Using Knowledge-Guided Machine Learning To Assess Patterns of Areal Change in Waterbodies across the Contiguous United States.

Lake and reservoir surface areas are an important proxy for freshwater availability. Advancements in machine learning (ML) techniques and increased accessibility of remote sensing data products have enabled the analysis of waterbody surface area dynamics on broad spatial scales. However, interpreting the ML results remains a challenge. While ML provides important tools for identifying patterns, the resultant models do not include mechanisms. Thus, the "black-box" nature of ML techniques often lacks ecological meaning. Using ML, we characterized temporal patterns in lake and reservoir surface area change from 1984 to 2016 for 103,930 waterbodies in the contiguous United States. We then employed knowledge-guided machine learning (KGML) to classify all waterbodies into seven ecologically interpretable groups representing distinct patterns of surface area change over time. Many waterbodies were classified as having "no change" (43%), whereas the remaining 57% of waterbodies fell into other groups representing both linear and nonlinear patterns. This analysis demonstrates the potential of KGML not only for identifying ecologically relevant patterns of change across time but also for unraveling complex processes that underpin those changes.

Cellular Visualization of G-Quadruplex RNA via Fluorescence- Lifetime Imaging Microscopy.

Over the past decade, appreciation of the roles of G-quadruplex (G4) structures in cellular regulation and maintenance has rapidly grown, making the establishment of robust methods to visualize G4s increasingly important. Fluorescent probes are commonly used for G4 detection in vitro; however, achieving sufficient selectivity to detect G4s in a dense and structurally diverse cellular environment is challenging. The use of fluorescent probes for G4 detection is further complicated by variations of probe uptake into cells, which may affect fluorescence intensity independently of G4 abundance. In this work, we report an alternative small-molecule approach to visualize G4s that does not rely on fluorescence intensity switch-on and, thus, does not require the use of molecules with exclusive G4 binding selectivity. Specifically, we have developed a novel thiazole orange derivative, TOR-G4, that exhibits a unique fluorescence lifetime when bound to G4s compared to other structures, allowing G4 binding to be sensitively distinguished from non-G4 binding, independent of the local probe concentration. Furthermore, TOR-G4 primarily colocalizes with RNA in the cytoplasm and nucleoli of cells, making it the first lifetime-based probe validated for exploring the emerging roles of RNA G4s in cellulo.

Dimeric Metal-Salphen Complexes Which Target Multimeric G-Quadruplex DNA.

G-Quadruplex DNA structures have attracted increasing attention due to their biological roles and potential as targets for the development of new drugs. While most guanine-rich sequences in the genome have the potential to form monomeric G-quadruplexes, certain sequences have enough guanine-tracks to give rise to multimeric quadruplexes. One of these sequences is the human telomere where tandem repeats of TTAGGG can lead to the formation of two or more adjacent G-quadruplexes. Herein we report on the modular synthesis via click chemistry of dimeric metal-salphen complexes (with NiII and PtII) bridged by either polyether or peptide linkers. We show by circular dichroism (CD) spectroscopy that they generally have higher selectivity for dimeric vs monomeric G-quadruplexes. The emissive properties of the PtII-salphen dimeric complexes have been used to study their interactions with monomeric and dimeric G-quadruplexes in vitro as well as to study their cellular uptake and localization.

Exploring the associations between neighbourhood food environment, household food insecurity and child weight-related outcomes in socio-economically and racially/ethnically diverse families.

OBJECTIVE: To examine associations among neighbourhood food environments (NFE), household food insecurity (HFI) and child's weight-related outcomes in a racially/ethnically diverse sample of US-born and immigrant/refugee families. DESIGN: This cross-sectional, observational study involving individual and geographic-level data used multilevel models to estimate associations between neighbourhood food environment and child outcomes. Interactions between HFI and NFE were employed to determine whether HFI moderated the association between NFE and child outcomes and whether the associations differed for US-born v. immigrant/refugee groups. SETTING: The sample resided in 367 census tracts in the Minneapolis/St. Paul, MN metropolitan area, and the data were collected in 2016-2019. PARTICIPANTS: The sample was from the Family Matters study of families (n 1296) with children from six racial/ethnic and immigrant/refugee groups (African American, Latino, Hmong, Native American, Somali/Ethiopian and White). RESULTS: Living in a neighbourhood with low perceived access to affordable fresh fruits and vegetables was found to be associated with lower food security (P < 0·01), poorer child diet quality (P < 0·01) and reduced availability of a variety of fruits (P < 0·01), vegetables (P < 0·05) and whole grains in the home (P < 0·01). Moreover, residing in a food desert was found to be associated with a higher child BMI percentile if the child's household was food insecure (P < 0·05). No differences in associations were found for immigrant/refugee groups. CONCLUSIONS: Poor NFE were associated with worse weight-related outcomes for children; the association with weight was more pronounced among children with HFI. Interventions aiming to improve child weight-related outcomes should consider both NFE and HFI.

