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Query Topic: CLOCK

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clock drawing test(140)

Cognitive Testing During Mild Acute Ischemic Stroke Predicts Long-Term Return to Work.
Many survivors of a mild ischemic stroke do not return to work or driving. Cognitive testing is commonly done to assess long-term cognitive impairment after stroke. Inpatient cognitive testing during the acute period of ischemic stroke may also be a predictor for workforce reengagement and functional outcome. At our comprehensive stroke center, we prospectively enrolled previously working adults < 65 years old who were diagnosed with first-ever ischemic stroke, had a prestroke modified Rankin Scale (mRS) ≤ 1 and NIHSS ≤ 3. Testing performed within 1 week of stroke included the Montreal Cognitive Assessment (MOCA), Clock Drawing Test (CDT), Trail Making Tests A and B, Backward Digit Span Test, and Hospital Anxiety and Depression Scale (HADS). Other data obtained included age, gender, years of education, occupation, stroke location, stroke laterality, and presence of white matter disease on imaging. Outcome measures assessed at 3 months, 6 months, and 12 months post-stroke included return to work, return to driving, and mRS. In a logistic regression analysis, we performed both univariate and multivariate analyses. Multivariate analysis was completed on variables with p-value ≤ 0.05 in the univariate analysis. Of 39 total stroke patients enrolled and tested (median [IQR] age 55 [46-60] years; 77.5% male; 22.5% female), 36 completed 3-month follow up, of which 58% returned to work, 78% returned to driving, and 72% had mRS of 0-1. In multivariate analysis, a single point increase in the clock drawing task score increased the odds of return to work by 3.79 (95% CI, 1.10-14.14) and return to driving by 6.74 (95% CI, 1.22-37.23) at 3 months. MOCA and HADS were both associated with mRS ≤ 1. MOCA was associated with return to work at 6 months and CDT was associated with return to work at 12 months. Cognitive testing with CDT and MOCA in the acute period after ischemic stroke may predict common patient goals post stroke, including return to work, driving, and independence. These tools can potentially be used for prognosis and identifying those who may benefit from further interventions.
Publication Date: 2021-10-28
Journal: Journal of stroke and cerebrovascular diseases : the official journal of National Stroke Association


core circadian clock(58)

Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in
The circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inverted relative to stomatal movement in C3 plants. The mechanisms behind how the circadian clock enabled physiological differences at the molecular level is not well understood. Recently, the rescheduling of gene expression was reported as a mechanism to explain how CAM evolved from C3. Therefore, we investigated whether core circadian clock genes in CAM plants were re-phased during evolution, or whether networks of phase-specific genes were simply re-wired to different core clock genes. We identified candidate core clock genes based on gene expression features and then applied the Local Edge Machine (LEM) algorithm to infer regulatory relationships between this new set of core candidates and known core clock genes in
Publication Date: 2021-09-29
Journal: Cells


mini-mental state examination(53)

Cognitive Assessment Tools Recommended in Geriatric Oncology Guidelines: A Rapid Review.
Cognitive assessment is a cornerstone of geriatric care. Cognitive impairment has the potential to significantly impact multiple phases of a person's cancer care experience. Accurately identifying this vulnerability is a challenge for many cancer care clinicians, thus the use of validated cognitive assessment tools are recommended. As international cancer guidelines for older adults recommend Geriatric Assessment (GA) which includes an evaluation of cognition, clinicians need to be familiar with the overall interpretation of the commonly used cognitive assessment tools. This rapid review investigated the cognitive assessment tools that were most frequently recommended by Geriatric Oncology guidelines: Blessed Orientation-Memory-Concentration test (BOMC), Clock Drawing Test (CDT), Mini-Cog, Mini-Mental State Examination (MMSE), Montreal Cognitive Assessment (MoCA), and Short Portable Mental Status Questionnaire (SPMSQ). A detailed appraisal of the strengths and limitations of each tool was conducted, with a focus on practical aspects of implementing cognitive assessment tools into real-world clinical settings. Finally, recommendations on choosing an assessment tool and the additional considerations beyond screening are discussed.
Publication Date: 2021-10-23
Journal: Current oncology (Toronto, Ont.)


circadian clock regulation(29)

Tobacco ubiquitin-specific protease 12 (NbUBP12) positively modulates drought resistance.
Deubiquitination, a type of post-translational modification, cleaves ubiquitin from target proteins, thereby regulating their stability or activity. Deubiquitination enzymes, ubiquitin-specific proteases (UBP/USP), have been reported to be involved in numerous cellular processes in plants, including meristem development, circadian clock regulation, and immunity. In contrast to model plants, however, the functions of UBP in other higher plants remain poorly understood. Here, we isolated a deubiquitination enzyme, ubiquitin-specific protease 12 (NbUBP12), from
Publication Date: 2021-10-19
Journal: Plant signaling & behavior


gene expression(231)

REGγ regulates circadian clock by modulating BMAL1 protein stability.
Endogenous clocks generate rhythms in gene expression, which facilitates the organisms to cope through periodic environmental variations in accordance with 24-h light/dark time. A core question that needs to be elucidated is how such rhythms proliferate throughout the cells and regulate the dynamic physiology. In this study, we demonstrate the role of REGγ as a new regulator of circadian clock in mice, primary MEF, and SY5Y cells. Assessment of circadian conduct reveals a difference in circadian period, wheel mode, and the ability to acclimate the external light stimulus between WT and KO littermates. Compared to WT mice, REGγ KO mice attain the phase delay behavior upon light shock at early night. During the variation of 12/12 h light/dark (LD) exposure, levels of Per1, Per2, Cry1, Clock, Bmal1, and Rorα circadian genes in suprachiasmatic nucleus are significantly higher in REGγ KO than in WT mice, concomitant with remarkable changes in BMAL1 and PER2 proteins. In cultured cells depleted of REGγ, serum shock induces early response of the circadian genes Per1 and Per2 with the cyclic rhythm maintained. Mechanistic study indicates that REGγ directly degrades BMAL1 by the non-canonical proteasome pathway independent of ATP and ubiquitin. Silencing BMAL1 abrogates the changes in circadian genes in REGγ-deficient cells. However, inhibition of GSK-3β, a known promoter for degradation of BMAL1, exacerbates the action of REGγ depletion. In conclusion, our findings define REGγ as a new factor, which functions as a rheostat of circadian rhythms to mitigate the levels of Per1 and Per2 via proteasome-dependent degradation of BMAL1.
Publication Date: 2021-11-07
Journal: Cell death discovery


circadian rhythm(160)

The Link between Circadian Clock Genes and Autophagy in Chronic Obstructive Pulmonary Disease.
Chronic obstructive pulmonary disease (COPD), a progressive respiratory disease, is characterized by the alveolar epithelium injury and persistent airway inflammation. It is documented that oscillation and dysregulated expression of circadian clock genes, like Bmal1, Per1, and Per2, involved in COPD pathogenies, including chronic inflammation and imbalanced autophagy level, and targeting the associations of circadian rhythm and autophagy is promising strategies in the management and treatment of COPD. Herein, we reviewed the mechanisms of the circadian clock and the unbalance of the autophagic level in COPD, as well as the link between the two, so as to provide further theoretical bases for the study on the pathogenesis of COPD.
Publication Date: 2021-11-05
Journal: Mediators of inflammation


biological clock(146)

