An inactivating mutation in the histone deacetylase SIRT6 causes human perinatal lethality.

It has been well established that histone and DNA modifications are critical to maintaining the equilibrium between pluripotency and differentiation during early embryogenesis. Mutations in key regulators of DNA methylation have shown that the balance between gene regulation and function is critical during neural development in early years of life. However, there have been no identified cases linking epigenetic regulators to aberrant human development and fetal demise. Here, we demonstrate that a homozygous inactivating mutation in the histone deacetylase SIRT6 results in severe congenital anomalies and perinatal lethality in four affected fetuses. In vitro, the amino acid change at Asp63 to a histidine results in virtually complete loss of H3K9 deacetylase and demyristoylase functions. Functionally, SIRT6 D63H mouse embryonic stem cells (mESCs) fail to repress pluripotent gene expression, direct targets of SIRT6, and exhibit an even more severe phenotype than Sirt6-deficient ESCs when differentiated into embryoid bodies (EBs). When terminally differentiated toward cardiomyocyte lineage, D63H mutant mESCs maintain expression of pluripotent genes and fail to form functional cardiomyocyte foci. Last, human induced pluripotent stem cells (iPSCs) derived from D63H homozygous fetuses fail to differentiate into EBs, functional cardiomyocytes, and neural progenitor cells due to a failure to repress pluripotent genes. Altogether, our study described a germline mutation in SIRT6 as a cause for fetal demise, defining SIRT6 as a key factor in human development and identifying the first mutation in a chromatin factor behind a human syndrome of perinatal lethality.

Expression of HIV-1 Intron-Containing RNA in Microglia Induces Inflammatory Responses.

Chronic neuroinflammation is observed in HIV+ individuals on suppressive combination antiretroviral therapy (cART) and is thought to cause HIV-associated neurocognitive disorders. We have recently reported that expression of HIV intron-containing RNA (icRNA) in productively infected monocyte-derived macrophages induces pro-inflammatory responses. Microglia, yolk sac-derived brain-resident tissue macrophages, are the primary HIV-1 infected cell type in the central nervous system (CNS). In this study, we tested the hypothesis that persistent expression of HIV icRNA in primary human microglia induces innate immune activation. We established multiple orthogonal primary human microglia-like cell cultures including peripheral blood monocyte-derived microglia (MDMG) and induced pluripotent stem cell (iPSC)-derived microglia. Unlike MDMG, human iPSC-derived microglia (hiMG), which phenotypically mimic primary CNS microglia, were robustly infected with replication competent HIV-1, and establishment of productive HIV-1 infection and de novo viral gene expression led to pro-inflammatory cytokine production. Blocking of HIV-1 icRNA expression, but not multiply spliced viral RNA, either via infection with virus expressing a Rev-mutant deficient for HIV icRNA nuclear export or infection in the presence of small molecule inhibitor of CRM1-mediated viral icRNA nuclear export pathway, attenuated induction of innate immune responses. These studies suggest that Rev-CRM1-dependent nuclear export and cytosolic sensing of HIV-1 icRNA induces pro-inflammatory responses in productively infected microglia. Novel strategies targeting HIV icRNA expression specifically are needed to suppress HIV-induced neuroinflammation.

Efficient production of retinol in Yarrowia lipolytica by increasing stability using antioxidant and detergent extraction.

