-
PloS One 2024Medaka fish (Oryzias latipes) is a powerful model to study genetics underlying the developmental and functional traits of the vertebrate visual system. We established a...
Medaka fish (Oryzias latipes) is a powerful model to study genetics underlying the developmental and functional traits of the vertebrate visual system. We established a simple and high-throughput optomotor response (OMR) assay utilizing medaka larvae to study visual functions including visual acuity and contrast sensitivity. Our assay presents multiple adjustable stripes in motion to individual fish in a linear arena. For that the OMR assay employs a tablet display and the Fish Stripes software to adjust speed, width, color, and contrast of the stripes. Our results demonstrated that optomotor responses were robustly induced by black and white stripes presented from below in the linear-pool-arena. We detected robust strain specific differences in the OMR when comparing long established medaka inbred strains. We observed an interesting training effect upon the initial exposure of larvae to thick stripes, which allowed them to better respond to narrower stripes. The OMR setup and protocol presented here provide an efficient tool for quantitative phenotype mapping, addressing visual acuity, trainability of cortical neurons, color sensitivity, locomotor response, retinal regeneration and others. Our open-source setup presented here provides a crucial prerequisite for ultimately addressing the genetic basis of those processes.
Topics: Animals; Oryzias; Larva; Visual Acuity; Photic Stimulation; Contrast Sensitivity; Vision, Ocular; High-Throughput Screening Assays
PubMed: 38941325
DOI: 10.1371/journal.pone.0302092 -
Bioinformatics (Oxford, England) Jun 2024Recently developed spatial lineage tracing technologies induce somatic mutations at specific genomic loci in a population of growing cells and then measure these...
MOTIVATION
Recently developed spatial lineage tracing technologies induce somatic mutations at specific genomic loci in a population of growing cells and then measure these mutations in the sampled cells along with the physical locations of the cells. These technologies enable high-throughput studies of developmental processes over space and time. However, these applications rely on accurate reconstruction of a spatial cell lineage tree describing both past cell divisions and cell locations. Spatial lineage trees are related to phylogeographic models that have been well-studied in the phylogenetics literature. We demonstrate that standard phylogeographic models based on Brownian motion are inadequate to describe the spatial symmetric displacement (SD) of cells during cell division.
RESULTS
We introduce a new model-the SD model for cell motility that includes symmetric displacements of daughter cells from the parental cell followed by independent diffusion of daughter cells. We show that this model more accurately describes the locations of cells in a real spatial lineage tracing of mouse embryonic stem cells. Combining the spatial SD model with an evolutionary model of DNA mutations, we obtain a phylogeographic model for spatial lineage tracing. Using this model, we devise a maximum likelihood framework-MOLLUSC (Maximum Likelihood Estimation Of Lineage and Location Using Single-Cell Spatial Lineage tracing Data)-to co-estimate time-resolved branch lengths, spatial diffusion rate, and mutation rate. On both simulated and real data, we show that MOLLUSC accurately estimates all parameters. In contrast, the Brownian motion model overestimates spatial diffusion rate in all test cases. In addition, the inclusion of spatial information improves accuracy of branch length estimation compared to sequence data alone. On real data, we show that spatial information has more signal than sequence data for branch length estimation, suggesting augmenting lineage tracing technologies with spatial information is useful to overcome the limitations of genome-editing in developmental systems.
AVAILABILITY AND IMPLEMENTATION
The python implementation of MOLLUSC is available at https://github.com/raphael-group/MOLLUSC.
Topics: Animals; Mice; Cell Movement; Cell Division; Cell Lineage; Likelihood Functions; Phylogeography; Mutation; Phylogeny
PubMed: 38940146
DOI: 10.1093/bioinformatics/btae221 -
Bioinformatics (Oxford, England) Jun 2024Eukaryotic cells contain organelles called mitochondria that have their own genome. Most cells contain thousands of mitochondria which replicate, even in nondividing...
