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While IFNγ is a well-known cytokine that actively promotes the type I immune response, it is also known to suppress the type II response by inhibiting the differentiation and proliferation of Th2 cells. However, the mechanism by which IFNγ suppresses Th2 cell proliferation is still not fully understood. We found that IFNγ decreases the expression of growth factor independent-1 transcriptional repressor (GFI1) in Th2 cells, resulting in the inhibition of Th2 cell proliferation. The deletion of the Gfi1 gene in Th2 cells results in the failure of their proliferation, accompanied by an impaired cell cycle progression. In contrast, the enforced expression of GFI1 restores the defective Th2 cell proliferation, even in the presence of IFNγ. These results demonstrate that GFI1 is a key molecule in the IFNγ-mediated inhibition of Th2 cell proliferation., Competing Interests: The authors declare no conflicts of interest in association with the present study.

Mutations in GBA (glucosylceramidase beta), which encodes the lysosomal enzyme glucocerebrosidase (GCase), are the strongest genetic risk factor for the neurodegenerative disorders Parkinson's disease (PD) and Lewy body dementia. Recent work has suggested that neuroinflammation may be an important factor in the risk conferred by GBA mutations. We therefore systematically tested the contributions of immune-related genes to neuropathology in a Drosophila model of GCase deficiency. We identified target immune factors via RNA-Seq and proteomics on heads from GCase-deficient flies, which revealed both increased abundance of humoral factors and increased macrophage activation. We then manipulated the identified immune factors and measured their effect on head protein aggregates, a hallmark of neurodegenerative disease. Genetic ablation of humoral (secreted) immune factors did not suppress the development of protein aggregation. By contrast, re-expressing Gba1b in activated macrophages suppressed head protein aggregation in Gba1b mutants and rescued their lifespan and behavioral deficits. Moreover, reducing the GCase substrate glucosylceramide in activated macrophages also ameliorated Gba1b mutant phenotypes. Taken together, our findings show that glucosylceramide accumulation due to GCase deficiency leads to macrophage activation, which in turn promotes the development of neuropathology. Author summary: Mutations in the gene GBA are the largest risk factor for developing Parkinson's disease and Lewy body dementia, diseases in which important brain cells die. We know that the immune system can be involved in these diseases, and that GBA mutations cause immune changes. We did experiments to learn how the immune system changes could make brain cells more likely to die. Using a fruit fly that was missing the fly version of GBA, we found out that inappropriately activated immune cells, but not secreted immune proteins, were important in the development of brain problems. We also learned that the abnormal activation was triggered by the lack of GBA function in the immune cells, not by signals from the brain or other parts of the body. We would like to find out next whether the immune cells get inside the brain or cause harm from a distance. What we learned matters because it could help us prevent or cure brain diseases associated with GBA mutations. Treating the abnormal activation of immune cells in people with these mutations might help prevent damage to the brain. [ABSTRACT FROM AUTHOR]

Hamstring injuries are associated with decreased hamstring strength. Matinlauri et al.'s 90:20 Isometric Posterior Chain Test (90:20 IPCT) efficiently assesses hamstring strength, but has not been validated so far. Furthermore, their rather unprecise original instruction allows high variability in test execution. We added a new instruction and variables and examined, whether this measure leads to increased reliability and validity. We assessed hamstring strength of 23 sport students via the 90:20 IPCT under the original instruction, to exert vertical force, and our new instruction, to exert vertical and horizontal force. Instead of only using bare vertical force as variable under the original (Fz_V) and our new instruction (Fz_VH), we also calculated the resultant force (Fres_VH) and the applied torque onto the force place (M_F_ortho_VH). To test for validity, we correlated the outcome variables with peak torque of gold standard dynamometry. Furthermore, we measured muscle activities of the mm. rectus femoris, biceps femoris, semitendinosus, and gluteus maximus under our new instruction and compared them to those under the original variable (Fz_V) via one sample t-tests. To evaluate reliability, tests were repeated on two separate days, for which we calculated intra class correlation coefficients (ICCs) and coefficients of variation (CVs). Our new instruction and variables (Fz_VH, Fres_VH, M_F_ortho_VH) showed better validity (mean r = 0.77, r = 0.81, and r = 0.85) and equally good or better reliability (ICCs: 0.87, 0.89, and 0.94; CVs: 4.7%, 4.1%, and 4.7%) than the original instruction and variable (Fz_V) (mean r = 0.70; ICC: 0.91; CV: 5.6%). There were no differences in muscle activities between the variables and instructions of the 90:20 IPCT. We recommend our new instruction and the applied torque onto the force plate as it makes the 90:20 IPCT a more reliable and valid tool to assess hamstring strength. [ABSTRACT FROM AUTHOR]

The hypersonic effect is a phenomenon in which sounds containing significant quantities of non-stationary high-frequency components (HFCs) above the human audible range (max. 20 kHz) activate the midbrain and diencephalon and evoke various physiological, psychological and behavioral responses. Yet important issues remain unverified, especially the relationship existing between the frequency of HFCs and the emergence of the hypersonic effect. In this study, to investigate the relationship between the hypersonic effect and HFC frequencies, we divided an HFC (above 16 kHz) of recorded gamelan music into 12 band components and applied them to subjects along with an audible component (below 16 kHz) to observe changes in the alpha2 frequency component (10-13 Hz) of spontaneous EEGs measured from centro-parieto-occipital regions (Alpha-2 EEG), which we previously reported as an index of the hypersonic effect. Our results showed reciprocal directional changes in Alpha-2 EEGs depending on the frequency of the HFCs presented with audible low-frequency component (LFC). When an HFC above approximately 32 kHz was applied, Alpha-2 EEG increased significantly compared to when only audible sound was applied (positive hypersonic effect), while, when an HFC below approximately 32 kHz was applied, the Alpha-2 EEG decreased (negative hypersonic effect). These findings suggest that the emergence of the hypersonic effect depends on the frequencies of inaudible HFC.

The TGF-β homolog Decapentaplegic (Dpp) acts as a secreted morphogen in the Drosophila wing disc, and spreads through the target tissue in order to form a long range concentration gradient. Despite extensive studies, the mechanism by which the Dpp gradient is formed remains controversial. Two opposing mechanisms have been proposed: receptor-mediated transcytosis (RMT) and restricted extracellular diffusion (RED). In these scenarios the receptor for Dpp plays different roles. In the RMT model it is essential for endocytosis, re-secretion, and thus transport of Dpp, whereas in the RED model it merely modulates Dpp distribution by binding it at the cell surface for internalization and subsequent degradation. Here we analyzed the effect of receptor mutant clones on the Dpp profile in quantitative mathematical models representing transport by either RMT or RED. We then, using novel genetic tools, experimentally monitored the actual Dpp gradient in wing discs containing receptor gain-of-function and loss-of-function clones. Gain-of-function clones reveal that Dpp binds in vivo strongly to the type I receptor Thick veins, but not to the type II receptor Punt. Importantly, results with the loss-of-function clones then refute the RMT model for Dpp gradient formation, while supporting the RED model in which the majority of Dpp is not bound to Thick veins. Together our results show that receptor-mediated transcytosis cannot account for Dpp gradient formation, and support restricted extracellular diffusion as the main mechanism for Dpp dispersal. The properties of this mechanism, in which only a minority of Dpp is receptor-bound, may facilitate long-range distribution., Competing Interests: The authors have declared that no competing interests exist.

The generalization of deep neural network algorithms to a broader population is an important challenge in the medical field. We aimed to apply self-supervised learning using masked autoencoders (MAEs) to improve the performance of the 12-lead electrocardiography (ECG) analysis model using limited ECG data. We pretrained Vision Transformer (ViT) models by reconstructing the masked ECG data with MAE. We fine-tuned this MAE-based ECG pretrained model on ECG-echocardiography data from The University of Tokyo Hospital (UTokyo) for the detection of left ventricular systolic dysfunction (LVSD), and then evaluated it using multi-center external validation data from seven institutions, employing the area under the receiver operating characteristic curve (AUROC) for assessment. We included 38,245 ECG-echocardiography pairs from UTokyo and 229,439 pairs from all institutions. The performances of MAE-based ECG models pretrained using ECG data from UTokyo were significantly higher than that of other Deep Neural Network models across all external validation cohorts (AUROC, 0.913–0.962 for LVSD, p < 0.001). Moreover, we also found improvements for the MAE-based ECG analysis model depending on the model capacity and the amount of training data. Additionally, the MAE-based ECG analysis model maintained high performance even on the ECG benchmark dataset (PTB-XL). Our proposed method developed high performance MAE-based ECG analysis models using limited ECG data. [ABSTRACT FROM AUTHOR]

The intercropping system is a promising approach to augmenting the soil nutrient status and promoting sustainable crop production. However, it is not known whether intercropping improves the soil phosphorus (P) status in alluvial soils with low P under subtropical climates. Over two growing seasons––2019–2020 and 2020–2021––two experimental fields were employed to explore the effect of durum wheat (Dw) and chickpea (Cp) cropping systems on the soil available P. A randomized complete block design was used in this experiment, with three blocks each divided into three plots. Each plot was used for one of the following three treatments with three replications: Dw monocrop (Dw-MC), Cp monocrop (Cp-MC), and Dw + Cp intercrop (CpDw-InC), with bulk soil (BS) used as a control. A reduction in the rhizosphere soil pH (-0.44 and -0.11 unit) was observed in the (Cp-MC) and (CpDw-InC) treatments over BS, occurring concomitantly with a significant increase in available P in the rhizosphere soil of around 28.45% for CpDw-InC and 24.9% for Cp-MC over BS. Conversely, the rhizosphere soil pH was significantly higher (+0.12 units) in the Dw-MC treatments. In addition, intercropping enhanced the soil microbial biomass P, with strong positive correlations observed between the biomass P and available P in the Cp-MC treatment, whereas this correlation was negative in the CpDw-InC and Dw-MC treatments. These findings suggested that Cp intercropped with Dw could be a viable approach in enhancing the available P through improved pH variation and biomass P when cultivated on alluvial soil under a subtropical climate. [ABSTRACT FROM AUTHOR]