G-quadruplexes Mark Sites of Methylation Instability Associated with Ageing and Cancer.

Regulation of the epigenome is critical for healthy cell function but can become disrupted with age, leading to aberrant epigenetic profiles including altered DNA methylation. Recent studies have indicated that DNA methylation homeostasis can be compromised by the formation of DNA secondary structures known as G-quadruplexes (G4s), which form in guanine-rich regions of the genome. G4s can be recognised and bound by certain methylation-regulating enzymes, and in turn perturb the surrounding methylation architecture. However, the effect G4 formation has on DNA methylation at critical epigenetic sites remains elusive and poorly explored. In this work, we investigate the association between G4 sequences and prominent DNA methylation sites, termed 'ageing clocks', that act as bona fide dysregulated regions in aged and cancerous cells. Using a combination of in vitro (G4-seq) and in cellulo (BG4-ChIP) G4 distribution maps, we show that ageing clocks sites are significantly enriched with G4-forming sequences. The observed enrichment also varies across species and cell lines, being least significant in healthy cells and more pronounced in tumorigenic cells. Overall, our results suggest a biological significance of G4s in the realm of DNA methylation, which may be important for further deciphering the driving forces of diseases characterised by epigenetic abnormality, including ageing.

Delayed sudden hearing recovery after treatment of a large vertebral artery aneurysm causing hearing loss and imbalance: a case report.

PURPOSE: Cerebral aneurysms that compress cranial nerve VIII can cause hearing loss and imbalance. Hearing function that does not recover after aneurysm occlusion can signal neurological damage with the potential for permanent deafness. CASE DESCRIPTION: A 72-year-old woman presented with gradually worsening left-sided hearing loss and imbalance over a period of 10 years. She was found to have a lesion of the cerebellopontine angle, which proved to be a large fusiform vertebral artery aneurysm with mass effect on cranial nerve VIII. The patient underwent surgical clip occlusion of the vertebral artery distal to the posterior inferior cerebellar artery and proximal to the aneurysm, which no longer filled on catheter angiography. Postoperatively, the patient experienced delayed complete loss of ipsilateral hearing on the third post-operative day. Otherwise, she made a good recovery with improvement in her balance issues. At that time, we suspected that delayed occlusion of a perforating vessel had probably caused irreversible hearing loss. Ten months later, the patient awoke with significant subjective recovery of her hearing. Audiometry confirmed substantial improvement in her hearing likely due to the aneurysm shrinking away from and decompressing the cranial nerve. CONCLUSION: This case highlights the continued usefulness of vascular occlusion in the management of selected cases of intracranial aneurysms and also that neurological function may recover suddenly, even in very delayed fashion, following treatment.

DNA G-quadruplex structures: more than simple roadblocks to transcription?

It has been >20 years since the formation of G-quadruplex (G4) secondary structures in gene promoters was first linked to the regulation of gene expression. Since then, the development of small molecules to selectively target G4s and their cellular application have contributed to an improved understanding of how G4s regulate transcription. One model that arose from this work placed these non-canonical DNA structures as repressors of transcription by preventing polymerase processivity. Although a considerable number of studies have recently provided sufficient evidence to reconsider this simplistic model, there is still a misrepresentation of G4s as transcriptional roadblocks. In this review, we will challenge this model depicting G4s as simple 'off switches' for gene expression by articulating how their formation has the potential to alter gene expression at many different levels, acting as a key regulatory element perturbing the nature of epigenetic marks and chromatin architecture.

Enhancement of alcohol aversion by the nicotinic acetylcholine receptor drug sazetidine-A.

