the decline and extinction of numerous vertebrate species. In New Zealand, human settlement in the late thirteenth century AD led to the rapid demise of a distinctive vertebrate fauna, and also a number of 'turnover' events where extinct lineages were subsequently replaced by closely related taxa. The recent genetic detection of an Australian little penguin (Eudyptula novaehollandiae) in southeastern New Zealand may potentially represent an additional 'cryptic' invasion. Here we use ancient-DNA (aDNA) analysis and radiocarbon dating of pre-human, archaeological and historical Eudyptula remains to reveal that the arrival of E. novaehollandiae in New Zealand probably occurred between AD 1500 and 1900, following the anthropogenic decline of its sister taxon, the endemic Eudyptula minor. This rapid turnover event, revealed by aDNA, suggests that native species decline can be masked by invasive taxa, and highlights the potential for human-mediated biodiversity shifts.

Human-mediated extirpation of the unique Chatham Islands sea lion and implications for the conservation management of remaining New Zealand sea lion populations.

While terrestrial megafaunal extinctions have been well characterized worldwide, our understanding of declines in marine megafauna remains limited. Here, we use ancient DNA analyses of prehistoric (<1450-1650 AD) sea lion specimens from New Zealand's isolated Chatham Islands to assess the demographic impacts of human settlement. These data suggest there was a large population of sea lions, unique to the Chatham Islands, at the time of Polynesian settlement. This distinct mitochondrial lineage became rapidly extinct within 200 years due to overhunting, paralleling the extirpation of a similarly large endemic mainland population. Whole mitogenomic analyses confirm substantial intraspecific diversity among prehistoric lineages. Demographic models suggest that even low harvest rates would likely have driven rapid extinction of these lineages. This study indicates that surviving Phocarctos populations are remnants of a once diverse and widespread sea lion assemblage, highlighting dramatic human impacts on endemic marine biodiversity. Our findings also suggest that Phocarctos bycatch in commercial fisheries may contribute to the ongoing population decline.

Geographically contrasting biodiversity reductions in a widespread New Zealand seabird.

Unravelling prehistoric anthropogenic impacts on biodiversity represents a key challenge for biologists and archaeologists. New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two distinct phylogeographic lineages, currently restricted to the country's south and southeast. However, fossil and archaeological remains suggest a far more widespread distribution at the time of Polynesian settlement ca. 1280 AD, encompassing much of coastal South Island. We used modern and ancient DNA, radiocarbon dating, and Bayesian modelling, to assess the impacts of human arrival on this taxon. Our analyses show that the southeast South Island (Otago) lineage was formerly widespread across coastal South Island, but experienced dramatic population extinctions, range retraction and lineage loss soon after human arrival. By comparison, the southernmost (Foveaux Strait) lineage has experienced a relatively stable demographic and biogeographic history since human arrival, retaining much of its mitochondrial diversity. Archaeological data suggest that these contrasting demographic histories (retraction vs. stability) reflect differential human impacts in mainland South Island vs. Foveaux Strait, highlighting the importance of testing for temporal and spatial variation in human-driven faunal declines.

Integrating multiple lines of evidence into historical biogeography hypothesis testing: a Bison bison case study.

One of the grand goals of historical biogeography is to understand how and why species' population sizes and distributions change over time. Multiple types of data drawn from disparate fields, combined into a single modelling framework, are necessary to document changes in a species's demography and distribution, and to determine the drivers responsible for change. Yet truly integrated approaches are challenging and rarely performed. Here, we discuss a modelling framework that integrates spatio-temporal fossil data, ancient DNA, palaeoclimatological reconstructions, bioclimatic envelope modelling and coalescence models in order to statistically test alternative hypotheses of demographic and potential distributional changes for the iconic American bison (Bison bison). Using different assumptions about the evolution of the bioclimatic niche, we generate hypothetical distributional and demographic histories of the species. We then test these demographic models by comparing the genetic signature predicted by serial coalescence against sequence data derived from subfossils and modern populations. Our results supported demographic models that include both climate and human-associated drivers of population declines. This synthetic approach, integrating palaeoclimatology, bioclimatic envelopes, serial coalescence, spatio-temporal fossil data and heterochronous DNA sequences, improves understanding of species' historical biogeography by allowing consideration of both abiotic and biotic interactions at the population level.

