Rapid age-grading and species identification of natural mosquitoes for malaria surveillance

The malaria parasite, which is transmitted by several Anopheles mosquito species, requires more time to reach its human-transmissible stage than the average lifespan of mosquito vectors. Monitoring the species-specific age structure of mosquito populations is critical to evaluating the impact of vector control interventions on malaria risk. We present a rapid, cost-effective surveillance method based on deep learning of mid-infrared spectra of mosquito cuticle that simultaneously identifies the species and age class of three main malaria vectors in natural populations. Using spectra from over 40, 000 ecologically and genetically diverse An. gambiae, An. arabiensis, and An. coluzzii females, we develop a deep transfer learning model that learns and predicts the age of new wild populations in Tanzania and Burkina Faso with minimal sampling effort. Additionally, the model is able to detect the impact of simulated control interventions on mosquito populations, measured as a shift in their age structures. In the future, we anticipate our method can be applied to other arthropod vector-borne diseases.

Knowing the age of malaria-transmitting mosquitoes is important to understand transmission risk as only old mosquitoes can transmit the disease. Here, the authors develop a method based on mid-infrared spectra of mosquito cuticle that can rapidly identify the species and age class of main malaria vectors.

Whole-Genome Transformation of Yeast Promotes Rare Host Mutations with a Single Causative SNP Enhancing Acetic Acid Tolerance

Whole-genome (WG) transformation (WGT) with DNA from the same or another species has been used to obtain strains with superior traits. Very few examples have been reported in eukaryotes—most apparently involving integration of large fragments of foreign DNA into the host genome. We show that WGT of a haploid acetic acid-sensitive Saccharomyces cerevisiae strain with DNA from a tolerant strain, but not from nontolerant strains, generated many tolerant transformants, some of which were stable upon subculturing under nonselective conditions. The most tolerant stable transformant contained no foreign DNA but only seven nonsynonymous single nucleotide polymorphisms (SNPs), of which none was present in the donor genome. The SNF4 mutation c.[805G→T], generating Snf4^E269*, was the main causative SNP. Allele exchange of SNF4^E269* or snf4Δ in industrial strains with unrelated genetic backgrounds enhanced acetic acid tolerance during fermentation under industrially relevant conditions. Our work reveals a surprisingly small number of mutations introduced by WGT, which do not bear any sequence relatedness to the genomic DNA (gDNA) of the donor organism, including the causative mutation. Spontaneous mutagenesis under protection of a transient donor gDNA fragment, maintained as extrachromosomal circular DNA (eccDNA), might provide an explanation. Support for this mechanism was obtained by transformation with genomic DNA of a yeast strain containing NatMX and selection on medium with nourseothricin. Seven transformants were obtained that gradually lost their nourseothricin resistance upon subculturing in nonselective medium. Our work shows that WGT is an efficient strategy for rapidly generating and identifying superior alleles capable of improving selectable traits of interest in industrial yeast strains.

Transcriptome Analysis on Key Metabolic Pathways in Rhodotorula mucilaginosa Under Pb(II) Stress

Rhodotorula mucilaginosa shows adaption to a broad range of Pb²⁺ stress. In this study, three key pathways, i.e., glycolysis (EMP), the tricarboxylic acid (TCA) cycle, and oxidative phosphorylation (OXPHOS), were investigated under 0-2,500 mg · L^-1 Pb stress, primarily based on biochemical analysis and RNA sequencing. R. mucilaginosa cells showed similar metabolic response to low/medium (500/1000 mg · L^-1) Pb²⁺ stress. High (2,500 mg · L^-1) Pb²⁺ stress exerted severe cytotoxicity to R. mucilaginosa. The downregulation of HK under low-medium Pb²⁺ suggested a correlation with the low hexokinase enzymatic activity in vivo. However, IDH3, regulating a key step of circulation in TCA, was upregulated to promote ATP feedstock for downstream OXPHOS. Then, through activation of complex I & IV in the electron transport chain (ETC) and ATP synthase, ATP production was finally enhanced. This mechanism enabled fungal cells to compensate for ATP consumption under low-medium Pb²⁺ toxicity. Hence, R. mucilaginosa tolerance to such a broad range of Pb²⁺ concentrations can be attributed to energy adaption. In contrast, high Pb²⁺ stress caused ATP deficiency. Then, the subsequent degradation of intracellular defense systems further intensified Pb toxicity. This study correlated responses of EMP, TCA, and OXPHOS pathways in R. mucilaginosa under Pb stress, hence providing new insights into the fungal resistance to heavy metal stress. IMPORTANCE Glycolysis (EMP), the tricarboxylic acid (TCA) cycle, and oxidative phosphorylation (OXPHOS) are critical metabolism pathways for microorganisms to obtain energy during the resistance to heavy metal (HM) stress. However, these pathways at the genetic level have not been elucidated to evaluate their cytoprotective functions for Rhodotorula mucilaginosa under Pb stress. In this study, we investigated these three pathways based on biochemical analysis and RNA sequencing. Under low-medium (500-1,000 mg · L^-1) Pb²⁺ stress, ATP production was stimulated mainly due to the upregulation of genes associated with the TCA cycle and the electron transport chain (ETC). Such an energy compensatory mechanism could allow R. mucilaginosa acclimation to a broad range of Pb²⁺ concentrations (up to 1000 mg · L^-1). In contrast, high (2500 mg · L^-1) Pb²⁺ stress exerted its excessive toxicity by provoking ATP deficiency and damage to intracellular resistance systems. This study provided new insights into R. mucilaginosa resistance to HM stress from the perspective of metabolism.

