Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of MBD3 and the cell cycle in the regulation of the epigenome

DNA methylation patterns were thought to be stable and unchanging throughout life. However more evidence has emerged suggesting that the DNA methylation pattern is dynamic, subject to changes in response to physiological and environmental cues. Thus, it is crucial to understand when these changes occur and how the DNA methylation pattern can be manipulated. This thesis focuses on alterations in the DNA methylation pattern during the cell cycle both globally and at a specific promoter, as well as how the methylated DNA binding domain protein MBD3 is involved in regulating these changes. During the cell cycle, the levels of DNA methylation are highest during S phase, and drop after DNA replication during G0/G1. These changes in DNA methylation are not occurring at repetitive sequences, but rather at specific sequences throughout the genome, as determined using a CpG island microarray. Conversely, the DNA methylation pattern of the ribosomal RNA (rRNA) promoter follows an opposite pattern, with decreased levels of DNA methylation at G1/S and S phase, with the levels increasing as the cell progresses through the cell cycle. These changes at the rRNA promoter correlate with other epigenetic changes, including histone acetylation and transcription factor binding, indicating a coordinated epigenetic change regulated with the different stages of the cell cycle. We further determined how the DNA methylation pattern of the rRNA promoter is regulated, and found a critical role for the methylated DNA binding domain protein MBD3. MBD3 was found to bind to unmethylated rRNA promoters, together with the transcription factor Upstream Binding Factor (UBF). Manipulating the levels of MBD3 expression resulted in a change in the levels of DNA meth%%%%Le patron de methylation de l'ADN est connu pour etre stable et fixes durant toute la vie. Cependant, plusieurs evidences suggerent que le patron de methylation de l'ADN soit dynamique, sujet aux changements en reponse a des stimuli physiologiques et environnementaux. Ainsi, il est crucial de comprendre quand ces changements se produisent et comment le patron de methylation d'ADN peut etre manipule. Cette these se concentre sur les changements dans le patron de methylation de l'ADN pendant le cycle cellulaire, a l'echelle globale et au niveau de promoteurs specifiques, et egalement sur le mecanisme par lequel la proteine MBD3, qui contient un domaine de liaison a l'ADN methyle, module ces changements. Pendant le cycle cellulaire, les niveaux de methylation de l'ADN sont plus eleves pendant la phase de S, et chute par la suite apres la replication de l'ADN lors de la phase G0/G1. Ces changements de methylation de l'ADN ne se…
The Natural History of Untreated Primary Hypogammaglobulinemia in Adults: Implications for the Diagnosis and Treatment of Common Variable Immunodeficiency Disorders (CVID)

Background: Adults with primary hypogammaglobulinemia are frequently encountered by clinicians. Where IgG levels are markedly decreased, most patients are treated with subcutaneous or intravenous immunoglobulin (SCIG/IVIG), because of the presumed risk of severe infections. The natural history of untreated severe asymptomatic hypogammaglobulinemia is thus unknown. Similarly, there are no long-term prospective studies examining the natural history of patients with moderate reductions in IgG. Methods: In 2006, we began a prospective cohort study of patients with symptomatic and asymptomatic reductions in IgG who were not immediately commenced on SCIG/IVIG. Over the course of 12 years, 120 patients were enrolled in the NZ hypogammaglobulinemia study (NZHS) including 59 who were asymptomatic. Results: Five patients with profound primary hypogammaglobulinemia (IgG < 3 g/l), who were not on regular SCIG/IVIG have remained well for a mean duration of 139 months. This study has also shown most asymptomatic patients with moderate hypogammaglobulinemia (IgG 3.0–6.9 g/l) have been in good health for a mean observation period of 96 months. We have only identified one asymptomatic patient with moderate hypogammaglobulinemia who experienced progressive decline in IgG levels to <3 g/l and was accepted for IVIG replacement. Prospective monitoring has shown that none have suffered catastrophic infections or any of the severe autoimmune or inflammatory sequelae associated with Common Variable Immunodeficiency Disorders (CVID). Unexpectedly, 18.1% of asymptomatic and 41.6% of symptomatic hypogammaglobulinemic patients spontaneously increased their IgG into the normal range (≥7.0 g/l) on at least one occasion, which we have termed transient hypogammaglobulinemia of adulthood (THA). In this study, vaccine challenge responses have correlated poorly with symptomatic state and long-term prognosis including subsequent SCIG/IVIG treatment. Conclusions: In spite of our favorable experience, we recommend patients with severe asymptomatic hypogammaglobulinemia are treated with SCIG/IVIG because of the potential risk of severe infections. Patients with moderate asymptomatic hypogammaglobulinemia have a good prognosis. Patients with symptomatic hypogammaglobulinemia are a heterogeneous group where some progress to SCIG/IVIG replacement, while many others spontaneously recover. This study has implications for the diagnosis and treatment of CVID.
Evaluation Lines and Their Half Diallel Crosses for Phenotypic Characteristics by Using Cluster Analysis of Maize(Zea mays L.)