Extinction and recolonization of coastal megafauna following human arrival in New Zealand.

Extinctions can dramatically reshape biological communities. As a case in point, ancient mass extinction events apparently facilitated dramatic new evolutionary radiations of surviving lineages. However, scientists have yet to fully understand the consequences of more recent biological upheaval, such as the megafaunal extinctions that occurred globally over the past 50 kyr. New Zealand was the world's last large landmass to be colonized by humans, and its exceptional archaeological record documents a vast number of vertebrate extinctions in the immediate aftermath of Polynesian arrival approximately AD 1280. This recently colonized archipelago thus presents an outstanding opportunity to test for rapid biological responses to extinction. Here, we use ancient DNA (aDNA) analysis to show that extinction of an endemic sea lion lineage (Phocarctos spp.) apparently facilitated a subsequent northward range expansion of a previously subantarctic-limited lineage. This finding parallels a similar extinction-replacement event in penguins (Megadyptes spp.). In both cases, an endemic mainland clade was completely eliminated soon after human arrival, and then replaced by a genetically divergent clade from the remote subantarctic region, all within the space of a few centuries. These data suggest that ecological and demographic processes can play a role in constraining lineage distributions, even for highly dispersive species, and highlight the potential for dynamic biological responses to extinction.

Why fishing magnifies fluctuations in fish abundance.

It is now clear that fished populations can fluctuate more than unharvested stocks. However, it is not clear why. Here we distinguish among three major competing mechanisms for this phenomenon, by using the 50-year California Cooperative Oceanic Fisheries Investigations (CalCOFI) larval fish record. First, variable fishing pressure directly increases variability in exploited populations. Second, commercial fishing can decrease the average body size and age of a stock, causing the truncated population to track environmental fluctuations directly. Third, age-truncated or juvenescent populations have increasingly unstable population dynamics because of changing demographic parameters such as intrinsic growth rates. We find no evidence for the first hypothesis, limited evidence for the second and strong evidence for the third. Therefore, in California Current fisheries, increased temporal variability in the population does not arise from variable exploitation, nor does it reflect direct environmental tracking. More fundamentally, it arises from increased instability in dynamics. This finding has implications for resource management as an empirical example of how selective harvesting can alter the basic dynamics of exploited populations, and lead to unstable booms and busts that can precede systematic declines in stock levels.

Sloppy model analysis identifies bifurcation parameters without normal form analysis.

Bifurcation phenomena are common in multidimensional multiparameter dynamical systems. Normal form theory suggests that bifurcations are driven by relatively few combinations of parameters. Models of complex systems, however, rarely appear in normal form, and bifurcations are controlled by nonlinear combinations of the bare parameters of differential equations. Discovering reparameterizations to transform complex equations into a normal form is often very difficult, and the reparameterization may not even exist in a closed form. Here we show that information geometry and sloppy model analysis using the Fisher information matrix can be used to identify the combination of parameters that control bifurcations. By considering observations on increasingly long timescales, we find those parameters that rapidly characterize the system's topological inhomogeneities, whether the system is in normal form or not. We anticipate that this novel analytical method, which we call time-widening information geometry (TWIG), will be useful in applied network analysis.

Modification of the structural stability of human serum albumin in rheumatoid arthritis.