Chrono-Pharmaceutical Approaches to Optimize Dosing Regimens Based on the Circadian Clock Machinery.
Daily rhythmic variations in biological functions affect the efficacy and/or toxicity of drugs: a large number of drugs cannot be expected to exhibit the same potency at different administration times. The "circadian clock" is an endogenous timing system that broadly regulates metabolism, physiology and behavior. In mammals, this clock governs the oscillatory expression of the majority of genes with a period length of approximately 24 h. Genetic studies have revealed that molecular components of the circadian clock regulate the expression of genes responsible for the sensitivity to drugs and their disposition. The circadian control of pharmacodynamics and pharmacokinetics enables 'chrono-pharmaceutical' applications, namely drug administration at appropriate times of day to optimize the therapeutic index (efficacy vs. toxicity). On the other hand, a variety of pathological conditions also exhibit marked day-night changes in symptom intensity. Currently, novel therapeutic approaches are facilitated by the development of chemical compound targeted to key proteins that cause circadian exacerbation of disease events. This review presents an overview of the current understanding of the role of the circadian biological clock in regulating drug efficacy and disease conditions, and also describes the importance of identifying the difference in the circadian machinery between diurnal and nocturnal animals to select the most appropriate times of day to administer drugs in humans.
Publication Date: 2021-11-02
Journal: Biological & pharmaceutical bulletin


nucleus scn(98)

[Internal circadian clock and liver metabolism].
Circadian clock is an internal autonomous time-keeping system, including central clocks located in the suprachiasmatic nucleus (SCN) and peripheral clocks. The molecular circadian clock consists of a set of interlocking transcriptional-translational feedback loops that take the clock-controlled genes 24 h to oscillate. The core mechanism of molecular circadian clock is that CLOCK/BMAL1 dimer activates the transcription of cryptochromes (CRYs) and Periods (PERs), which act as transcriptional repressors of further CLOCK/BMAL1-mediated transcription. In addition to this basic clock, there is an additional sub-loop of REV-ERBα and RORα regulating the transcription of BMAL1. Approximately 80% protein-coding genes demonstrate significant rhythmicity. The earth rotation is responsible for the generation of the daily circadian rhythms. To coordinate metabolic balance and energy availability, almost all organisms adapt to the rhythm. Studies have shown that circadian clock integrating with metabolic homeostasis increases the efficiency of energy usage and coordinates with different organs in order to adapt to internal physiology and external environment soon. As the central organ of metabolism, the liver performs various physiological activities nearly all controlled by the circadian clock. There are multiple interactive regulation mechanisms between the circadian clock and the regulation of liver metabolism. The misalignment of metabolism with tissue circadian is identified as a high-risk factor of metabolic diseases. This article reviews the recent studies on circadian physiological regulation of liver glucose, lipid and protein metabolism and emphasizes oscillation of mitochondrial function. We also take an outlook for new methods and application of circadian clock research in the future.
Publication Date: 2021-10-29
Journal: Sheng li xue bao : [Acta physiologica Sinica]


clock protein(70)

TOC1 clock protein phosphorylation controls complex formation with NF-YB/C to repress hypocotyl growth.
Plant photoperiodic growth is coordinated by interactions between circadian clock and light signaling networks. How post-translational modifications of clock proteins affect these interactions to mediate rhythmic growth remains unclear. Here, we identify five phosphorylation sites in the Arabidopsis core clock protein TIMING OF CAB EXPRESSION 1 (TOC1) which when mutated to alanine eliminate detectable phosphorylation. The TOC1 phospho-mutant fails to fully rescue the clock, growth, and flowering phenotypes of the toc1 mutant. Further, the TOC1 phospho-mutant shows advanced phase, a faster degradation rate, reduced interactions with PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) and HISTONE DEACETYLASE 15 (HDA15), and poor binding at pre-dawn hypocotyl growth-related genes (PHGs), leading to a net de-repression of hypocotyl growth. NUCLEAR FACTOR Y subunits B and C (NF-YB/C) stabilize TOC1 at target promoters, and this novel trimeric complex (NF-TOC1) acts as a transcriptional co-repressor with HDA15 to inhibit PIF-mediated hypocotyl elongation. Collectively, we identify a molecular mechanism suggesting how phosphorylation of TOC1 alters its phase, stability, and physical interactions with co-regulators to precisely phase PHG expression to control photoperiodic hypocotyl growth.
Publication Date: 2021-11-03
Journal: The EMBO journal


epigenetic clocks(65)

Impact of large granular lymphocyte leukemia on blood DNA methylation and epigenetic clock modeling in Fischer 344 rats.
Age-dependent differences in methylation at specific cytosine-guanosine sites (CpGs) have been used in "epigenetic clock" formulas to predict age. Deviations of epigenetic age from chronological age are informative of health status and are associated with adverse health outcomes, including mortality. In most cases, epigenetic clocks are performed on methylation from DNA extracted from circulating blood cells. However, the effect of neoplastic cells in the circulation on estimation and interpretation of epigenetic clocks is not well understood. Here, we explored this using Fischer 344 (F344) rats, a strain that often develops large granular lymphocyte leukemia (LGL). We found clear histological markers of LGL pathology in the spleens and livers of 27 out of 61 rats aged 17-27 months. We assessed DNA methylation by reduced representation bisulfite sequencing with coverage of 3 million cytosine residues. Although LGL broadly increased DNA methylation variability, it did not change epigenetic aging. Despite this, inclusion of rats with LGL in clock training sets significantly altered predictor selection probability at 83 of 121 commonly utilized CpGs. Furthermore, models trained on rat samples that included individuals with LGL had greater absolute age error than those trained exclusively on LGL-free rats (39% increase; p<0.0001). We conclude that the epigenetic signals for aging and LGL are distinct, such that LGL assessment is not necessary for valid measures of epigenetic age in F344 rats. The precision and architecture of constructed epigenetic clock formulas, however, can be influenced by the presence of neoplastic hematopoietic cells in training set populations.
Publication Date: 2021-11-01
Journal: The journals of gerontology. Series A, Biological sciences and medical sciences


clock components(64)

nan
The core of the plant circadian clock involves multiple interlocking gene expression loops and post-translational controls along with inputs from light and metabolism. The complexity of the interactions is such that few specific functions can be ascribed to single components. In previous work, we reported differences in the operation of the clocks in Arabidopsis shoots and roots, including the effects of mutations of key clock components. Here, we have used luciferase imaging to study
Publication Date: 2021-11-05
Journal: Frontiers in plant science


peripheral clocks(62)

Synchronization between peripheral circadian clock and feeding-fasting cycles in microfluidic device sustains oscillatory pattern of transcriptome.
The circadian system cyclically regulates many physiological and behavioral processes within the day. Desynchronization between physiological and behavioral rhythms increases the risk of developing some, including metabolic, disorders. Here we investigate how the oscillatory nature of metabolic signals, resembling feeding-fasting cycles, sustains the cell-autonomous clock in peripheral tissues. By controlling the timing, period and frequency of glucose and insulin signals via microfluidics, we find a strong effect on Per2::Luc fibroblasts entrainment. We show that the circadian Per2 expression is better sustained via a 24 h period and 12 h:12 h frequency-encoded metabolic stimulation applied for 3 daily cycles, aligned to the cell-autonomous clock, entraining the expression of hundreds of genes mostly belonging to circadian rhythms and cell cycle pathways. On the contrary misaligned feeding-fasting cycles synchronize and amplify the expression of extracellular matrix-associated genes, aligned during the light phase. This study underlines the role of the synchronicity between life-style-associated metabolic signals and peripheral clocks on the circadian entrainment.
Publication Date: 2021-10-28
Journal: Nature communications


central clock(57)

