Changes In DNA Content Research Articles

In vitro induction of tetraploids and their phenotypic and transcriptome analysis in Glehnia littoralis

BackgroundGlehnia littoralis is a medicinal and edible plant species having commercial value and has several hundred years of cultivation history. Polyploid breeding is one of the most important and fastest ways to generate novel varieties. To obtain tetraploids of G. littoralis in vitro, colchicine treatment was given to the seeds and then were screened based on morphology, flow cytometry, and root tip pressing assays. Furthermore, transcriptome analysis was performed to identity the differentially expressed genes associated with phenotypic changes in tetraploid G. littoralis.ResultsThe results showed that 0.05% (w/v) colchicine treatment for 48 h was effective in inducing tetraploids in G. littoralis. The tetraploid G. littoralis (2n = 4x = 44) was superior in leaf area, leaf thickness, petiole diameter, SPAD value (Chl SPAD), stomatal size, epidermal tissues thickness, palisade tissues thickness, and spongy tissues thickness to the diploid ones, while the stomatal density of tetraploids was significantly lower. Transcriptome sequencing revealed, a total of 1336 differentially expressed genes (DEGs) between tetraploids and diploids. Chromosome doubling may lead to DNA content change and gene dosage effect, which directly affects changes in quantitative traits, with changes such as increased chlorophyll content, larger stomata and thicker tissue of leaves. Several up-regulated DEGs were found related to growth and development in tetraploid G. littoralis such as CKI, PPDK, hisD and MDP1. KEGG pathway enrichment analyses showed that most of DEGs were enriched in metabolic pathways.ConclusionsThis is the first report of the successful induction of tetraploids in G. littoralis. The information presented in this study facilitate breeding programs and molecular breeding of G. littoralis varieties.

Foraminifera as a model of eukaryotic genome dynamism.

In contrast to the canonical view that genomes cycle only between haploid and diploid states, many eukaryotes have dynamic genomes that change content throughout an individual's life cycle. However, the few detailed studies of microeukaryotic life cycles render our understanding of eukaryotic genome dynamism incomplete. Foraminifera (Rhizaria) are an ecologically important, yet understudied, clade of microbial eukaryotes with complex life cycles that include changes in ploidy and genome organization. Here, we apply fluorescence microscopy and image analysis techniques to over 2,800 nuclei in 110 cells to characterize the life cycle of Allogromia laticollaris strain Cold Spring Harbor (CSH), one of few cultivable foraminifera species. We show that haploidy and diploidy are brief moments in the A. laticollaris life cycle and that A. laticollaris nuclei endoreplicate up to 12,000 times the haploid genome size. We find that A. laticollaris reorganizes a highly endoreplicated nucleus into thousands of haploid genomes through a non-canonical mechanism called Zerfall, in which the nuclear envelope degrades and extrudes chromatin into the cytoplasm. Based on these findings, along with changes in nuclear architecture across the life cycle, we believe that A. laticollaris uses spatio-temporal mechanisms to delineate germline and somatic DNA within a single nucleus. The analyses here extend our understanding of the genome dynamics across the eukaryotic tree of life.IMPORTANCEIn traditional depictions of eukaryotes (i.e., cells with nuclei), life cycles alternate only between haploid and diploid phases, overlooking studies of diverse microeukaryotic lineages (e.g., amoebae, ciliates, and flagellates) that show dramatic variation in DNA content throughout their life cycles. Endoreplication of genomes enables cells to grow to large sizes and perhaps to also respond to changes in their environments. Few microeukaryotic life cycles have been studied in detail, which limits our understanding of how eukaryotes regulate and transmit their DNA across generations. Here, we use microscopy to study the life cycle of Allogromia laticollaris strain CSH, an early-diverging lineage within the Foraminifera (an ancient clade of predominantly marine amoebae). We show that DNA content changes significantly throughout their life cycle and further describe an unusual process called Zerfall, by which this species reorganizes a large nucleus with up to 12,000 genome copies into hundreds of small gametic nuclei, each with a single haploid genome. Our results are consistent with the idea that all eukaryotes demarcate germline DNA to pass on to offspring amidst more flexible somatic DNA and extend the known diversity of eukaryotic life cycles.

Surface-enhanced Raman spectroscopy for the study of interaction of an antibacterial agent ([bis(1,3-dipentyl-1H-imidazol-2(3H)-ylidene)silver(i)]bromide) with Bacillus subtilis bacterial biofilms.