Cell adhesion requires linkage of transmembrane receptors to the cytoskeleton through intermediary linker proteins. Integrin-based adhesion to the extracellular matrix (ECM) involves large adhesion complexes that contain multiple cytoskeletal adapters that connect to the actin cytoskeleton. Many of these adapters, including the essential cytoskeletal linker Talin, have been shown to contain multiple actin-binding sites (ABSs) within a single protein. To investigate the possible role of having such a variety of ways of linking integrins to the cytoskeleton, we generated mutations in multiple actin binding sites in Drosophila talin. Using this approach, we have been able to show that different actin-binding sites in talin have both unique and complementary roles in integrin-mediated adhesion. Specifically, mutations in either the C-terminal ABS3 or the centrally located ABS2 result in lethality showing that they have unique and non-redundant function in some contexts. On the other hand, flies simultaneously expressing both the ABS2 and ABS3 mutants exhibit a milder phenotype than either mutant by itself, suggesting overlap in function in other contexts. Detailed phenotypic analysis of ABS mutants elucidated the unique roles of the talin ABSs during embryonic development as well as provided support for the hypothesis that talin acts as a dimer in in vivo contexts. Overall, our work highlights how the ability of adhesion complexes to link to the cytoskeleton in multiple ways provides redundancy, and consequently robustness, but also allows a capacity for functional specialization. Author summary: The construction of tissues in animals requires cells to form attachments (adhesions), to other cells or the surrounding mixture of proteins and molecules known as the Extracellular matrix (ECM). Cell adhesion to the ECM has an important role in providing the mechanical stability that allows cells to arrange into different shapes during animal development. Key to this stability is their ability to connect to and organise the intracellular cytoskeleton such that it forms a scaffold that is both strong and flexible. To study the strategies used by cells to link the ECM to the cytoskeleton we introduced mutations into a protein called talin that is a key intermediary in adhesions between the outside environment and the cytoskeleton. Talin has different ways of linking to the actin cytoskeleton as it contains multiple domains that bind actin. Using a genetic approach, we disrupted these domains separately or together to block actin binding. We found these domains have both unique and complementary roles in cell-ECM adhesion indicating that having multiple actin-binding sites provides functional redundancy and specialization. Overall, our findings provide mechanistic insight into how cells can regulate cell adhesions by changing how they link to the cytoskeleton. [ABSTRACT FROM AUTHOR]

Amyotrophic Lateral Sclerosis (ALS) is a progressive neurodegenerative disease that affects motor neurons, resulting in muscle weakness, paralysis, and eventually patient mortality. In recent years, neuromodulation techniques have emerged as promising potential therapeutic approaches to slow disease progression and improve the quality of life of ALS patients. A systematic review was conducted until August 8, 2023, to evaluate the neuromodulation methods used and their potential in the treatment of ALS. The search strategy was applied in the Cochrane Central database, incorporating results from other databases such as PubMed, Embase, CTgov, CINAHL, and ICTRP. Following the exclusion of papers that did not fulfil the inclusion criteria, a total of 2090 records were found, leaving a total of 10 studies. R software was used to conduct meta-analyses based on the effect sizes between the experimental and control groups. This revealed differences in muscle stretch measures with manual muscle testing (p = 0.012) and resting motor threshold (p = 0.0457), but not with voluntary isometric contraction (p = 0.1883). The functionality of ALS was also different (p = 0.007), but not the quality of life. Although intracortical facilitation was not seen in motor cortex 1 (M1) (p = 0.1338), short-interval intracortical inhibition of M1 was significant (p = 0.0001). BDNF showed no differences that were statistically significant (p = 0.2297). Neuromodulation-based treatments are proposed as a promising therapeutic approach for ALS that can produce effects on muscle function, spasticity, and intracortical connections through electrical, magnetic, and photonic stimulation. Photobiomodulation stands out as an innovative approach that uses specific wavelengths to influence mitochondria, with the aim of improving mitochondrial function and reducing excitotoxicity. The lack of reliable placebo controls and the variation in stimulation frequency are some of the drawbacks of neuromodulation. [ABSTRACT FROM AUTHOR]

Several lines of evidence demonstrate that increased neuronal excitability can enhance proteomic stress. For example, epilepsy can enhance the proteomic stress caused by the expression of certain aggregation-prone proteins implicated in neurodegeneration. However, unanswered questions remain concerning the mechanisms by which increased neuronal excitability accomplishes this enhancement. Here we test whether increasing neuronal excitability at a particular identified glutamatergic synapse, the Drosophila larval neuromuscular junction, can enhance the proteomic stress caused by mutations in the ER fusion/GTPase gene atlastin (atl). It was previously shown that larval muscle from the atl2 null mutant is defective in autophagy and accumulates protein aggregates containing ubiquitin (poly-UB aggregates). To determine if increased neuronal excitability might enhance the increased proteomic stress caused by atl2, we activated the TrpA1-encoded excitability channel within neurons. We found that TrpA1 activation had no effect on poly-UB aggregate accumulation in wildtype muscle, but significantly increased poly-UB aggregate number in atl2 muscle. Previous work has shown that atl loss from either neuron or muscle increases muscle poly-UB aggregate number. We found that neuronal TrpA1 activation enhanced poly-UB aggregate number when atl was removed from muscle, but not from neuron. Neuronal TrpA1 activation enhanced other phenotypes conferred by muscle atl loss, such as decreased pupal size and decreased viability. Taken together, these results indicate that the proteomic stress caused by muscle atl loss is enhanced by increasing neuronal excitability. [ABSTRACT FROM AUTHOR]

WNK (With no Lysine [K]) kinases have critical roles in the maintenance of ion homeostasis and the regulation of cell volume. Their overactivation leads to pseudohypoaldosteronism type II (Gordon syndrome) characterized by hyperkalemia and high blood pressure. More recently, WNK family members have been shown to be required for the development of the nervous system in mice, zebrafish, and flies, and the cardiovascular system of mice and fish. Furthermore, human WNK2 and Drosophila Wnk modulate canonical Wnt signaling. In addition to a well-conserved kinase domain, animal WNKs have a large, poorly conserved C-terminal domain whose function has been largely mysterious. In most but not all cases, WNKs bind and activate downstream kinases OSR1/SPAK, which in turn regulate the activity of various ion transporters and channels. Here, we show that Drosophila Wnk regulates Wnt signaling and cell size during the development of the wing in a manner dependent on Fray, the fly homolog of OSR1/SPAK. We show that the only canonical RF(X)V/I motif of Wnk, thought to be essential for WNK interactions with OSR1/SPAK, is required to interact with Fray in vitro. However, this motif is unexpectedly dispensable for Fray-dependent Wnk functions in vivo during fly development and fluid secretion in the Malpigian (renal) tubules. In contrast, a structure function analysis of Wnk revealed that the less-conserved C-terminus of Wnk, that recently has been shown to promote phase transitions in cell culture, is required for viability in vivo. Our data thus provide novel insights into unexpected in vivo roles of specific WNK domains. Author summary: Members of the conserved WNK kinase family are large proteins that have essential developmental roles, as well as crucial functions in the regulation of ion transporters in kidneys via the intermediary kinases OSR1 and SPAK. Using Drosophila as model system, we show that the fly homolog of the intermediary kinases, Fray, acts downstream of Wnk during the development of the fly wing to regulate cell size. Surprisingly though, our work reveals that Wnk does not need the canonical motif that binds to Fray for function in vivo. In contrast, we find an essential function for the less-well conserved C-terminus of Wnk that recently was shown to form membraneless organelles. Our findings thus reveal unanticipated roles of WNK domains. [ABSTRACT FROM AUTHOR]

Goal: To evaluate the acute impact of a nutraceutical blend on immune surveillance. Study design: A randomized, double-blind, placebo-controlled, cross-over trial was conducted in 11 healthy subjects. Blood samples were taken immediately before and at 1, 2, and 3 hours after consuming placebo or 500 mg of UP360, which is a blend of botanicals from Aloe vera, Poria cocos, and rosemary (APR extract). Immunophenotyping and flow cytometry quantified numbers of monocytes, NK cells, NKT cells, CD8+ cytotoxic T cells, γδT cells, and total T cells, and expression of CD25 and CD69 activation markers. Plasma was tested for cytokines, chemokines, growth factors, and enzymatic activity of superoxide dismutase and catalase. Results: Compared to the placebo, consumption of APR extract triggered rapid increases in chemokine levels starting at 1 hour, including IP-10 (P<0.05) and MCP-1 (P<0.1), which peaked at 2 hours (P<0.01) and 3 hours (P<0.05), respectively. The stem cell-mobilizing growth factor G-CSF increased at 2 hours (P<0.05). Increased immune surveillance involved a transient effect for monocytes at 1 hour, followed by NKT cells, CD8+ cytotoxic T cells, and γδT cells at 2–3 hours. Increased immune cell alertness was seen at 1 hour by increased CD25 expression on monocytes (P<0.01), NKT cells (P<0.01), and T cells (P<0.05). NKT cells showed upregulation of CD69 at 2 hours (P<0.01). Increased enzymatic activity was seen at 2 hours for the antioxidant enzymes superoxide dismutase (P<0.05) and catalase (P<0.01). Conclusion: Consumption of APR extract triggered acute changes to chemokine levels. In addition, immune alertness was increased via the expression of activation markers on multiple types of innate immune cells, followed by increased immune surveillance and antioxidant protection. This suggests a beneficial enhancement of natural immune surveillance, likely via a combination of gut-mediated cytokine release and vagus nerve communication, in combination with cellular protection from oxidative stress. [ABSTRACT FROM AUTHOR]

