Melanin‐based ornament darkness positively correlates with across‐season nutritional condition

Sexually dimorphic ornamental traits are widely regarded as indicators of nutritional condition. However, variation of nutritional condition outside the reproductive and the ornament production seasons has rarely been considered, although it affects the generality of information content, especially for ornaments that may be used across the year. We measured several indicators of migratory and molt condition in male and female blackcaps (Sylvia atricapilla) during their autumn migration, and quantified their crown reflectance. We detected robust correlations between migratory and molt condition indices, and the correlation structure was similar in the two sexes. Furthermore, the across‐season measure of body condition was positively related to the darkness of the black crown in males, while being unrelated to reflectance traits of the reddish crown in females. Our results reinforce the possibility that some melanin‐based ornaments may be year‐round indicators of individual quality via their dependence on nutritional condition.     

Using fractal self‐similarity to increase precision of shrub biomass estimates

We show that aerial tips are self‐similar fractals of whole shrubs and present a field method that applies this fact to improves accuracy and precision of biomass estimates of tall‐shrubs, defined here as those with diameter at root collar (DRC) ≥ 2.5 cm. Power function allometry of biomass to stem diameter generates a disproportionate prediction error that increases rapidly with diameter. Thus, biomass should be modeled as a single measure of stem diameter only if stem diameter is less than a threshold D_max. When stem diameter exceeds D_max, then the stem internode should be treated as a conic frustrum requiring two additional measures: a second, node‐adjacent diameter and a length. If the second diameter is less than D_max, then the power function allometry can be applied to the aerial tip; otherwise an additional internode is measured. This “two‐component” allometry—internodes as frustra and aerial tips as shrubs—can reduce estimated biomass error propagated to the plot‐level by as much as 50% or more where very large shrubs are present D_max is any diameter such that the ratio of single‐component to two‐component uncertainty exceeds the ratio of two‐component to single‐component measurement time. Guidelines for estimating D_max based on pilot field data are provided. Tall shrubs are increasing in abundance and distribution across Arctic, alpine, boreal, and dryland ecosystems. Estimating their biomass is important for both ecological studies and carbon accounting. Reducing field‐sample prediction error increases precision in multi‐stage modeling because additional measures efficiently improve plot‐level biomass precision, reducing uncertainty for shrub biomass estimates.     

Sex‐ and strain‐specific effects of mitochondrial uncoupling on age‐related metabolic diseases in high‐fat diet‐fed mice

Mild uncoupling of oxidative phosphorylation is an intrinsic property of all mitochondria and may have evolved to protect cells against the production of damaging reactive oxygen species. Therefore, compounds that enhance mitochondrial uncoupling are potentially attractive anti‐aging therapies; however, chronic ingestion is associated with a number of unwanted side effects. We have previously developed a controlled‐release mitochondrial protonophore (CRMP) that is functionally liver‐directed and promotes oxidation of hepatic triglycerides by causing a subtle sustained increase in hepatic mitochondrial inefficiency. Here, we sought to leverage the higher therapeutic index of CRMP to test whether mild mitochondrial uncoupling in a liver‐directed fashion could reduce oxidative damage and improve age‐related metabolic disease and lifespan in diet‐induced obese mice. Oral administration of CRMP (20 mg/[kg‐day] × 4 weeks) reduced hepatic lipid content, protein kinase C epsilon activation, and hepatic insulin resistance in aged (74‐week‐old) high‐fat diet (HFD)‐fed C57BL/6J male mice, independently of changes in body weight, whole‐body energy expenditure, food intake, or markers of hepatic mitochondrial biogenesis. CRMP treatment was also associated with a significant reduction in hepatic lipid peroxidation, protein carbonylation, and inflammation. Importantly, long‐term (49 weeks) hepatic mitochondrial uncoupling initiated late in life (94–104 weeks), in conjugation with HFD feeding, protected mice against neoplastic disorders, including hepatocellular carcinoma (HCC), in a strain and sex‐specific manner. Taken together, these studies illustrate the complex variation of aging and provide important proof‐of‐concept data to support further studies investigating the use of liver‐directed mitochondrial uncouplers to promote healthy aging in humans.     