MOTIVATION
Eukaryotic cells contain organelles called mitochondria that have their own genome. Most cells contain thousands of mitochondria which replicate, even in nondividing cells, by means of a relatively error-prone process resulting in somatic mutations in their genome. Because of the higher mutation rate compared to the nuclear genome, mitochondrial mutations have been used to track cellular lineage, particularly using single-cell sequencing that measures mitochondrial mutations in individual cells. However, existing methods to infer the cell lineage tree from mitochondrial mutations do not model "heteroplasmy," which is the presence of multiple mitochondrial clones with distinct sets of mutations in an individual cell. Single-cell sequencing data thus provide a mixture of the mitochondrial clones in individual cells, with the ancestral relationships between these clones described by a mitochondrial clone tree. While deconvolution of somatic mutations from a mixture of evolutionarily related genomes has been extensively studied in the context of bulk sequencing of cancer tumor samples, the problem of mitochondrial deconvolution has the additional constraint that the mitochondrial clone tree must be concordant with the cell lineage tree.
RESULTS
We formalize the problem of inferring a concordant pair of a mitochondrial clone tree and a cell lineage tree from single-cell sequencing data as the Nested Perfect Phylogeny Mixture (NPPM) problem. We derive a combinatorial characterization of the solutions to the NPPM problem, and formulate an algorithm, MERLIN, to solve this problem exactly using a mixed integer linear program. We show on simulated data that MERLIN outperforms existing methods that do not model mitochondrial heteroplasmy nor the concordance between the mitochondrial clone tree and the cell lineage tree. We use MERLIN to analyze single-cell whole-genome sequencing data of 5220 cells of a gastric cancer cell line and show that MERLIN infers a more biologically plausible cell lineage tree and mitochondrial clone tree compared to existing methods.
AVAILABILITY AND IMPLEMENTATION
https://github.com/raphael-group/MERLIN.
Topics: Single-Cell Analysis; Humans; Cell Lineage; Mitochondria; Mutation; Genome, Mitochondrial; Algorithms; Evolution, Molecular
PubMed: 38940122
DOI: 10.1093/bioinformatics/btae231 -
Frontiers in Bioscience (Scholar... May 2024The ETS transcription factor PU.1 plays an essential role in blood cell development. Its precise expression pattern is governed by cis-regulatory elements (CRE) acting... (Review)
Review
The ETS transcription factor PU.1 plays an essential role in blood cell development. Its precise expression pattern is governed by cis-regulatory elements (CRE) acting at the chromatin level. CREs mediate the fine-tuning of graded levels of , deviations of which can cause acute myeloid leukemia. In this review, we perform an in-depth analysis of the regulation of expression in normal and malignant hematopoiesis. We elaborate on the role of trans-acting factors and the biomolecular interplays in mediating local chromatin dynamics. Moreover, we discuss the current understanding of CRE bifunctionality exhibiting enhancer or silencer activities in different blood cell lineages and future directions toward gene-specific chromatin-targeted therapeutic development.
Topics: Humans; Hematopoiesis; Proto-Oncogene Proteins; Trans-Activators; Cell Lineage; Animals; Transcription, Genetic; Gene Expression Regulation; Leukemia, Myeloid, Acute; Chromatin
PubMed: 38939973
DOI: 10.31083/j.fbs1602010 -
Frontiers in Bioscience (Elite Edition) May 2024Fall armyworm () is a highly destructive maize pest that significantly threatens agricultural productivity. Existing control methods, such as chemical insecticides and...
BACKGROUND
Fall armyworm () is a highly destructive maize pest that significantly threatens agricultural productivity. Existing control methods, such as chemical insecticides and entomopathogens, lack effectiveness, necessitating alternative approaches.