The demand for bio-based retinol (vitamin A) is currently increasing, however its instability represents a major bottleneck in microbial production. Here, we developed an efficient method to selectively produce retinol in Yarrowia lipolytica. The ß-carotene 15,15'-dioxygenase (BCO) cleaves ß-carotene into retinal, which is reduced to retinol by retinol dehydrogenase (RDH). Therefore, to produce retinol, we first generated ß-carotene-producing strain based on a high-lipid-producer via overexpressing genes including heterologous ß-carotene biosynthetic genes, GGS1F43I mutant of endogenous geranylgeranyl pyrophosphate synthase isolated by directed evolution, and FAD1 encoding flavin adenine dinucleotide synthetase, while deleting several genes previously known to be beneficial for carotenoid production. To produce retinol, 11 copies of BCO gene from marine bacterium 66A03 (Mb.Blh) were integrated into the rDNA sites of the ß-carotene overproducer. The resulting strain produced more retinol than retinal, suggesting strong endogenous promiscuous RDH activity in Y. lipolytica. The introduction of Mb.Blh led to a considerable reduction in ß-carotene level, but less than 5% of the consumed ß-carotene could be detected in the form of retinal or retinol, implying severe degradation of the produced retinoids. However, addition of the antioxidant butylated hydroxytoluene (BHT) led to a >20-fold increase in retinol production, suggesting oxidative damage is the main cause of intracellular retinol degradation. Overexpression of GSH2 encoding glutathione synthetase further improved retinol production. Raman imaging revealed co-localization of retinol with lipid droplets, and extraction of retinol using Tween 80 was effective in improving retinol production. By combining BHT treatment and extraction using Tween 80, the final strain CJ2104 produced 4.86 g/L retinol and 0.26 g/L retinal in fed-batch fermentation in a 5-L bioreactor, which is the highest retinol production titer ever reported. This study demonstrates that Y. lipolytica is a suitable host for the industrial production of bio-based retinol.

Prenatal Octamethylcyclotetrasiloxane Exposure Impaired Proliferation of Neuronal Progenitor, Leading to Motor, Cognition, Social and Behavioral Functions.

Cyclic siloxane octamethylcyclotetrasiloxane (D4) has raised concerns as an endocrine-disrupting chemical (EDC). D4 is widely used in detergent products, cosmetics, and personal care products. Recently, robust toxicological data for D4 has been reported, but the adverse effects of D4 on brain development are unknown. Here, pregnant mice on gestational day 9.5 were treated daily with D4 to postnatal day 28, and the offspring mice were studied. The prenatal D4-treated mice exhibited cognitive dysfunction, limited memory, and motor learning defect. Moreover, prenatal D4 exposure reduced the proliferation of neuronal progenitors in the offspring mouse brain. Next, the mechanisms through which D4 regulated the cell cycle were investigated. Aberrant gene expression, such as cyclin-dependent kinases CDK6 and cyclin-dependent kinase inhibitor p27, were found in the prenatal D4-treated mice. Furthermore, the estrogen receptors ERa and ERb were increased in the brain of prenatal D4-treated mice. Overall, these findings suggest that D4 exerts estrogen activity that affects the cell cycle progression of neuronal progenitor cells during neurodevelopment, which may be associated with cognitive deficits in offspring.

Loss of Nckx3 Exacerbates Experimental DSS-Induced Colitis in Mice through p53/NF-κB Pathway.

Inflammatory bowel diseases (IBDs) comprises a range of chronic inflammatory conditions of the intestinal tract. The incidence and prevalence of IBDs are increasing worldwide, but the precise etiology of these diseases is not completely understood. Calcium signaling plays a regulatory role in cellular proliferation. Nckx3, a potassium-dependent Na+/Ca2+ exchanger, is not only expressed in the brain but also in the aortic, uterine, and intestinal tissues, which contain abundant smooth muscle cells. This study investigated the role of Nckx3 in intestinal inflammation. Microarray analyses revealed the upregulation of the innate immune response-associated genes in the duodenum of Nckx3 knockout (KO) mice. The Nckx3 KO mice also showed an increase in IBD- and tumorigenesis-related genes. Using dextran sodium sulfate (DSS)-induced experimental colitis mice models, the Nckx3 KO mice showed severe colitis. Furthermore, the pathways involving p53 and NF-κB signaling were significantly upregulated by the absence of Nckx3. Overall, Nckx3 plays a critical role in the innate immune and immune response and may be central to the pathogenesis of IBD.

Effects of Homologous instrument assisted mobilization (HIM) on ankle movement, gait-related muscle activation, and plantar pressure distribution in ankle dorsiflexion syndrome: A randomized single control trial.

