An adaptive landscape concept outlined by G.G. Simpson constitutes the major conceptual bridge between the fields of micro- and macroevolutionary study. Despite some important theoretical extensions ...since 1944, this conceptual bridge has been ignored in many empirical studies. In this article, we review the status of theoretical work and emphasize the importance of models for peak movement. Although much theoretical work has been devoted to evolution on stationary, unchanging landscapes, an important new development is a focus on the evolution of the landscape itself. We also sketch an agenda of empirical issues that is inspired by theoretical developments.
Recent research has highlighted the importance of dissolved organic matter (DOM) for ecosystem function and because of this paradigm shift, it has become crucial to not only quantify its contribution ...to river nutrient loads but also to characterise its composition. There has been a significant research effort utilising optical methods, such as fluorescence and UV–Vis spectrophotometry, in order to start exploring DOM character. However, these methods still lack the granularity to understand the chemical composition at the molecular level, which is vital to properly understanding its functional role in freshwater ecosystems. As a direct result, there has been a shift towards including molecular-scale analyses to investigate the in-stream processing of the material. Alongside this, recent methodological advancements, particularly in mass spectrometry are opening new opportunities for probing one of the most complex environmental mixtures. However, in order to fully exploit these opportunities, it is key that the way that samples are collected, processed and stored is considered carefully such that sample integrity is maintained. There are additional challenges when collecting water samples for analysis at molecular scale, for example the ultra-low concentrations of individual compounds within DOM means that the samples are sensitive to contamination. This paper discusses current sample collection, processing and storage protocols for this C, N and P quantification and characterisation in freshwaters, and proposes a new standardised protocol suitable for both nutrient fraction quantification and molecular scale analyses, based on method development and testing undertaken in our UK Natural Environment Research Council large grant programme, characterising the nature, origins and ecological significance of Dissolved Organic Matter IN freshwater Ecosystems (DOMAINE).
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•Sample collection, processing and storage protocols are set for molecular analysis.•A glass-only apparatus should be used to avoid sample contamination.•Samples should be stored below 4 °C then filtered and analysed within 24 h.•Samples should be frozen or freeze-dried for long-term storage and archiving.
Proteus mirabilis is a common pathogen of the catheterized urinary tract and often described as intrinsically resistant to the biocide chlorhexidine (CHD). Here, we demonstrate that derepression of ...the smvA efflux system has occurred in clinical isolates of P. mirabilis and reduces susceptibility to CHD and other cationic biocides. Compared with other isolates examined, P. mirabilis RS47 exhibited a significantly higher CHD MIC (≥512 μg/ml) and significantly greater expression of smvA. Comparison of the RS47 smvA and cognate smvR repressor with sequences from other isolates indicated that RS47 carries an inactivated smvR. Complementation of RS47 with a functional smvR from isolate RS50a (which exhibited the lowest smvA expression and lowest CHD MIC) reduced smvA expression by ∼59-fold and markedly lowered the MIC of CHD and other cationic biocides. Although complementation of RS47 did not reduce MICs to concentrations observed in isolate RS50a, the significantly lower polymyxin B MIC of RS50a indicated that differences in lipopolysaccharide (LPS) structure are also a factor in P. mirabilis CHD susceptibility. To determine if exposure to CHD can select for mutations in smvR, clinical isolates with the lowest CHD MICs were adapted to grow at increasing concentrations of CHD up to 512 μg/ml. Analysis of the smvR in adapted populations indicated that mutations predicted to inactivate smvR occurred following CHD exposure in some isolates. Collectively, our data show that smvA derepression contributes to reduced biocide susceptibility in P. mirabilis, but differences in LPS structure between strains are also likely to be an important factor.
Philadelphia chromosome-positive (Ph+) B-cell precursor acute lymphoblastic leukemia (ALL) expressing BCR-ABL1 oncoprotein is a major subclass of ALL with poor prognosis. BCR-ABL1-expressing leukemic ...cells are highly dependent on double-strand break (DSB) repair signals for their survival. Here we report that a first-in-class HDAC1,2 selective inhibitor and doxorubicin (a hyper-CVAD chemotherapy regimen component) impair DSB repair networks in Ph+ B-cell precursor ALL cells using common as well as distinct mechanisms. The HDAC1,2 inhibitor but not doxorubicin alters nucleosomal occupancy to impact chromatin structure, as revealed by MNase-Seq. Quantitative mass spectrometry of the chromatin proteome along with functional assays showed that the HDAC1,2 inhibitor and doxorubicin either alone or in combination impair the central hub of DNA repair, the Mre11-Rad51-DNA ligase 1 axis, involved in BCR-ABL1-specific DSB repair signaling in Ph+ B-cell precursor ALL cells. HDAC1,2 inhibitor and doxorubicin interfere with DISC (DNA damage-induced transcriptional silencing in cis)) or transcriptional silencing program in cis around DSB sites via chromatin remodeler-dependent and -independent mechanisms, respectively, to further impair DSB repair. HDAC1,2 inhibitor either alone or when combined with doxorubicin decreases leukemia burden in vivo in refractory Ph+ B-cell precursor ALL patient-derived xenograft mouse models. Overall, our novel mechanistic and preclinical studies together demonstrate that HDAC1,2 selective inhibition can overcome DSB repair 'addiction' and provide an effective therapeutic option for Ph+ B-cell precursor ALL.