Differential scanning calorimetry (DSC) can indicate changes in structure and/or concentration of the most abundant proteins in a biological sample via heat denaturation curves (HDCs). In blood serum for example, HDC changes result from either concentration changes or altered thermal stabilities for 7-10 proteins and has previously been shown capable of differentiating between sick and healthy human subjects. Here, we compare HDCs and proteomic profiles of 50 patients experiencing joint-inflammatory symptoms, 27 of which were clinically diagnosed with rheumatoid arthritis (RA). The HDC of all 50 subjects appeared significantly different from expected healthy curves, but comparison of additional differences between the RA and the non-RA subjects allowed more specific understanding of RA samples. We used mass spectrometry (MS) to investigate the reasons behind the additional HDC changes observed in RA patients. The HDC differences do not appear to be directly related to differences in the concentrations of abundant serum proteins. Rather, the differences can be attributed to modified thermal stability of some fraction of the human serum albumin (HSA) proteins in the sample. By quantifying differences in the frequency of artificially induced post translational modifications (PTMs), we found that HSA in RA subjects had a much lower surface accessibility, indicating potential ligand or protein binding partners in certain regions that could explain the shift in HSA melting temperature in the RA HDCs. Several low abundance proteins were found to have significant changes in concentration in RA subjects and could be involved in or related to binding of HSA. Certain amino acid sites clusters were found to be less accessible in RA subjects, suggesting changes in HSA structure that may be related to changes in protein-protein interactions. These results all support a change in behavior of HSA which may give insight into mechanisms of RA pathology.

Suture Anchor Repair of a Combined Tear of the Proximal Iliotibial Band and Tensor Fascia Lata.

A combined tear of the proximal iliotibial band and tensor fascia lata is an uncommon injury, and currently, the body of literature on the topic is limited. The suture anchor repair technique described in this article allows anatomic restoration of the proximal iliotibial band and tensor fascia lata.

Assessment of Skeletal Maturity and Postoperative Growth Disturbance After Anterior Cruciate Ligament Reconstruction in Skeletally Immature Patients: A Systematic Review.

BACKGROUND: Growth disturbance is an uncommon but potentially serious complication after anterior cruciate ligament (ACL) reconstruction in skeletally immature patients. PURPOSE: To describe how the pediatric ACL literature has assessed preoperative skeletal maturity and the amount of growth remaining and to comprehensively review the incidence, reporting, and monitoring of postoperative growth disturbance. STUDY DESIGN: Systematic review; Level of evidence, 4. METHODS: This review included studies reporting original research of clinical outcomes of skeletally immature patients after ACL reconstruction. Patient characteristics, surgical techniques, preoperative assessments of skeletal maturity or growth remaining, and postoperative assessments of growth disturbances were extracted. RESULTS: A total of 100 studies met inclusion criteria. All studies reported chronological age, and 28 studies (28%) assessed skeletal age. A total of 44 studies (44%) used Tanner staging, and 12 studies (12%) obtained standing hip-to-ankle radiographs preoperatively. In total, 42 patients (2.1%) demonstrated a leg length discrepancy (LLD) >10 mm postoperatively, including 9 patients (0.5%) with LLD >20 mm; furthermore, 11 patients (0.6%) with LLD underwent growth modulation. Shortening was the most common deformity overall, but overgrowth was reported more frequently in patients who had undergone all-epiphyseal techniques. Most LLDs involved the femur (83%). A total of 26 patients (1.3%) demonstrated a postoperative angular deformity ≥5°, and 9 of these patients underwent growth modulation. The most common deformities were femoral valgus (41%), tibial recurvatum (33%), and tibial varus (22%). Although standing hip-to-ankle radiographs were the most common radiographic assessment of growth disturbance, most studies inadequately reported the clinical and radiographic methods of assessment for growth disturbance. Additionally, only 35% of studies explicitly followed patients to skeletal maturity. CONCLUSION: This systematic review described significant variability in the reporting and monitoring of growth-related complications after ACL reconstruction in skeletally immature patients. The incidence of LLD and angular deformity appeared to be low, but the quality of research was not comprehensive enough for accurate assessment. REGISTRATION: CRD42019136059 (PROSPERO).