Seven pure lines of maize (Zea mays L.) (Agr-183, ZM47W, CML494, IK58, ZP505, ZP670, ZP197)were used in a half Diallel crosses program according to the second Griffing method (1956),in autumn 2014 season ,at the farm field in Tuz /Salahaddin , planted 21 single crosses and parents as well as the check variety (Drachma) on 20 July 2015 by using Randomized Completely Block Design with three replications to study the Genetic distance between parents and crosses for the flowing characters: ( days to 50% male of male and female flowering, plant height(cm), main ear height(cm), leaves no. upper main ear , leaf area surrounding main ear(cm2), no. ears per plant, ear length(cm), ear diameter(cm), no. of rows per ear, no. of grains per row, no. of grains per ear, 300 grain weight(gm), plant yield(gm), and protein and oil content(%). The genotypes ( parents and first filial hybrids and commercial cross )showed significant differences at 1% level probability for all studied traits except no. ears per plant which was significant at 5%level in the parents. Parents (CML494 and ZP505 and ZP670) were superior in four characters. The hybrid (ZM47W × CML494) had been marked superiority in five characters(plant height, main ear height, number of ears per plant, number of leaves over main ear , area of leaf surrounding main ear, ear length, 300 grain weight) compare with the other crosses also (Agr-183 × ZP505) hybrid was remarkably superior in the number of ears per plant, ear length, number of grains per row, plant yield . The crosses (1 × 4) and (1 × 5) and (2 × 4) and (5 × 6) Showed significant hybrid vigor for the most traits studied towards desired direction comparison with the best parents and check variety as interpretation of large genetic distance of their parents that laid in different major and minor groups. The highest genetic distance(22661.37) was between 2and4 parents which would be useful for exploiting hybrid vigor.
Faster response to water level increase facilitates Salix cavaleriei survival in Lake Erhai

Abstract The roles that adventitious roots play in flooding tolerance have been well-studied in willows, while which of the maximum height of adventitious roots and the abundance of adventitious roots in willows is more important for their flooding tolerance is not well known. In this study, we analyzed the effects of adventitious roots on the flooding tolerance of Salix cavaleriei by comparing the maximum height of adventitious roots and the abundance of adventitious roots in dead and live willows along a flooding gradient from 0 to 180 cm in Lake Erhai, China. The results showed that willow mortality increased drastically when the water depth suffered by willows exceeded 100 cm. Live willows developed more adventitious roots and produced them higher on the trees compared with dead willows, however, the pest infestation percentage of the dead willows was larger. Additionally, both the maximum height and the abundance of adventitious roots in live willows were significantly correlated with water depth, whereas in dead willows, these variables were not significantly correlated or only weakly correlated with water depth. The results indicate that producing adventitious roots higher on the trees may be more important than developing abundant adventitious roots lower on the trees when S. cavaleriei is subjected to high flooding levels. Our data highlight that a faster adventitious root response promotes this species’ survival under flood stress, although pest infestation accounts for a small percentage of willow mortality. Accordingly, we should choose those willows that can develop more abundant adventitious roots and higher on the stems to plant in regions with abrupt water-level fluctuations.
The Appropriate Marker for Astrocytes: Comparing the Distribution and Expression of Three Astrocytic Markers in Different Mouse Cerebral Regions