Pluripotency defines the unlimited potential of individual cells of vertebrate embryos, from which all adult somatic cells and germ cells are derived. Understanding how the programming of pluripotency evolved has been obscured in part by a lack of data from lower vertebrates; in model systems such as frogs and zebrafish, the function of the pluripotency genes NANOG and POU5F1 have diverged. Here, we investigated how the axolotl ortholog of NANOG programs pluripotency during development. Axolotl NANOG is absolutely required for gastrulation and germ-layer commitment. We show that in axolotl primitive ectoderm (animal caps; ACs) NANOG and NODAL activity, as well as the epigenetic modifying enzyme DPY30, are required for the mass deposition of H3K4me3 in pluripotent chromatin. We also demonstrate that all 3 protein activities are required for ACs to establish the competency to differentiate toward mesoderm. Our results suggest the ancient function of NANOG may be establishing the competence for lineage differentiation in early cells. These observations provide insights into embryonic development in the tetrapod ancestor from which terrestrial vertebrates evolved. The role of Nanog and Nodal in establishing pluripotency in an amphibian, the axolotl, indicates that the gene regulatory networks underlying pluripotency are conserved and provided the basis for the evolution of mesoderm. [ABSTRACT FROM AUTHOR]

Background: Muscle strain injuries (MSIs) in the hamstrings are among the most prevalent injuries in elite soccer. We aimed to examine the relation between biomechanical maladaptation in eccentric strength and neuromuscular factors separated by their time and frequency domains. Methods: 20 elite soccer players with a previous history of unilateral MSI in the M. biceps femoris (BF) long head and 20 without MSI participated. Knee flexion torques, rate of torque development (RTD) and electromyographic signals (EMG) of the BF, the M. semitendinosus (SMT) and knee extensors were obtained during unilateral maximal eccentric knee flexions performed at slow (30°/s) and fast (120°/s) angular speeds. Root mean squares and mean power frequency (MF) was calculated. Results: In the group with a history of MSI, reduced maximal eccentric flexion torque (slow eccentrics -8±11, p<0.05; fast eccentrics -18±13 N*m, p<0.05) and RTD (-33±28 N*m/s, p<0.05; -95±47 N*m/s, p<0.05) concomitantly occurred with diminished agonistic myoelectrical activities (-4±5% of MVC, p<0.05; -10±7% of MVC, p<0.05) and MFs (-24±13 Hz, p<0.05; -24±18 Hz, p<0.05) in the BF. Simultaneously, antagonistic myoelectric activity was elevated (+4±3% of MVC, p<0.05; +3±3% of MVC, p<0.05) in MSI affected legs as compared to unaffected legs for both eccentric contractions. Deficits in myoelectrical activity (r2 = 0.715, p<0.05; r2 = 0.601, p<0.05) and MF (r2 = 0.484, p<0.05; r2 = 0.622, p<0.05) correlated with deficits in maximal torque in the affected leg in the MSI group. Analysis of SMT demonstrated no significant differences. Conclusion: Positive relationships between neuromuscular deficits and the reduced eccentric strength profile underpin neuronal inhibition after MSI. This persistent involvement of dysfunctional synergist and antagonist neural hamstring function in strength weakness is of clinical relevance in sports medicine for prevention and rehabilitation. [ABSTRACT FROM AUTHOR]

YES-associated protein (YAP), a critical actor of the mammalian Hippo signaling pathway involved in diverse biological events, has gained increased recognition as a cellular factor regulated by viral infections, but very few studies have investigated their relationship vice versa. In this study, we show that YAP impairs HCMV replication as assessed by viral gene expression analysis and progeny assays, and that this inhibition occurs at the immediate-early stages of the viral life cycle, at the latest. Using YAP mutants lacking key functional domains and shRNA against TEAD, we show that the inhibitory effects of YAP on HCMV replication are nuclear localization- and TEAD cofactor-dependent. Quantitative real-time PCR (qPCR) and subcellular fractionation analyses reveal that YAP does not interfere with the viral entry process but inhibits transport of the HCMV genome into the nucleus. Most importantly, we show that the expression of stimulator of interferon genes (STING), recently identified as an important component for nuclear delivery of the herpesvirus genome, is severely downregulated by YAP at the level of gene transcription. The functional importance of STING is further confirmed by the observation that STING expression restores YAP-attenuated nuclear transport of the HCMV genome, viral gene expression, and progeny virus production. We also show that HCMV-upregulated YAP reduces expression of STING. Taken together, these findings indicate that YAP possesses both direct and indirect regulatory roles in HCMV replication at different infection stages. Author summary: Human cytomegalovirus (HCMV) infections in immunocompromised patients cause morbidity and mortality, and congenital infections can lead to severe neurodevelopmental deficits such as microcephaly. This study shows that YAP, a transcription factor renowned for its roles in diverse cellular events, potently inhibits HCMV viral gene expression and subsequent infectious progeny production. Furthermore, we find that these inhibitory effects of YAP on HCMV replication are due to inefficient delivery of the HCMV genome into the nuclei of the host cells, thus hindering a key early step of the viral life cycle. Importantly, we pinpoint that YAP reduces STING protein levels, contributing to the impaired nuclear transport of the HCMV genome. Taken together, our findings provide insight into the molecular features of YAP regulation of viral replication, and novel antiviral approaches against HCMV and other herpesvirus infections. [ABSTRACT FROM AUTHOR]

Understanding the regulatory interactions that control gene expression during the development of novel tissues is a key goal of evolutionary developmental biology. Here, we show that Mbnl3 has undergone a striking process of evolutionary specialization in eutherian mammals resulting in the emergence of a novel placental function for the gene. Mbnl3 belongs to a family of RNA-binding proteins whose members regulate multiple aspects of RNA metabolism. We find that, in eutherians, while both Mbnl3 and its paralog Mbnl2 are strongly expressed in placenta, Mbnl3 expression has been lost from nonplacental tissues in association with the evolution of a novel promoter. Moreover, Mbnl3 has undergone accelerated protein sequence evolution leading to changes in its RNA-binding specificities and cellular localization. While Mbnl2 and Mbnl3 share partially redundant roles in regulating alternative splicing, polyadenylation site usage and, in turn, placenta maturation, Mbnl3 has also acquired novel biological functions. Specifically, Mbnl3 knockout (M3KO) alone results in increased placental growth associated with higher Myc expression. Furthermore, Mbnl3 loss increases fetal resource allocation during limiting conditions, suggesting that location of Mbnl3 on the X chromosome has led to its role in limiting placental growth, favoring the maternal side of the parental genetic conflict. This study reveals that the RNA binding protein Mbnl3 has undergone a process of evolutionary divergence in eutherian mammals associated with the emergence of a role in restricting placental growth, favoring the maternal side of the parental genetic conflict, and likely driven by its location on the X chromosome. [ABSTRACT FROM AUTHOR]

Few reports exist regarding the expression and function of Wilms' tumor 1-associated protein (WTAP) in colorectal cancer (CRC), and the evidence is controversial. Our analysis explored the expression of WTAP in CRC tissue, and analyzed its clinical and prognostic significance. WTAP expression was significantly higher in CRC tissue than in colorectal adenoma and normal colorectal tissue. WTAP was highest in left colon tumor samples and negatively associated with tumor differentiation, as well as depth of tumor invasion. In multiple logistic regression analysis, independent predictors of WTAP expression in CRC included tumor in the left colon (odds ratio = 2.634; 95% confidence interval: 1.129–6.142; P = 0.025) and poorly differentiated tissue (0.072; 0.014–0.367; P = 0.002). No clear relationship was observed between CRC patient prognosis and WTAP expression. We suggest that WTAP expression is upregulated in CRC, highly expressed in left colon cancer and negatively correlated with tumor differentiation. [ABSTRACT FROM AUTHOR]

Majority of Pakistani soils are deficient in phosphorus. Phosphorus is usually applied in form of synthetic fertilizer. However integrated use of P from synthetic and organic sources can be more profitable and beneficial on sustainable basis. Field trials were conducted at research farm University of Poonch, Rawalakot, AJK, Pakistan for two consecutive years to check the comparative effects of synthetic fertilizer and organic manures applied alone and in combinations on the phosphorus use efficiency (PUE), wheat yield and yield components. Shafaq-06 cultivar of wheat was used as test cultivar. Ten treatments were included: (I) Control (P0) without application of fertilizer; (II) SSP @ 60 kg/ha (P60SSP); (III) SSP @ 90 kg/ha (P90SSP); (IV) SSP @ 120 kg/ha (P120SSP); (V) PM @60 kg/ha (P60PM); (VI) PM @90 kg/ha (P90PM); (VII) PM @120 kg/ha (P120PM); (VIII) SSP @30 kg/ha + PM @30 kg/ha (P30SSP+30PM); (IX) SSP @45 kg/ha + PM @45 kg/ha (P45SSP+45PM); (X) SSP @60 kg/ha + PM @60 kg/ha (P60SSP+60PM) which were laid out under the Randomized Complete Block Design. Significantly higher values for yield of grain (2397 kg/ha) was recorded with PM + SSP @ 60 kg P2O5 ha-1 each. Likewise, FPUE, PIR of wheat and AFPUE was quite higher with combined use of PM and SSP i.e. P60SSP+60PM treatment. Additionally, increase in PUE, wheat yield and yield components associated with combined treated plot would help to minimize the use of high cost synthetic mineral fertilizers and represents an environmentally and agronomically sound management strategy. [ABSTRACT FROM AUTHOR]