Bacterial resistance towards antibiotics is a significant challenge for public health, and surface-enhanced Raman spectroscopy (SERS) has great potential to be a promising technique to provide detailed information about the effect of antibiotics against biofilms. SERS is employed to check the antibacterial potential of a lab synthesized drug ([bis(1,3-dipentyl-1H-imidazol-2(3H)-ylidene)silver(i)] bromide) against Bacillus subtilis and to analyze various SERS spectral features of unexposed and exposed Bacillus strains by observing biochemical changes in DNA, protein, lipid and carbohydrate contents induced by the lab synthesized imidazole derivative. Further, PCA and PLS-DA are employed to differentiate the SERS features. PCA was employed to differentiate the biochemical contents of unexposed and exposed Bacillus strains in the form of clusters of their representative SERS spectra and is also helpful in the pairwise comparison of two spectral data sets. PLS-DA provides authentic information to discriminate different unexposed and exposed Bacillus strains with 91% specificity, 93% sensitivity and 97% accuracy. SERS can be employed to characterize the complex and heterogeneous system of biofilms and to check the changes in spectral features of Bacillus strains by exposure to the lab synthesized imidazole derivative.

Centromere-proximal suppression of meiotic crossovers in Drosophila is robust to changes in centromere number, repetitive DNA content, and centromere-clustering.

Accurate segregation of homologous chromosomes during meiosis depends on both the presence and the regulated placement of crossovers (COs). The centromere effect, or CO exclusion in pericentromeric regions of the chromosome, is a meiotic CO patterning phenomenon that helps prevent nondisjunction, thereby protecting against chromosomal disorders and other meiotic defects. Despite being identified nearly a century ago, the mechanisms behind this fundamental cellular process remain unknown, with most studies of the Drosophila centromere effect focusing on local influences of the centromere and pericentric heterochromatin. In this study, we sought to investigate whether dosage changes in centromere number and repetitive DNA content affect the strength of the centromere effect, using phenotypic recombination mapping. Additionally, we studied the effects of repetitive DNA function on centromere effect strength using satellite DNA-binding protein mutants displaying defective centromere-clustering in meiotic nuclei. Despite what previous studies suggest, our results show that the Drosophila centromere effect is robust to changes in centromere number, repetitive DNA content, as well as repetitive DNA function. Our study suggests that the centromere effect is unlikely to be spatially controlled, providing novel insight into the mechanisms behind the Drosophila centromere effect.

Cardiomyocyte nuclear remodeling after mechanical unloading.

Cardiomyocytes increase DNA content in response to stress in humans. DNA content is reported to decrease in association with increased markers of proliferation in cardiomyocytes following left ventricular assist device (LVAD) unloading. However, cardiac recovery resulting in LVAD explant is rare. Thus, we sought to test the hypothesis that changes in DNA content with mechanical unloading occurs independent of cardiomyocyte proliferation by quantifying cardiomyocyte nuclear number, cell size, DNA content, and the frequency of cell-cycling markers using a novel imaging flow cytometry methodology comparing human subjects undergoing LVAD implantation or primary transplantation. We found that cardiomyocyte size was 15% smaller in unloaded versus loaded samples without differences in the percentage of mono-, bi-, or multinuclear cells. DNA content per nucleus was significantly decreased in unloaded hearts versus loaded controls. Cell-cycle markers, Ki67 and phospho-histon3 (H3P), were not increased in unloaded samples. In conclusion, unloading of failing hearts is associated with decreased DNA content of nuclei independent of nucleation state within the cell. As these changes were associated with a trend to decreased cell size but not increased cell-cycle markers, they may represent a regression of hypertrophic nuclear remodeling and not proliferation.NEW & NOTEWORTHY Our data suggest that increases in DNA content that occur with cardiomyocyte hypertrophy in heart failure may reverse with mechanical unloading.

Effective micropropagation of kale (Brassica oleracea convar. Acephala var. sabellica): one of the most important representatives of cruciferous crops

Kale (Brassica oleracea convar. acephala var. sabellica) is one of the oldest Brassica vegetable varieties with the highest nutritional value and stress resistance. This work aimed to establish an efficient kale micropropagation protocol. Shoot tips were used as explants during axillary shoots multiplication. The most effective cytokinin (6 and 10 shoots per explant after the 1st and 2nd passage, respectively) was 2.5 mg dm−3 6-benzylaminopurine. Rooting was the most effective on MS medium supplemented with 1.0 mg dm−3 indole-3-acetic acid (IAA; 95% rooted shoots). The highest survival rate during acclimatization to ex vitro conditions occurred when plantlets were planted in a soil and perlite mixture. No changes in DNA content were detected using flow cytometry. This paper additionally emphasizes problems associated with the abnormal development of some multiplied Brassicaceae shoots. Nevertheless, the results confirmed that kale micropropagation was successful without any phenotypic aberration.