Picornavirus translation strategies

The genome of viruses classified as picornaviruses consists of a single monocistronic positive strand RNA. The coding capacity of these RNA viruses is rather limited, and thus, they rely on the cellular machinery for their viral replication cycle. Upon the entry of the virus into susceptible cells, the viral RNA initially competes with cellular mRNAs for access to the protein synthesis machinery. Not surprisingly, picornaviruses have evolved specialized strategies that successfully allow the expression of viral gene products, which we outline in this review. The main feature of all picornavirus genomes is the presence of a heavily structured RNA element on the 5´UTR, referred to as an internal ribosome entry site (IRES) element, which directs viral protein synthesis as well and, consequently, triggers the subsequent steps required for viral replication. Here, we will summarize recent studies showing that picornavirus IRES elements consist of a modular structure, providing sites of interaction for ribosome subunits, eIFs, and a selective group of RNA‐binding proteins.

Fine-mapping of Parkinson's disease susceptibility loci identifies putative causal variants

Recent genome-wide association studies have identified 78 loci associated with Parkinson's disease susceptibility but the underlying mechanisms remain largely unclear. To identify likely causal variants for disease risk, we fine-mapped these Parkinson's-associated loci using four different fine-mapping methods. We then integrated multi-assay cell type-specific epigenomic profiles to pinpoint the likely mechanism of action of each variant, allowing us to identify Consensus single nucleotide polymorphism (SNPs) that disrupt LRRK2 and FCGR2A regulatory elements in microglia, an MBNL2 enhancer in oligodendrocytes, and a DYRK1A enhancer in neurons. This genome-wide functional fine-mapping investigation of Parkinson's disease substantially advances our understanding of the causal mechanisms underlying this complex disease while avoiding focus on spurious, non-causal mechanisms. Together, these results provide a robust, comprehensive list of the likely causal variants, genes and cell-types underlying Parkinson's disease risk as demonstrated by consistently greater enrichment of our fine-mapped SNPs relative to lead GWAS SNPs across independent functional impact annotations. In addition, our approach prioritized an average of 3/85 variants per locus as putatively causal, making downstream experimental studies both more tractable and more likely to yield disease-relevant, actionable results. Large-scale studies comparing individuals with Parkinson's disease to age-matched controls have identified many regions of the genome associated with the disease. However, there is widespread correlation between different parts of the genome, making it difficult to tell which genetic variants cause Parkinson's and which are simply co-inherited with causal variants. We therefore applied a suite of statistical models to identify the most likely causal genetic variants (i.e. fine-mapping). We then linked these genetic variants with epigenomic and gene expression signatures across a wide variety of tissues and cell types to identify how these variants cause disease. Therefore, this study provides a comprehensive and robust list of cellular and molecular mechanisms that may serve as targets in the development of more effective Parkinson's therapeutics.

Vascularized Co-Culture Clusteroids of Primary Endothelial and Hep-G2 Cells Based on Aqueous Two-Phase Pickering Emulsions

Three-dimensional cell culture has been extensively involved in biomedical applications due to its high availability and relatively mature biochemical properties. However, single 3D cell culture models based on hydrogel or various scaffolds do not meet the more in-depth requirements of in vitro models. The necrotic core formation inhibits the utilization of the 3D cell culture ex vivo as oxygen permeation is impaired in the absence of blood vessels. We report a simple method to facilitate the formation of angiogenic HUVEC (human umbilical vein endothelial cells) and Hep-G2 (hepatocyte carcinoma model) co-culture 3D clusteroids in a water-in-water (w/w) Pickering emulsions template which can overcome this limitation. This method enabled us to manipulate the cells proportion in order to achieve the optimal condition for stimulating the production of various angiogenic protein markers in the co-cultured clusteroids. The HUVEC cells respond to the presence of Hep-G2 cells and their byproducts by forming endothelial cell sprouts in Matrigel without the exogenous addition of vascular endothelial growth factor (VEGF) or other angiogenesis inducers. This culture method can be easily replicated to produce other types of cell co-culture spheroids. The w/w Pickering emulsion template can facilitate the fabrication of 3D co-culture models to a great extent and be further utilized in drug testing and tissue engineering applications.