Astrocytes possess different morphological characteristics depending on the cerebral region in which they are found. However, none of the current astrocytic markers can label all subpopulations successfully. Thus, identifying the appropriate marker for a specific scientific investigation is critical. Here, we compared the distribution and protein expression of three astrocyte markers: NDRG2, GFAP, and S100β, in the cortex, hippocampus, and thalamus. NDRG2- and S100β-positive astrocytes were distributed more uniformly than GFAP-positive astrocytes throughout the whole cerebrum. NDRG2 and S100β immunoreactivities were the strongest in the dorsal cortex and thalamus, while GFAP immunoreactivity was the strongest in the hippocampus. Moreover, protein expression levels of NDRG2, GFAP, and S100β in adult mice were the highest in the cortex, hippocampus, and thalamus, respectively. We also detected astrocyte morphology and found that, in the corpus callosum and cerebral peduncle, GFAP-positive astrocytes were found with more numerous and longer processes than NDRG2- and S100β-positive astrocytes. These results demonstrate that NDRG2 and S100β are more suitably used to visualize the overall distribution and changes in the number of astrocytes, as well as label astrocytes in the cortex and thalamus. GFAP, however, is more appropriately used to label astrocytes in the corpus callosum, cerebral peduncle, and the hippocampus. These results help to guide researchers in the choice of appropriate astrocyte marker and suggest differences in immunological qualities of astrocytes based on the tissue in which they are found.
Targeting pathogenic Lafora bodies in Lafora disease using an antibody-enzyme fusion

Lafora disease (LD) is a fatal childhood epilepsy and a non-classical glycogen storage disorder with no effective therapy or cure. LD is caused by recessive mutations in the EPM2A or EPM2B genes that encode the glycogen phosphatase laforin and an E3 ubiquitin ligase malin, respectively. A hallmark of LD is the intracellular accumulation of abnormal and insoluble α-linked polysaccharide deposits known as Lafora bodies (LBs) in several tissues, including most regions of the brain. In mouse models of LD, genetic reduction of glycogen synthesis eliminates LB formation and rescues the neurological phenotype. Since multiple groups have confirmed that neurodegeneration and epilepsy result from LB accumulation, a major focus in the field has shifted toward the development of therapies that reduce glycogen synthesis or target LBs for degradation with the goal of treating LD. Herein, we identify the optimal enzymes for degrading LBs, and we develop a novel therapeutic agent by fusing human pancreatic α-amylase to a cellpenetrating antibody fragment. This antibody-enzyme fusion (VAL-0417) degrades LBs in vitro, shows robust cellular uptake, and significantly reduces the LB load in vivo in Epm2a-/- mice. VAL-0417 is a promising therapeutic for the treatment of LD and a putative precision therapy for an intractable epilepsy. Antibody-enzyme fusions represent a new class of antibody-based drugs that could be utilized to treat glycogen storage disorders and other diseases. One Sentence Summary An antibody-enzyme fusion delivering an amylase degrades the toxic polyglucosan bodies that cause Lafora disease, a fatal childhood epilepsy.
A generalized linear model for decomposing genetic, parent-of-origin, and maternal effects on allele-specific gene expression

Joint quantification of genetic and epigenetic effects on gene expression is important for understanding the establishment of complex gene regulation systems in living organisms. In particular, genomic imprinting and maternal effects play important roles in the developmental process of mammals and flowering plants. However, the influence of these effects on gene expression are difficult to quantify because they act simultaneously with cis-regulatory mutations. Here we propose a simple method to decompose cis-regulatory mutational (i.e., allelic genotype, AG), genomic imprinting (i.e., parent-of-origin, PO), and maternal (i.e., maternal genotype, MG) effects on allele-specific gene expression using RNA-seq data obtained from reciprocal crosses. We evaluated the methodologic efficiency using a simulated dataset and applied the method to whole-body Drosophila and mouse trophoblast stem cell (TSC) and liver RNA-seq data. Consistent with previous studies, we found no evidence of PO and MG effects in adult Drosophila samples. In contrast, we identified hundreds of mouse genes with significant PO and MG effects. Interestingly, the PO effect was mostly conserved between mouse TSCs and livers, whereas the MG effect was mostly observed in livers. Further method application studies will clarify how these three effects influence gene expression levels in different tissues and developmental stages, and provide novel insight into the evolution of gene expression regulation.
Biological evaluation of a springbok-farming enterprise