Murine Norovirus Interaction with Enterobacter cloacae Leads to Changes in Membrane Stability and Packaging of Lipid and Metabolite Vesicle Content.

Outer membrane vesicles (OMVs) are a primary means of communication for Gram-negative bacteria. The specific role of vesicle components in cellular communication and how components are packaged are still under investigation, but a correlation exists between OMV biogenesis and content. The two primary mechanisms of OMV biogenesis are membrane blebbing and explosive cell lysis, and vesicle content is based on the biogenesis mechanism. Hypervesiculation, which can be induced by stress conditions, also influences OMV content. Norovirus interaction with Enterobacter cloacae induces stress responses leading to increased OMV production and changes in DNA content, protein content, and vesicle size. The presence of genomic DNA and cytoplasmic proteins in these OMVs suggests some of the vesicles are formed by explosive cell lysis, so reduction or loss of these components indicates a shift away from this mechanism of biogenesis. Based on this, further investigation into bacterial stability and OMV content was conducted. Results showed that norovirus induced a dramatic shift in OMV lipid content. Specifically, the increased accumulation of phospholipids is associated with increased blebbing, thereby supporting previous observations that noroviruses shift the mechanism of OMV biogenesis. Slight differences in OMV metabolite content were also observed. While norovirus induced changes in OMV content, it did not change the lipid content of the bacterial outer membrane or the metabolite content of the bacterial cell. Overall, these results indicate that norovirus induces significant changes to OMV lipid architecture and cargo, which may be linked to a change in the mechanism of vesicle biogenesis. IMPORTANCE Extracellular vesicles from commensal bacteria are recognized for their importance in modulating host immune responses, and vesicle content is related to their impact on the host. Therefore, understanding how vesicles are formed and how their content shifts in response to stress conditions is necessary for elucidating their downstream functions. Our recent work has demonstrated that interactions between noroviruses and Enterobacter cloacae induce bacterial stress responses leading to hypervesiculation. In this article, we characterize and compare the lipid and metabolomic cargo of E. cloacae vesicles generated in the presence and absence of norovirus and show that viral interactions induce significant changes in vesicle content. Furthermore, we probe how these changes and changes to the bacterial cell may be indicative of a shift in the mechanism of vesicle biogenesis. Importantly, we find that noroviruses induce significant changes in vesicle lipid architecture and cargo that may be responsible for the immunogenic activity of these vesicles.

Various technique of cell culture and slide preparation for human chromosome

The cell culture and slide preparation method of human chromosome is the mechanism that is a corresponding change in DNA content. In this research we used various techniques of cell culture and slide preparation for human chromosome and examined for 2 days, 3 days and 4 days cell culture because these are average days for approximately the good results and the treatment will still be good also the result has minimum bias. The research objectives were to determine the appropriate length of cell culture needed for human chromosome with different lengths and to determine the appropriate method for staining the slide for human chromosome with different lengths. Based on the data analysis, the result of this research shows that the appropriate length of cell culture needed for human chromosome with different lengths is 2 days of incubation. Although there were no significant differences between 2,3 and 4 days length based on statistical analysis, still there is little difference between them and the best is 2 days rather than 3 and 4 days based on the graph analysis. The appropriate method for staining the slide for human chromosome with different lengths is hot plate rather than another technique

Analysis of Nuclear DNA Content and Karyotype of Phaseolus vulgaris L.