Assessment of medium and large‐sized mammals and their behavioral response toward anthropogenic activities in Jorgo‐Wato Protected Forest,Western Ethiopia

Medium and large‐sized mammals of Jorgo‐Wato Protected Forest have not yet been documented though the forest established before four decades. Hence, this study aims to document medium and large mammals and the behavioral responses of selected mammals toward anthropogenic activities in the study area. The study was conducted from February 2015 to June 2016, encompassing the wet and dry seasons. Data were collected mainly through camera traps, indirect and direct evidence. The study revealed about 23 medium and large‐sized mammals that belong to seven orders namely Bovidae, Carnivora, Primates, Rodentia, Tubulidentata, Lagomorpha, and Hyracoidea. Papio anubis, C. guereza, and C. aethiops were the most abundant large mammals in JWPF. Because of high anthropogenic activities, African buffalo shifted its activity period from diurnal into crepuscular and nocturnal. African buffalo traveled longer distances during the wet season (mean = 14.33 km, SD = 1.25 km) than during the dry season (mean = 9.00 km, SD = 2.16 km). This could be due to the fact that the local people were less likely to go to the forest for resource exploitation during the wet season as they are fully engaged in agricultural activities. However, low agricultural activities during the dry season allow the local people to extract resources and involve in bushmeat hunting which could limit the movement of mammals to their refugia. African buffalo preferred to rest on and adjacent to a gravel road (22.1%) in the forest, followed by on open rocky hilltops (14.7%) at night time, but rest in the bottomland thicket vegetation during the dry daytime. Regardless of high human pressure in the area, this study has revealed a good number of medium and large‐sized mammals that could be used as baseline information to design a sound conservation and management action plan of large mammals and their habitat in Jorgo‐Wato Protected Forest.     

Compartment‐specific 13C metabolic flux analysis reveals boosted NADPH availability coinciding with increased cell‐specific productivity for IgG1 producing CHO cells after MTA treatment

Increasing cell‐specific productivities (CSPs) for the production of heterologous proteins in Chinese hamster ovary (CHO) cells is an omnipresent need in the biopharmaceutical industry. The novel additive 5′‐deoxy‐5′‐(methylthio)adenosine (MTA), a chemical degradation product of S‐(5′‐adenosyl)‐ʟ‐methionine (SAM) and intermediate of polyamine biosynthesis, boosts the CSP of IgG1‐producing CHO cells by 50%. Compartment‐specific ¹³C flux analysis revealed a fundamental reprogramming of the central metabolism after MTA addition accompanied by cell‐cycle arrest and increased cell volumes. Carbon fluxes into the pentose‐phosphate pathway increased 22 fold in MTA‐treated cells compared to that in non‐MTA‐treated reference cells. Most likely, cytosolic ATP inhibition of phosphofructokinase mediated the carbon detour. Mitochondrial shuttle activity of the α‐ketoglurarate/malate antiporter (OGC) reversed, reducing cytosolic malate transport. In summary, NADPH supply in MTA‐treated cells improved three fold compared to that in non‐MTA‐treated cells, which can be regarded as a major factor for explaining the boosted CSPs.     

Population dynamics of the glacial relict amphipods in a subarctic lake: role of density‐dependent and density‐independent factors