Circadian Rhythm, Clock Genes, and Hypertension: Recent Advances in Hypertension.
Accumulating evidence suggests that the molecular circadian clock is crucial in blood pressure (BP) control. Circadian rhythms are controlled by the central clock, which resides in the suprachiasmatic nucleus of the hypothalamus and peripheral clocks throughout the body. Both light and food cues entrain these clocks but whether these cues are important for the circadian rhythm of BP is a growing area of interest. The peripheral clocks in the smooth muscle, perivascular adipose tissue, liver, adrenal gland, and kidney have been recently implicated in the regulation of BP rhythm. Dysregulation of the circadian rhythm of BP is associated with adverse cardiorenal outcomes and increased risk of cardiovascular mortality. In this review, we summarize the most recent advances in peripheral clocks as BP regulators, highlight the adverse outcomes of disrupted circadian BP rhythm in hypertension, and provide insight into potential future work in areas exploring the circadian clock in BP control and chronotherapy. A better understanding of peripheral clock function in regulating the circadian rhythm of BP will help pave the way for targeted therapeutics in the treatment of circadian BP dysregulation and hypertension.
Publication Date: 2021-10-05
Journal: Hypertension (Dallas, Tex. : 1979)


present study(50)

Are Analogue or Digital Clocks Friendlier for People Living with Dementia?
In ageing population, it is desirable to reduce the impact of cognitive decline on daily life. While various types of dementia-friendly environments have been proposed, the question still remains regarding whether analogue or digital clocks are friendlier for people with dementia. In clinical practice, we normally use our original clock reading test (10 analogue and 10 digital clocks) to assess patients' ability to read a clock. In the present study, a retrospective medical record survey was conducted. Fifty-five participants who had done the test were identified. The result of the test was compared between analogue and digital clocks. Additionally, to assess specific ability to read analogue clocks, an "analogue-digital gap" was defined as the difference between patients' performance for analogue and digital clocks. Univariate and multivariate analyses were conducted to detect significant factors associated with reading ability specific to analogue clocks. The analogue clock proved less readable than the digital clock, even after adjusting for MMSE total score ( In the present study, the digital clock was friendlier than the analogue clock for patients with dementia. Compared to the digital clock, reading analogue clocks might require more widespread cognition, such as working memory and visuospatial processing. While our finding was a general tendency, and individual assessment is necessary, it might help the development of personalized environmental adjustments.
Publication Date: 2021-10-28
Journal: Dementia and geriatric cognitive disorders extra


clock bmal1(47)

Cell-associated HIV RNA has a Circadian Cycle in Males Living with HIV on Antiretroviral Therapy.
Circadian transcription factors that regulate cell-autonomous circadian clocks can also increase HIV transcription in vitro. We aimed to determine if circadian variation in HIV transcription exists in people living with HIV (PLHIV) on antiretroviral therapy (ART). We performed a prospective observational study of male PLHIV on ART, sampling blood every four hours for 24 hours. Using qPCR, we quantified expression of circadian associated genes, HIV DNA and cell-associated unspliced (CA-US) RNA in peripheral blood CD4+ T-cells. Plasma sex hormones were quantified alongside plasma and salivary cortisol. The primary outcome was to identify temporal variations in CA-US HIV RNA using a linear mixed effect regression framework and maximum likelihood estimation. Salivary and plasma cortisol, and circadian genes including Clock, Bmal1, and Per3 varied with a circadian rhythm. CA-US HIV RNA and the ratio of CA-US HIV RNA-to-DNA in CD4+ T-cells also demonstrated circadian variations, with no variation in HIV DNA. Circulating oestradiol was highly predictive of CA-US HIV RNA variation in vivo. CA-US HIV RNA in PLHIV on ART varies temporally with a circadian rhythm. These findings have implications for the design of clinical trials and biomarkers to assess HIV cure interventions.
Publication Date: 2021-10-17
Journal: The Journal of infectious diseases


kaput clock(26)

Understanding the Associations of Prenatal Androgen Exposure on Sleep Physiology, Circadian Proteins, Anthropometric Parameters, Hormonal Factors, Quality of Life, and Sex Among Healthy Young Adults: Protocol for an International, Multicenter Study.
The ratio of the second finger length to the fourth finger length (2D:4D ratio) is considered to be negatively correlated with prenatal androgen exposure (PAE) and positively correlated with prenatal estrogen. Coincidentally, various brain regions are sensitive to PAE, and their functions in adults may be influenced by the prenatal actions of sex hormones. This study aims to assess the relationship between PAE (indicated by the 2D:4D ratio) and various physiological (sex hormone levels and sleep-wake parameters), psychological (mental health), and sexual parameters in healthy young adults. This study consists of two phases. In phase 1, we will conduct a survey-based study and anthropometric assessments (including 2D:4D ratio and BMI) in healthy young adults. Using validated questionnaires, we will collect self-reported data on sleep quality, sexual function, sleep chronotype, anxiety, and depressive symptoms. In phase 2, a subsample of phase 1 will undergo polysomnography and physiological and genetic assessments. Sleep architecture data will be obtained using portable polysomnography. The levels of testosterone, estradiol, progesterone, luteinizing hormone, follicle-stimulating hormone, prolactin, melatonin, and circadian regulatory proteins (circadian locomotor output cycles kaput [CLOCK], timeless [TIM], and period [PER]) and the expression levels of some miRNAs will be measured using blood samples. The rest and activity cycle will be monitored using actigraphy for a 7-day period. In Poland, 720 participants were recruited for phase 1. Among these, 140 completed anthropometric measurements. In addition, 25 participants joined and completed phase 2 data collection. Recruitment from other sites will follow. Findings from our study may help to better understand the plausible role of PAE in sleep physiology, mental health, and sexual quality of life in young adults. DERR1-10.2196/29199.
Publication Date: 2021-10-07
Journal: JMIR research protocols


95 ci(15)

Exploring determinants of community pharmacist-led influenza vaccination in a Middle Eastern country: a national web-based cross-sectional study.
Utilizing community pharmacists (CPs) as immunizers has being adopted in various countries as approach to boost influenza vaccination coverage. Our study aims to explore the Lebanese CPs' willingness to administer influenza vaccine, and to identify factors associated with this willingness. This is a web-based, cross-sectional study, conducted over 2 months, from the 1st of November to the end of December 2020. Self-reported data were collected electronically from Lebanese CPs through an anonymous, questionnaire using google form. The collected data were analyzed using the statistical software SPSS (Statistical Package for Social Sciences). Bivariate and multivariable analyses were performed to examine factors associated with the willingness of CPs to administer influenza vaccine. A total of 412 CPs participated in this survey of which 76.9% are willing to administer influenza vaccines. More than 90% of them had a good overall knowledge score and 88.8% of CPs showed a positive overall attitude score, particularly towards involvement of CPs in influenza vaccine provision. Their willingness to administer vaccine was positively associated with the younger age (aOR = 3.12 with 95% CI (1.597-4.040)), higher education level (aOR = 2.02 with 95% CI (1.093-3.741)), previous experience in immunization (aOR = 2.72 with 95% CI (1.320-5.627)) and urbanicity of pharmacy (aOR = 1.542 with 95% CI (1.219-4.627)). Extensive working hours (aOR = 2.34 with 95% CI (1.131-4.845)), working in pharmacies that are operating round-the-clock, showing positive attitude towards immunization (aOR = 3.01 with 95% CI (1.872-6.422)) and towards provision of influenza vaccines (aOR = 13.72 with 95% CI (13.721-38.507)) were also positively associated to this willingness. Conversely, patient privacy (aOR = 0.55 with 95% CI (0.079-0.983)), time and cost for professional development (aOR = 0.55 with 95% CI (0.172-0.918)), limited patient's trust (aOR = 0.39 with 95% CI (0.203-0.784)), financial remuneration (aOR = 0.18 with 95% CI (0.088-0.377)), and requirement of formal certification in vaccine administration (aOR = 0.07 with 95% CI (0.020-0.279)) were negatively associated to this willingness. Addressing the unearthed concerns related to utilizing CPs as influenza immunizers through a concerted effort is a key to success in any future implementation of vaccination services in pharmacies.
Publication Date: 2021-09-22
Journal: Journal of pharmaceutical policy and practice


system(343)