Microdeletion of 16q24.1-q24.2-A unique etiology of Lymphedema-Distichiasis syndrome and neurodevelopmental disorder

Interstitial deletions of 16q24.1–q24.2 are associated with alveolar capillary dysplasia, congenital renal malformations, neurodevelopmental disorders, and congenital abnormalities. Lymphedema–Distichiasis syndrome (LDS; OMIM # 153400) is a dominant condition caused by heterozygous pathogenic variants in FOXC2. Usually, lymphedema and distichiasis occur in puberty or later on, and affected individuals typically achieve normal developmental milestones. Here, we describe a boy with congenital lymphedema, distichiasis, bilateral hydronephrosis, and global developmental delay, with a de novo microdeletion of 894 kb at 16q24.1–q24.2. This report extends the phenotype of both 16q24.1–q24.2 microdeletion syndrome and of LDS. Interestingly, the deletion involves only the 3′‐UTR part of FOXC2.

Acidity-responsive nanocages as robust reactive oxygen species generators with butterfly effects for maximizing oxidative damage and enhancing cancer therapy

Recently, with the rational design of transition metal-containing nanoagents, chemodynamic therapy (CDT) has been developed and considered a promising method for cancer therapy through Fenton and Fenton-like reaction-induced hydroxyl radical (·OH) generation and cellular oxidative damage. However, it is still a great challenge to realize high reactive oxygen species (ROS) generation and therapeutic efficiency under the strict conditions of the tumor microenvironment (TME). Herein, we design and fabricate a TME-responsive core-shell nanocage composed of a CaCO₃ nanolayer and a heterogeneous CoP core (CaCO₃@CoP, CCP) with the synergy of CDT and calcium overload to maximize oxidative damage and enhance cancer therapy. The CaCO₃ nanoshell is sensitive to pH and can be rapidly degraded upon endocytosis, leading to intracellular Ca²⁺ accumulation, which further triggers the production of mitochondrial ROS. Subsequently, the CoP hollow nanocage with fully exposed Co active sites has high Fenton-like reactive activity to produce ·OH and induce mitochondrial damage. Mitochondrial damage and ROS elevation, in turn, can modulate Ca²⁺ dynamics and augment calcium overload. The reciprocal interaction and loop feedback between calcium overload and photoenhanced ROS generation via photothermal therapy (PTT) can further trigger the immunogenic cell death (ICD) process to activate the maturation of dendritic cells (DCs), activation of cytotoxic and helper T cells, and excretion of proinflammatory cytokines to enhance antitumor immunity in vivo. With the butterfly effect, CCP finally brings forth a greatly enhanced cancer therapeutic outcome in murine models.

Combination of Electrochemistry and Mass Spectrometry to Study Nitric Oxide Metabolism and Its Modulation by Compound K in Breast Cancer Cells

The levels of l-arginine and asymmetric dimethylarginine (ADMA) and the amount of the nitric oxide (NO) production have recently been linked to breast cancer and pharmaceutical effect evaluation. Herein, a method combining electrochemistry and high-resolution mass spectrometry (HRMS) was established and used to study NO metabolism and its modulation by ginsenoside compound K (CK) in breast cancer cells. Platinum nanoparticles-decorated fluorine tin oxide was employed as an electrochemical sensor for in situ detection of NO release, while HRMS was used for the analysis of the NO-related metabolites. Through the combination of the electrochemical and HRMS results, decreases in arginine and NO and increases in ADMA and ornithine were observed after modulation by CK, and two highly correlated metabolic pathways including arginine and proline metabolism and vascular smooth muscle contraction were found. This method offers a new strategy for fast evaluation of pharmaceutical efficacy based on NO metabolism.

Solving neurodegeneration: common mechanisms and strategies for new treatments

Across neurodegenerative diseases, common mechanisms may reveal novel therapeutic targets based on neuronal protection, repair, or regeneration, independent of etiology or site of disease pathology. To address these mechanisms and discuss emerging treatments, in April, 2021, Glaucoma Research Foundation, BrightFocus Foundation, and the Melza M. and Frank Theodore Barr Foundation collaborated to bring together key opinion leaders and experts in the field of neurodegenerative disease for a virtual meeting titled "Solving Neurodegeneration". This "think-tank" style meeting focused on uncovering common mechanistic roots of neurodegenerative disease and promising targets for new treatments, catalyzed by the goal of finding new treatments for glaucoma, the world's leading cause of irreversible blindness and the common interest of the three hosting foundations. Glaucoma, which causes vision loss through degeneration of the optic nerve, likely shares early cellular and molecular events with other neurodegenerative diseases of the central nervous system. Here we discuss major areas of mechanistic overlap between neurodegenerative diseases of the central nervous system: neuroinflammation, bioenergetics and metabolism, genetic contributions, and neurovascular interactions. We summarize important discussion points with emphasis on the research areas that are most innovative and promising in the treatment of neurodegeneration yet require further development. The research that is highlighted provides unique opportunities for collaboration that will lead to efforts in preventing neurodegeneration and ultimately vision loss.