Relative role of intrinsic density‐dependent factors (such as inter‐ and intraspecific competition, predation) and extrinsic density‐independent factors (environmental changes) in population dynamics is a key issue in ecology. Density‐dependent mechanisms are considered as important drivers of population dynamics in many vertebrate and insect species; however, their influence on the population dynamics of freshwater invertebrates is not clearly understood. In this study, I examined interannual variations in the abundance of the glacial relict amphipod Monoporeia affinis in a small subarctic lake based on long‐term (2002–2019) monitoring data. The results suggest that the population dynamics of amphipods in the lake is influenced by the combined effects of both intrinsic and extrinsic factors. The reproductive success of amphipod cohorts was inversely related to its initial abundance, indicating it is influenced by density‐dependent factors. M. affinis recruitment was negatively correlated with population density and near‐bottom temperature but positively correlated with food availability, which is defined as the concentration of chlorophyll a. Multiple regression with chlorophyll, temperature, and abundance of parent cohort as independent factors explained about 80% of the variation in the reproductive success of amphipods. The negative correlation between amphipod recruitment and water temperature indicates that the current climate conditions adversely affect the populations of glacial relict amphipods even in cold‐water lakes of the subarctic zone. Results of this study can be useful in environmental assessments to separate population oscillations connected with density‐dependent mechanisms from human‐mediated changes.     

Limited contributions of plant pathogens to density‐dependent seedling mortality of mast fruiting Bornean trees

Fungal pathogens are implicated in driving tropical plant diversity by facilitating strong, negative density‐dependent mortality of conspecific seedlings (C‐NDD). Assessment of the role of fungal pathogens in mediating coexistence derives from relatively few tree species and predominantly the Neotropics, limiting our understanding of their role in maintaining hyper‐diversity in many tropical forests. A key question is whether fungal pathogen‐mediated C‐NDD seedling mortality is ubiquitous across diverse plant communities. Using a manipulative shadehouse experiment, we tested the role of fungal pathogens in mediating C‐NDD seedling mortality of eight mast fruiting Bornean trees, typical of the species‐rich forests of South East Asia. We demonstrate species‐specific responses of seedlings to fungicide and density treatments, generating weak negative density‐dependent mortality. Overall seedling mortality was low and likely insufficient to promote overall community diversity. Although conducted in the same way as previous studies, we find little evidence that fungal pathogens play a substantial role in determining patterns of seedling mortality in a SE Asian mast fruiting forest, questioning our understanding of how Janzen‐Connell mechanisms structure the plant communities of this globally important forest type.     

Understanding of mouse and human bladder at single‐cell resolution: integrated analysis of trajectory and cell‐cell interactive networks based on multiple scRNA‐seq datasets

ObjectivesTo elaborately decipher the mouse and human bladders at single‐cell levels.Materials and MethodsWe collected more than 50,000 cells from multiple datasets and created, up to date, the largest integrated bladder datasets. Pseudotime trajectory of urothelium and interstitial cells, as well as dynamic cell‐cell interactions, was investigated. Biological activity scores and different roles of signaling pathways between certain cell clusters were also identified.ResultsThe glucose score was significantly high in most urothelial cells, while the score of H3 acetylation was roughly equally distributed across all cell types. Several genes via a pseudotime pattern in mouse (Car3, Dkk2, Tnc, etc.) and human (FBLN1, S100A10, etc.) were discovered. S100A6, TMSB4X, and typical uroplakin genes seemed as shared pseudotime genes for urothelial cells in both human and mouse datasets. In combinational mouse (n = 16,688) and human (n = 22,080) bladders, we verified 1,330 and 1,449 interactive ligand‐receptor pairs, respectively. The distinct incoming and outgoing signaling was significantly associated with specific cell types. Collagen was the strongest signal from fibroblasts to urothelial basal cells in mouse, while laminin pathway for urothelial basal cells to smooth muscle cells (SMCs) in human. Fibronectin 1 pathway was intensely sent by myofibroblasts, received by urothelial cells, and almost exclusively mediated by SMCs in mouse bladder. Interestingly, the cell cluster of SMCs 2 was the dominant sender and mediator for Notch signaling in the human bladder, while SMCs 1 was not. The expression of integrin superfamily (the most common communicative pairs) was depicted, and their co‐expression patterns were located in certain cell types (eg, Itgb1 and Itgb4 in mouse and human basal cells).ConclusionsThis study provides a complete interpretation of the normal bladder at single‐cell levels, offering an in‐depth resource and foundation for future research.     