Morphogen gradients are crucial for the development of organisms. The biochemical properties of many morphogens prevent their extracellular free diffusion, indicating the need of an active mechanism for transport. The involvement of filopodial structures (cytonemes) has been proposed for morphogen signaling. Here, we describe an in silico model based on the main general features of cytoneme-meditated gradient formation and its implementation into Cytomorph, an open software tool. We have tested the spatial and temporal adaptability of our model quantifying Hedgehog (Hh) gradient formation in two Drosophila tissues. Cytomorph is able to reproduce the gradient and explain the different scaling between the two epithelia. After experimental validation, we studied the predicted impact of a range of features such as length, size, density, dynamics and contact behavior of cytonemes on Hh morphogen distribution. Our results illustrate Cytomorph as an adaptive tool to test different morphogens gradients and to generate hypotheses that are difficult to study experimentally. Author summary: Graded distribution of signaling molecules (morphogens) is crucial for the development of organisms. Signaling membrane protrusions, called Cytonemes, have been experimentally demonstrated to be involved in morphogen transport and reception. Here, we have developed an in silico model for gradient formation based on key features of cytoneme mediated signaling. We have also implemented the model into an open software tool we named Cytomorph, and validated it by comparing its simulations with experimental data obtained from Hedgehog morphogen distribution. Finally, we have generated in silico predictions for the impact of different cytoneme features such as length, size, density, dynamics and contact behavior. Our results show that Cytomorph is an adaptive tool that can facilitate the study of other cytoneme-dependent morphogen gradients, besides being able to generate hypotheses about aspects that remain elusive to experimental approaches. [ABSTRACT FROM AUTHOR]

The Epstein-Barr virus (EBV) human herpesvirus is associated with B-cell and epithelial-cell malignancies, and both the latent and lytic forms of viral infection contribute to the development of EBV-associated tumors. Here we show that the Hippo signaling effectors, YAP and TAZ, promote lytic EBV reactivation in epithelial cells. The transcriptional co-activators YAP/TAZ (which are inhibited by Hippo signaling) interact with DNA-binding proteins, particularly TEADs, to induce transcription. We demonstrate that depletion of either YAP or TAZ inhibits the ability of phorbol ester (TPA) treatment, cellular differentiation or the EBV BRLF1 immediate-early (IE) protein to induce lytic EBV reactivation in oral keratinocytes, and show that over-expression of constitutively active forms of YAP and TAZ reactivate lytic EBV infection in conjunction with TEAD family members. Mechanistically, we find that YAP and TAZ interact with, and activate, the EBV BZLF1 immediate-early promoter. Furthermore, we demonstrate that YAP, TAZ, and TEAD family members are expressed at much higher levels in epithelial cell lines in comparison to B-cell lines, and find that EBV infection of oral keratinocytes increases the level of activated (dephosphorylated) YAP and TAZ. Finally, we have discovered that lysophosphatidic acid (LPA), a known YAP/TAZ activator that plays an important role in inflammation, induces EBV lytic reactivation in epithelial cells through a YAP/TAZ dependent mechanism. Together these results establish that YAP/TAZ are powerful inducers of the lytic form of EBV infection and suggest that the ability of EBV to enter latency in B cells at least partially reflects the extremely low levels of YAP/TAZ and TEADs in this cell type. Author summary: EBV causes infectious mononucleosis and persists in latently infected B cells for life. The virus periodically reactivates to a lytic form that produces infectious virus particles, allowing the virus to infect new cells and be transmitted to new hosts. Oral epithelial cells are an important site of lytic viral infection, promoting secretion of infectious virus into saliva. Rarely, EBV infection results in B-cell and epithelial-cell human tumors, and both the latent and lytic forms of infection contribute to these malignancies. However, the viral and cellular factors that determine whether the virus remains latent or lytic are still incompletely understood. Here we have discovered that the Hippo signaling pathway is an important regulator of lytic EBV reactivation, particularly in epithelial cells. We show that transcriptional co-activators YAP and TAZ (which are turned off by Hippo signaling) are strong inducers of lytic EBV reactivation, collaborating with DNA-binding TEAD proteins to activate EBV immediate-early genes. Furthermore, we demonstrate that epithelial cells express much higher levels of YAP/TAZ/TEADs in comparison to B cells, helping to explain why B cells support latent infection. Finally, we find that lysophosphatidic acid, a YAP/TAZ activator, induces lytic reactivation through a YAP/TAZ-dependent mechanism. [ABSTRACT FROM AUTHOR]

Drosophila larvae and pupae are at high risk of parasitoid infection in nature. To circumvent parasitic stress, fruit flies have developed various survival strategies, including cellular and behavioral defenses. We show that adult Drosophila females exposed to the parasitic wasps, Leptopilina boulardi, decrease their total egg-lay by deploying at least two strategies: Retention of fully developed follicles reduces the number of eggs laid, while induction of caspase-mediated apoptosis eliminates the vitellogenic follicles. These reproductive defense strategies require both visual and olfactory cues, but not the MB247-positive mushroom body neuronal function, suggesting a novel mode of sensory integration mediates reduced egg-laying in the presence of a parasitoid. We further show that neuropeptide F (NPF) signaling is necessary for both retaining matured follicles and activating apoptosis in vitellogenic follicles. Whereas previous studies have found that gut-derived NPF controls germ stem cell proliferation, we show that sensory-induced changes in germ cell development specifically require brain-derived NPF signaling, which recruits a subset of NPFR-expressing cell-types that control follicle development and retention. Importantly, we found that reduced egg-lay behavior is specific to parasitic wasps that infect the developing Drosophila larvae, but not the pupae. Our findings demonstrate that female fruit flies use multimodal sensory integration and neuroendocrine signaling via NPF to engage in parasite-specific cellular and behavioral survival strategies. Author summary: Behavioral adaptation to environmental threats such as infectious diseases or predators increases the survival and fitness of an organism. Here, we studied behavioral immunity in adult Drosophila females that protect their progeny from the parasitic infection. We show that Drosophila females modify their oviposition behavior in the presence of a parasitic wasp. This change in reproductive behavior is highly specific to Leptopilina wasps, which necessitates both visual as well as the parasitoid-specific olfactory cues. In addition, we find that the transient retention of matured follicles and increased apoptosis of the developing follicles in the parasitoid-exposed Drosophila ovaries results in an egg-lay reduction. We also identify that the neuroendocrine signaling involving neuropeptide F (NPF) and its cognate receptor, NPFR, mediates the parasitoid-induced egg-lay depression and germline physiological modifications. Based on the innate recognition of the predatory threat, our study unravels the cellular and physiological mechanisms that underlie an ecological relevant form of behavioral adaptation in Drosophila. [ABSTRACT FROM AUTHOR]

Development of the Drosophila wing—a paradigm of organ development—is governed by 2 morphogens, Decapentaplegic (Dpp, a BMP) and Wingless (Wg, a Wnt). Both proteins are produced by defined subpopulations of cells and spread outwards, forming gradients that control gene expression and cell pattern as a function of concentration. They also control growth, but how is unknown. Most studies have focused on Dpp and yielded disparate models in which cells throughout the wing grow at similar rates in response to the grade or temporal change in Dpp concentration or to the different amounts of Dpp "equalized" by molecular or mechanical feedbacks. In contrast, a model for Wg posits that growth is governed by a progressive expansion in morphogen range, via a mechanism in which a minimum threshold of Wg sustains the growth of cells within the wing and recruits surrounding "pre-wing" cells to grow and enter the wing. This mechanism depends on the capacity of Wg to fuel the autoregulation of vestigial (vg)—the selector gene that specifies the wing state—both to sustain vg expression in wing cells and by a feed-forward (FF) circuit of Fat (Ft)/Dachsous (Ds) protocadherin signaling to induce vg expression in neighboring pre-wing cells. Here, we have subjected Dpp to the same experimental tests used to elucidate the Wg model and find that it behaves indistinguishably. Hence, we posit that both morphogens act together, via a common mechanism, to control wing growth as a function of morphogen range. Drosophila wing growth depends on the progressive outward spread of the morphogens Decapentaplegic (a member of the BMP family) and Wingless (a member of the Wnt family) via their capacity to sustain the growth of wing cells and to induce neighboring cells to grow and enter the wing. [ABSTRACT FROM AUTHOR]

This study aimed to investigate the influence of the task type on the relative electromyography (EMG) activity of biceps femoris long head (BFlh) to semitendinosus (ST) muscles, and of proximal to distal regions during isometric leg-curl (LC) and hip-extension (HE). Twenty male volunteers performed isometric LC with the knee flexed to 30° (LC30) and 90° (LC90), as well as isometric HE with the knee extended (HE0) and flexed to 90° (HE90), at 40% and 100% maximal voluntary contraction (MVIC). Hip position was neutral in all conditions. EMG activity was recorded from the proximal and distal region of the BFlh and ST muscles. BFlh/ST was calculated from the raw root-mean-square (RMS) amplitudes. The RMS of 40% MVIC was normalized using MVIC data and the proximal/distal (P/D) ratio of normalized EMG (NEMG) was calculated. The BFlh/ST ratio was higher in HE0 than in LC90 during MVIC and 40% MVIC (p<0.05), and was higher in HE90 than in LC90 (p<0.05) during 40% MVIC at the proximal region, whereas no difference was observed between HE0 and LC30. There was no inter-task difference in BFlh/ST ratio in the distal region. Furthermore, the P/D ratio was higher in LC90 than in LC30 and HE0 (p<0.05) in BFlh and ST muscles, and was higher in HE90 than in LC30 and HE0 (p<0.05) in BFlh during 40% MVIC. However, there was no difference in P/D ratio between LC30 and LC90, and HE0 and HE90. This showed that there was no task-dependent difference in the EMG activity of the BFlh muscle relative to the ST muscle between prone hip extension and prone knee flexion when the knee joint was set at an equivalent angle. Similarly, there was no task-dependent difference in the NEMG of the proximal region relative to the distal region in BFlh and ST muscles during 40% MVIC. [ABSTRACT FROM AUTHOR]