Circadian Regulation and Clock-Controlled Mechanisms of Glycerophospholipid Metabolism from Neuronal Cells and Tissues to Fibroblasts.
Along evolution, living organisms developed a precise timekeeping system, circadian clocks, to adapt life to the 24-h light/dark cycle and temporally regulate physiology and behavior. The transcriptional molecular circadian clock and metabolic/redox oscillator conforming these clocks are present in organs, tissues, and even in individual cells, where they exert circadian control over cellular metabolism. Disruption of the molecular clock may cause metabolic disorders and higher cancer risk. The synthesis and degradation of glycerophospholipids (GPLs) is one of the most highly regulated metabolisms across the 24-h cycle in terms of total lipid content and enzyme expression and activity in the nervous system and individual cells. Lipids play a plethora of roles (membrane biogenesis, energy sourcing, signaling, and the regulation of protein-chromatin interaction, among others), making control of their metabolism a vital checkpoint in the cellular organization of physiology. An increasing body of evidence clearly demonstrates an orchestrated and sequential series of events occurring in GPL metabolism across the 24-h day in diverse retinal cell layers, immortalized fibroblasts, and glioma cells. Moreover, the clock gene Per1 and other circadian-related genes are tightly involved in the regulation of GPL synthesis in quiescent cells. However, under proliferation, the metabolic oscillator continues to control GPL metabolism of brain cancer cells even after molecular circadian clock disruption, reflecting the crucial role of the temporal metabolism organization in cell preservation. The aim of this review is to examine the control exerted by circadian clocks over GPL metabolism, their synthesizing enzyme expression and activities in normal and tumorous cells of the nervous system and in immortalized fibroblasts.
Publication Date: 2021-10-27
Journal: Molecular neurobiology


function(277)

The SEEL motif and members of the MYB-related REVEILLE transcription factor family are important for the expression of LORELEI in the synergid cells of the Arabidopsis female gametophyte.
Synergid cells in the micropylar end of the female gametophyte are required for critical cell-cell signaling interactions between the pollen tube and the ovule that precede double fertilization and seed formation in flowering plants. LORELEI (LRE) encodes a putative GPI-anchored protein that is expressed primarily in the synergid cells, and together with FERONIA, a receptor-like kinase, it controls pollen tube reception by the receptive synergid cell. Still, how LRE expression is controlled in synergid cells remains poorly characterized. We identified candidate cis-regulatory elements enriched in LRE and other synergid cell-expressed genes. One of the candidate motifs ('TAATATCT') in the LRE promoter was an uncharacterized variant of the Evening Element motif that we named as the Short Evening Element-like (SEEL) motif. Deletion or point mutations in the SEEL motif of the LRE promoter resulted in decreased reporter expression in synergid cells, demonstrating that the SEEL motif is important for expression of LRE in synergid cells. Additionally, we found that LRE expression is decreased in the loss of function mutants of REVEILLE (RVE) transcription factors, which are clock genes known to bind the SEEL and other closely related motifs. We propose that RVE transcription factors regulate LRE expression in synergid cells by binding to the SEEL motif in the LRE promoter. Identification of cis-regulatory elements and transcription factors involved in the expression of LRE will serve as a foundation to characterize the gene regulatory networks in synergid cells.
Publication Date: 2021-10-31
Journal: Plant reproduction


cell(243)

HNF4A defines tissue-specific circadian rhythms by beaconing BMAL1::CLOCK chromatin binding and shaping the rhythmic chromatin landscape.
Transcription modulated by the circadian clock is diverse across cell types, underlying circadian control of peripheral metabolism and its observed perturbation in human diseases. We report that knockout of the lineage-specifying Hnf4a gene in mouse liver causes associated reductions in the genome-wide distribution of core clock component BMAL1 and accessible chromatin marks (H3K4me1 and H3K27ac). Ectopically expressing HNF4A remodels chromatin landscape and nucleates distinct tissue-specific BMAL1 chromatin binding events, predominantly in enhancer regions. Circadian rhythms are disturbed in Hnf4a knockout liver and HNF4A-MODY diabetic model cells. Additionally, the epigenetic state and accessibility of the liver genome dynamically change throughout the day, synchronized with chromatin occupancy of HNF4A and clustered expression of circadian outputs. Lastly, Bmal1 knockout attenuates HNF4A genome-wide binding in the liver, likely due to downregulated Hnf4a transcription. Our results may provide a general mechanism for establishing circadian rhythm heterogeneity during development and disease progression, governed by chromatin structure.
Publication Date: 2021-11-05
Journal: Nature communications


processes(236)

PER2 mediates CREB-dependent light induction of the clock gene Per1.
Light affects many physiological processes in mammals such as entrainment of the circadian clock, regulation of mood, and relaxation of blood vessels. At the molecular level, a stimulus such as light initiates a cascade of kinases that phosphorylate CREB at various sites, including serine 133 (S133). This modification leads CREB to recruit the co-factor CRCT1 and the histone acetyltransferase CBP to stimulate the transcription of genes containing a CRE element in their promoters, such as Period 1 (Per1). However, the details of this pathway are poorly understood. Here we provide evidence that PER2 acts as a co-factor of CREB to facilitate the formation of a transactivation complex on the CRE element of the Per1 gene regulatory region in response to light or forskolin. Using in vitro and in vivo approaches, we show that PER2 modulates the interaction between CREB and its co-regulator CRTC1 to support complex formation only after a light or forskolin stimulus. Furthermore, the absence of PER2 abolished the interaction between the histone acetyltransferase CBP and CREB. This process was accompanied by a reduction of histone H3 acetylation and decreased recruitment of RNA Pol II to the Per1 gene. Collectively, our data show that PER2 supports the stimulus-dependent induction of the Per1 gene via modulation of the CREB/CRTC1/CBP complex.
Publication Date: 2021-11-07
Journal: Scientific reports


model(223)

Discrete coalescent trees.
In many phylogenetic applications, such as cancer and virus evolution, time trees, evolutionary histories where speciation events are timed, are inferred. Of particular interest are clock-like trees, where all leaves are sampled at the same time and have equal distance to the root. One popular approach to model clock-like trees is coalescent theory, which is used in various tree inference software packages. Methodologically, phylogenetic inference methods require a tree space over which the inference is performed, and the geometry of this space plays an important role in statistical and computational aspects of tree inference algorithms. It has recently been shown that coalescent tree spaces possess a unique geometry, different from that of classical phylogenetic tree spaces. Here we introduce and study a space of discrete coalescent trees. They assume that time is discrete, which is natural in many computational applications. This tree space is a generalisation of the previously studied ranked nearest neighbour interchange space, and is built upon tree-rearrangement operations. We generalise existing results about ranked trees, including an algorithm for computing distances in polynomial time, and in particular provide new results for both the space of discrete coalescent trees and the space of ranked trees. We establish several geometrical properties of these spaces and show how these properties impact various algorithms used in phylogenetic analyses. Our tree space is a discretisation of a previously introduced time tree space, called t-space, and hence our results can be used to approximate solutions to various open problems in t-space.
Publication Date: 2021-11-06
Journal: Journal of mathematical biology


cycle(202)