BACKGROUND: While the limited ankle dorsiflexion syndrome (ADS) is common in neuro-musculoskeletal conditions, the instrument-assisted mobilization focused on the shortened gastro-soleus myofascial structure (IMI) rather than the homologous structure (both gastrosoleus and tibiliais anterior muscles, HIM). OBJECTIVE: We aimed to compare the immediate therapeutic effects between IMH and IMI treatment groups on the ankle dorsiflexion angle, muscle activation and foot pressure distribution during dynamic gait in ADS. METHODS: Neuromechanical tests including kinematics (ankle mobility), kinetics (center of pressure distribution), and electromyography were used to determine the immediate therapeutic effects between HIM and IMI treatment groups in 24 participants with ADS. RESULTS: The ankle joint angle analysis demonstrated a more improved active DF angle in the group who received HIM intervention when compared to the group who received IMI intervention. (11.26% and 3.58%, respectively) EMG analysis showed more decreased mean and peak TA activation amplitudes in the group who received HIM intervention (9.1% and 9%) when compared to the group who received IMI intervention (11.48% and 1.48%). Plantar pressure distribution analysis showed difference that the forefoot/area decreased in the group who received HIM intervention (8.1%), but rather increased in the group who received IMI intervention (14.3%). CONCLUSIONS: Our neuromechanical results demonstrated promising positive effects on ankle joint mobility, muscle activation and foot pressure distribution during gait in ADS.

Clinical machine learning predicting best stroke rehabilitation responders to exoskeletal robotic gait rehabilitation.

BACKGROUND: Although clinical machine learning (ML) algorithms offer promising potential in forecasting optimal stroke rehabilitation outcomes, their specific capacity to ascertain favorable outcomes and identify responders to robotic-assisted gait training (RAGT) in individuals with hemiparetic stroke undergoing such intervention remains unexplored. OBJECTIVE: We aimed to determine the best predictive model based on the international classification of functioning impairment domain features (Fugl- Meyer assessment (FMA), Modified Barthel index related-gait scale (MBI), Berg balance scale (BBS)) and reveal their responsiveness to robotic assisted gait training (RAGT) in patients with subacute stroke. METHODS: Data from 187 people with subacute stroke who underwent a 12-week Walkbot RAGT intervention were obtained and analyzed. Overall, 18 potential predictors encompassed demographic characteristics and the baseline score of functional and structural features. Five predictive ML models, including decision tree, random forest, eXtreme Gradient Boosting, light gradient boosting machine, and categorical boosting, were used. RESULTS: The initial and final BBS, initial BBS, final Modified Ashworth scale, and initial MBI scores were important features, predicting functional improvements. eXtreme Gradient Boosting demonstrated superior performance compared to other models in predicting functional recovery after RAGT in patients with subacute stroke. CONCLUSION: eXtreme Gradient Boosting may be an invaluable prognostic tool, providing clinicians and caregivers with a robust framework to make precise clinical decisions regarding the identification of optimal responders and effectively pinpoint those who are most likely to derive maximum benefits from RAGT interventions.

Spatiotemporal Niche Separation among Passeriformes in the Halla Mountain Wetland of Jeju, Republic of Korea: Insights from Camera Trap Data.

This study analyzed 5322 camera trap photographs from Halla Mountain Wetland, documenting 1427 independent bird sightings of 26 families and 49 species of Passeriformes. Key observations include morning activities in Cyanoptila cyanomelana and Horornis canturians and afternoon activity in Muscicapa dauurica and Phoenicurus auroreus. Wetlands were significantly preferred (P_i = 0.398) despite their smaller area, contrasting with underutilized grasslands (P_i = 0.181). Seasonal activity variations were notable, with overlap coefficients ranging from 0.08 to 0.81 across species, indicating diverse strategies in resource utilization and thermoregulation. Population density was found to be a critical factor in habitat usage, with high-density species showing more consistent activity patterns. The study's results demonstrate the ecological adaptability of Passeriformes in the Halla Mountain Wetland while highlighting the limitations of camera trapping methods. These limitations include their fixed field of view and intermittent recording capability, which may not fully capture the spectrum of complex avian behaviors. This research underlines the need for future studies integrating various methodologies, such as direct observation and acoustic monitoring, to gain a more comprehensive understanding of avian ecology.

Abnormal synaptic architecture in iPSC-derived neurons from a multi-generational family with genetic Creutzfeldt-Jakob disease.