The prevalence of alcohol use disorders (AUDs) has steadily increased in the United States over the last 30 years. Alcohol acts on multiple receptor systems including the nicotinic acetylcholine receptors (nAChRs), which are known to mediate alcohol consumption and reward. We previously reported that the preclinical drug sazetidine-A, a nAChR agonist and desensitizer, reduces alcohol consumption without affecting nicotine consumption in C57BL/6J mice. Here, we found that sazetidine-A enhances the expression of alcohol aversion without affecting the expression or acquisition of conditioned alcohol reward in C57BL/6J mice. Microinjection of sazetidine-A into the ventral midbrain targeting the ventral tegmental area (VTA) reduced binge alcohol consumption, implicating this region in mediating the effects of sazetidine-A. Furthermore, the sazetidine-A-induced reduction in alcohol consumption was mediated by non-α4 containing nAChRs, as sazetidine-A reduced binge alcohol consumption in both α4 knock-out and wild-type mice. Finally, we found that in mice pretreated with sazetidine-A, alcohol induced Fos transcript in Th-, but not Gad2-expressing neurons in the VTA as measured by increased Fos transcript expression. In summary, we find that sazetidine-A enhances the expression of alcohol aversion, which may underlie the reduction in alcohol consumption induced by sazetidine-A. Elucidating the identity of non-α4 nAChRs in alcohol aversion mechanisms will provide a better understanding the complex role of nAChRs in alcohol addiction and potentially reveal novel drug targets to treat AUDs.

A Chemical Biology Approach to Probing the Folding Pathways of the Inhibitory Cystine Knot (ICK) Peptide ProTx-II.

Peptide toxins that adopt the inhibitory cystine knot (ICK) scaffold have very stable three-dimensional structures as a result of the conformational constraints imposed by the configuration of the three disulfide bonds that are the hallmark of this fold. Understanding the oxidative folding pathways of these complex peptides, many of which are important therapeutic leads, is important in order to devise reliable synthetic routes to correctly folded, biologically active peptides. Previous research on the ICK peptide ProTx-II has shown that in the absence of an equilibrating redox buffer, misfolded intermediates form that prevent the formation of the native disulfide bond configuration. In this paper, we used tandem mass spectrometry to examine these misfolded peptides, and identified two non-native singly bridged peptides, one with a Cys(III)-Cys(IV) linkage and one with a Cys(V)-Cys(VI) linkage. Based on these results, we propose that the C-terminus of ProTx-II has an important role in initiating the folding of this peptide. To test this hypothesis, we have also studied the folding pathways of analogs of ProTx-II containing the disulfide-bond directing group penicillamine (Pen) under the same conditions. We find that placing Pen residues at the C-terminus of the ProTx-II analogs directs the folding pathway away from the singly bridged misfolded intermediates that represent a kinetic trap for the native sequence, and allows a fully oxidized final product to be formed with three disulfide bridges. However, multiple two-disulfide peptides were also produced, indicating that further study is required to fully control the folding pathways of this modified scaffold.

Differential patterns of alcohol and nicotine intake: Combined alcohol and nicotine binge consumption behaviors in mice.

Late adolescence and young adulthood, corresponding to the high school and college years, are vulnerable periods for increased alcohol and nicotine use. The dramatic increase in the prevalence of electronic cigarette use is particularly concerning in these age groups. Late adolescents and young adults are more likely to engage in cycles of binge drug consumption, and alcohol and nicotine are frequently used together. However, there are few data examining the combination of alcohol and nicotine in binge models in animal models. In this study, our objectives were to determine how voluntary nicotine consumption beginning in late adolescence influenced subsequent binge alcohol consumption in young adulthood, how a combination of alcohol and nicotine binge consumption differed from alcohol-only binge consumption, and whether nicotine would be consumed when presented in a binge procedure. Male C57BL/6J mice voluntarily consumed unsweetened alcohol and nicotine in continuous-access bottle-choice procedures in combination with cycles of drinking-in-the-dark. Our results show that experience with voluntary nicotine consumption in late adolescence did not affect subsequent binge alcohol consumption in early adulthood. However, mice that consumed nicotine in adolescence showed an initial decrease in alcohol preference, and consequently increase in nicotine preference, on the first session of combined ethanol and nicotine binge consumption in adulthood compared with mice that drank only water during late adolescence. Lastly, we found that mice readily consumed unsweetened nicotine when presented in a binge procedure, and the level of consumption exceeded the nicotine consumption observed in the combination alcohol and nicotine binge. Our data show that expansion of the patterns of alcohol and nicotine co-consumption in a mouse models is possible, which will enable us to dissect relevant molecular targets underlying these consumption patterns and better inform drug development efforts.

Unequal interactions between alcohol and nicotine co-consumption: suppression and enhancement of concurrent drug intake.