Timeless in animal circadian clocks and beyond.
TIMELESS (TIM) was first identified as a molecular cog in the Drosophila circadian clock. Almost three decades of investigations have resulted in an insightful model describing the critical role of Drosophila TIM (dTIM) in circadian timekeeping in insects, including its function in mediating light entrainment and temperature compensation of the molecular clock. Furthermore, exciting discoveries on its sequence polymorphism and thermosensitive alternative RNA splicing have also established its role in regulating seasonal biology. Although mammalian TIM (mTIM), its mammalian paralog, was first identified as a potential circadian clock component in 1990s due to sequence similarity to dTIM, its role in clock regulation has been more controversial. Mammalian TIM has now been characterized as a DNA replication fork component and has been shown to promote fork progression and participate in cell cycle checkpoint signaling in response to DNA damage. Despite defective circadian rhythms displayed by mtim mutants, it remains controversial whether the regulation of circadian clocks by mTIM is direct, especially given the interconnection between the cell cycle and circadian clocks. In this review, we provide a historical perspective on the identification of animal tim genes, summarize the roles of TIM proteins in biological timing and genomic stability, and draw parallels between dTIM and mTIM despite apparent functional divergence.
Publication Date: 2021-10-27
Journal: The FEBS journal


age(199)

Loxl2 is a mediator of cardiac aging in Drosophila melanogaster; genetically examining the role of aging clock genes.
Transcriptomic, proteomic, and methylation aging clocks demonstrate that aging has a predictable preset program, while Transcriptome Trajectory Turning Points indicate that the 20 to 40 age range in humans is the likely stage at which the progressive loss of homeostatic control, and in turn aging, begins to have detrimental effects. Turning points in this age range overlapping with human aging clock genes revealed five candidates that we hypothesized could play a role in aging or age-related physiological decline. To examine these gene's effects on lifespan and health-span, we utilized whole body and heart specific gene knockdown of human orthologs in Drosophila melanogaster. Whole body Loxl2, fz3, and Glo1 RNAi positively affected lifespan as did heart-specific Loxl2 knockdown. Loxl2 inhibition concurrently reduced age-related cardiac arrythmia and collagen (Pericardin) fiber width. Loxl2 binds several transcription factors in humans and RT-qPCR confirmed that a conserved transcriptional target CDH1 (Drosophila CadN2), has expression levels which correlate with Loxl2 reduction in Drosophila. These results point to conserved pathways and multiple mechanisms by which inhibition of Loxl2 can be beneficial to heart health and organismal aging.
Publication Date: 2021-11-05
Journal: G3 (Bethesda, Md.)


physiological(190)

PER1 as a Tumor Suppressor Attenuated in the Malignant Phenotypes of Breast Cancer Cells.
Circadian clock genes play a crucial role in physiological and pathological processes, and their aberrant expressions were involved in various human cancers. The objective of this study was to investigate the expression level of Period circadian regulator 1 (PER1), an important circadian clock gene, and its biological roles in the development and progression of breast cancer. The expression level of PER1 in breast cancer samples was analyzed using the Oncomine database, and the correlation between PER1 expression and clinicopathologic parameters was assessed by bc-GenExMiner v4.5. In addition, Kaplan-Meier plotter database was used to determine the prognostic significance of PER1 expression for breast cancer patients. The expressions of PER1 in breast cancer tissues and cells were validated by Western blot. The loss-or-gain assay of PER1 was conducted to investigate the effects of its expression on cell proliferation, migration and invasion of breast cancer. The relationship between PER1 expression and epigenetic modifications was further explored by Western blot. The results of the bioinformatics analysis revealed that the expression level of PER1 was markedly reduced in breast cancer tissues (P<0.001), and patients with high expression of PER1 had a better overall survival (HR:0.78, 95% CI:0.63-0.97, P=0.026) and recurrence-free survival (HR:0.83, 95% CI:0.75-0.93, P=0.001) than those with low expression. The assay of gene loss-or-gain indicated that downregulation of PER1 expression markedly promoted cell proliferation, migration and invasion (P<0.05), whereas these malignant phenotypes of breast cancer cells were inhibited by PER1 overexpression (P<0.05). Further studies showed that trichostatin A (TSA), a histone deacetylase inhibitor, induced the expression of PER1 protein in breast cancer cells (P<0.05). PER1 functions as a tumor suppressor in the development and progression of breast cancer, and its expression silencing might be regulated by epigenetic modifications.
Publication Date: 2021-10-30
Journal: International journal of general medicine


brain(185)

Methylation studies in Peromyscus: aging, altitude adaptation, and monogamy.
DNA methylation-based biomarkers of aging have been developed for humans and many other mammals and could be used to assess how stress factors impact aging. Deer mice (Peromyscus) are long-living rodents that have emerged as an informative model to study aging, adaptation to extreme environments, and monogamous behavior. In the present study, we have undertaken an exhaustive, genome-wide analysis of DNA methylation in Peromyscus, spanning different species, stocks, sexes, tissues, and age cohorts. We describe DNA methylation-based estimators of age for different species of deer mice based on novel DNA methylation data generated on highly conserved mammalian CpGs measured with a custom array. The multi-tissue epigenetic clock for deer mice was trained on 3 tissues (tail, liver, and brain). Two human-Peromyscus clocks accurately measure age and relative age, respectively. We present CpGs and enriched pathways that relate to different conditions such as chronological age, high altitude, and monogamous behavior. Overall, this study provides a first step towards studying the epigenetic correlates of monogamous behavior and adaptation to high altitude in Peromyscus. The human-Peromyscus epigenetic clocks are expected to provide a significant boost to the attractiveness of Peromyscus as a biological model.
Publication Date: 2021-10-27
Journal: GeroScience


proteins(175)

Biphasic Roles of Clock Genes and Bone Morphogenetic Proteins in Gonadotropin Expression by Mouse Gonadotrope Cells.
Roles of Clock genes and the bone morphogenetic protein (BMP) system in the regulation of gonadotropin secretion by gonadotropin-releasing hormone (GnRH) were investigated using mouse gonadotropin LβT2 cells. It was found that luteinizing hormone (LH)β mRNA expression level in LβT2 cells changed gradually over time, with LHβ expression being suppressed in the early phase up to 12 h and then elevated in the late phase 24 h after GnRH stimulation. In addition, the mRNA expression levels of Clock genes, including Bmal1, Clock, Per2, and Cry1, also showed temporal changes mimicking the pattern of LHβ expression in the presence and absence of GnRH. Notably, the expression levels of Bmal1 and Clock showed strong positive correlations with LHβ mRNA expression levels. Moreover, a functional link of the ERK signaling of mitogen-activated protein kinases (MAPKs) in the suppression of LHβ mRNA expression, as well as Bmal1 and Clock mRNA expression by GnRH at the early phase, was revealed. Inhibition of Bmal1 and Clock expression using siRNA was involved in the reduction in LHβ mRNA levels in the late phase 24 h after GnRH stimulation. Furthermore, in the presence of BMP-6 and -7, late-phase Bmal1 and LHβ mRNA expression after GnRH stimulation was significantly attenuated. Collectively, the results indicated that LH expression in gonadotrope cells exhibits Bmal1/Clock-dependent fluctuations under the influence of GnRH and that the fluctuations are regulated by ERK and BMPs in the early and late stages, respectively, in a phase-dependent manner after GnRH stimulation.
Publication Date: 2021-10-24
Journal: International journal of molecular sciences


internal(172)

A flexible system-on-a-chip control hardware for atomic, molecular, and optical physics experiments.
We have implemented a control system core for experiments in atomic, molecular, and optical physics based on a commercial low-cost board, featuring a field-programmable gate array as part of a system-on-a-chip on which a Linux operating system is running. The board features Gigabit Ethernet, allowing for fast data transmission and operation of remote experimental systems. A single board can control a set of devices generating digital, analog, and radio frequency signals with precise timing given either by an external or internal clock. Contiguous output and input sampling rates of up to 40 MHz are achievable. Several boards can run synchronously with a timing error approaching 1 ns. For this purpose, a novel auto-synchronization scheme is demonstrated, with possible application in complex distributed experimental setups with demanding timing requests.
Publication Date: 2021-11-01
Journal: The Review of scientific instruments


regulates(159)