The C4 crop maize (Zea mays) is the most widely grown cereal crop worldwide and is an essential feedstock for food and bioenergy. Improving maize yield is important to achieve food security and agricultural sustainability in the 21st century. One potential means to improve crop productivity is to enhance photosynthesis. ictB, a membrane protein that is highly conserved across cyanobacteria, has been shown to improve photosynthesis, and often biomass, when introduced into diverse C3 plant species. Here, ictB from Synechococcus sp. strain PCC 7942 was inserted into maize using Agrobacterium-mediated transformation. In three controlled-environment experiments, ictB insertion increased leaf starch and sucrose content by up to 25% relative to controls. Experimental field trials in four growing seasons, spanning the Midwestern United States (Summers 2018 & 2019) and Argentina (Winter 2018 & 2019), showed an average of 3.49% grain yield improvement, by as much as 5.4% in a given season and up to 9.4% at certain trial locations. A subset of field trial locations was used to test for modification of ear traits and ФPSII, a proxy for photosynthesis. Results suggested that yield gain in transgenics could be associated with increased ФPSII, and the production of longer, thinner ears with more kernels. ictB localized primarily to the microsome fraction of leaf bundle-sheath cells, but not to chloroplasts. Extramembrane domains of ictB interacted in vitro with proteins involved in photosynthesis and carbohydrate metabolism. To our knowledge, this is the first published evidence of ictB insertion into a species using C4 photosynthesis and the largest-scale demonstration of grain yield enhancement from ictB insertion in planta. Results show that ictB is a valuable yield gene in the economically important crop maize, and are an important proof of concept that transgenic manipulation of photosynthesis can be used to create economically viable crop improvement traits. [ABSTRACT FROM AUTHOR]

Mosaic animals have provided the platform for many fundamental discoveries in developmental biology, cell biology, and other fields. Techniques to produce mosaic animals by mitotic recombination have been extensively developed in Drosophila melanogaster but are less common for other laboratory organisms. Here, we report mosaic analysis by gRNA-induced crossing-over (MAGIC), a new technique for generating mosaic animals based on DNA double-strand breaks produced by CRISPR/Cas9. MAGIC efficiently produces mosaic clones in both somatic tissues and the germline of Drosophila. Further, by developing a MAGIC toolkit for 1 chromosome arm, we demonstrate the method's application in characterizing gene function in neural development and in generating fluorescently marked clones in wild-derived Drosophila strains. Eliminating the need to introduce recombinase-recognition sites in the genome, this simple and versatile system simplifies mosaic analysis in Drosophila and can in principle be applied in any organism that is compatible with CRISPR/Cas9. Analysis of mosaic animals has been crucial in developmental and cell biology; this study describes a versatile, simple, and likely widely-applicable technique, MAGIC (mosaic analysis by gRNA-induced crossing-over), for generating mosaic animals based on DNA double-strand breaks produced by CRISPR/Cas9. [ABSTRACT FROM AUTHOR]

The lack of information regarding the water requirement of tree species results in water waste in the seedlings production in nurseries. Water requirement, the growth plant factors and water efficiencies for height and diameter were determined for Schizolobium parahyba (Vell.) Blake, Cytharexylum myrianthum Cham. and Ceiba speciosa Ravenna seedlings, under automated irrigation management and greenhouse conditions, located at 22o45'53" S and 43o41'50" W. We used sewage sludge biosolids as substrate in the seedling phase (280 cm-3 tube), and sandy soil material in the initial pot growth phase (18 dm-3 pot). In the seedlings phase, four water replacement levels were applied to the substrate, by drip irrigation, corresponding to average replacement ranging from 40 (V1) to 100% (V4) of the species water requirement. Seedlings developed properly and 80 days after emergence, S. parahyba, C. myrianthum and C. speciosa seedlings received, respectively, 2.40, 1.08 and 0.85 L per plant, for V4. After growth phase (230 DAE), the total water volumes were, respectively, 70.0, 50.3 and 52.7 L per plant. Under adequate water supply, there were rapid recovery and growth of the species, even for the seedlings which showed different height and diameter in the tube phase. The growth plant factors values found were below 0.5 for all species indicating low sensitivity to growth, both in height and in diameter, in response to water deficit. Water efficiency indicators point to distinct trends between the two phases, and C. speciosa has higher values of water efficiencies for height (80.7 and 17.0 cm L-1) and diameter (2.1 and 0.5 mm L-1) in both phases. [ABSTRACT FROM AUTHOR]

Taste bud cells arise from local epithelial stem cells in the oral cavity and are continuously replaced by newborn cells throughout an animal's life. However, little is known about the molecular and cellular mechanisms of taste cell turnover. Recently, it has been demonstrated that SOX2, a transcription factor expressed in epithelial stem/progenitor cells of the oral cavity, regulates turnover of anterior tongue epithelium including gustatory and non-gustatory papillae. Yet, the role of SOX2 in regulating taste cell turnover in the posterior tongue is unclear. Prompted by the fact that there are regional differences in the cellular and molecular composition of taste buds and stem/progenitor cells in the anterior and posterior portions of tongue, which are derived from distinct embryonic origins, we set out to determine the role of SOX2 in epithelial tissue homeostasis in the posterior tongue. Here we report the differential requirement of SOX2 in the stem/progenitor cells for the normal turnover of lingual epithelial cells in the posterior tongue. Sox2 deletion in the stem/progenitor cells neither induced active caspase 3-mediated apoptotic cell death nor altered stem/progenitor cell population in the posterior tongue. Nevertheless, morphology and molecular feature of non-gustatory epithelial cells were impaired in the circumvallate papilla but not in the filiform papillae. Remarkably, taste buds became thinner, collapsed, and undetectable over time. Lineage tracing of Sox2-deleted stem/progenitor cells demonstrated an almost complete lack of newly generated basal precursor cells in the taste buds, suggesting mechanistically that Sox2 is involved in determining stem/progenitor cells to differentiate to gustatory lineage cells. Together, these results demonstrate that SOX2 plays key roles in regulating epithelial tissue homeostasis in the posterior tongue, similar but not identical to its function in the anterior tongue. [ABSTRACT FROM AUTHOR]

The Ikzf1 locus encodes the lymphoid specific transcription factor Ikaros, which plays an essential role in both T and B cell differentiation, while deregulation or mutation of IKZF1/Ikzf1 is involved in leukemia. Tissue-specific and cell identity genes are usually associated with clusters of enhancers, also called super-enhancers, which are believed to ensure proper regulation of gene expression throughout cell development and differentiation. Several potential regulatory regions have been identified in close proximity of Ikzf1, however, the full extent of the regulatory landscape of the Ikzf1 locus is not yet established. In this study, we combined epigenomics and transcription factor binding along with high-throughput enhancer assay and 4C-seq to prioritize an enhancer element located 120 kb upstream of the Ikzf1 gene. We found that deletion of the E120 enhancer resulted in a significant reduction of Ikzf1 mRNA. However, the epigenetic landscape and 3D topology of the locus were only slightly affected, highlighting the complexity of the regulatory landscape regulating the Ikzf1 locus. [ABSTRACT FROM AUTHOR]

Aims: Much work has been done to find markers of cancer stem cells (CSCs) that distinguish them from the tumor bulk cells and normal cells. Recent CSC research has applied the induced pluripotent stem cell (iPSC) concept. In this study, we investigated the expression of a panel of iPSC markers in primary colon adenocarcinoma (CA)-derived cell lines. Materials and methods: Expression of iPSC markers by CA-derived primary cell lines was interrogated using immunocytochemistry, western blotting and RT-qPCR. The stem cell function of these cells was then assessed in vitro using differentiation and tumorsphere assays. Results: Expression of iPSC markers OCT4, SOX2, NANOG, KLF4 and c-MYC was more widespread in high-grade CA (HGCA) cell lines than low-grade CA (LGCA) cell lines, as demonstrated by western blotting and RT-qPCR. These cells could be induced to differentiate down the three embryonic lineages. Cells derived from HGCA were more capable of forming tumorspheres than those derived from LGCA. EpCAM sorting revealed that a population enriched for EpCAMHigh cells formed larger tumorspheres than EpCAMLow cells. Pluripotency markers, SSEA4 and TRA-1-60, were co-expressed by a small subpopulation of cells that also co-expressed SOX2 in 75% and OCT4 in 50% of the cell lines. Conclusions: CA-derived primary cell lines contain tumorsphere-forming cells which express key pluripotency genes and can differentiate down 3 embryonic lineages, suggesting a pluripotent CSC-like phenotype. There appear to be two iPSC-like subpopulations, one with high EpCAM expression which forms larger tumorspheres than another with low EpCAM expression. Furthermore, these cells can be characterized based on iPSC marker expression, as we have previously demonstrated in the original CA tumor tissues. [ABSTRACT FROM AUTHOR]

During mammalian blastocyst development, inner cell mass (ICM) cells differentiate into epiblast (Epi) or primitive endoderm (PrE). These two fates are characterized by the expression of the transcription factors NANOG and GATA6, respectively. Here, we investigate the spatio-temporal distribution of NANOG and GATA6 expressing cells in the ICM of the mouse blastocysts with quantitative three-dimensional single cell-based neighbourhood analyses. We define the cell neighbourhood by local features, which include the expression levels of both fate markers expressed in each cell and its neighbours, and the number of neighbouring cells. We further include the position of a cell relative to the centre of the ICM as a global positional feature. Our analyses reveal a local three-dimensional pattern that is already present in early blastocysts: 1) Cells expressing the highest NANOG levels are surrounded by approximately nine neighbours, while 2) cells expressing GATA6 cluster according to their GATA6 levels. This local pattern evolves into a global pattern in the ICM that starts to emerge in mid blastocysts. We show that FGF/MAPK signalling is involved in the three-dimensional distribution of the cells and, using a mutant background, we further show that the GATA6 neighbourhood is regulated by NANOG. Our quantitative study suggests that the three-dimensional cell neighbourhood plays a role in Epi and PrE precursor specification. Our results highlight the importance of analysing the three-dimensional cell neighbourhood while investigating cell fate decisions during early mouse embryonic development. [ABSTRACT FROM AUTHOR]