Multienzyme interactions of the de novo purine biosynthetic protein PAICS facilitate purinosome formation and metabolic channeling

There is growing evidence that mammalian cells deploy a mitochondria-associated metabolon called the purinosome to perform channeled de novo purine biosynthesis (DNPB). However, the molecular mechanisms of this substrate-channeling pathway are not well defined. Here, we present molecular evidence of protein-protein interactions (PPIs) between the human bifunctional phosphoribosylaminoimidazole carboxylase/succinocarboxamide synthetase (PAICS) and other known DNPB enzymes. We employed two orthogonal approaches: bimolecular fluorescence complementation, to probe PPIs inside live, intact cells, and co-immunoprecipitation using StrepTag-labeled PAICS that was reintegrated into the genome of PAICS-knockout HeLa cells (crPAICS). With the exception of amidophosphoribosyltransferase, the first enzyme of the DNPB pathway, we discovered PAICS interacts with all other known DNPB enzymes and with MTHFD1, an enzyme which supplies the 10-formyltetrahydrofolate cofactor essential for DNPB. We show these interactions are present in cells grown in both purine-depleted and purine-rich conditions, suggesting at least a partial assembly of these enzymes may be present regardless of the activity of the DNPB pathway. We also demonstrate that tagging of PAICS on its C terminus disrupts these interactions and that this disruption is correlated with disturbed DNPB activity. Finally, we show that crPAICS cells with reintegrated N-terminally tagged PAICS regained effective DNPB with metabolic signatures of channeled synthesis, whereas crPAICS cells that reintegrated C-terminally tagged PAICS exhibit reduced DNPB intermediate pools and a perturbed partitioning of inosine monophosphate into AMP and GMP. Our results provide molecular evidence in support of purinosomes and suggest perturbing PPIs between DNPB enzymes negatively impact metabolite flux through this important pathway.

Structural analysis of M1AP variants associated with severely impaired spermatogenesis causing male infertility

Background

Impaired meiosis can result in absence of sperm in the seminal fluid. This condition, namely non-obstructive azoospermia (NOA), is one of the reasons of male infertility. Despite the low number of studies on meiosis 1-associated protein (M1AP) in the literature, M1AP is known to be crucial for spermatogenesis. Recently, seven variants (five missense, one frameshift, one splice-site) have been reported in the M1AP gene as associated with NOA, cryptozoospermia and oligozoospermia in two separate studies. However, all missense variants were evaluated as variant of uncertain significance by these studies. Therefore, we aimed to analyze their structural impacts on the M1AP protein that could lead to NOA.

Methods

We firstly performed an evolutionary conservation analysis for the variant positions. Afterwards, a comprehensive molecular modelling study was performed for the M1AP structure. By utilizing this model, protein dynamics were sampled for the wild-type and variants by performing molecular dynamics (MD) simulations.

Results

All variant positions are highly conserved, indicating that they are potentially important for function. In MD simulations, none of the variants led to a general misfolding or loss of stability in the protein structure, but they did cause severe modifications in the conformational dynamics of M1AP, particularly through changes in local interactions affecting flexibility, hinge and secondary structure.

Conclusions

Due to critical perturbations in protein dynamics, we propose that these variants may cause NOA by affecting important interactions regulating meiosis, particularly in wild-type M1AP deficiency since the variants are reported to be homozygous or bi-allelic in the infertile individuals. Our results provided reasonable insights about the M1AP structure and the effects of the variants to the structure and dynamics, which should be further investigated by experimental studies to validate.

Engineering nanobodies for next-generation molecular imaging

In recent years, nanobodies have emerged as ideal imaging agents for molecular imaging. Molecular nanobody imaging combines the specificity of nanobodies with the sensitivity of state-of-the-art molecular imaging modalities, such as positron emission tomography (PET). Given that modifications of nanobodies alter their pharmacokinetics (PK), the engineering strategies that combine nanobodies with radionuclides determine the effectiveness, reliability, and safety of the molecular imaging probes. In this review, we introduce conjugation strategies that have been applied to nanobodies, including random conjugation, ^99mTc tricarbonyl chemistry, sortase A-mediated site-specific conjugation, maleimide-cysteine chemistry, and click chemistries. We also summarize the latest advances in nanobody tracers, emphasizing their preclinical and clinical use. In addition, we elaborate on nanobody-based near-infrared fluorescence (NIRF) imaging and image-guided surgery.

Integrating Long-Range Regulatory Interactions to Predict Gene Expression Using Graph Convolutional Networks

Long-range regulatory interactions among genomic regions are critical for controlling gene expression, and their disruption has been associated with a host of diseases. However, when modeling the effects of regulatory factors, most deep learning models either neglect long-range interactions or fail to capture the inherent 3D structure of the underlying genomic organization. To address these limitations, we present a Graph Convolutional Model for Epigenetic Regulation of Gene Expression (GC-MERGE). Using a graph-based framework, the model incorporates important information about long-range interactions via a natural encoding of genomic spatial interactions into the graph representation. It integrates measurements of both the global genomic organization and the local regulatory factors, specifically histone modifications, to not only predict the expression of a given gene of interest but also quantify the importance of its regulatory factors. We apply GC-MERGE to data sets for three cell lines-GM12878 (lymphoblastoid), K562 (myelogenous leukemia), and HUVEC (human umbilical vein endothelial)-and demonstrate its state-of-the-art predictive performance. Crucially, we show that our model is interpretable in terms of the observed biological regulatory factors, highlighting both the histone modifications and the interacting genomic regions contributing to a gene's predicted expression. We provide model explanations for multiple exemplar genes and validate them with evidence from the literature. Our model presents a novel setup for predicting gene expression by integrating multimodal data sets in a graph convolutional framework. More importantly, it enables interpretation of the biological mechanisms driving the model's predictions.