The mechanism of how patatin‐like phospholipase domain‐containing protein 3 (PNPLA3) variant M148 is associated with increased risk of development of hepatic steatosis is still debated. Here, we ...propose a novel role of PNPLA3 as a key player during autophagosome formation in the process of lipophagy. A human hepatocyte cell line, HepG2 cells, expressing recombinant I148 or 148M, was used to study lipophagy under energy deprived conditions, and lipid droplet morphology was investigated using florescence microscopy, image analysis and biochemical assays. Autophagic flux was studied using the golden‐standard of LC3‐II turnover in combination with the well characterized GFP‐RFP‐LC3 vector. To discriminate between, perturbed autophagic initiation and lysosome functionality, lysosomes were characterized by Lysotracker staining and LAMP1 protein levels as well as activity and activation of cathepsin B. For validation, human liver biopsies genotyped for I148 and 148M were analyzed for the presence of LC3‐II and PNPLA3 on lipid droplets. We show that the M148‐PNPLA3 variant is associated with lipid droplets that are resistant to starvation‐mediated degradation. M148 expressing hepatocytes reveal decreased autophagic flux and reduced lipophagy. Both I148‐PNPLA3 and M148‐PNPLA3 colocalize and interact with LC3‐II, but the M148‐PNPLA3 variant has lower ability to bind LC3‐II. Together, our data indicate that PNPLA3 might play an essential role in lipophagy in hepatocytes and furthermore that the M148‐PNPLA3 variant appears to display a loss in this activity, leading to decreased lipophagy.
M148‐PNPLA3 overexpressing hepatocytes are characterized by lipid droplets resistant to degradation, decreased autophagic flux and lipophagy and impaired autophagosome formation.
PNPLA3 colocalizes with LC3‐II on lipid droplets, interacts with LC3‐II, but is not degraded by the lysosome.
Hepatocytes in Liver Samples from M148 Individuals Reveal Accumulation of LC3‐II + LDs with increased area and colocalized PNPLA3 and LC3 Puncta on LDs.
This paper investigates the extraction of acoustic signatures from small boats using a passive sonar system. Noise radiated from a small boats consists of broadband noise and harmonically related ...tones that correspond to engine and propeller specifications. A signal processing method to automatically extract the harmonic structure of noise radiated from small boats is developed. The Harmonic Extraction and Analysis Tool (HEAT) estimates the instantaneous fundamental frequency of the harmonic tones, refines the fundamental frequency estimate using a Kalman filter, and automatically extracts the amplitudes of the harmonic tonals to generate a harmonic signature for the boat. Results are presented that show the HEAT algorithms ability to extract these signatures.
Abstract
OBJECTIVES
(i) To monitor cerebral blood flow velocity (CBFv) throughout aortic arch repair surgery and during the recovery period. (ii) To examine the relationship between transcranial ...doppler ultrasound (TCD) and near-infrared spectroscopy (NIRS) during cardiac surgery. (iii) To examine CBFv in patients cooled to 20°C and 25°C.
METHODS
During aortic arch repair and after surgery, measurements of TCD, NIRS, blood pH, pO2, pCO2, HCO3, lactate, Hb, haematocrit (%) and temperature (core and rectal) were recorded in 24 neonates. General linear mixed models were used to examine differences over time and between two cooling temperatures. Repeated measures correlations were used to determine the relationship between TCD and NIRS.
RESULTS
CBFv changed during arch repair (main effect of time: P = 0.001). During cooling, CBFv increased by 10.0 cm/s (5.97, 17.7) compared to normothermia (P = 0.019). Once recovering in paediatric intensive care unit (PICU), CBFv had increased from the preoperative measurement by 6.2 cm/s (0.21, 13.4; P = 0.045). CBFv changes were similar between patients cooled to 20°C and 25°C (main effect of temperature: P = 0.22). Repeated measures correlations (rmcorr) identified a statistically significant but weak positive correlation between CBFv and NIRS (r = 0.25, P≤0.001).