A hierarchical deep learning based approach for multi‐functional enzyme classification

Enzymes are critical proteins in every organism. They speed up essential chemical reactions, help fight diseases, and have a wide use in the pharmaceutical and manufacturing industries. Wet lab experiments to figure out an enzyme''s function are time consuming and expensive. Therefore, the need for computational approaches to address this problem are becoming necessary. Usually, an enzyme is extremely specific in performing its function. However, there exist enzymes that can perform multiple functions. A multi‐functional enzyme has vast potential as it reduces the need to discover/use different enzymes for different functions. We propose an approach to predict a multi‐functional enzyme''s function up to the most specific fourth level of the hierarchy of the Enzyme Commission (EC) number. Previous studies can only predict the function of the enzyme till level 1. Using a dataset of 2,583 multi‐functional enzymes, we achieved a hierarchical subset accuracy of 71.4% and a Macro F₁ Score of 96.1% at the fourth level. The robustness of the network was further tested on a multi‐functional isoforms dataset. Our method is broadly applicable and may be used to discover better enzymes. The web‐server can be freely accessed at http://hecnet.cbrlab.org/.     

A machine learning method for estimating the probability of presence using presence‐background data

Estimating the prevalence or the absolute probability of the presence of a species from presence‐background data has become a controversial topic in species distribution modelling. In this paper, we propose a new method by combining both statistics and machine learning algorithms that helps overcome some of the known existing problems. We have also revisited the popular but highly controversial Lele and Keim (LK) method by evaluating its performance and assessing the RSPF condition it relies on. Simulations show that the LK method with the RSPF assumptions would render fragile estimation/prediction of the desired probabilities. Rather, we propose the local knowledge condition, which relaxes the predetermined population prevalence condition that has so often been used in much of the existing literature. Simulations demonstrate the performance of the new method utilizing the local knowledge assumption to successfully estimate the probability of presence. The local knowledge extends the local certainty or the prototypical presence location assumption, and has significant implications for demonstrating the necessary condition for identifying absolute (rather than relative) probability of presence from presence background without absence data in species distribution modelling.     

Scale‐dependent effects of neighborhood biodiversity on individual tree productivity in a coniferous and broad‐leaved mixed forest in China

The relationship between biodiversity and productivity has stimulated an increasing body of research over the past decades, and this topic still occupies a central place in ecology. While most studies have focused on biomass production in quadrats or plots, few have investigated the scale‐dependent relationship from an individual plant perspective. We present an analysis of the effects of biodiversity (species diversity and functional diversity) on individual tree growth with a data set of 16,060 growth records from a 30‐ha temperate forest plot using spatially explicit individual tree‐based methods. A significant relationship between species diversity and tree growth was found at the individual tree level in our study. The magnitude and direction of biodiversity effects varies with the spatial scale. We found positive effects of species diversity on tree growth at scales exceeding 9 m. Individual tree growth rates increased when there was a greater diversity of species in the neighborhood of the focal tree, which provides evidence of a niche complementarity effect. At small scales (3–5 m), species diversity had negative effects on tree growth, suggesting that competition is more prevalent than complementarity or facilitation in these close neighborhoods. The results also revealed many confounding factors which influence tree growth, such as elevation and available sun light. We conclude that the use of individual tree‐based methods may lead to a better understanding of the biodiversity‐productivity relationship in forest communities.     

Bcl‐xL expression following articular cartilage injury and its effects on the biological function of chondrocytes