Mix and wait - a relaxed way for synthesizing ZIF-8

Herein we report the synthesis of a zeolitic imidazolate framework (ZIF-8) by an easy "mix and wait" procedure. In a closed vial, without any interference, the mixture of 2-methylimidazole and basic zinc carbonate assembles into the crystalline product with approx. 90% conversion after 70 h. The reaction exhibits sigmoidal kinetics due to the self-generated water which accelerates the reaction.

Persistent DNA damage associated with ATM kinase deficiency promotes microglial dysfunction

The autosomal recessive genome instability disorder Ataxia-telangiectasia, caused by mutations in ATM kinase, is characterized by the progressive loss of cerebellar neurons. We find that DNA damage associated with ATM loss results in dysfunctional behaviour of human microglia, immune cells of the central nervous system. Microglial dysfunction is mediated by the pro-inflammatory RELB/p52 non-canonical NF-κB transcriptional pathway and leads to excessive phagocytic clearance of neuronal material. Activation of the RELB/p52 pathway in ATM-deficient microglia is driven by persistent DNA damage and is dependent on the NIK kinase. Activation of non-canonical NF-κB signalling is also observed in cerebellar microglia of individuals with Ataxia-telangiectasia. These results provide insights into the underlying mechanisms of aberrant microglial behaviour in ATM deficiency, potentially contributing to neurodegeneration in Ataxia-telangiectasia.

The Acute Effect of a Novel Miso-Type Sauce, Enhanced with a Carotenoid-Rich Extract from Fruit By-Products, on Postprandial Biomarkers of Oxidative Stress and Inflammation

Several fruit by-products may exert a beneficial role on oxidative stress and inflammation modulation, providing essential bioactive components, such as polyphenols and carotenoids. Recently, the potential bioactivity of miso has been reported. The aim of this dietary intervention−clinical study was to evaluate the acute effect of a novel, functional miso-type sauce based on legumes, on postprandial biomarkers of oxidative stress and inflammation. In this randomized, cross-over design, intervention−clinical trial, 14 healthy volunteers, aged 20−30 years old, consumed a rice meal rich in fat and carbohydrates (258 g), containing a legume-based sauce. After a 1-week washout period, the same subjects consumed the same meal, containing the novel fermented miso-type sauce, enhanced with 50% carotenoid-rich, fruit peel extract. Differences in postprandial total plasma antioxidant capacity according to the FRAP method, serum lipids, glucose, uric acid levels, and antithrombotic activity in platelet-rich plasma were evaluated before, 30 min, 1.5 h, and 3 h after consumption. The results showed that, in comparison to the control group, consumption of the novel sauce resulted in a significantly increased total plasma antioxidant capacity 3 h after consumption (p < 0.05). In addition, we observed a significant attenuation of triglycerides concentration increase in the last 1.5 h in the functional group (p < 0.05). A significant decrease in serum aggregation was found at 30 min and 3 h after functional sauce intake in comparison with the baseline (p < 0.05). Finally, LDL-cholesterol concentrations were significantly reduced 3 h after the functional meal consumption, in comparison with baseline values (p < 0.05). The remaining biomarkers did not show statistically significant differences (p > 0.05). Further investigation is needed in order to validate the current results.

Cold atmospheric pressure plasma for attenuation of SARS-CoV-2 spike protein binding to ACE2 protein and the RNA deactivation

Cold atmospheric pressure (CAP) plasma has a profound effect on protein-protein interactions. In this work, we have highlighted the deactivation of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spike protein by CAP plasma treatment. Complete deactivation of spike protein binding to the human ACE2 protein was observed within an exposure time of 5 minutes which is correlated to the higher concentration of hydrogen peroxide formation due to the interaction with the reactive oxygen species present in the plasma. On the other hand, we have established that CAP plasma is also capable of degrading RNA of SARS-CoV-2 virus which is also linked to hydrogen peroxide concentration. The reactive oxygen species is produced in the plasma by using noble gases such as helium, in the absence of any other chemicals. Therefore, it is a green process with no chemical waste generated and highly advantageous from the environmental safety prospects. Results of this work could be useful in designing plasma-based disinfection systems over those based on environmentally hazardous chemical-based disinfection and biomedical applications.

Single-Cell Multiomics Techniques: From Conception to Applications

Recent advances in methods for single-cell analyses and barcoding strategies have led to considerable progress in research. The development of multiplexed assays offers the possibility to conduct parallel analyses of multiple factors and processes for comprehensive characterization of cellular and molecular states in health and disease. These technologies have expanded extremely rapidly in the past years and constantly evolve and provide better specificity, precision and resolution. This review summarizes recent progress in single-cell multiomics approaches, and focuses, in particular, on the most innovative techniques that integrate genome, epigenome and transcriptome profiling. It describes the methodologies, discusses their advantages and limitations, and explains how they have been applied to studies on cell heterogeneity and differentiation, and epigenetic reprogramming.