The common bean (Phaseolus vulgaris L.), whose annual production is 26 million tons worldwide, is one of the main sources of protein and is known as one of the most important food sources. In this study, the karyotype variations and the genome size of four common bean genotypes in Turkey were investigated to determine whether the geographic variables in these regions affected the genome size and the karyotype parameters. In addition, it is known that as that the cytological and chromosomal parameters change under the influence of the climatic conditions of each region, appropriate and stable cytological methods for each plant facilitate and enable the determination of the chromosomal structure and the identification of specific chromosomes in the genotypes of the relevant region. Correct and valuable information such as this enables breeders and researchers to determine the correct shape and actual size of chromosomes. The genome size of the genotypes was measured with a flow cytometer, and chromosome analyses were performed with the squash method. For each genotype, the karyotype parameters, such as the number of somatic chromosomes, the Mean Total Chromosome Length (MTCL), the Mean Centromere Index (MCI), and the Mean Arm Ratio (MAR), were measured. The results showed that the highest and the lowest amounts of DNA per nucleus (3.28 pg and 1.49 pg) were observed in the Bitlis and Elaziğ genotypes. In addition, all genotype chromosome numbers were counted to be 2n = 2x = 22. The Mean Total Chromosome Length varied from 15.65 µm in Elaziğ to 34.24 µm in the Bitlis genotype. The Mean Chromosome Length ranged between 1.42 µm and 3.11 µm in the Elaziğ and Bitlis genotypes. The Hakkari and Van genotypes consist of eleven metacentric chromosomes, while the Bitlis and Elaziğ genotypes consist of ten metacentric chromosomes and one sub-metacentric chromosome. However, the Mean Centromere Index and Arm Ratio differed considerably among the genotypes. The highest (46.88) and the lowest (43.18) values of the Mean Centromere Index were observed in the Hakkari and Elaziğ genotypes, respectively. On the other hand, the lowest (1.15) and the highest (1.36) values of the Mean Arm Ratio were obtained in the Bitlis and Elaziğ genotypes, respectively. Eventually, intraspecies variations in genome size and chromosomal parameters were observed, and it was determined that the changes in nuclear DNA content and different chromosomal parameters among the four Phaseolus genotypes from four different regions of Turkey indicate the effect of climate change in the regions on these parameters. Such information in these areas can be used as useful information for the improvement of this plant and breeding programs.

BODY WEIGHT, MUSCLE WIGHT, PROTEIN, DNA AND RNA CONTENTS IN BREAST MUSCLE (M. Pectoralis Major) OF SELECTED LOCAL MEAT CHICKEN FED ON A DIFFERENT LEVEL OF KIAPU (Pistia stratiotes L.) IN FERMENTED DIET

The study to evaluate changes in body weight, muscle weight, muscle protein content and total DNA and RNA on breast muscle of selectedlocal chicken due to different levels of fermented feed containing Kiapu (Pistia stratiotes L.) was conducted using a factorial randomized designfor 7 weeks. This study used 72 selected local chickens, which were separated into 2 groups (male and female) and fed on 3 types of feedtreatment, namely P0 (control treatment with 100% commercial feed), P1 (80% commercial feed + 20% fermented Kiapu feed), and P2 (70%commercial feed + 30% fermented Kiapu feed). Parameters were body weight, muscle weight, muscle protein content and total DNA and RNAon breast muscle of chicken. Total protein, DNA and RNA content were analysed by enzymatic reactions of prokaryotic cell and measured with aUV-Spectrophotometer according to the specified OD (optical density). The results showed that feeding Kiapu fermented 20-30% increased bodyweight and protein content of breast muscle of female chicken by change in DNA content. However, the feeding treatment had no changes inmuscle weight and RNA content of both in male and female chicken. On the other hand, substitution of 20-30% Kiapu fermented feed causednegative changes in DNA level of breast muscle. From this study, it was concluded that substitution of fermented feed containing 20-30% Kiapuassociated with the growth process of breast muscle protein is suitable for female but not suitable for male chicken.

Abstract P5-08-06: MDX-124, a novel annexin-A1 antibody, shows anti-tumor efficacy in several preclinical models of triple-negative breast cancer