This study aimed to investigate the expression of B‐cell lymphoma‐extra large (Bcl‐xL) in cartilage tissues following articular cartilage injury and to determine its effects on the biological function of chondrocytes. A total of 25 necrotic cartilage tissue samples and 25 normal tissue samples were collected from patients diagnosed with osteoarthritis at our hospital from December 2015 to December 2018. The mRNA expression levels of Bcl‐xL, caspase‐3, and matrix metalloproteinase‐3 (MMP‐3) in the normal and necrotic tissues were examined via quantitative polymerase chain reaction, and their protein expression levels were detected via western blotting. The expression levels of Bcl‐xL, insulin‐like growth factor‐1 (IGF‐1), and bone morphogenetic protein (BMP) were significantly lower but those of caspase‐3, MMP‐3, interleukin‐1β (IL‐1β), and chemokine‐like factor 1 (CKLF1) levels were markedly higher in necrotic cartilage tissues than in normal tissues. Following cell transfection, the expression levels of Bcl‐xL, IGF‐1, and BMP were remarkably higher but those of caspase‐3, MMP‐3, IL‐1β, and CKLF1 were notably lower in the Si‐Bcl‐xL group than in the NC group. The Si‐Bcl‐xL group showed significantly lower cell growth and noticeably higher apoptosis rate than the NC group (normal control group). The expression of Bcl‐xL is reduced following articular cartilage injury, and this reduction promotes the proliferation and inhibits the apoptosis of chondrocytes. Therefore, Bcl‐xL could serve as a relevant molecular target in the clinical practice of osteoarthritis and other diseases causing cartilage damage.     

Diagnostics and correction of batch effects in large‐scale proteomic studies: a tutorial

Advancements in mass spectrometry‐based proteomics have enabled experiments encompassing hundreds of samples. While these large sample sets deliver much‐needed statistical power, handling them introduces technical variability known as batch effects. Here, we present a step‐by‐step protocol for the assessment, normalization, and batch correction of proteomic data. We review established methodologies from related fields and describe solutions specific to proteomic challenges, such as ion intensity drift and missing values in quantitative feature matrices. Finally, we compile a set of techniques that enable control of batch effect adjustment quality. We provide an R package, "proBatch", containing functions required for each step of the protocol. We demonstrate the utility of this methodology on five proteomic datasets each encompassing hundreds of samples and consisting of multiple experimental designs. In conclusion, we provide guidelines and tools to make the extraction of true biological signal from large proteomic studies more robust and transparent, ultimately facilitating reliable and reproducible research in clinical proteomics and systems biology.     

Role of miR‐218‐GREM1 axis in epithelial‐mesenchymal transition of oral squamous cell carcinoma: An in vivo and vitro study based on microarray data

Oral squamous cell carcinoma (OSCC) is a prevalent cancer that develops in the head and neck area and has high annual mortality despite optimal treatment. microRNA‐218 (miR‐218) is a tumour inhibiting non‐coding RNA that has been reported to suppress the cell proliferation and invasion in various cancers. Thus, our study aims to determine the mechanism underlying the inhibitory role of miR‐218 in OSCC. We conducted a bioinformatics analysis to screen differentially expressed genes in OSCC and their potential upstream miRNAs. After collection of surgical OSCC tissues, we detected GREM1 expression by immunohistochemistry, RT‐qPCR and Western blot analysis, and miR‐218 expression by RT‐qPCR. The target relationship between miR‐218 and GREM1 was assessed by dual‐luciferase reporter gene assay. After loss‐ and gain‐of‐function experiments, OSCC cell proliferation, migration and invasion were determined by MTT assay, scratch test and Transwell assay, respectively. Expression of TGF‐β1, Smad4, p21, E‐cadherin, Vimentin and Snail was measured by RT‐qPCR and Western blot analysis. Finally, effects of miR‐218 and GREM1 on tumour formation and liver metastasis were evaluated in xenograft tumour‐bearing nude mice. GREM1 was up‐regulated, and miR‐218 was down‐regulated in OSCC tissues, and GREM1 was confirmed to be the target gene of miR‐218. Furthermore, after up‐regulating miR‐218 or silencing GREM1, OSCC cell proliferation, migration and invasion were reduced. In addition, expression of TGF‐β signalling pathway‐related genes was diminished by overexpressing miR‐218 or down‐regulating GREM1. Finally, up‐regulated miR‐218 or down‐regulated GREM1 reduced tumour growth and liver metastasis in vivo. Taken together, our findings suggest that the overexpression of miR‐218 may inhibit OSCC progression by inactivating the GREM1‐dependent TGF‐β signalling pathway.     