Cell differentiation is a complex process orchestrated by sets of regulators precisely appearing at certain time points, resulting in regulatory cascades that affect the expression of broader sets of genes, ending up in the formation of different tissues and organ parts. The identification of stage-specific master regulators and the mechanism by which they activate each other is a key to understanding and controlling differentiation, particularly in the fields of tissue regeneration and organoid engineering. Here we present a workflow that combines a comprehensive general regulatory network based on binding site predictions with user-provided temporal gene expression data, to generate a a temporally connected series of stage-specific regulatory networks, which we call a temporal regulatory cascade (TRC). A TRC identifies those regulators that are unique for each time point, resulting in a cascade that shows the emergence of these regulators and regulatory interactions across time. The model was implemented in the form of a user-friendly, visual web-tool, that requires no expert knowledge in programming or statistics, making it directly usable for life scientists. In addition to generating TRCs the tool links multiple interactive visual workflows, in which a user can track and investigate further different regulators, target genes, and interactions, directing the tool along the way into biologically sensible results based on the given dataset. We applied the TRC model on two different expression datasets, one based on experiments conducted on human induced pluripotent stem cells (hiPSCs) undergoing differentiation into mature cardiomyocytes and the other based on the differentiation of H1-derived human neuronal precursor cells. The model was successful in identifying previously known and new potential key regulators, in addition to the particular time points with which these regulators are associated, in cardiac and neural development. [ABSTRACT FROM AUTHOR]

Genetically encoded pH indicators (GEpHI) have emerged as important tools for investigating intracellular pH (pHi) dynamics in Drosophila. However, most of the indicators are based on the Gal4/UAS binary expression system. Here, we report the generation of a ubiquitously-expressed GEpHI. The fusion protein of super ecliptic pHluorin and FusionRed was cloned under the tubulin promoter (tpHusion) to drive it independently of the Gal4/UAS system. The function of tpHusion was validated in various tissues from different developmental stages of Drosophila. Differences in pHi were also indicated correctly in fixed tissues. Finally, we describe the use of tpHusion for comparative analysis of pHi in manipulated clones and the surrounding cells in epithelial tissues. Our findings establish tpHusion as a robust tool for studying pHi in Drosophila. [ABSTRACT FROM AUTHOR]

Objective: Macmoondongtang has been used as a traditional medicine to treat pulmonary disease in Korea. However, the mechanism underlying its therapeutic effect has yet to be reported. In the present study, the role of macmoondongtang as a respiratory medicine, especially as an anti-asthmatic agent, has been attributed to the down-regulation of interleukin (IL)-4 and tumor necrosis factor (TNF)-α. Materials & methods: BALB/c mice were divided into five groups: control, asthma-induced control, dexamethasone treatment, treatment with 150 mg/kg macmoondongtang, and treatment with 1500 mg/kg macmoondongtang. To evaluate the anti-asthmatic effect of macmoondongtang, we investigated its suppressive or inhibitory effects against typical asthmatic changes such as differential cell count in bronchioalveolar fluid (BALF), serum IgE levels, lung morphology, expression of Th1/Th2 cell transcription factors such as T-bet and GATA-3, and Th1-/Th2-/Th17-related cytokines such as interferon (IFN)-γ, IL-12p40, IL-4, -5, -13, TNF-α, and IL-6. The active ingredients in macmoondongtang were further analyzed. Results: Macmoondongtang treatment down-regulated serum IgE level, a very important marker of hyper-responsiveness. It reversed typical morphological changes such as mucous hypersecretion, lung epithelial cell hyperplasia, and inflammatory cell infiltration near bronchioalveolar space and veins. Macmoondongtang significantly decreased neutrophil count in BALF, as well as reduced T-bet, IFN-γ, and TNF-α expression in the lung. It also showed a dose-dependent control of inflammatory cells in BALF, controlled the expression of IL-12, IL-4, and IL-5 genes in the lung, and the protein expression of IL12p40, GATA-3, IL-4, IL-5, and IL-13. The component analysis revealed glycyrrhizin and liquiritin as the active ingredients. Conclusions: Macmoondongtang treatment alleviates asthma symptoms and modulate the Th1-/Th2- related cytokines. Glycyrrhizin and liquiritin could be the major the active therapeutic components. [ABSTRACT FROM AUTHOR]

The purpose of this study was to present and biomechanically evaluate several variations of the Nordic hamstring exercise (NHE), achieved by altering the slope of the lower leg support and by asumming different hip flexion angles. Electromyographic and 2D kinematic measurements were conducted to analyse muscle activity (biceps femoris, semitendinosus, gluteus maximus, erector spine and lateral head of the gastrocnemius), knee and hip joint torques during 6 variations of NHE. The study involved 18 adults (24.9 ± 3.7 years) with previous experience in resistance training, but with little or no experience with NHE. Increasing the slope of the lower leg support from 0° (standard NHE) to 20° and 40° enabled the participants to perform the exercise through a larger range of motion, while achieving similar peak knee and hip torques. Instructions for increased hip flexion from 0° (standard NHE) to 25°, 50° and 75° resulted in greater peak knee and hip torque, although the participants were not able to maintain the hip angle at 50° nor 75°. Muscle activity decreased or remained similar in all modified variations compared to the standard NHE for all measured muscles. Our results suggest that using the presented variations of NHE might contribute to optimization of hamstring injury prevention and rehabilitation programs, by providing appropriate difficulty for the individual's strength level and also allow eccentric strengthening at longer hamstring lengths. [ABSTRACT FROM AUTHOR]

During vertebrate early embryogenesis, the ventral development is directed by the ventral-to-dorsal activity gradient of the bone morphogenetic protein (BMP) signaling. As secreted ligands, the extracellular traffic of BMP has been extensively studied. However, it remains poorly understood that how BMP ligands are secreted from BMP-producing cells. In this work, we show the dominant role of Marcksb controlling the secretory process of Bmp2b via interaction with Hsp70 in vivo. We firstly carefully characterized the role of Marcksb in promoting BMP signaling during dorsoventral axis formation through knockdown approach. We then showed that Marcksb cell autonomously regulates the trafficking of Bmp2b from producing cell to the extracellular space and both the total and the extracellular Bmp2b was decreased in Marcksb-deficient embryos. However, neither the zygotic mutant of marcksb (Zmarcksb) nor the maternal zygotic mutant of marcksb (MZmarcksb) showed any defects of dorsalization. In contrast, the MZmarcksb embryos even showed increased BMP signaling activity as measured by expression of BMP targets, phosphorylated Smad1/5/9 levels and imaging of Bmp2b, suggesting that a phenomenon of “genetic over-compensation” arose. Finally, we revealed that the over-compensation effects of BMP signaling in MZmarcksb was achieved through a sequential up-regulation of MARCKS-family members Marcksa, Marcksl1a and Marcksl1b, and MARCKS-interacting protein Hsp70.3. We concluded that the Marcksb modulates BMP signaling through regulating the secretory pathway of Bmp2b. [ABSTRACT FROM AUTHOR]

Aims: The cancer stem cell concept proposes that tumor growth and recurrence is driven by a small population of cancer stem cells (CSCs). In this study we investigated the expression of induced-pluripotent stem cell (iPSC) markers and their localization in primary low-grade adenocarcinoma (LGCA) and high-grade adenocarcinoma (HGCA) and their patient-matched normal colon samples. Materials and methods: Transcription and translation of iPSC markers OCT4, SOX2, NANOG, KLF4 and c-MYC were investigated using immunohistochemical (IHC) staining, RT-qPCR and in-situ hybridization (ISH). Results: All five iPSC markers were detected at the transcriptional and translational levels. Protein abundance was found to be correlated with tumor grade. Based on their protein expression within the tumors, two sub-populations of cells were identified: a NANOG+/OCT4- epithelial subpopulation and an OCT4+/NANOG- stromal subpopulation. All cases were accurately graded based on four pieces of iPSC marker-related data. Conclusions: This study suggests the presence of two putative sub-populations of CSCs: a NANOG+/OCT4- epithelial subpopulation and an OCT4+/NANOG- stromal subpopulation. Normal colon, LGCA and HGCA could be accurately distinguished from one another using iPSC marker expression. Once validated, novel combinations of iPSC markers may provide diagnostic and prognostic value to help guide patient management. [ABSTRACT FROM AUTHOR]

The inherent capacity of somatic cells to switch their phenotypic status in response to damage stimuli in vivo might have a pivotal role in ageing and cancer. However, how the entry-exit mechanisms of phenotype reprogramming are established remains poorly understood. In an attempt to elucidate such mechanisms, we herein introduce a stochastic model of combined epigenetic regulation (ER)-gene regulatory network (GRN) to study the plastic phenotypic behaviours driven by ER heterogeneity. To deal with such complex system, we additionally formulate a multiscale asymptotic method for stochastic model reduction, from which we derive an efficient hybrid simulation scheme. Our analysis of the coupled system reveals a regime of tristability in which pluripotent stem-like and differentiated steady-states coexist with a third indecisive state, with ER driving transitions between these states. Crucially, ER heterogeneity of differentiation genes is for the most part responsible for conferring abnormal robustness to pluripotent stem-like states. We formulate epigenetic heterogeneity-based strategies capable of unlocking and facilitating the transit from differentiation-refractory (stem-like) to differentiation-primed epistates. The application of the hybrid numerical method validates the likelihood of such switching involving solely kinetic changes in epigenetic factors. Our results suggest that epigenetic heterogeneity regulates the mechanisms and kinetics of phenotypic robustness of cell fate reprogramming. The occurrence of tunable switches capable of modifying the nature of cell fate reprogramming might pave the way for new therapeutic strategies to regulate reparative reprogramming in ageing and cancer. [ABSTRACT FROM AUTHOR]