Abstract Triple-negative breast cancer (TNBC) accounts for 10-15% of all breast cancer cases and is a particularly aggressive form of the disease, with poorer prognosis compared to other breast cancer subtypes. Advances in TNBC treatment have been made with the introduction of checkpoint inhibitors, PARP inhibitors and antibody drug conjugates. However, these therapies still have several limitations including low patient response rates, treatment resistance or relapse, and considerable side effects. Therefore, a significant unmet clinical need remains to develop novel targeted agents to treat TNBC. Annexin-A1 (ANXA1) is a phospholipid binding protein secreted in response to several physiological stimuli where it activates formyl peptide receptors (FPR1/2) triggering multiple oncogenic cell signaling pathways. Overexpression of ANXA1 by TNBC cells has been shown to influence several cancer-related processes including cell growth, cell cycle progression, angiogenesis, migration and invasion. In addition, ANXA1 has been shown to have immunomodulatory effects on T-cells, macrophages and dendritic cells. High ANXA1 expression in TNBC patients correlates with both poor overall survival and progression-free survival, indicating ANXA1 is a therapeutic target in TNBC. MDX-124 is a novel humanized antibody targeting ANXA1, and we have previously demonstrated its significant anti-proliferative activity. Here we present additional data showing the efficacy of MDX-124 in preclinical models of TNBC. Methods: The impact of MDX-124 on cell cycle progression was evaluated by measuring changes in DNA content using flow cytometry and analyzed with FlowJo™ software.The modulation of key oncogenic cell signalling pathways by MDX-124 was assessed using human phospho-kinase and XL Oncology Proteome Profiler™ antibody arrays. The effect of MDX-124 in combination therapy with chemotherapy was studied in-vitro using MTT cell proliferation assays, whilst synergy with anti-PD-1 therapy was evaluated using the EMT6 syngeneic mouse model of TNBC. Results: MDX-124 treatment dramatically decreased the proportion of HCC1806 TNBC cells in S-phase by 29.1% with a concomitant increase in G1 of 33.5% versus untreated cells. This occurred in a dose-dependent manner and is consistent with an MDX-124 mediated increase in cell cycle arrest.Treatment of HCC1806 TNBC cells with MDX-124 altered the expression of key oncogenic proteins and the phosphorylation of several kinases that regulate cell signaling pathways involved in proliferation, survival and migration. Notably, MDX-124 substantially reduced ERK and AKT phosphorylation by 84% and 72% respectively versus untreated control cells. In the HCC1806 TNBC cell line, proliferation was significantly reduced after 72 h treatment with MDX-124 and chemotherapy versus control.In the EMT6 syngeneic mouse model of TNBC, the murine analogue of MDX-124 (MDX-001) potentiated mean tumor growth inhibition of single agent anti-PD-1 treatment by 15%. Additionally, 30% of treated mice showed tumor regression in the MDX-001 combination therapy group versus 10% in the single agent anti-PD-1 group. This suggest that anti-ANXA1 antibody therapy acts synergistically with anti-PD-1 immunotherapy.Conclusion: MDX-124 binds to secreted and extracellular ANXA1 disrupting interactions with FPR1/2. This results in altered expression levels of several key cancer-related proteins preventing the activation of oncogenic signaling pathways that promote cancer progression. MDX-124 has demonstrated anti-cancer activity in several TNBC cell line and mouse models, as both a single agent and in combination with other drugs, including anti-PD-1 immunotherapy. Medannex plan to initiate a First-In-Human study in Q4 2021 to evaluate MDX-124 in solid malignancies, including TNBC. Citation Format: Fiona C Dempsey, Hussein Al-Ali, Scott J Crichton, Charlene Fabian, Chris Pepper, Christopher N Parris. MDX-124, a novel annexin-A1 antibody, shows anti-tumor efficacy in several preclinical models of triple-negative breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-08-06.

Morphological, molecular and phytochemical variations induced by colchicine and EMS chemical mutagens in Crocus sativus L.

Crocus sativus L., also known as saffron, is one of the most important medicinal and spice plants throughout the world. The plant is a rich source of apocarotenoids such as crocetin esters, picrocrocin, and safranal. The purpose of this study was to investigate the effect of colchicine and ethyl methanesulfonate (EMS) mutagens on possible inducing new variation in C. sativus. Accordingly, corms were exposed to EMS (0.1% and 0.2%) and colchicine (0.05% and 0.025%) for three incubation times. The lowest survival rate of corms was related to EMS treatments. The relative expression of ALDH, BGL, and CCD2 genes under 0.025% colchicine treatment for 12 h revealed a 2 fold increase compared with the control. The flow cytometric measurements (FCM) of the nuclear DNA content of the colchicine-treated plants did not reveal any significant changes in 2C DNA content. The results, manifest the potential of mutagens to create new variations in the plant.

Efficacy of MDX-124, a novel anti-annexin-A1 antibody, in preclinical models of pancreatic cancer.