Sensor-based phenotyping of above-ground plant-pathogen interactions

Plant pathogens cause yield losses in crops worldwide. Breeding for improved disease resistance and management by precision agriculture are two approaches to limit such yield losses. Both rely on detecting and quantifying signs and symptoms of plant disease. To achieve this, the field of plant phenotyping makes use of non-invasive sensor technology. Compared to invasive methods, this can offer improved throughput and allow for repeated measurements on living plants. Abiotic stress responses and yield components have been successfully measured with phenotyping technologies, whereas phenotyping methods for biotic stresses are less developed, despite the relevance of plant disease in crop production. The interactions between plants and pathogens can lead to a variety of signs (when the pathogen itself can be detected) and diverse symptoms (detectable responses of the plant). Here, we review the strengths and weaknesses of a broad range of sensor technologies that are being used for sensing of signs and symptoms on plant shoots, including monochrome, RGB, hyperspectral, fluorescence, chlorophyll fluorescence and thermal sensors, as well as Raman spectroscopy, X-ray computed tomography, and optical coherence tomography. We argue that choosing and combining appropriate sensors for each plant-pathosystem and measuring with sufficient spatial resolution can enable specific and accurate measurements of above-ground signs and symptoms of plant disease.

BTG2 as a tumor target for the treatment of luminal A breast cancer

As one of the most common breast cancer subtypes, luminal A breast cancer is sensitive to endocrine-based therapy and insensitive to chemotherapy. Patients with luminal A subtype of breast cancer have a relatively good prognosis compared with that of patients with other subtypes of breast cancer. However, with the increased incidence in endocrine resistance and severe side effects, simple endocrine therapy has become unsuitable for the treatment of luminal A breast cancer. Therefore, identifying novel therapeutic targets for luminal A breast cancer may accelerate the development of an effective therapeutic strategy. The bioinformatical analysis of the current study, which included KEGG and GO analyses of the GSE20437 dataset containing 24 healthy and 18 breast cancer tissue samples, identified key target genes associated with breast cancer. Moreover, survival analysis results revealed that a low expression of BTG2 was significantly associated with the low survival rate of patients with breast cancer, indicated that B-cell translocation gene 2 (BTG2) may be a potential target in breast cancer. However, BTG2 may be cancer type-dependent, as overexpression of BTG2 has been demonstrated to suppress the proliferation of pancreatic and lung cancer cells, but promote the proliferation of bladder cancer cells. Since the association between BTG2 and luminal A-subtype breast cancer remains unclear, it is important to understand the biological function of BTG2 in luminal A breast cancer. Based on the expression levels of estrogen receptor, progesterone receptor and human epidermal growth factor receptor, MCF-7 cells were selected in the present study as a luminal A breast cancer cell type. MTT, Transwell invasion and wound healing assays revealed that overexpression of BTG2 suppressed the levels of MCF-7 cell proliferation, migration and invasion. In addition, the downregulation of BTG2 at the mRNA and protein level was also confirmed in luminal A breast tumor tissue, which was consistent with the results in vitro. These results indicated that BTG2 may act as an effective target for the treatment of luminal A breast cancer.

Rapid identification of tumor-reactive T-cell receptors by RNA preamplification-based single-cell sequencing

T-cell receptor (TCR)-transduced T (TCR-T) cell therapy has shown promising efficacy in the clinical treatment of malignant cancers. However, the populations covered by reported TCRs are still limited. Tumor infiltrating lymphocytes (TILs) are natural reservoirs of tumor-reactive T cells and TCRs. Approaches are required for the fast and cost-effective identification of tumor-reactive TCRs from TILs. The widely employed TCR identification approaches by the clonal expansion of TILs involve a TCR singularization process for the direct pairing of TCR Vα and the Vβ chain. However, the clonal expansion of T cells is well known to require extensive time and effort due to the involvement of T cell cultures. Several single-cell multiplexing PCR methods followed by Sanger sequencing have been developed, representing a cost-effective and fast approach for single-cell TCR identification. In this study, an RNA-based preamplification step was included in the single-cell TCR sequencing, which can reduce the multiplexing PCR amplification to one round. Moreover, the cDNA product of RNA preamplification is derived from the whole genome mRNA, instead of TCR mRNA only by multiplexing primers-based DNA preamplification, which is valuable for many other analyses (e.g., phenotypic analysis) of the tumor-reactive T cells that can be correlated with the identified TCRs. The feasibility for both single α chain and dual α chain TILs of this approach highlights its potential value as a rapid and cost-effective sequencing strategy for the development of TCR-T therapies for solid cancers.