Genetic prion diseases are caused by mutations in PRNP, which encodes the prion protein (PrPC). Why these mutations are pathogenic, and how they alter the properties of PrPC are poorly understood. We have consented and accessed 22 individuals of a multi-generational Israeli family harboring the highly penetrant E200K PRNP mutation and generated a library of induced pluripotent stem cells (iPSCs) representing nine carriers and four non-carriers. iPSC-derived neurons from E200K carriers display abnormal synaptic architecture characterized by misalignment of postsynaptic NMDA receptors with the cytoplasmic scaffolding protein PSD95. Differentiated neurons from mutation carriers do not produce PrPSc, the aggregated and infectious conformer of PrP, suggesting that loss of a physiological function of PrPC may contribute to the disease phenotype. Our study shows that iPSC-derived neurons can provide important mechanistic insights into the pathogenesis of genetic prion diseases and can offer a powerful platform for testing candidate therapeutics.

Effects of Decamethylcyclopentasiloxane on Reproductive Systems in Female Rats.

The female reproductive system becomes fertile through the action of hormones involved in the hypothalamic-pituitary-ovarian axis. On the other hand, estrogen-like endocrine disruptors released into the environment come into contact with humans by various routes and affect the reproductive system. Exposure to these chemicals can cause problems with the reproductive process, from egg ovulation to implantation, or cause female reproductive diseases. These reproductive problems cause infertility. Decamethylcyclopentasiloxane (D5) is used for lubrication in silicone polymers, households, and personal care products. In the case of D5, it is discharged through factory wastewater and can bioaccumulate. Therefore, it accumulates in the human body. In this study, D5 was administered orally for four weeks to determine the effects of D5 on the reproductive process. As a result, D5 increases the number of follicles in the ovary and suppresses the expression of genes related to the growth of follicles. In addition, it increases the gonadotropin hormone, inducing estradiol enhancement and progesterone reduction. Because of these changes in the reproductive system when exposed to D5, the industry should reconsider using D5.

GATA1 deletion in human pluripotent stem cells increases differentiation yield and maturity of neutrophils.

Human pluripotent stem cell (hPSC)-derived tissues can be used to model diseases in cell types that are challenging to harvest and study at-scale, such as neutrophils. Neutrophil dysregulation, specifically neutrophil extracellular trap (NET) formation, plays a critical role in the prognosis and progression of multiple diseases, including COVID-19. While hPSCs can generate limitless neutrophils (iNeutrophils) to study these processes, current differentiation protocols generate heterogeneous cultures of granulocytes and precursors. Here, we describe a method to improve iNeutrophil differentiations through the deletion of GATA1. GATA1 knockout (KO) iNeutrophils are nearly identical to primary neutrophils in form and function. Unlike wild-type iNeutrophils, GATA1 KO iNeutrophils generate NETs in response to the physiologic stimulant lipopolysaccharide, suggesting they are a more accurate model when performing NET inhibitor screens. Furthermore, through deletion of CYBB, we demonstrate that GATA1 KO iNeutrophils are a powerful tool in determining involvement of a given protein in NET formation.

Notch activation during early mesoderm induction modulates emergence of the T/NK cell lineage from human iPSCs.

A robust method of producing mature T cells from iPSCs is needed to realize their therapeutic potential. NOTCH1 is known to be required for the production of hematopoietic progenitor cells with T cell potential in vivo. Here we identify a critical window during mesodermal differentiation when Notch activation robustly improves access to definitive hematopoietic progenitors with T/NK cell lineage potential. Low-density progenitors on either OP9-hDLL4 feeder cells or hDLL4-coated plates favored T cell maturation into TCRab+CD3+CD8+ cells that express expected T cell markers, upregulate activation markers, and proliferate in response to T cell stimulus. Single-cell RNAseq shows Notch activation yields a 6-fold increase in multi-potent hematopoietic progenitors that follow a developmental trajectory toward T cells with clear similarity to post-natal human thymocytes. We conclude that early mesodermal Notch activation during hematopoietic differentiation is a missing stimulus with broad implications for producing hematopoietic progenitors with definitive characteristics.

Molecular Evidence Reveals the Sympatric Distribution of Cervus nippon yakushimae and Cervus nippon taiouanus on Jeju Island, South Korea.