590 Background: Pancreatic cancer is a highly fatal disease with poor survival and response to both chemotherapy and immunotherapy. Novel approaches to treat this disease are urgently required. Annexin-A1 (ANXA1) is secreted in response to several physiological stimuli where it activates formyl peptide receptors (FPR1/2) triggering multiple oncogenic processes. High ANXA1 expression in pancreatic cancer patients is associated with poor overall survival, and influences cancer progression, drug sensitivity, migration and invasion. MDX-124 is a novel humanized antibody targeting ANXA1 and we have previously presented data demonstrating its significant antiproliferative activity. Here we present further data showing the efficacy of MDX-124 in several preclinical models of pancreatic cancer. Methods: In-vitro models utilized MIA PaCa-2, PANC-1 or BxPC-3 human pancreatic cancer cell lines. Cell cycle progression was evaluated by measuring changes in DNA content via flow cytometry. Pancreatic cancer cell viability following incubation with MDX-124 (0-10 µM) and 5FU (IC50) was assessed via MTT assay. A transwell migration assay was used to evaluate the effect of MDX-124 (0-50 µM) on pancreatic cancer cell migration. In-vivo efficacy was evaluated using an orthotopic mouse model of metastatic pancreatic cancer (FC1242luc/zsGreen; KPC-derived cell line) with bioluminescent imaging used to quantify the incidence and burden of lung metastases. Results: When compared to untreated MIA PaCa-2 pancreatic cancer cells, MDX-124 treatment decreased the proportion of cells in S-phase by 29% and G2 phase by 9.1%, with a concomitant increase in G1 of 38.1%. This occurred in a dose-dependent manner and is consistent with an MDX-124 mediated increase in cell cycle arrest. MDX-124 significantly reduced the viability of MIA PaCa-2 and PANC-1 cell lines versus an IgG control in a dose-dependent manner. Additionally in these two cell lines, combination of MDX-124 with 5FU (IC50) had a significant synergistic impact reducing cancer cell viability by 99.8% and 91.2% respectively. Furthermore, MDX-124 significantly reduced the migratory ability of MIA PaCa-2 and BxPC-3 pancreatic cancer cells. In the orthotopic model of metastatic pancreatic cancer, the murine analog of MDX-124 (MDX-001), markedly reduced both the incidence and size of lung metastases. Conclusions: MDX-124 demonstrated significant anti-tumor efficacy in several preclinical models of pancreatic cancer as a single agent, with increased potency observed when used in combination with 5FU. Medannex will initiate a First-In-Human study in Q4 2021 to evaluate MDX-124 in solid malignancies, including pancreatic cancer.

Lack of variation in nuclear DNA content in avian muscle.

The avian pectoralis muscle demonstrates plasticity with regard to size, so that temperate birds facing winter conditions or birds enduring a migration bout tend to have significant increases in the size and mass of this tissue due to muscular hypertrophy. Myonuclear domain (MND), the volume of cytoplasm a myonuclei services, in the pectoralis muscle of birds seems to be altered during thermal stress or changing seasons. However, there is no information available regarding muscle DNA content or ploidy level within the avian pectoralis. Changes in muscle DNA content can be used in this tissue to aid in size and mass changes. Here, we hypothesized that long-distance migrants or temperate residents would use the process of endoreduplication to aid in altering muscle size. Mostly contradictory to our hypotheses, we found no differences in the mean muscle DNA content in any of the 62 species of birds examined in this study. We also found no correlations between mean muscle DNA content and other muscle structural measurements, such as the number of nuclei per millimeter of fiber, myonuclear domain, and fiber cross-sectional area. Thus, while avian muscle seems more phenotypically plastic than mammalian muscle, the biological processes surrounding myonuclear function may be more closely related to those seen in mammals.

Skeletal Muscle Phenotype in Patients Undergoing Long-Term Hemodialysis Awaiting Kidney Transplantation.

Age and comorbidity-related sarcopenia represent a main cause of muscle dysfunction in patients on long-term hemodialysis. However, recent findings suggest muscle abnormalities that are not associated with sarcopenia. The aim of this study was to isolate functional and cellular muscle abnormalities independently of other major confounding factors, including malnutrition, age, comorbidity, or sedentary lifestyle, which are common in patients on maintenance hemodialysis. To overcome these confounding factors, alterations in skeletal muscle were analyzed in highly selected patients on long-term hemodialysis undergoing kidney transplantation. In total, 22 patients on long-term hemodialysis scheduled for kidney transplantation with few comorbidities, but with a long-term uremic milieu exposure, and 22 age, sex, and physical activity level frequency-matched control participants were recruited. We compared biochemical, functional, and molecular characteristics of the skeletal muscle using maximal voluntary force and endurance of the quadriceps, 6-minute walking test, and muscle biopsy of vastus lateralis. For statistical analysis, mean comparison and multiple regression tests were used. In patients on long-term hemodialysis, muscle endurance was lower, whereas maximal voluntary force was not significantly different. We observed a transition from type I (oxidative) to type II (glycolytic) muscle fibers, and an alteration of mitochondrial structure (swelling) without changes in DNA content, genome replication (peroxisome proliferator activator receptor γ coactivator-1α and mitochondrial transcription factor A), regulation of fusion (mitofusin and optic atrophy 1), or fission (dynamin-related protein 1). Notably, there were autophagosome structures containing glycogen along with mitochondrial debris, with a higher expression of light chain 3 (LC3) protein, indicating phagophore formation. This was associated with a greater conversion of LC3-I to LC3-II and the expression of Gabaralp1 and Bnip3l genes involved in mitophagy. In this highly selected long-term hemodialysis population, a low oxidative phenotype could be defined by a poor endurance, a fiber-type switch, and an alteration of mitochondria structure, without evidence of sarcopenia. This phenotype could be related to uremia through the activation of autophagy/mitophagy. NCT02794142 and NCT02040363.