METHODS
Gut-associated bacteria were isolated from the gut samples of fall armyworm and screened based on their chitinase and protease-producing ability before characterization through 16S rRNA gene sequence analysis. The efficient chitinase-producing FGE4 and FGE18 were chosen to test the biocontrol efficacy. As their respective cell suspensions and extracted crude chitinase enzyme, these two isolates were applied topically on the larvae, supplemented with their feed, and analyzed for their quantitative food use efficiency and survivability.
RESULTS
Twenty-one high chitinase and protease-producing bacterial isolates were chosen. Five genera were identified by 16S rRNA gene sequencing: , , , , and . In the biocontrol efficacy test, the consumption index and relative growth rate were lowered in larvae treated with FGE18 by topical application and feed supplementation. Similarly, topical treatment of FGE4 to larvae decreased consumption index, relative growth rate, conversion efficiency of ingested food, and digested food values.
CONCLUSION
The presence of gut bacteria with high chitinase activity negatively affects insect health. Utilizing gut-derived bacterial isolates with specific insecticidal traits offers a promising avenue to control fall armyworms. This research suggests a potential strategy for future pest management.
Topics: Animals; Spodoptera; Chitinases; RNA, Ribosomal, 16S; Bacteria; Bacillus licheniformis; Enterobacter cloacae; Larva; Pest Control, Biological; Gastrointestinal Tract
PubMed: 38939914
DOI: 10.31083/j.fbe1602015 -
Frontiers in Cellular and Infection... 2024The Asian citrus psyllid (ACP) Kuwayama is the leading vector of Liberibacter asiaticus (Las), the causative agent of citrus Huanglongbing (HLB) disease. The...
The Asian citrus psyllid (ACP) Kuwayama is the leading vector of Liberibacter asiaticus (Las), the causative agent of citrus Huanglongbing (HLB) disease. The distribution and dynamics of Las within ACP are critical to understanding how the transmission, spread and infection of Las occurs within its host vector in nature. In this study, the distribution and titer changes of Las in various tissues of ACP 5 instar nymphs and adults were examined by (FISH) and real-time quantitative PCR (qPCR) techniques. Results demonstrated that 100% of ACP 5 instar nymphs and adults were infected with Las following feeding on infected plants, and that Las had widespread distribution in most of the tissues of ACP. The titers of Las within the midgut, salivary glands and hemolymph tissues were the highest in both 5 instar nymphs and adults. When compared with adults, the titers of Las in these three tissues of 5 instar nymphs were significantly higher, while in the mycetome, ovary and testes they were significantly lower than those of adults. FISH visualization further confirmed these findings. Dynamic analysis of Las demonstrated that it was present across all the developmental ages of ACP adults. There was a discernible upward trend in the presence of Las with advancing age in most tissues of ACP adults, including the midgut, hemolymph, salivary glands, foot, head, cuticula and muscle. Our findings have significant implications for the comprehensive understanding of the transmission, dissemination and infestation of Las, which is of much importance for developing novel strategies to halt the spread of Las, and therefore contribute to the efficient prevention and control of HLB.
Topics: Animals; Hemiptera; Insect Vectors; Plant Diseases; Nymph; Citrus; In Situ Hybridization, Fluorescence; Rhizobiaceae; Real-Time Polymerase Chain Reaction; Salivary Glands; Hemolymph
PubMed: 38938879
DOI: 10.3389/fcimb.2024.1408362 -
Open Veterinary Journal May 2024Canine Legg Calvé Perthes disease (LCPD) occurs during the growth period, and the cause of ischemic necrosis of the femoral head during growth remains unclear. If...
BACKGROUND
Canine Legg Calvé Perthes disease (LCPD) occurs during the growth period, and the cause of ischemic necrosis of the femoral head during growth remains unclear. If LCPD-affected femoral head-derived mesenchymal stem cells (LCPD-MSCs) can be generated, they can be used as a new tool for the pathophysiological analysis of canine LCPD.