Modular Bioreactor Design for Directed Tendon/Ligament Tissue Engineering

Functional tissue-engineered tendons and ligaments remain to be prepared in a reproducible and scalable manner. This study evaluates an acellular 3D extracellular matrix (ECM) scaffold for tendon/ligament tissue engineering and their ability to support strain-induced gene regulation associated with the tenogenesis of cultured mesenchymal stromal cells. Preliminary data demonstrate unique gene regulation patterns compared to other scaffold forms, in particular in Wnt signaling. However, the need for a robust bioreactor system that minimizes process variation was also evident. A design control process was used to design and verify the functionality of a novel bioreactor. The system accommodates 3D scaffolds with clinically-relevant sizes, is capable of long-term culture with customizable mechanical strain regimens, incorporates in-line load measurement for continuous monitoring and feedback control, and allows a variety of scaffold configurations through a unique modular grip system. All critical functional specifications were met, including verification of physiological strain levels from 1–10%, frequency levels from 0.2–0.5 Hz, and accurate load measurement up to 50 N, which can be expanded on the basis of load cell capability. The design process serves as a model for establishing statistical functionality and reliability of investigative systems. This work sets the stage for detailed analyses of ECM scaffolds to identify critical differentiation signaling responses and essential matrix composition and cell–matrix interactions.

Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species

We investigated the potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250 km² island. The island scrub-jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine-oak ecotones on Santa Cruz Island, California (USA) similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3,000 single nucleotide polymorphisms (SNPs) in 123 adult island scrub-jay males from across Santa Cruz Island using restriction site-associated DNA sequencing (RADseq). Neutral landscape genomic analyses revealed that genome-wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis (RDA) while controlling for spatial effects. Finally, two genome-wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow.

Single amino acid bionanozyme for environmental remediation

Enzymes are extremely complex catalytic structures with immense biological and technological importance. Nevertheless, their widespread environmental implementation faces several challenges, including high production costs, low operational stability, and intricate recovery and reusability. Therefore, the de novo design of minimalistic biomolecular nanomaterials that can efficiently mimic the biocatalytic function (bionanozymes) and overcome the limitations of natural enzymes is a critical goal in biomolecular engineering. Here, we report an exceptionally simple yet highly active and robust single amino acid bionanozyme that can catalyze the rapid oxidation of environmentally toxic phenolic contaminates and serves as an ultrasensitive tool to detect biologically important neurotransmitters similar to the laccase enzyme. While inspired by the laccase catalytic site, the substantially simpler copper-coordinated bionanozyme is ∼5400 times more cost-effective, four orders more efficient, and 36 times more sensitive compared to the natural protein. Furthermore, the designed mimic is stable under extreme conditions (pH, ionic strength, temperature, storage time), markedly reusable for several cycles, and displays broad substrate specificity. These findings hold great promise in developing efficient bionanozymes for analytical chemistry, environmental protection, and biotechnology.

Dendritic epidermal T cells secreting exosomes promote the proliferation of epidermal stem cells to enhance wound re-epithelialization

Background

Efficient re-epithelialization is important for successful skin wound healing. The proportion of epidermal stem cells (EpSCs) and dendritic epidermal T cells (DETCs) determines the extent of wound re-epithelialization, especially in large areas of skin tissue loss. However, it remains unknown whether and how DETCs regulate the status of EpSCs to impact wound re-epithelialization.

Methods

To investigate how DETCs regulate EpSCs in skin re-epithelialization, we utilized normal or full-thickness skin deficient wide type (WT) mice and Tcrσ knockout (Tcrσ^−/−) mice with DETCs or DETCs-derived exosomes (Exos) treatment. Flow cytometry analysis (FCAS), BrdU labelled experiments, immunofluorescence and immunohistochemical assays were performed to detect the proportion of EpSCs in the epidermis. Wound closure rate and re-epithelialization were assayed by a macroscopical view and hematoxylin–eosin (H&E) staining. EpSCs in vitro were co-cultured with DETCs in a transwell-dependent or -independent manner, or supplement with GW4869 or Exos (5 µg/mL, 15 µg/mL and 45 µg/mL), and the proliferation of EpSCs was detected by means of FCAS and CFSE.

Results

Our data showed that the proportion of CD49f^briCD71^dim cells, K15⁺ cells and BrdU⁺ cells in the normal epidermis of Tcrδ^−/− mice had no significant difference compared to WT mice. For wounded Tcrδ^−/− mice, DETCs treatment increase the proportion of CD49f^briCD71^dim cells, K15⁺ cells and BrdU⁺ cells in the epidermis around the wound in comparison to PBS treatment. DETCs significantly increased the number of CD49f^briCD7^dim cells and K15⁺ cells through transwell-dependent or -independent manners relative to control group. Furthermore, Exos stimuli remarkedly promote the proliferation of EpSCs compared to control group, while the increasement was suppressed when DETCs were interfered with GW4869. Gross observation and H&E staining showed that Exos significantly accelerated wound closure and increased re-epithelialization length in Tcrδ^−/− mice when compared to control mice. Additionally, we found in vivo that Exos observably facilitated the proliferation of CD49f^briCD7^dim cells and K15⁺ cells.

Conclusions

We revealed that DETCs enhanced the proliferation of EpSCs in the epidermis around the wounds to accelerate re-epithelialization in which Exos played important roles in the remote regulation of EpSCs proliferation. Together, these findings suggest a mechanistic link among DETC-derived exosomes, the proliferation of EpSCs, and wound re-epithelialization in the skin.