Non-native species threaten native ecosystems and species, particularly on islands where rates of endemism and vulnerability to threats are high. Understanding species invasion will aid in providing insights into ecological and evolutionary processes. To identify the non-native sika deer (Cervus nippon) population in Jeju, South Korea, and their phylogenetic affinities, we collected tissue samples from roadkill and the World Natural Heritage Headquarters in Jeju. Mitochondrial DNA cytochrome B (CytB) gene sequences were analyzed to determine two distinct CytB haplotypes. Phylogenetic analysis using maximum likelihood tree revealed two haplotypes of CytB clustered into two different groups representing two subspecies: C. n. yakushimae, native to Japan, and C. n. taiouanus, native to Taiwan. The tentative divergence time between the two subspecies was estimated at 1.81 million years. Our study confirmed that the two subspecies of sika deer are sympatric in the natural ecosystem of Jeju Island. This study provides valuable information to help government and conservation agencies understand alien species and determine control policies for conserving native biodiversity in South Korea.

Pre-validation of an alternative test method for prediction of developmental neurotoxicity.

Exposure to neurodevelopmental toxicants can cause permanent brain injury. Hance, determining the neurotoxicity of unknown substances is essential for the safety of substance. As an alternative method to animal studies, developmental neurotoxicity test (DNT) and the first discriminant function (DF) were established in previous study. This study aimed to increase the predictability of the DNT method and perform a mobility test. Two endpoints of 29 newly investigated substances were used to establish a second-generation DF (2nd GDF). As two endpoints, the half-inhibitory concentration of the cell viability (IC50) was determined using a cell counting kit-8 assay. The half-inhibitory concentration of differentiation (ID50) was determined by measuring the green fluorescent protein (GFP) intensity in 46C cells. The substances were treated dose-dependently to measure IC50 and ID50. The 2nd GDF classified 29 chemicals accurately as toxic and non-toxic. Four participants of three independent laboratories were enrolled to test the mobility. The results of the test set were highly accurate in reproducibility (100% of accuracy, sensitivity, and specificity) and mobility (accuracy 93.33%, sensitivity 90.91%, and specificity 100%). In conclusion, the protocol is transferable, reproducible, and accurate. Therefore, this could be a standardizing method for determining a neurotoxicant as an alternative for animal experiments.

Anti-apoptotic effect of melatonin on preimplantation development of porcine parthenogenetic embryos.

In the present study, we investigated the effect of melatonin on the preimplantation development of porcine parthenogenetic and somatic cell nuclear transfer (SCNT) embryos. Parthenogenetic embryos were cultured in mNCSU-23 supplemented with various concentrations of melatonin for 7 days. The results revealed that 100 pM was the optimal concentration, which resulted in significantly increased cleavage and blastocyst formation rates. Additionally, 100 pM melatonin provided the highest increase in total cell number of blastocysts. Therefore, the subsequent experiments were performed with 100 pM melatonin. ROS level in 2-8 cell stage embryos in the presence or absence of melatonin was evaluated. Embryos cultured with melatonin showed significantly decreased ROS. Blastocysts cultured with melatonin for 7 days were analyzed by the TUNEL assay. It was observed that melatonin not only increased (P < 0.05) the total cell number but also decreased (P < 0.05) the rate of apoptotic nuclei. Blastocysts cultured with melatonin were assessed for the expression of apoptosis-related genes Bcl-xl and Bax, and of pluripotency marker gene Oct-4 by real-time quantitative PCR. Analysis of data showed that the expression of Bcl-xl was higher (1.7-fold) compared to the control while the expression of Bax was significantly decreased relative to the control (0.7-fold) (P < 0.05). Moreover, the expression of Oct-4 was 1.7-fold higher than the control. These results indicated that melatonin had beneficial effects on the development of porcine parthenogenetic embryos. Based on the findings of parthenogenetic embryos, we investigated the effect of melatonin on the development of porcine SCNT embryos. The results also demonstrated increased cleavage and blastocyst formation rates, and the total cell numbers in blastocysts were significantly higher when the embryos were cultured with melatonin. Therefore, these data suggested that melatonin may have important implications for improving porcine preimplantation SCNT embryo development.

Generation of Human Induced Pluripotent Stem Cells Using a Defined, Feeder-Free Reprogramming System.