AIM
To generate affected femoral head-derived mesenchymal stem cells (MSCs) from dogs with LCPD and investigate the mRNA expression levels of angiogenesis-related factors and osteogenic differentiation potency of LCPD-MSCs.
METHODS
This study was performed using affected femoral heads from dogs diagnosed with LCPD and underwent femoral head and neck ostectomy. The necrotic tissue was harvested from the LCPD-affected femoral head and cultured statically (LCPD group, = 6). Canine bone marrow-derived MSCs (BM-MSCs) were used as controls (control group, = 6). First, the morphology of the cultured cells was observed, and the expression of CD29, CD34, CD44, CD45, CD90, and major histocompatibility complex class II was analyzed using flow cytometry. Additionally, the trilineage differentiation potency of the LCPD-affected head-derived adherent cells was examined. Furthermore, the expression levels of , , , and mRNAs and the bone differentiation potency of LCPD-affected head-derived adherent cells were investigated.
RESULTS
LCPD-affected femoral head-derived adherent cells showed a fibroblast-like morphology, and the expression of cell surface antigens was similar to that of BM-MSCs. In addition, LCPD-affected femoral head-derived adherent cells showed the same trilineage differentiation potency as BM-MSCs and were consistent with MSC characteristics. Furthermore, the mRNA expression levels of angiogenesis-related factors could be objectively measured in LCPD-MSCs and those MSCs had bone differentiation potency.
CONCLUSION
In the present study, canine LCPD-MSCs were successfully generated, suggesting their usefulness as a tool for pathological analysis of LCPD in dogs.
Topics: Animals; Dogs; Legg-Calve-Perthes Disease; Mesenchymal Stem Cells; Dog Diseases; Femur Head; Cell Differentiation; Osteogenesis; Male; Cells, Cultured; Female
PubMed: 38938425
DOI: 10.5455/OVJ.2024.v14.i5.12 -
Open Veterinary Journal May 2024Oxygen deprivation (OD) is a critical condition that can lead to brain damage and even death. Current hypoxia management approaches are limited in effectiveness. (CA),...
BACKGROUND
Oxygen deprivation (OD) is a critical condition that can lead to brain damage and even death. Current hypoxia management approaches are limited in effectiveness. (CA), known for its neuroprotective properties, offers a potential alternative for OD treatment.
AIMS
This study aims to investigate the neuroprotective effects of CA on the expression of brain-derived neurotrophic factor (BDNF) and vesicular glutamate transporter 1 (VGLUT1) in zebrafish larvae under oxygen-deficient conditions.
METHODS
Zebrafish embryos were subjected to low oxygen levels (1.5 mg/l) 0-2 hours post-fertilization (hpf) until 3 days post-fertilization (dpf), simulating the early stages of OD. Subsequent treatment involved varying concentrations of CA (1.25-5 µg/ml) up to 9 days post-fertilization. The expression levels of BDNF and VGLUT1 were measured using PCR methods. Statistical analysis was conducted using a two-way analysis of variance to evaluate the impact of CA on the expression of BDNF and VGLUT1 in zebrafish larvae aged 3 and 9 dpf in oxygen-deprived conditions.
RESULTS
CA significantly influenced the expression of BDNF and VGLUT1 under OD ( < 0.001). An increase in BDNF expression ( < 0.001) and a decrease in VGLUT1 ( < 0.01) were observed in zebrafish larvae experiencing OD and treated with CA. There was no significant difference in BDNF and VGLUT1 expression across age variations in zebrafish larvae at 3 dpf and 9 dpf in the treatment groups ( > 0.05). CA concentration of 2.5 µg/ml effectively enhanced BDNF and reduced VGLUT1 in 3-9 dpf zebrafish larvae.
CONCLUSION
CA demonstrates potential as a neuroprotective agent, modulating increased BDNF expression and reduced VGLUT1 under OD conditions. These findings lay a foundation for further research in developing therapies for oxygen deficiency.