Application of T‐cell receptor repertoire as a novel monitor in dynamic tracking and assessment: A cohort‐study based on RA patients

T‐cell receptor repertoire (TCRR) sequencing has been widely applied in many fields as a novel tool. This study explored characteristics of TCRR in detail with a cohort of 598 rheumatoid arthritis (RA) patients before and after anti‐rheumatic treatments. We highlighted the abnormal TCRR distribution in RA characterized by decreased diversity and increased proportion of hyperexpanded clones (HECs), which was potentially attributed to skewed usage of global V/J segments but not a few certain ones. Enriched motifs analysis in RA community demonstrated the huge heterogeneity of CDR3 sequences, so that individual factors are strongly recommended to be taken into consideration when it comes to clinical application of TCRR. Disease‐modifying antirheumatic drugs (DMARDs) can regulate immune system through recovery of TCRR richness to relieve symptoms. Remarkably, sensitive gene profile and advantageous gene profile were identified in this study as new biomarkers for different DMARDs regimens.     

Mass‐ratio and complementarity effects simultaneously drive aboveground biomass in temperate Quercus forests through stand structure

Forests play a key role in regulating the global carbon cycle, a substantial portion of which is stored in aboveground biomass (AGB). It is well understood that biodiversity can increase the biomass through complementarity and mass‐ratio effects, and the contribution of environmental factors and stand structure attributes to AGB was also observed. However, the relative influence of these factors in determining the AGB of Quercus forests remains poorly understood. Using a large dataset retrieved from 523 permanent forest inventory plots across Northeast China, we examined the effects of integrated multiple tree species diversity components (i.e., species richness, functional, and phylogenetic diversity), functional traits composition, environmental factors (climate and soil), stand age, and structure attributes (stand density, tree size diversity) on AGB based on structural equation models. We found that species richness and phylogenetic diversity both were not correlated with AGB. However, functional diversity positively affected AGB via an indirect effect in line with the complementarity effect. Moreover, the community‐weighted mean of specific leaf area and height increased AGB directly and indirectly, respectively; demonstrating the mass‐ratio effect. Furthermore, stand age, density, and tree size diversity were more important modulators of AGB than biodiversity. Our study highlights that biodiversity–AGB interaction is dependent on the regulation of stand structure that can be even more important for maintaining high biomass than biodiversity in temperate Quercus forests.     

Agent‐based modeling of the effects of forest dynamics,selective logging,and fragment size on epiphyte communities

1. Forest canopies play a crucial role in structuring communities of vascular epiphytes by providing substrate for colonization, by locally varying microclimate, and by causing epiphyte mortality due to branch or tree fall. However, as field studies in the three‐dimensional habitat of epiphytes are generally challenging, our understanding of how forest structure and dynamics influence the structure and dynamics of epiphyte communities is scarce.
2. Mechanistic models can improve our understanding of epiphyte community dynamics. We present such a model that couples dispersal, growth, and mortality of individual epiphytes with substrate dynamics, obtained from a three‐dimensional functional–structural forest model, allowing the study of forest–epiphyte interactions. After validating the epiphyte model with independent field data, we performed several theoretical simulation experiments to assess how (a) differences in natural forest dynamics, (b) selective logging, and (c) forest fragmentation could influence the long‐term dynamics of epiphyte communities.
3. The proportion of arboreal substrate occupied by epiphytes (i.e., saturation level) was tightly linked with forest dynamics and increased with decreasing forest turnover rates. While species richness was, in general, negatively correlated with forest turnover rates, low species numbers in forests with very‐low‐turnover rates were due to competitive exclusion when epiphyte communities became saturated. Logging had a negative impact on epiphyte communities, potentially leading to a near‐complete extirpation of epiphytes when the simulated target diameters fell below a threshold. Fragment size had no effect on epiphyte abundance and saturation level but correlated positively with species numbers.
4. Synthesis: The presented model is a first step toward studying the dynamic forest–epiphyte interactions in an agent‐based modeling framework. Our study suggests forest dynamics as key factor in controlling epiphyte communities. Thus, both natural and human‐induced changes in forest dynamics, for example, increased mortality rates or the loss of large trees, pose challenges for epiphyte conservation.