Human induced pluripotent stem cells (hiPSCs) offer great opportunities for the study of human development and disease modeling and have enormous potential for use in future clinical cell-based therapies. However, most current systems to create hiPSCs often expose the cells to animal feeder layers or xenogeneic reagents; this raises safety concerns about using hiPSC-derived cells for therapeutic purposes. Here, we describe protocols to generate hiPSCs without exposing the cells to xenogeneic materials that uses a defined, feeder-free reprogramming system. With this method, we were able to successfully reprogram not only patient-derived peripheral blood mononuclear cells but also amniocytes from the amniotic fluid of stillborn fetuses using two independent reprogramming platforms. Importantly, hiPSCs generated in this fashion expressed pluripotent markers and had normal karyotypes. The protocols allowed us to generate and culture hiPSCs under Good Manufacturing Practice-like conditions, a necessary step for the future clinical application of these cells. © 2018 by John Wiley & Sons, Inc.

Complete mitochondrial genome of the far eastern Myotis, Myotis bombinus (Chiroptera, Vespertilionidae).

The complete mitochondrial genome of the Far Eastern Myotis, Myotis bombinus (Chiroptera, Vespertilionidae) is determined in this study. It is 17 128 base pairs in length with 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a non-coding control region. Its gene order is identical to that of other typical vertebrates. There are two tandem repeat sequences in the non-coding control region. Each repeat sequences contains 5 copies of 81 nucleotides and 42 copies of 6 nucleotides. Phylogenetic tree of mt 13 protein-coding gene sequences of 18 species in the family Vespertilionidae shows two distinct clades. Clade I consists of Myotis and Murina, while Clade II contains all other species analyzed.

Complete mitochondrial genome of the Ussuri white-toothed shrew Crocidura lasiura (Insectivora, Soricidae).

We obtained the complete mitochondrial genome of the Ussuri white-toothed shrew Crocidura lasiura (Insectivora, Soricidae) at 17 362 base pairs (bp) containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a non-coding control region. Its gene order is identical to that of other vertebrates. Several repeat elements were identified in the non-coding control region (D-loop). Phylogenetic tree using mt protein-coding gene sequences showed that C. lasiura was closely related to C. attenuata. The reports of mt genome sequences of Crocidura were not enough to study phylogenetic relationships in genome levels. However, this report may help us to understand the phylogenetic relationships and evolutionary history of Crocidura.

A Comprehensive, Ethnically Diverse Library of Sickle Cell Disease-Specific Induced Pluripotent Stem Cells.

Sickle cell anemia affects millions of people worldwide and is an emerging global health burden. As part of a large NIH-funded NextGen Consortium, we generated a diverse, comprehensive, and fully characterized library of sickle-cell-disease-specific induced pluripotent stem cells (iPSCs) from patients of different ethnicities, ß-globin gene (HBB) haplotypes, and fetal hemoglobin (HbF) levels. iPSCs stand to revolutionize the way we study human development, model disease, and perhaps eventually, treat patients. Here, we describe this unique resource for the study of sickle cell disease, including novel haplotype-specific polymorphisms that affect disease severity, as well as for the development of patient-specific therapeutics for this phenotypically diverse disorder. As a complement to this library, and as proof of principle for future cell- and gene-based therapies, we also designed and employed CRISPR/Cas gene editing tools to correct the sickle hemoglobin (HbS) mutation.

Crystallization and preliminary X-ray crystallographic studies of glutamate racemase from Lactobacillus fermenti.

Glutamate racemase catalyzes the conversion of L-glutamic acid to D-glutamic acid and vice versa. Since D-glutamic acid is one of the essential amino acids present in peptidoglycan, glutamate racemase has been considered to be an attractive target for the design of new antibacterial drugs. Glutamate racemase from Lactobacillus fermenti has been crystallized by the hanging-drop vapour-diffusion method using polyethylene glycol 8000 as a precipitant. The crystals belong to the orthorhombic space group C222(1), with unit-cell parameters a = 98.32, b = 184.09, c = 45.99 A. The asymmetric unit contains one molecule, corresponding to a VM value of 1.84 A3 Da(-1). A complete data set has been collected from the native enzyme at 2.28 A resolution using a synchrotron-radiation source.