Loss of myeloid Bmal1 exacerbates hypertensive vascular remodelling through interaction with STAT6 in mice.
In addition to its involvement of inflammatory responses, limited information is available on the phenotype and behaviour of vascular macrophages during hypertensive vascular remodelling. Here we aim at studying the contribution of BMAL1 to the pro-fibrotic macrophage phenotype in the vasculature during hypertension, which leads to enhanced vascular remodelling and promoted blood pressure increase. Wild type Bmal1f/f and myeloid cell selective Bmal1 knockout Bmal1f/f; LysMCre/+ mice were infused with AngII for four weeks to induce hypertension. AngII-induced blood pressure increase, vascular media thickness and vascular dysfunction were enhanced in Bmal1f/f; LysMCre/+ mice, accompanied with a pro-fibrotic M2 phenotype of the vascular macrophages. Bmal1f/f; LysMCre/+ mice also have more upregulations of MMP9 and MMP13 expression in the vascular wall, accompanied by enhanced collagen deposition after AngII infusion. Loss of Bmal1 in bone marrow derived macrophages enhanced STAT6 activation induced by IL4, and the subsequent MMP13 upregulation and activity. In macrophages, loss of Bmal1 enhanced the phosphorylation and nuclear translocation of STAT6 triggered by IL4, through possibly a direct interaction between BMAL1 and STAT6. To further determine whether IL4 induced signalling in macrophage contributes to enhanced vascular remodelling in hypertensive mice, we showed that deletion of myeloid IL4Rα in Il4raf/f; LysMCre/+ mice attenuated blood pressure increase and hypertensive vascular remodelling after AngII infusion. Our results suggested a tonic effect of BMAL1 deletion on hypertensive vascular remodelling. BMAL1 might inhibit IL4-STAT6 signalling in macrophages through the interaction with STAT6 to reduce STAT6 activation and target gene transcription, especially MMP9 and MMP13, contributing to vascular remodelling. Many recent studies emphasized the contribution of macrophage, especially those reside within the vasculture, in modulating vessel function and structure, under physiological and pathological conditions such as hypertension. Our study showed that clock gene BMAL1 not only regulates rhythmic gene expression in macrophages, but also interacts with other factors to maintain homeostasis of macrophage functon. Pro-fibrotic M2 macrophages contributes to hypertensive vascular remodeling. These findings add the complexity of blood pressure regulation and vascular remodeling, also indicate that it is important to consider the individual differences for blood pressure control and anti-hypertensive treatments.
Publication Date: 2021-11-03
Journal: Cardiovascular research


transcription(153)

Understanding the Logistics for the Distribution of Heme in Cells.
Heme is essential for the survival of virtually all living systems-from bacteria, fungi, and yeast, through plants to animals. No eukaryote has been identified that can survive without heme. There are thousands of different proteins that require heme in order to function properly, and these are responsible for processes such as oxygen transport, electron transfer, oxidative stress response, respiration, and catalysis. Further to this, in the past few years, heme has been shown to have an important regulatory role in cells, in processes such as transcription, regulation of the circadian clock, and the gating of ion channels. To act in a regulatory capacity, heme needs to move from its place of synthesis (in mitochondria) to other locations in cells. But while there is detailed information on how the heme lifecycle begins (heme synthesis), and how it ends (heme degradation), what happens in between is largely a mystery. Here we summarize recent information on the quantification of heme in cells, and we present a discussion of a mechanistic framework that could meet the logistical challenge of heme distribution.
Publication Date: 2021-11-02
Journal: JACS Au


factors(143)

New integrative approaches to discovery of pathophysiological mechanisms triggered by night shift work.
Synchronization to periodic cues such as food/water availability and light/dark cycles is crucial for living organisms' homeostasis. Both factors have been heavily influenced by human activity, with artificial light at night (ALAN) being an evolutionary challenge imposed over roughly the last century. Evidence from studies in humans and animal models shows that overt circadian misalignment, such as that imposed to about 20% of the workforce by night shift work (NSW), negatively impinges on the internal temporal order of endocrinology, physiology, metabolism, and behavior. Moreover, NSW is often associated to mistimed feeding, with both unnatural behaviors being known to increase the risk of chronic diseases, such as eating disorders, overweight, obesity, cardiovascular, metabolic (particularly type 2 diabetes mellitus) and gastrointestinal disorders, some types of cancer, as well as mental disease including sleep disturbances, cognitive disorders, and depression. Regarding deleterious effects of ALAN on reproduction, increased risk of miscarriage, preterm delivery and low birth weight have been reported in shift-worker women. These mounting lines of evidence prompt further efforts to advance our understanding of the effects of long-term NSW on health. Emerging data suggest that NSW with or without mistimed feeding modify gene expression and functional readouts in different tissues/organs, which seem to translate into persistent cardiometabolic and endocrine dysfunction. However, this research avenue still faces multiple challenges, such as functional characterization of new experimental models more closely resembling human long-term NSW and mistimed feeding in males versus females; studying further target organs; identifying molecular changes by means of deep multi-omics analyses; and exploring biomarkers of NSW with translational medicine potential. Using high-throughput and systems biology is a relatively new approach to study NSW, aimed to generate experiments addressing new biological factors, pathways, and mechanisms, going beyond the boundaries of the circadian clock molecular machinery.
Publication Date: 2021-11-04
Journal: Chronobiology international


feedback(143)

Circadian clock dysfunction of epithelial cells in pulmonary diseases.
Highly-differentiated pulmonary epithelial cells are essential for maintaining lung homeostasis by exerting various physiological functions, which are regulated by circadian clock consisted of an autoregulatory feedback loop of clock genes, including Brain-Muscle Aryl-hydrocarbon Receptor Nuclear Translocator-Like 1 (BMAL1) and Nuclear Heme Receptor Reverse Erythroblastosis Virus α (REV-ERB-α). The circadian clock dysfunction of epithelial cells has been increasingly associated with the pulmonary diseases: BMAL1 and REV-ERB-α regulates inflammatory response of club cells induced by lipopolysaccharide and cigarette smoke (CS) respectively; the clock disfunction in alveolar epithelial type2 cells (AEC-II) has been implicated in CS-induced airway inflammation and early-life hyperoxia-related susceptibility to influenza infection; the ciliary beat frequency of ciliated cells also shows circadian rhythms. Here, we review the current knowledge on the circadian regulation of different epithelial-cell subtypes, attempting to provide insights into how clock dysfunction contributes to pulmonary diseases, and explore possible pharmacological therapies and future directions for fundamental studies.
Publication Date: 2021-10-27
Journal: The international journal of biochemistry & cell biology


per2(138)

Food reward induction of rhythmic clock gene expression in the prefrontal cortex of rats is accompanied by changes in miR-34a-5p expression.
The current study is focused on mechanisms by which the peripheral circadian oscillator in the prefrontal cortex (PFC) participates in food reward-induced activity. The experimental group of male Wistar rats was trained to receive a food reward with a low hedonic and caloric value. Afterwards, animals were exposed to a 5h phase advance. Experimental animals could access a small food reward as they had been accustomed to while control rats were exposed to the same phase shift without access to a food reward. When synchronisation to a new light:dark cycle was accompanied by intake of food reward, animals exerted more exact phase shift compared to the controls. In rats with access to a food reward, a rhythm in dopamine receptors type 1 and 2 in the PFC was detected. Rhythmic clock gene expression was induced in the PFC of rats when a food reward was provided together with a phase shift. The per2 and clock genes are predicted targets of miR-34a-5p. The precursor form of miR-34a-5p (pre-miR-34a-5p) showed a daily rhythm in expression in the PFC of the control and experimental groups. On the other hand, the mature form of miR-34a-5p exerted an inverted rhythm compared to pre-miR-34a-5p and negative correlation with per and clock genes expression only in the PFC of rewarded rats. A difference in the pattern of mature and pre-miR-34a-5p values was not related to expression of enzymes drosha, dicer and dgcr8. A role of the clock genes and miR-34a-5p in reward-facilitated synchronisation has been hypothesised.
Publication Date: 2021-11-05
Journal: The European journal of neuroscience


showed(134)