Topics: Animals; Zebrafish; Centella; Plant Extracts; Larva; Triterpenes; Brain-Derived Neurotrophic Factor; Neuroprotective Agents; Oxygen; Fish Diseases; Hypoxia
PubMed: 38938421
DOI: 10.5455/OVJ.2024.v14.i5.9 -
BMC Surgery Jun 2024Although many prognostic factors in neonates with congenital diaphragmatic hernia (CDH) have been described, no consensus thus far has been reached on which and how many...
OBJECTIVES
Although many prognostic factors in neonates with congenital diaphragmatic hernia (CDH) have been described, no consensus thus far has been reached on which and how many factors are involved. The aim of this study is to analyze the association of multiple prenatal and postnatal factors with 1-month mortality of neonates with CDH and to construct a nomogram prediction model based on significant factors.
METHODS
A retrospective analysis of neonates with CDH at our center from 2013 to 2022 was conducted. The primary outcome was 1-month mortality. All study variables were obtained either prenatally or on the first day of life. Risk for 1-month mortality of CDH was quantified by odds ratio (OR) with 95% confidence interval (CI) in multivariable logistic regression models.
RESULTS
After graded multivariable adjustment, six factors were found to be independently and consistently associated with the significant risk of 1-month mortality in neonates with CDH, including gestational age of prenatal diagnosis (OR, 95% CI, P value: 0.845, 0.772 to 0.925, < 0.001), observed-to-expected lung-to-head ratio (0.907, 0.873 to 0.943, < 0.001), liver herniation (3.226, 1.361 to 7.648, 0.008), severity of pulmonary hypertension (6.170, 2.678 to 14.217, < 0.001), diameter of defect (1.560, 1.084 to 2.245, 0.017), and oxygen index (6.298, 3.383 to 11.724, < 0.001). Based on six significant factors identified, a nomogram model was constructed to predict the risk for 1-month mortality in neonates with CDH, and this model had decent prediction accuracy as reflected by the C-index of 94.42%.
CONCLUSIONS
Our findings provide evidence for the association of six preoperational and intraoperative factors with the risk of 1-month mortality in neonates with CDH, and this association was reinforced in a nomogram model.
Topics: Humans; Hernias, Diaphragmatic, Congenital; Nomograms; Infant, Newborn; Retrospective Studies; Female; Male; Prognosis; Gestational Age; Infant Mortality; Risk Factors; Risk Assessment
PubMed: 38937726
DOI: 10.1186/s12893-024-02479-z -
Scientific Reports Jun 2024Marine Heatwaves (MHWs) can directly influence survival of marine fishes, particularly for early life stages, including age-0 juveniles during their residence in coastal...
Marine Heatwaves (MHWs) can directly influence survival of marine fishes, particularly for early life stages, including age-0 juveniles during their residence in coastal nursery habitats. However, the ability of nurseries to support high fish densities, optimize foraging and growth, and protect against predators may be altered during MHWs. Gulf of Alaska Pacific cod (Gadus macrocephalus) larval, juvenile, and adult abundances declined dramatically following MHW events in 2014-2016 and 2019. To evaluate coastal nursery function during MHWs, we compared diet composition, recent growth, size, condition, and abundance of age-0 juveniles throughout their first summer before, during, and between MHWs. Diet shifted to larger prey during MHWs, particularly mysids, but diet did not appear to influence growth. We observed faster growth rates during MHWs, yet even when accounting for growth, we could not explain the higher body sizes observed in August during MHWs. Together with lower abundance and the near absence of small fish in the nursery by August during MHWs, these patterns highlight potential for size-selection and a reduced ability of nursery habitats to buffer against environmental variability during MHWs, with only a small number of large "super survivors" persisting through the summer.
Topics: Animals; Ecosystem; Alaska; Gadiformes; Larva; Seasons; Body Size
PubMed: 38937554
DOI: 10.1038/s41598-024-63897-w