Genetic and Phenotypic Diversities in Experimental Populations of Diploid Inter-Lineage Hybrids in the Human Pathogenic Cryptococcus.

To better understand the potential factors contributing to genome instability and phenotypic diversity, we conducted mutation accumulation (MA) experiments for 120 days for 7 diploid cryptococcal hybrids under fluconazole (10 MA lines each) and non-fluconazole conditions (10 MA lines each). The genomic DNA content, loss of heterozygosity (LOH) rate, growth ability, and fluconazole susceptibility were determined for all 140 evolved cultures. Compared to that of their ancestral clones, the evolved clones showed: (i) genomic DNA content changes ranging from ~22% less to ~27% more, and (ii) reduced, similar, and increased phenotypic values for each tested trait, with most evolved clones displaying increased growth at 40 °C and increased fluconazole resistance. Aside from the ancestral multi-locus genotypes (MLGs) and heterozygosity patterns (MHPs), 77 unique MLGs and 70 unique MPHs were identified among the 140 evolved cultures at day 120. The average LOH rates of the MA lines in the absence and presence of fluconazole were similar at 1.27 × 10−4 and 1.38 × 10−4 LOH events per MA line per mitotic division, respectively. While LOH rates varied among MA lines from different ancestors, there was no apparent correlation between the genetic divergence of the parental haploid genomes within ancestral clones and LOH rates. Together, our results suggest that hybrids between diverse lineages of the human pathogenic Cryptococcus can generate significant genotypic and phenotypic diversities during asexual reproduction.

Loss of SHMT2 and Folate Deficiency Impair Energy Metabolism in Mouse Embryonic Fibroblasts Cells

ObjectivesSerine hydroxymethyltransferase 2 (SHMT2) catalyzes the reversible conversion of tetrahydrofolate (THF) and serine producing THF-conjugated one-carbon units and glycine in the mitochondria. Recently biallelic SHMT2 variants were identified in humans and suggested to alter the protein’s active site, potentially disrupting enzymatic function. Indeed, patient fibroblasts exhibited impaired oxidative capacity, however, with no changes in oxidative phosphorylation protein levels. Furthermore, immortalized cells models of total SHMT2 loss or folate deficiency exhibit decreased oxidative capacity and impaired mitochondrial complex I assembly and protein levels suggesting folate-mediated one-carbon metabolism (FOCM) and the oxidative phosphorylation system are functionally coordinated. We have developed a mouse model of reduced Shmt2 expression that provides an appropriate reference model to further study the deleterious human SHMT2 variants and their connection to folate metabolism. MethodsPrimary mouse embryonic fibroblasts (MEF) were isolated from a C57Bl/6 dam crossed with a heterozygous Shmt2+/– (HET) male. MEF embryos were genotyped, and Shmt2+/+ (wild type) or Shmt2+/– MEF cells were cultured for 4 doubling in 2 nM (deficient) or 25 nM folate (sufficient) medium. Cells were examined for proliferation, total folate levels, mtDNA content, protein levels of pyruvate kinase and PGC1α, pyruvate kinase enzyme activity, and mitochondrial membrane potential and function. ResultsLoss of Shmt2 and folate deficiency significantly reduced cell proliferation and oxygen consumption rate. Total cellular folate levels and pyruvate kinase enzyme activity and protein levels were reduced with folate deficiency. While there were no changes in mitochondrial DNA content or complex 1 proteins NDUFA9 or ND3, mitochondrial membrane potential was impaired and PGC1α protein levels were elevated in Shmt2+/– MEF cells. ConclusionsOur results demonstrate that loss of SHMT2 impairs cellular proliferation and that SHMT2 expression and folate status impact cellular energy metabolism and mitochondrial health. Funding SourcesThis study was financially supported by a President’s Council of Cornell Women Award and Cornell University Division of Nutritional Sciences funds.

Endopolyploidy Variation in Wild Barley Seeds across Environmental Gradients in Israel.