     

Aboveground competition influences density‐dependent effects of cordgrass on sediment biogeochemistry

Interspecific interactions between plants influence plant phenotype, distribution, abundance, and community structure. Each of these can, in turn, impact sediment biogeochemistry. Although the population and community level impacts of these interactions have been extensively studied, less is known about their effect on sediment biogeochemistry. This is surprising given that many plants are categorized as foundation species that exert strong control on community structure. In southern California salt marshes, we used clipping experiments to manipulate aboveground neighbor presence to study interactions between two dominant plants, Pacific cordgrass (Spartina foliosa) and perennial pickleweed (Sarcocornia pacifica). We also measured how changes in cordgrass stem density influenced sediment biogeochemistry. Pickleweed suppressed cordgrass stem density but had no effect on aboveground biomass. For every cordgrass stem lost per square meter, porewater ammonium increased 0.3–1.0 µM. Thus, aboveground competition with pickleweed weakened the effects of cordgrass on sediment biogeochemistry. Predictions about plant–soil feedbacks, especially under future climate scenarios, will be improved when plant–plant interactions are considered, particularly those containing dominant and foundation species.     

An efficient and precise method for generating knockout cell lines based on CRISPR‐Cas9 system

Although the efficiency and versatility of CRISPR‐Cas9 system has been greatly improved over conventional genome editing methods such as zinc finger or TALEN, it is still time‐consuming and labor‐intensive for screening knockout/knock‐in cell clones due to differences of the targeted location or efficacies of guide RNAs (gRNAs). Here, we adapted a targeted knock‐in strategy with CRISPR‐Cas9 system and characterized the efficiency for generating single or double knockout cell lines. Specifically, a homology‐arm based donor cassette consisting of genes encoding a fluorescence protein and antibiotic selection marker driven by a constitutive promoter was co‐transfected with a gRNA expressing unit. Based on FACS sorting and antibiotic drug selection, positive cell clones were confirmed by genotyping and at the protein expression level. The results indicated that more than 70% of analyzed clones identified by cell sorting and selection were successfully targeted in both single and double knockout experiments. The procedure takes less than three weeks to obtain knockout cell lines. We believe that this methodology could be applicable and versatile in generating knockout cell clones with high efficiency in most cell lines.     

Therapeutic effects of CXCR4+ subpopulation of transgene‐free induced cardiosphere‐derived cells on experimental myocardial infarction

ObjectivesMyocardial infarction (MI) is the most predominant type of cardiovascular diseases with high mortality and morbidity. Stem cell therapy, especially cardiac progenitor cell therapy, has been proposed as a promising approach for cardiac regeneration and MI treatment. Previously, we have successfully generated cardiac progenitor‐like cells, induced cardiosphere (iCS), via somatic reprogramming. However, the genome integration characteristic of virus‐based reprogramming approach hampered their therapeutic applications due to the risk of tumour formation. In the current study, we aim to establish a safer iCS generation strategy with transgene‐free approaches.Materials and MethodsFour transgene‐free approaches for somatic reprogramming, including episome, minicircle, self‐replicative RNA, and sendai virus, were compared, from the perspective of cardiac progenitor marker expression, iCS formation, and cardiac differentiation. The therapeutic effects were assessed in the mouse model of MI, from the perspective of survival rate, cardiac function, and structural alterations.ResultsThe self‐replicative RNA approach produced more iCS, which had cardiomyocyte differentiation ability and therapeutic effects on the mouse model of MI with comparable levels with endogenous cardiospheres and iCS generated with retrovirus. In addition, the CXCR4 (C‐X‐C chemokine receptor 4) positive subpopulation of iCS derived cells (iCSDC) delivered by intravenous injection was found to have similar therapeutic effects with intramyocardial injection on the mouse model of MI, representing a safer delivery approach.ConclusionThus, the optimized strategy for iCS generation is safer and has more therapeutic potentials.