Association Between CLOCK Gene Variants and Restless Legs Syndrome in Koreans.
Previous studies have suggested various causes of restless legs syndrome (RLS), including iron and dopamine concentrations in the brain. Genetic influences have also been reported in many studies. There is also a possibility that circadian clock genes may be involved because symptoms of RLS worsen at night. We investigated whether CLOCK and NPAS2 gene polymorphisms were associated with RLS. A total of 227 patients with RLS and 229 non-RLS matched controls were assessed according to the International Restless Legs Syndrome Study Group diagnostic criteria. Genotyping was performed using reverse transcription polymerase chain reaction and high-resolution melting curve analyses. Although the genotype distributions of the CLOCK variants (rs1801260 and rs2412646) were not significantly different between patients with RLS and non-RLS controls, the allele frequencies of CLOCK rs1801260 showed marginally significant differences between the two groups (X2 =2.98, p=0.085). Furthermore, there was a significant difference in the distribution of CLOCK haplotypes (rs1801260-rs2412646) between patients with RLS and non-RLS controls (p=0.013). The distributions of allelic, genotypic, and haplotypic variants of NPAS2 (rs2305160 and rs6725296) were not significantly different between the two groups. Our results suggest that CLOCK variants may be associated with decreased susceptibility to RLS.
Publication Date: 2021-11-05
Journal: Psychiatry investigation


significantly(113)

Effect of anesthesia on the expression of clock gene Clock and Bmal1 in New Zealand rabbits.
To evaluate the effect of anesthetic drugs on the expression of circadian gene Clock and Bmal1 in the brain of New Zealand rabbits, and to explore their change pattern. A total of 90 New Zealand rabbits were randomly divided into 5 groups ( At 0 and 24 h after anesthesia, compared with the group S, the levels of Clock and Bmal1 proteins were decreased significantly in the group P, the group D, and the group SEV (all Anesthetic SEV, propofol, and dexmedetomidine can inhibit the expression of clock gene Clock and Bmal1 protein in the brain fissues of the New Zealand rabbits, and the suppression effect continues for at least 24 h after anesthesia, whereas the suppression decreases significantly at 72 h after anesthesia.
Publication Date: 2021-09-28
Journal: Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences


years(92)

Citrullination was introduced into animals by horizontal gene transfer from cyanobacteria.
Protein post-translational modifications (PTMs) add great sophistication to biological systems. Citrullination, a key regulatory mechanism in human physiology and pathophysiology, is enigmatic from an evolutionary perspective. Although the citrullinating enzymes peptidylarginine deiminases (PADIs) are ubiquitous across vertebrates, they are absent from yeast, worms and flies. Based on this distribution PADIs were proposed to have been horizontally transferred, but this has been contested. Here, we map the evolutionary trajectory of PADIs into the animal lineage. We present strong phylogenetic support for a clade encompassing animal and cyanobacterial PADIs that excludes fungal and other bacterial homologues. The animal and cyanobacterial PADI proteins share functionally relevant primary and tertiary synapomorphic sequences that are distinct from a second PADI type present in fungi and actinobacteria. Molecular clock calculations and sequence divergence analyses using the fossil record estimate the last common ancestor of the cyanobacterial and animal PADIs to be less than one billion years old. Additionally, under an assumption of vertical descent, PADI sequence change during this evolutionary time frame is anachronistically low, even when compared to products of likely endosymbiont gene transfer, mitochondrial proteins and some of the most highly conserved sequences in life. The consilience of evidence indicates that PADIs were introduced from cyanobacteria into animals by horizontal gene transfer (HGT). The ancestral cyanobacterial PADI is enzymatically active and can citrullinate eukaryotic proteins, suggesting that the PADI HGT event introduced a new catalytic capability into the regulatory repertoire of animals. This study reveals the unusual evolution of a pleiotropic protein modification.
Publication Date: 2021-11-04
Journal: Molecular biology and evolution


growth(91)

Epidemiological dynamics of SARS-CoV-2 VOC Gamma in Rio de Janeiro, Brazil.
The emergence and widespread circulation of severe acute respiratory syndrome coronavirus 2 variants of concern (VOCs) or interest impose an enhanced threat to global public health. In Brazil, one of the countries most severely impacted throughout the pandemic, a complex dynamics involving variants co-circulation and turnover events has been recorded with the emergence and spread of VOC Gamma in Manaus in late 2020. In this context, we present a genomic epidemiology investigation based on samples collected between December 2020 and May 2021 in the second major Brazilian metropolis, Rio de Janeiro. By sequencing 244 novel genomes through all epidemiological weeks in this period, we were able to document the introduction and rapid dissemination of VOC Gamma in the city, driving the rise of the third local epidemic wave. Molecular clock analysis indicates that this variant has circulated locally since the first weeks of 2021 and only 7 weeks were necessary for it to achieve a frequency above 70 per cent, consistent with rates of growth observed in Manaus and other states. Moreover, a Bayesian phylogeographic reconstruction indicates that VOC Gamma spread throughout Brazil between December 2020 and January 2021 and that it was introduced in Rio de Janeiro through at least 13 events coming from nearly all regions of the country. Comparative analysis of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) cycle threshold (Ct) values provides further evidence that VOC Gamma induces higher viral loads (N1 target; mean reduction of Ct: 2.7, 95 per cent confidence interval = ± 0.7). This analysis corroborates the previously proposed mechanistic basis for this variant-enhanced transmissibility and distinguished epidemiological behavior. Our results document the evolution of VOC Gamma and provide independent assessment of scenarios previously studied in Manaus, therefore contributing to the better understanding of the epidemiological dynamics currently being surveyed in other Brazilian regions.
Publication Date: 2021-11-03
Journal: Virus evolution


performance(89)

DCTclock: Clinically-Interpretable and Automated Artificial Intelligence Analysis of Drawing Behavior for Capturing Cognition.
Developing tools for efficiently measuring cognitive change specifically and brain health generally-whether for clinical use or as endpoints in clinical trials-is a major challenge, particularly for conditions such as Alzheimer's disease. Technology such as connected devices and advances in artificial intelligence offer the possibility of creating and deploying clinical-grade tools with high sensitivity, rapidly, cheaply, and non-intrusively. Starting from a widely-used paper and pencil cognitive status test-The Clock Drawing Test-we combined a digital input device to capture time-stamped drawing coordinates with a machine learning analysis of drawing behavior to create DCTclock™, an automated analysis of nuances in cognitive performance beyond successful task completion. Development and validation was conducted on a dataset of 1,833 presumed cognitively unimpaired and clinically diagnosed cognitively impaired individuals with varied neurological conditions. We benchmarked DCTclock against existing clock scoring systems and the Mini-Mental Status Examination, a widely-used but lengthier cognitive test, and showed that DCTclock offered a significant improvement in the detection of early cognitive impairment and the ability to characterize individuals along the Alzheimer's disease trajectory. This offers an example of a robust framework for creating digital biomarkers that can be used clinically and in research for assessing neurological function.
Publication Date: 2021-11-02
Journal: Frontiers in digital health


however(87)