RATIONALE: Alcohol and nicotine addiction are prevalent conditions that co-occur. Despite the prevalence of co-use, factors that influence the suppression and enhancement of concurrent alcohol and nicotine intake are largely unknown. OBJECTIVES: Our goals were to assess how nicotine abstinence and availability influenced concurrent alcohol consumption and to determine the impact of quinine adulteration of alcohol on aversion-resistant alcohol consumption and concurrent nicotine consumption. METHODS: Male and female C57BL/6J mice voluntarily consumed unsweetened alcohol, nicotine, and water in a chronic 3-bottle choice procedure. In experiment 1, nicotine access was removed for 1 week and re-introduced the following week, while the alcohol and water bottles remained available at all times. In experiment 2, quinine (100-1000 µM) was added to the 20% alcohol bottle, while the nicotine and water bottles remained unaltered. RESULTS: In experiment 1, we found that alcohol consumption and preference were unaffected by the presence or absence of nicotine access in both male and female mice. In experiment 2a, we found that quinine temporarily suppressed alcohol intake and enhanced concurrent nicotine, but not water, preference in both male and female mice. In experiment 2b, chronic quinine suppression of alcohol intake increased nicotine consumption and preference in female mice without affecting water preference, whereas it increased water and nicotine preference in male mice. CONCLUSIONS: Quinine suppression of alcohol consumption enhanced the preference for concurrent nicotine preference in male and female mice, suggesting that mice compensate for the quinine adulteration of alcohol by increasing their nicotine preference.

Assessment of steroid use as a key performance indicator in inflammatory bowel disease-analysis of data from 2385 UK patients.

BACKGROUND: Patients with IBD are at risk of excess corticosteroids. AIMS: To assess steroid excess in a large IBD cohort and test associations with quality improvement and prescribing. METHODS: Steroid exposure was recorded for outpatients attending 19 centres and associated factors analysed. Measures taken to avoid excess were assessed. RESULTS: Of 2385 patients, 28% received steroids in the preceding 12 months. 14.8% had steroid excess or dependency. Steroid use was significantly lower at 'intervention centres' which participated in a quality improvement programme (exposure: 23.8% vs 31.0%, P < .001; excess 11.5% vs 17.1%, P < .001). At intervention centres, steroid use fell from 2015 to 2017 (steroid exposure 30.0%-23.8%, P = .003; steroid excess 13.8%-11.5%, P = .17). Steroid excess was judged avoidable in 50.7%. Factors independently associated with reduced steroid excess in Crohn's disease included maintenance with anti-TNF agents (OR 0.61 [95% CI 0.24-0.95]), treatment in a centre with a multi-disciplinary team (OR 0.54 [95% CI 0.20-0.86]) and treatment at an intervention centre (OR 0.72 [95% CI 0.46-0.97]). Treatment with 5-ASA in CD was associated with higher rates of steroid excess (OR 1.72 [95% CI 1.24-2.09]). In ulcerative colitis (UC), thiopurine monotherapy was associated with steroid excess (OR 1.97 [95% CI 1.19-3.01]) and treatment at an intervention centre with less steroid excess (OR 0.72 [95% CI 0.45-0.95]). CONCLUSIONS: This study validates steroid assessment as a meaningful quality measure and provides a benchmark for this performance indicator in a large cohort. A programme of quality improvement was associated with lower steroid use.

Mc1r gene in Astroblepus pholeter and Astyanax mexicanus: Convergent regressive evolution of pigmentation across cavefish species.

Cave-adapted organisms are often characterized by a reduction in pigmentation, eyesight, and enhanced mechanosensory functions. Previous studies have described the genetic basis for a depigmented phenotype in multiple independent populations of the Blind Mexican Tetra, Astyanax mexicanus; the reduction in melanin content (brown; Mc1r). At least seven wild populations express the brown phenotype. In three populations, there are two different coding sequence alterations affecting Mc1r and the remaining four populations show the accumulation of sequence mutations affecting the 5' regulatory region. Thus, the Mc1r gene has been the repeated and independent location of mutations in Astyanax. As such, it would appear that this gene is a target during regressive evolution of cave adapted organisms. If this is the case, it would be expected that other cave adapted fish would have mutations in the same gene. We study here the stygobitic catfish Astroblepus pholeter, a depigmented fish found within some river caves in Ecuador. A. pholeter displays mutations in ultra-conserved areas of the pigment-controlling gene, Mc1r, that have been linked to pigment regulation in other organisms. It is thus concluded that Mc1r, a gene known to control pigment variation in many organisms, may be the target of cavernicole regressive evolution across species in different families of fish.