CONCLUSIONS
Our data suggested that CBFv changed throughout aortic arch repair and was higher during the cooling period. A weak relationship was found between NIRS and TCD. Overall, these findings could provide clinicians with information on how to optimise long-term cerebrovascular health.
Survival rates in patients born with congenital heart disease have increased due to improvements in clinical care and treatment options 1.
Background
Substance P (SP) is a pain‐ and inflammation‐related neuropeptide which preferentially binds to the neurokinin receptor 1 (NK1). SP and NK1 receptors have been implicated in joint pain, ...inflammation and damage in animal models and human studies of osteoarthritis (OA). The aim of this study was to test if genetic variation at the neurokinin 1 receptor gene (TACR1) is associated with pain in individuals with radiographic knee OA.
Methods
Participants from the Genetics of OA and Lifestyle study were used for the discovery group (n = 1615). Genotype data for six SNPs selected to cover most variation in the TACR1 gene were used to test for an association with symptomatic OA. Replication analysis was performed using data from the Chingford 1000 Women Study, Hertfordshire Cohort Study, Tasmanian Older Adult Cohort Study and the Clearwater OA Study. In total, n = 1715 symptomatic OA and n = 735 asymptomatic OA individuals were analysed.
Results
Out of six SNPs tested in the TACR1 gene, one (rs11688000) showed a nominally significant association with a decreased risk of symptomatic OA in the discovery cohort. This was then replicated in four additional cohorts. After adjusting for age, gender, body mass index and radiographic severity, the G (minor) allele at rs11688000 was associated with a decreased risk of symptomatic OA compared to asymptomatic OA cases (p = 9.90 × 10−4, OR = 0.79 95% 0.68–0.90 after meta‐analysis).
Conclusions
This study supports a contribution from the TACR1 gene in human OA pain, supporting further investigation of this gene's function in OA.
Significance
This study contributes to the knowledge of the genetics of painful osteoarthritis, a condition which affects millions of individuals worldwide. Specifically, a contribution from the TACR1 gene to modulating pain sensitivity in osteoarthritis is suggested.
Cerebellar ataxia, neuropathy and vestibular areflexia syndrome (CANVAS) is an autosomal recessive neurodegenerative disease, usually caused by biallelic AAGGG repeat expansions in RFC1. In this ...study, we leveraged whole genome sequencing data from nearly 10 000 individuals recruited within the Genomics England sequencing project to investigate the normal and pathogenic variation of the RFC1 repeat. We identified three novel repeat motifs, AGGGC (n = 6 from five families), AAGGC (n = 2 from one family) and AGAGG (n = 1), associated with CANVAS in the homozygous or compound heterozygous state with the common pathogenic AAGGG expansion. While AAAAG, AAAGGG and AAGAG expansions appear to be benign, we revealed a pathogenic role for large AAAGG repeat configuration expansions (n = 5). Long-read sequencing was used to characterize the entire repeat sequence, and six patients exhibited a pure AGGGC expansion, while the other patients presented complex motifs with AAGGG or AAAGG interruptions. All pathogenic motifs appeared to have arisen from a common haplotype and were predicted to form highly stable G quadruplexes, which have previously been demonstrated to affect gene transcription in other conditions. The assessment of these novel configurations is warranted in CANVAS patients with negative or inconclusive genetic testing. Particular attention should be paid to carriers of compound AAGGG/AAAGG expansions when the AAAGG motif is very large (>500 repeats) or the AAGGG motif is interrupted. Accurate sizing and full sequencing of the satellite repeat with long-read sequencing is recommended in clinically selected cases to enable accurate molecular diagnosis and counsel patients and their families.
We present optical spectroscopy of galaxies in clusters detected through the Sunyaev-Zel'dovich (SZ) effect with the South Pole Telescope (SPT). We report our own measurements of 61 spectroscopic ...cluster redshifts, and 48 velocity dispersions each calculated with more than 15 member galaxies. This catalog also includes 19 dispersions of SPT-observed clusters previously reported in the literature. The majority of the clusters in this paper are SPT-discovered; of these, most have been previously reported in other SPT cluster catalogs, and five are reported here as SPT discoveries for the first time. By performing a resampling analysis of galaxy velocities, we find that unbiased velocity dispersions can be obtained from a relatively small number of member galaxies (lap30), but with increased systematic scatter. We use this analysis to determine statistical confidence intervals that include the effect of membership selection.We fit scaling relations between the observed cluster velocity dispersions and mass estimates from SZ and X-ray observables. In both cases, the results are consistent with the scaling relation between velocity dispersion and mass expected from dark-matter simulations. We measure a ~30% log-normal scatter in dispersion at fixed mass, and a ~10% offset in the normalization of the dispersion-mass relation when compared to the expectation from simulations, which is within the expected level of systematic uncertainty.
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