A practical game-cropping enterprise on a Merino wool production farm in the Karoo was evaluated by collecting samples of the shot springbok and analysing the data in terms of growth, carcass composition, age structure and reproduction. Veld utilization was investigated by rumen content analysis and the data are summarized in terms of species eaten, importance in the diet, and selection. The springbok is a productive animal and seems to complement the Merino sheep in its veld utilization. There seems to be scope for increasing the efficiency of production and for this more research on reproduction and population biology are needed.
Targeting the Autonomic Nervous System Balance in Patients with Chronic Low Back Pain Using Transcranial Alternating Current Stimulation: A Randomized, Crossover, Double-Blind, Placebo-Controlled Pilot Study

Background Chronic low back pain (CLBP) is characterized by an alteration in pain processing by the central nervous system that may affect autonomic nervous system (ANS) balance. Heart rate variability (HRV) reflects the balance of parasympathetic and sympathetic ANS activation. In particular, respiratory sinus arrhythmia (RSA) solely reflects parasympathetic input and is reduced in CLBP patients. Yet, it remains unknown if non-invasive brain stimulation can alter ANS balance in CLBP patients. Objective To evaluate if non-invasive brain stimulation modulates the ANS, we analyzed HRV metrics collected in a previously published study of transcranial alternating current stimulation (tACS) for the modulation of CLBP through enhancing alpha oscillations. We hypothesized that tACS would increase RSA. Methods A randomized, crossover, double-blind, sham-controlled pilot study was conducted to investigate the effects of 10Hz-tACS on metrics of ANS balance calculated from electrocardiogram (ECG). ECG data were collected for 2 minutes before and after 40 minutes of 10Hz-tACS or sham stimulation. Results There were no significant changes in RSA or other frequency-domain HRV components from 10Hz-tACS. However, exploratory time-domain HRV analysis revealed a significant increase in the standard deviation of normal RR intervals (SDNN) for 10Hz-tACS relative to sham. Conclusion(s) Although tACS did not significantly increase RSA, we found in an exploratory analysis that tACS modulated an integrated HRV measure of both ANS branches. These findings support the further study of how the ANS and alpha oscillations interact and are modulated by tACS.
Membrane curvature and the Tol-Pal complex determine polar localization of the chemoreceptor Tar in E. coli

Chemoreceptors are localized at the cell poles of Escherichia coli and other rod-shaped bacteria. Over the years different mechanisms have been put forward to explain this polar localization; from stochastic clustering, membrane curvature driven localization, interactions with the Tol-Pal complex, to nucleoid exclusion. To evaluate these mechanisms, we monitored the cellular localization of the aspartate chemoreceptor Tar in different deletion mutants. We did not find any indication for either stochastic cluster formation or nucleoid exclusion. However, the presence of a functional Tol-Pal complex appeared to be essential to retain Tar at cell poles. This finding also implies that the curvature of cell poles does not attract chemoreceptor complexes. Interestingly, Tar still accumulated at midcell in tol and in pal deletion mutants. In these mutants, the protein appears to gather at the base of division septa, a region characterised by strong membrane curvature. Chemoreceptors, like Tar, form trimer-of-dimers that bend the cell membrane due to a rigid tripod structure with an estimated curvature of approximately 37 nm. This curvature approaches the curvature of the cell membrane generated during cell division, and localization of chemoreceptor tripods at curved membrane areas is therefore energetically favourable as it lowers membrane tension. Indeed, when we introduced mutations in Tar that abolish the rigid tripod structure, the protein was no longer able to accumulate at midcell or cell poles. These findings favour a model where chemoreceptor localization in E. coli is driven by strong membrane curvature and association with the Tol-Pal complex. Importance Bacteria have exquisite mechanisms to sense and to adapt to the environment they live in. One such mechanism involves the chemotaxis signal transduction pathway, in which chemoreceptors specifically bind certain attracting or repelling molecules and transduce the signals to the cell. In different rod-shaped bacteria, these chemoreceptors localize specifically to cell poles. Here, we examined the polar localization of the aspartate chemoreceptor Tar in E. coli, and found that membrane curvature at cell division sites and interaction with the Tal-pol protein complex, localize Tar at cell division sites, the future cell poles. This study shows how membrane curvature can guide localization of proteins in a cell.
Conservatism of thermal preferences between parthenogenetic Aspidoscelis cozumela complex (Squamata: Teiidae) and their parental species