Wild barley is abundant, occupying large diversity of sites, ranging from the northern mesic Mediterranean meadows to the southern xeric deserts in Israel. This is also reflected in its wide phenotypic heterogeneity. We investigated the dynamics of DNA content changes in seed tissues in ten wild barley accessions that originated from an environmental gradient in Israel. The flow cytometric measurements were done from the time shortly after pollination up to the dry seeds. We show variation in mitotic cell cycle and endoreduplication dynamics in both diploid seed tissues (represented by seed maternal tissues and embryo) and in the triploid endosperm. We found that wild barley accessions collected at harsher xeric environmental conditions produce higher proportion of endoreduplicated nuclei in endosperm tissues. Also, a comparison of wild and cultivated barley strains revealed a higher endopolyploidy level in the endosperm of wild barley, that is accompanied by temporal changes in the timing of the major developmental phases. In summary, we present a new direction of research focusing on connecting spatiotemporal patterns of endoreduplication in barley seeds and possibly buffering for stress conditions.

An Optimized and Versatile Counter-Flow Centrifugal Elutriation Workflow to Obtain Synchronized Eukaryotic Cells.

Cell synchronization is a powerful tool to understand cell cycle events and its regulatory mechanisms. Counter-flow centrifugal elutriation (CCE) is a more generally desirable method to synchronize cells because it does not significantly alter cell behavior and/or cell cycle progression, however, adjusting specific parameters in a cell type/equipment-dependent manner can be challenging. In this paper, we used the unicellular eukaryotic model organism, Tetrahymena thermophila as a testing system for optimizing CCE workflow. Firstly, flow cytometry conditions were identified that reduced nuclei adhesion and improved the assessment of cell cycle stage. We then systematically examined how to achieve the optimal conditions for three critical factors affecting the outcome of CCE, including loading flow rate, collection flow rate and collection volume. Using our optimized workflow, we obtained a large population of highly synchronous G1-phase Tetrahymena as measured by 5-ethynyl-2′-deoxyuridine (EdU) incorporation into nascent DNA strands, bulk DNA content changes by flow cytometry, and cell cycle progression by light microscopy. This detailed protocol can be easily adapted to synchronize other eukaryotic cells.

DDB2 regulates DNA replication through PCNA-independent degradation of CDT2

BackgroundTargeting ubiquitin-dependent proteolysis is one of the strategies in cancer therapy. CRLCDT2 and CRLDDB2 are two key E3 ubiquitin ligases involved in DNA replication and DNA damage repair. But CDT2 and DDB2 are opposite prognostic factors in kinds of cancers, and the underlining mechanism needs to be elucidated.MethodsSmall interfering RNAs were used to determine the function of target genes. Co-immunoprecipitation (Co-IP) was performed to detect the interaction between DDB2 and CDT2. Immunofluorescence assays and fluorescence activating cell sorting (FACS) were used to measure the change of DNA content. In vivo ubiquitination assay was carried out to clarify the ubiquitination of CDT2 mediated by DDB2. Cell synchronization was performed to arrest cells at G1/S and S phase. The mechanism involved in DDB2-mediated CDT2 degradation was investigated by constructing plasmids with mutant variants and measured by Western blot. Immunohistochemistry was performed to determine the relationship between DDB2 and CDT2. Paired two-side Student’s t-test was used to measure the significance of the difference between control group and experimental group.ResultsKnockdown of DDB2 stabilized CDT2, while over-expression of DDB2 enhanced ubiquitination of CDT2, and subsequentially degradation of CDT2. Although both DDB2 and CDT2 contain PIP (PCNA-interacting protein) box, PIP box is dispensable for DDB2-mediated CDT2 degradation. Knockdown of PCNA had negligible effects on the stability of CDT2, but promoted accumulation of CDT1, p21 and SET8. Silencing of DDB2 arrested cell cycle in G1 phase, destabilized CDT1 and reduced the chromatin loading of MCMs, thereby blocked the formation of polyploidy induced by ablation of CDT2. In breast cancer and ovarian teratoma tissues, high level of DDB2 was along with lower level of CDT2.ConclusionsWe found that CRL4DDB2 is the novel E3 ubiquitin ligases of CDT2, and DDB2 regulates DNA replication through indirectly regulates CDT1 protein stability by degrading CDT2 and promotes the assembly of pre-replication complex. Our results broaden the horizon for understanding the opposite function of CDT2 and DDB2 in tumorigenesis, and may provide clues for drug discovery in cancer therapy.