BMAL1 induces colorectal cancer metastasis by stimulating exosome secretion.
To adapt to daily changes in the external environment, organisms have developed circadian rhythm systems with a period of approximately 24 h. Many studies have reported that both circadian rhythms and exosomes play important roles in the development and metastasis of tumors. However, whether circadian clock genes can affect the progression of tumors by regulating exosomes remains unclear. In this study, we isolated exosomes from the supernatant of human colorectal cancer (CRC) cells, including SW480, SW620, and HCT116 cells, by differential centrifugation and characterized exosomes by transmission electron microscopy, nanoparticle tracking analysis, and Western blot analysis. Then, we found that exosomes derived from SW480, SW620 and HCT116 cells could promote the migration of HCT116 and human umbilical vein endothelial cells. Exosomes derived from SW620 cells showed increased stimulating effects when we increased the expression of BMAL1, a core circadian protein. In contrast, exosomes derived from SW480 and HCT116 cells showed decreased stimulating effects when we knocked down the expression of BMAL1. Furthermore, we discovered that BMAL1 promotes the release of exosomes by HCT116 and SW620 cells. In addition, by luciferase assay, we confirmed that BMAL1 transcriptionally regulates the expression of Rab27a, a key molecule related to the secretion of exosomes. Our data reveal a new mechanism by which BMAL1 induces CRC metastasis by stimulating exosome secretion. This finding may help further clarify the role of circadian rhythm in the progression of CRC.
Publication Date: 2021-11-03
Journal: Molecular biology reports


neurons(85)

Mesencephalic Astrocyte-Derived Neurotrophic Factor Regulates Morphology of Pigment-Dispersing Factor-Positive Clock Neurons and Circadian Neuronal Plasticity in
Mesencephalic Astrocyte-derived Neurotrophic Factor (MANF) is one of a few neurotrophic factors described in
Publication Date: 2021-10-15
Journal: Frontiers in physiology


group(82)

Pneumatic retinopexy: an update.
Pneumatic retinopexy (PR) is a minimally invasive, non-incisional procedure for repairing uncomplicated rhegmatogenous retinal detachment. It consists of an intravitreal gas injection followed by the maintenance of a postoperative head position and the use of laser or cryopexy to seal the retinal breaks. It was initially indicated for a single or a group of retinal breaks no larger than 1 clock hour involving the superior 8 clock hours in phakic eyes with no proliferative vitreoretinopathy. We aim to perform a narrative review on pneumatic retinopexy since the last major review of 2008, based on a Medline search up to June 20 2021 using multiple search words including pneumatic retinopexy, pneumoretinopexy, retinal detachment, and pars plana vitrectomy. Indications for PR have been expanded and include pseudophakic eyes, eyes with mild PVR, and even breaks in the inferior fundus. Depending on the case selection, PR has a single-operation success rate ranging from 45 to 80%. Despite the lower single operation success rate, the functional outcomes of those eyes repaired successfully by primary PR exceed those of scleral buckling (SB) and pars plana vitrectomy (PPV). Best corrected visual acuity, metamorphopsia scores, mental health scores, and vision-related functioning scores were all better in PR-treated eyes compared to PPV-treated eyes. PR should be strongly considered for eligible patients with a primary uncomplicated rhegmatogenous retinal detachments.
Publication Date: 2021-10-13
Journal: Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie


cry1(71)

An observational study investigating the CRY1Δ11 variant associated with delayed sleep-wake patterns and circadian metabolic output.
We conducted an observational research study to collect information on sleep-wake patterns from participants with a confirmed status of the cryptochrome circadian clock 1 (CRY1) splicing variant, CRY1Δ11 c.1657 + 3A > C, and their controls, defined as wild-type (WT) family members. Altogether, 67 participants were enrolled and completed this study in Turkey, recruited from a list of families with at least one CRY1-confirmed member. We measured sleep-wake patterns and metabolic output, specifically time and frequency of bowel movements, for all participants by daily post-sleep diaries over 28 days. The sleep diary measured self-reported bed time, wake time, midpoint of sleep, and latency to persistent sleep (LPS), and accounted for naps and awakenings for religious purposes. Wake time and midpoint of sleep were significantly later in the CRY1Δ11 variant group versus WT, and LPS was significantly greater in participants in the CRY1Δ11 variant group. The mean bed time on all nights of sleep was later in participants with a CRY1Δ11 variant versus WT. Additionally, participants with a CRY1Δ11 variant had significantly affected metabolic outputs, measured by later bowel movements than WT participants. These results demonstrate that, on average, individuals with the studied splicing variant experience pronounced delays in sleep period and circadian-related metabolic processes.
Publication Date: 2021-10-13
Journal: Scientific reports


respectively(41)

Quantitative digital clock drawing test as a sensitive tool to detect subtle cognitive impairments in early stage Parkinson's disease.
The prevalence of subtle cognitive decline in the early stages of Parkinson's Disease (PD) is common and is thought to be even greater in patients carrying genetic mutations in the GBA gene. Current cognitive tests often lack sensitivity to identify subtle impairments. Technological advancements may offer greater precision. We explored the utility of a digitized cognitive clock-drawing test to assess cognition in patients with PD compared to healthy controls (HC) and its sensitivity compared to that of standardized neuropsychological tests. Further, we investigated the existence of a cognitive profile based on genotype. The study included 75 early stage PD patients (24 with GBA-PD, 23 LRRK2-PD, 28 idiopathic PD cases) and 59 HC. Participants underwent a cognitive assessment which included the Montreal Cognitive Assessment (MoCA), the Color Trails Test (CTT) and a digital clock drawing test (DCTclock). Patients with PD presented lower scores than HC on all cognitive tests. The DCTclock best discriminated PD from HC (AUC: 0.807) compared to the MoCA (0.590) and CTT (0.636 and 0.717 for CTT-1 and CTT-2 respectively). In-depth quantitative analysis of the DCTclock revealed that LRRK2-PD showed better performance than other PD sub-groups. The use of quantitative digital cognitive assessment showed greater sensitivity in identifying subtle cognitive decline than the current standardized tests. Differences in cognitive profiles were observed based on genotype. The identification of early cognitive decline may improve the clinical management of PD patients and be useful for cognitive related clinical trials.
Publication Date: 2021-08-21
Journal: Parkinsonism & related disorders


per3(35)

Variants in clock genes could be associated with lower risk of type 2 diabetes in an elderly Greek population.
Recent evidence has linked circadian rhythm dysregulation to an increased risk of metabolic disorders. This study explores a potential association between variation in genes regulating the endogenous circadian timing system (clock genes) and the risk of type 2 diabetes (T2D) in a sample of Greek elderly people. Variants within and upstream or downstream of PPARA, PPARD, CLOCK/TMEM165, PER1, PER2 and PER3 genes were genotyped in 716 individuals with T2D (A) and 569 normoglycemic controls (B), and allele frequencies were compared between the groups in a case control study design. Samples were genotyped on Illumina Human PsychArray. Permutation test analysis was implemented to determine statistical significance. To avoid the possibility of subjects with prediabetes being included in the control group, people with HbA1c <5.7% and fasting glucose <100 mg/dl comprised group C (n = 393), for whom a separate analysis was performed (secondary analysis). A protective role against T2D was identified for 14 variants in the PPARA gene. The rs7291444, rs36125344, rs6008384 in PKDREJ, located upstream of PPARA, and rs2859389 in UTS2, located upstream of PER3, demonstrated a protective role against T2D in both analyses. In contrast, rs6744132, located between HES6 and PER2, was positively correlated with T2D risk. Only in the secondary analysis, rs2278637 in VAMP2, located downstream of PER1, and rs11943456 in CLOCK/TMEM165 were found to confer protection against T2D. In a recessive model analysis of all groups, PPARD variants exhibited a protective role against disease. Our findings suggest a possible implication of clock genes in T2D susceptibility. Further studies are needed to clarify the mechanisms that connect circadian rhythm dysfunction and T2D pathogenesis.
Publication Date: 2021-10-23
Journal: Maturitas