Correspondence: Fausto R. Méndez-de la Cruz (faustor@ibiologia.unam.mx) Closely-related species can exhibit similar thermal requirements despite inhabiting different environments. Hybrid species between them can exhibit a diversity of thermal requirements, or can be similar to parental species. In this study, we investigated thermal preference and efficiency in parthenogenetic Aspidoscelis cozumela complex lizards (A. cozumela, A. rodecki, A. maslini) and their parental species (A. angusticeps and A. deppii), to determine whether thermal preferences are conservative. We found that thermal preferences are similar among species and determined by phylogenetic relationships. Aspidoscelis deppii (paternal species), A. cozumela and A. maslini showed similar thermal preferences, whereas A. rodecki was similar to the maternal species (A. angusticeps). These results suggest that thermal preferences of parthenogenetic lineages match with one of the parental species and are not restricted to one gender. These findings support the “frozen niche variation” hypothesis.
Differential Effects of Prostaglandin E2 Production and Signaling through the Prostaglandin EP3 Receptor on Human Beta-cell Compensation

Objective Signaling through Prostaglandin E3 Receptor (EP3), a G protein-coupled receptor for E series prostaglandins such as prostaglandin E2 (PGE2), has been linked to the beta-cell dysfunction and loss of beta-cell mass in type 2 diabetes (T2D). In the beta-cell, EP3 is specifically coupled to the unique cAMP-inhibitory G protein, Gz. Divergent effects of EP3 agonists and antagonists or Gαz loss on beta-cell function, replication, and survival depending on whether islets are isolated from mice or humans in the lean and healthy, type 1 diabetic, or T2D state suggest a divergence in biological effects downstream of EP3/Gαz dependent on the physiological milieu in which the islets reside. Methods We determined the expression of a number of genes in the EP3/Gαz signaling pathway; PGE2 production pathway; and the beta-cell metabolic, proliferative, and survival responses to insulin resistance and its corresponding metabolic and inflammatory derangements in a panel of 80 islet preparations from non-diabetic human organ donors spanning a BMI range of approximately 20-45. In a subset of islet preparations, we also performed glucose-stimulated insulin secretion assays with and without the addition of an EP3 agonist, L798,106, and a glucagon-like peptide 1 receptor agonist, exendin-4, allowing us to compare the gene expression profile of each islet preparation with its (1) total islet insulin content (2), functional responses to glucose and incretin hormones, and (3) intrinsic influence of endogenous EP3 signaling in regulating these functional responses. We also transduced two independent islet preparations from three human organ donors with adenoviruses encoding human Gαz or a GFP control in order to determine the impact of Gαz hyperactivity (a mimic of the T2D state) on human islet insulin content and functional response to glucose. Results In contrast to results from islets isolated from T2D mice and human organ donors, where PGE2-mediated EP3 signaling actively contributes to beta-cell dysfunction, PGE2 production and EP3 expression appeared positively associated with various measurements of functional beta-cell compensation. While Gαz mRNA expression was negatively associated with islet insulin content, that of each of the Gαz-sensitive adenylate cyclase (AC) isoforms were positively associated with BMI and cyclin A1 mRNA expression, suggesting increased expression of AC1, AC5, and AC6 is a compensatory mechanism to augment beta-cell mass. Human islets over-expressing Gαz via adenoviral transduction had reduced islet insulin content and secretion of insulin in response to stimulatory glucose as a percent of content, consistent with the effects of hyperactivation of Gαz by PGE2/EP3 signaling observed in islets exposed to the T2D physiological milieu. Conclusions Our work sheds light on critical mechanisms in the human beta-cell compensatory response, before the progression to frank T2D.