Objectives: To evaluate frequency and severity of complications after CT-guided lung biopsy using the Society of Interventional Radiology (SIR) classification, and to assess risk factors for overall and major complications. Materials and methods: 311 consecutive biopsies with a non-coaxial semi-automated 18 gauge biopsy system were retrospectively evaluated. Complications after biopsy were classified into minor SIR1-2 and major SIR3-6. Studied risk factors for complications were patient-related (age, sex and underlying emphysema), lesion-related (size, location, morphologic characteristic, depth from the pleura and histopathology), and technique-related (patient position during procedure, thoracic wall thickness at needle path, procedure time length and number of procedural CT images, number of pleural passes, fissure penetration and needle-to-blood vessel angle). Data were analyzed using logistic and ordinal regression. Results: Complications were pneumothorax and pulmonary hemorrhage. The complications were minor SIR1-2 in 142 patients (45.6%), and major SIR3-4 in 25 patients (8%). SIR5-6 complications were not present. Emphysema, smaller deeply located lesion, increased puncture time length and number of procedural CT images, multiple pleural passes and fissure puncture were significant risk factors for complication severity in univariate analysis. Emphysema (OR = 8.8, p<0.001), lesion depth from the pleura (OR = 1.9 per cm, p<0.001), and fissure puncture (OR = 9.4, p = 0.01) were the independent factors for major complications in a multiple logistic regression model. No statistical difference of complication rates between the radiologists performing biopsies was observed. Conclusions: Knowledge about risk factors influencing complication severity is important for planning and performing CT-guided lung biopsies. [ABSTRACT FROM AUTHOR]

How cells communicate to initiate a regenerative response after damage has captivated scientists during the last few decades. It is known that one of the main signals emanating from injured cells is the Reactive Oxygen Species (ROS), which propagate to the surrounding tissue to trigger the replacement of the missing cells. However, the link between ROS production and the activation of regenerative signaling pathways is not yet fully understood. We describe here the non-autonomous ROS sensing mechanism by which living cells launch their regenerative program. To this aim, we used Drosophila imaginal discs as a model system due to its well-characterized regenerative ability after injury or cell death. We genetically-induced cell death and found that the Apoptosis signal-regulating kinase 1 (Ask1) is essential for regenerative growth. Ask1 senses ROS both in dying and living cells, but whose activation is selectively attenuated in living cells by Akt1, the core kinase component of the insulin/insulin-like growth factor pathway. Akt1 phosphorylates Ask1 in a secondary site outside the kinase domain, which attenuates its activity. This modulation of Ask1 activity results in moderate levels of JNK signaling in the living tissue, as well as in activation of p38 signaling, both pathways required to turn on the regenerative response. Our findings demonstrate a non-autonomous activation of a ROS sensing mechanism by Ask1 and Akt1 to replace the missing tissue after damage. Collectively, these results provide the basis for understanding the molecular mechanism of communication between dying and living cells that triggers regeneration. [ABSTRACT FROM AUTHOR]

There is an established relationship between primary DNA sequence, secondary and tertiary chromatin structure, and transcriptional activity, suggesting that observed differences in one of these properties may reflect changes in the others. Here, we exploit these relationships to show that variations in DNA structure can be used to identify a wide range of genomic alterations in mammalian samples. In this proof-of-concept study we characterized and compared genome-wide histone occupancy by ChIP-Seq, DNA accessibility by ATAC-Seq, and chromosomal conformation by Hi-C for five CRISPR/Cas9-modified mammalian cell lines and their unmodified parent strains, as well as in one modified tissue sample and its parent strain. The results showed that the impact of genomic alterations on each of the levels of DNA organization varied depending on mutation type (insertion or deletion), size, and genomic location. The largest genomic alterations we identified included chromosomal rearrangements and deletions (greater than 200 Kb) in four of the modified cell lines, which can be difficult to identify by standard whole genome sequencing analysis. This multi-level DNA organizational analysis provides a sensitive approach for identifying a wide range of genomic and epigenomic perturbations that can be utilized for biomedical and biosecurity applications. [ABSTRACT FROM AUTHOR]

Mouse embryonic stem cells (ESCs) are pluripotent stem cells, which have the ability to differentiate into all three germ layers: mesoderm, endoderm, and ectoderm. Proper levels of phosphorylated extracellular signal-regulated kinase (pERK) are critical for maintaining pluripotency, as elevated pERK evoked by fibroblast growth factor (FGF) receptor activation results in differentiation of ESCs, while, conversely, reduction of pERK by a MEK inhibitor maintains a pluripotent ground state. However, mechanisms underlying proper control of pERK levels in mouse ESCs are not fully understood. Here, we find that Klf5, a Krüppel-like transcription factor family member, is a component of pERK regulation in mouse ESCs. We show that ERK signaling is overactivated in Klf5-KO ESCs and the overactivated ERK in Klf5-KO ESCs is suppressed by the introduction of Klf5, but not Klf2 or Klf4, indicating a unique role for Klf5 in ERK suppression. Moreover, Klf5 regulates Spred1, a negative regulator of the FGF-ERK pathway. Klf5 also facilitates reprogramming of EpiSCs into a naïve state in combination with a glycogen synthase kinase 3 inhibitor and LIF, and in place of a MEK inhibitor. Taken together, these results show for the first time that Klf5 has a unique role suppressing ERK activity in mouse ESCs. [ABSTRACT FROM AUTHOR]

Background: Key regulators of developmental processes can be prioritized through integrated analysis of ChIP-Seq data of master transcriptional factors (TFs) such as Nanog and Oct4, active histone modifications (HMs) such as H3K4me3 and H3K27ac, and repressive HMs such as H3K27me3. Recent studies show that broad enrichment signals such as super-enhancers and broad H3K4me3 enrichment signals play more dominant roles than short enrichment signals of the master TFs and H3K4me3 in epigenetic regulatory mechanism. Besides the broad enrichment signals, up to ten thousands of short enrichment signals of these TFs and HMs exist in genome. Prioritization of these broad enrichment signals from ChIP-Seq data is a prerequisite for such integrated analysis. Results: Here, we present a method named Clustering-Local-Unique-Enriched-Signals (CLUES), which uses an adaptive-size-windows strategy to identify enriched regions (ERs) and cluster them into broad enrichment signals. Tested on 62 ENCODE ChIP-Seq datasets of Ctcf and Nrsf, CLUES performs equally well as MACS2 regarding prioritization of ERs with the TF’s motif. Tested on 165 ENCODE ChIP-Seq datasets of H3K4me3, H3K27me3, and H3K36me3, CLUES performs better than existing algorithms on prioritizing broad enrichment signals implicating cell functions influenced by epigenetic regulatory mechanism in cells. Most importantly, CLUES helps to confirm several novel regulators of mouse ES cell self-renewal and pluripotency through integrated analysis of prioritized broad enrichment signals of H3K4me3, H3K27me3, Nanog and Oct4 with the support of a CRISPR/Cas9 negative selection genetic screen. Conclusions: CLUES holds promise for prioritizing broad enrichment signals from ChIP-Seq data. The download site for CLUES is . [ABSTRACT FROM AUTHOR]

Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genome-wide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cell-cycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescence-associated (SA) β-galactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycle-dependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidy limiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM. [ABSTRACT FROM AUTHOR]

Mammalian oocytes and zygotes have nucleoli that are transcriptionally inactive and structurally distinct from nucleoli in somatic cells. These nucleoli have been termed nucleolus precursor bodies (NPBs). Recent research has shown that NPBs are important for embryonic development, but they are only required during pronuclear formation. After fertilization, multiple small NPBs are transiently formed in male and female pronuclei and then fuse into a single large NPB in zygotes. In cloned embryos produced by somatic cell nuclear transfer (SCNT), multiple NPBs are formed and maintained in the pseudo-pronucleus, and this is considered an abnormality of the cloned embryos. Despite this difference between SCNT and normal embryos, it is unclear how the size and number of NPBs in pronuclei is determined. Here, we show that in mouse embryos, the volume of NPB materials plays a major role in the NPB scaling through a limiting component mechanism and determines whether a single or multiple NPBs will form in the pronucleus. Extra NPB- and extra MII spindle-injection experiments demonstrated that the total volume of NPBs was maintained regardless of the pronucleus number and the ratio of pronucleus/NPB is important for fusion into a single NPB. Based on these results, we examined whether extra-NPB injection rescued multiple NPB maintenance in SCNT embryos. When extra-NPBs were injected into enucleated-MII oocytes before SCNT, the number of NPBs in pseudo-pronuclei of SCNT embryos was reduced. These results indicate that multiple NPB maintenance in SCNT embryos is caused by insufficient volume of NPB. [ABSTRACT FROM AUTHOR]

The crosstalk between cells is important for differentiation of cells. Murine-derived feeder cells, SNL76/7 feeder cells (SNLs) or mouse primary embryonic fibroblast feeder cells (MEFs) are widely used for culturing undifferentiated human induced pluripotent stem cells (hiPSCs). It is still unclear whether different culture conditions affect the induction efficiency of definitive endoderm (DE) differentiation from hiPSCs. Here we show that the efficiency of DE differentiation from hiPSCs cultured on MEFs was higher than that of hiPSCs cultured on SNLs. The qPCR, immunofluorescent and flow cytometry analyses revealed that the expression levels of mRNA and/or proteins of the DE marker genes, SOX17, FOXA2 and CXCR4, in DE cells differentiated from hiPSCs cultured on MEFs were significantly higher than those cultured on SNLs. Comprehensive RNA sequencing and molecular network analyses showed the alteration of the gene expression and the signal transduction of hiPSCs cultured on SNLs and MEFs. Interestingly, the expression of non-coding hXIST exon 4 was up-regulated in hiPSCs cultured on MEFs, in comparison to that in hiPSCs cultured on SNLs. By qPCR analysis, the mRNA expression of undifferentiated stem cell markers KLF4, KLF5, OCT3/4, SOX2, NANOG, UTF1, and GRB7 were lower, while that of hXIST exon 4, LEFTY1, and LEFTY2 was higher in hiPSCs cultured on MEFs than in those cultured on SNLs. Taken together, our finding indicated that differences in murine-feeder cells used for maintenance of the undifferentiated state alter the expression of pluripotency-related genes in hiPSCs by the signaling pathways and affect DE differentiation from hiPSCs, suggesting that the feeder cells can potentiate hiPSCs for DE differentiation. [ABSTRACT FROM AUTHOR]

NK-4 is the main component of the antiallergic drug Lumin, which has been in popular usage since the early 1950s. In this study, we examined whether NK-4 exerts a regulatory effect on the activation and effector function of Th2 cells. NK-4 inhibited IL-4 production by anti-CD3ε mAb-stimulated BALB/c mouse spleen cells, whereas NK-4 had little effect on IFN-γ production. IL-4 and IL-5 secretion by anti-CD3ε mAb- or antigen-stimulated Th2 cells (D10.G4.1) was abrogated by NK-4 without affecting cell numbers, whereas IFN-γ secretion by activated Th1 cells was unchanged. Mechanistic analysis revealed that NK-4 inhibited mRNA expression of the Th2-associated transcription factors GATA-3 and NFATc1 in anti-CD3ε mAb-stimulated D10.G4.1 cells. Regarding the regulation of Th2 cell effector functions, NK-4 inhibited the secretion of eotaxin and thymus and activation-regulated chemokine (TARC) by normal human dermal fibroblasts in response to IL-4 and/or TNF-α. NK-4 achieved TARC attenuation comparable to what is observed with suplatast tosilate, an antiallergic drug that selectively inhibits Th2 cytokine production, at 14-fold lower concentrations of suplatast tosilate. Dexamethasone increased TARC production by 2.2- to 2.6-fold of control cultures. NK-4 successfully inhibited the STAT6 signaling pathway, suggesting a potential mechanism for down-regulating chemokines expression. In addition, NK-4 abrogated IL-4-driven modulation of cytokine production profile in human monocytic THP-1 cells from proinflammatory to anti-inflammatory response, as seen in the inverted ratio of TNF-α to IL-10 produced in response to LPS. These results suggest that NK-4 could prevent IL-4-driven polarization to alternatively activated macrophages, which are proposed to have pathogenic roles in allergic asthma. The importance of Th2 cytokines and chemokines in the development and progression of type 2 inflammatory disorders has been highlighted by recent advance in our understanding the immunological mechanism underlying allergic disease. Our results support the use of NK-4 as a reasonable therapeutic option to alleviate Th2-mediated allergic inflammation. [ABSTRACT FROM AUTHOR]

Functional mapping of the 5’LTR has shown that the U3 and the R regions (U3R) contain a cluster of regulatory elements involved in the control of HIV-1 transcription and expression. As the HIV-1 genome is characterized by extensive variability, here we aimed to describe mutations in the U3R from various HIV-1 clades and CRFs in order to highlight strain specific differences that may impact the biological properties of diverse HIV-1 strains. To achieve our purpose, the U3R sequence of plasma derived virus belonging to different clades (A1, B, C, D, F2) and recombinants (CRF02_AG, CRF01_AE and CRF22_01A1) was obtained using Illumina technology. Overall, the R region was very well conserved among and across different strains, while in the U3 region the average inter-strains nucleotide dissimilarity was up to 25%. The TAR hairpin displayed a strain-distinctive cluster of mutations affecting the bulge and the loop, but mostly the stem. Like in previous studies we found a motif in U3 promoter region from the majority of HIV-1 strains and a motif in CRF01_AE; but also in LTRs from CRF22_01A1 isolates. Although LTRs from CRF22_01A1 specimens were assigned CRF01_AE, they contained two NF-kB sites instead of the single TFBS described in CRF01_AE. Also, as previously describe in clade C isolates, we found no C/EBP binding site directly upstream of the enhancer region in CRF22_01A1 specimens. In our study, one-third of CRF02_AG LTRs displayed three NF-kB sites which have been mainly described in clade C isolates. Overall, the number, location and binding patterns of potential regulatory elements found along the U3R might be specific to some HIV-1 strains such as clade F2, CRF02_AG, CRF01_AE and CRF22_01A1. These features may be worth consideration as they may be involved in distinctive regulation of HIV-1 transcription and replication by different and diverse infecting strains. [ABSTRACT FROM AUTHOR]

Extracellular vesicles (EVs) released by virtually every cell of all organisms are involved in processes of intercellular communication through the delivery of their functional mRNAs, proteins and bioactive lipids. We previously demonstrated that mouse embryonic stem cell-released EVs (mESEVs) are able to transfer their content to different target retinal cells, inducing morphological and biochemical changes in them. The main objective of this paper is to characterize EVs derived from human embryonic stem cells (hESEVs) and investigate the effects that they have on cultured retinal glial, progenitor Müller cells, which are known to give rise to retinal neurons under specific conditions. This would allow us to establish if hESEVs have a pro-regenerative potential not yet described that could be used in the future for treatment of human retinal degenerative diseases. Initially, we showed that hESEVs are heterogeneous in size, contain mRNAs and proteins involved in the induction and maintenance of stem cell pluripotency and can be internalized by cultured Müller cells. After a single exposure to hESEVs these cells display changes in their gene expression profile, and with multiple exposures they de-differentiate and trans-differentiate into retinal neuronal precursors. hESEVs were then fractionated into microvesicles (MVs) and exosomes (EXOs), which were characterized by size, specific surface proteins and biochemical/molecular components. We demonstrate that despite the similar internalization of non-fractionated hESEVs, MVs and EXOs by Müller progenitor cells, in vitro, only the release of MVs’ cargo into the cells’ cytoplasm induces specific changes in their levels of pluripotency mRNAs and early retinal proteins. EXOs do not produce any detectable effect. Thus, we conclude that MVs and MVs-containing hESEVs are promising agents that possibly could promote the regeneration of diseased or damaged retinas in vivo through inducing glial Müller cells to become replacement neurons. [ABSTRACT FROM AUTHOR]

Pluripotent embryonic stem cells are of paramount importance for biomedical sciences because of their innate ability for self-renewal and differentiation into all major cell lines. The fateful decision to exit or remain in the pluripotent state is regulated by complex genetic regulatory networks. The rapid growth of single-cell sequencing data has greatly stimulated applications of statistical and machine learning methods for inferring topologies of pluripotency regulating genetic networks. The inferred network topologies, however, often only encode Boolean information while remaining silent about the roles of dynamics and molecular stochasticity inherent in gene expression. Herein we develop a framework for systematically extending Boolean-level network topologies into higher resolution models of networks which explicitly account for the promoter architectures and gene state switching dynamics. We show the framework to be useful for disentangling the various contributions that gene switching, external signaling, and network topology make to the global heterogeneity and dynamics of transcription factor populations. We find the pluripotent state of the network to be a steady state which is robust to global variations of gene switching rates which we argue are a good proxy for epigenetic states of individual promoters. The temporal dynamics of exiting the pluripotent state, on the other hand, is significantly influenced by the rates of genetic switching which makes cells more responsive to changes in extracellular signals. [ABSTRACT FROM AUTHOR]

Naïve CD4 T (NCD4T) cells post-activation undergo programming for inducible production of cytokines leading to generation of memory cells with various functions. Based on cytokine based polarization of NCD4T cells in vitro, programming for either ‘Th1’ (interferon-gamma [IFNg]) or ‘Th2’ (interleukin [IL]-4/5/13) cytokines is thought to occur via mutually exclusive expression and functioning of T-bet or GATA-3 transcription factors (TFs). However, we show that a high proportion of mouse and human memory-phenotype CD4 T (MCD4T) cells generated in vivo which expressed either Th1 or Th2 cytokines commonly co-expressed T-bet and GATA-3. While T-bet levels did not differ between IFNg-expressing and IL-4/5/13-expressing MCD4T cells, GATA-3 levels were higher in the latter. These observations were also confirmed in MCD4T cells from FVB/NJ or aged C57BL/6 or IFNg-deficient mice. While MCD4T cells from these strains showed greater Th2 commitment than those from young C57BL/6 mice, pattern of co-expression of TF was similar. Effector T cells generated in vivo following immunization also showed TF co-expression in Th1 or Th2 cytokine producing cells. We speculated that the difference in TF expression pattern of MCD4T cells generated in vivo and those generated in cytokine polarized cultures in vitro could be due to relative absence of polarizing conditions during activation in vivo. We tested this by NCD4T cell activation in non-polarizing conditions in vitro. Anti-CD3 and anti-CD28-mediated priming of polyclonal NCD4T cells in vitro without polarizing milieu generated cells that expressed either IFNg or IL-4/5/13 but not both, yet both IFNg- and IL-4/5/13-expressing cells showed upregulation of both TFs. We also tested monoclonal T cell populations activated in non-polarizing conditions. TCR-transgenic NCD4T cells primed in vitro by cognate peptide in non-polarizing conditions which expressed either IFNg or IL-4/5/13 also showed a high proportion of cells co-expressing TFs, and their cytokine commitment varied depending on genetic background or priming conditions, without altering pattern of TF co-expression. Thus, the model of mutually antagonistic differentiation programs driven by mutually exclusively expressed T-bet or GATA-3 does not completely explain natural CD4 T cell priming outcomes. [ABSTRACT FROM AUTHOR]