Isorhamnetin alleviates lipopolysaccharide-induced acute lung injury by inhibiting mTOR signaling pathway

Aim: Acute Lung Injury (ALI) is an acute hypoxic respiratory insufficiency caused by various traumatic factors, manifested as progressive hypoxemia and respiratory distress, and lung imaging shows a heterogeneous osmotic outbreak. Isorhamnetin (ISO) is a flavonoid compound isolated and purified from medicinal plants, such as Hippophae rhamnoides L. and Ginkgo, and has multiple pharmacological functions, such as anti-tumor, anti-myocardial hypoxia, and cardiovascular protection. Our previous study has shown that ISO could attenuate lipopolysaccharide (LPS)-induced acute lung injury in mice, but its mechanism is not clear.Methods: In this study, we used LPS-induced mouse and cell models to research the mechanism of ISO alleviating acute lung injury.Results: The results showed that ISO could attenuate the injury of type II alveolar epithelial cells by inhibiting the TLR4/NF-κB pathway. Further studies showed that ISO could inhibit the activation of mTOR signal in vivo and in vitro and promote autophagy in alveolar epithelial cells to reduce lung injury caused by LPS. In addition, ISO could inhibit LPS-induced epithelial cell apoptosis.Conclusion: Overall, ISO could suppress injury and apoptosis of epithelial cells and activate autophagy to protect epithelial cells via inhibiting mTOR signal and attenuating LPS-induced acute lung injury in mice.

Loss-of-function of KMT5B leads to neurodevelopmental disorder and impairs neuronal development and neurogenesis

Autism spectrum disorder (ASD) is a group of neurodevelopmental disorders that cause severe social, communication and behavioral problems. Recent studies show that the variants of a histone methyltransferase gene KMT5B, cause neurodevelopmental disorders (NDDs), including ASD and the knockout of Kmt5b in mice is embryonic lethal. However, the detailed genotype-phenotype correlations and functional effects of KMT5B in neurodevelopment are unclear. By targeted sequencing of a large Chinese ASD cohort, analyzing published genome-wide sequencing data, and mining literature, we curated 39 KMT5B variants identified from NDD individuals. A genotype-phenotype correlation analysis for ten individuals with KMT5B pathogenic variants reveals common symptoms, including ASD, intellectual disability, languages problem and macrocephaly. In vitro knockdown of the expression of Kmt5b in cultured mouse primary cortical neurons leads to a decrease in neuronal dendritic complexity and an increase in dendritic spine density, which can be rescued by expression of human KMT5B but not that of pathogenic de novo missense mutants. In vivo knockdown of the Kmt5b expression in the mouse embryonic cerebral cortex by in utero electroporation results in decreased proliferation and accelerated migration of neural progenitor cells. Our findings reveal essential roles of histone methyltransferase KMT5B in neuronal development, prenatal neurogenesis, and neuronal migration.

Fluxomics - New Metabolomics Approaches to Monitor Metabolic Pathways

Fluxomics is an innovative -omics research field that measures the rates of all intracellular fluxes in the central metabolism of biological systems. Fluxomics gathers data from multiple different -omics fields, portraying the whole picture of molecular interactions. Recently, fluxomics has become one of the most relevant approaches to investigate metabolic phenotypes. Metabolic flux using 13C-labeled molecules is increasingly used to monitor metabolic pathways, to probe the corresponding gene-RNA and protein-metabolite interaction networks in actual time. Thus, fluxomics reveals the functioning of multi-molecular metabolic pathways and is increasingly applied in biotechnology and pharmacology. Here, we describe the main fluxomics approaches and experimental platforms. Moreover, we summarize recent fluxomic results in different biological systems.

Thyroid hormone enhances stem cell maintenance and promotes lineage-specific differentiation in human embryonic stem cells

Background

Thyroid hormone triiodothyronine (T3) is essential for embryogenesis and is commonly used during in vitro fertilization to ensure successful implantation. However, the regulatory mechanisms of T3 during early embryogenesis are largely unknown.

Method

To study the impact of T3 on hPSCs, cell survival and growth were evaluated by measurement of cell growth curve, cloning efficiency, survival after passaging, cell apoptosis, and cell cycle status. Pluripotency was evaluated by RT-qPCR, immunostaining and FACS analysis of pluripotency markers. Metabolic status was analyzed using LC–MS/MS and Seahorse XF Cell Mito Stress Test. Global gene expression was analyzed using RNA-seq. To study the impact of T3 on lineage-specific differentiation, cells were subjected to T3 treatment during differentiation, and the outcome was evaluated using RT-qPCR, immunostaining and FACS analysis of lineage-specific markers.

Results

In this report, we use human pluripotent stem cells (hPSCs) to show that T3 is beneficial for stem cell maintenance and promotes trophoblast differentiation. T3 enhances culture consistency by improving cell survival and passaging efficiency. It also modulates cellular metabolism and promotes energy production through oxidative phosphorylation. T3 helps maintain pluripotency by promoting ERK and SMAD2 signaling and reduces FGF2 dependence in chemically defined culture. Under BMP4 induction, T3 significantly enhances trophoblast differentiation.

Conclusion

In summary, our study reveals the impact of T3 on stem cell culture through signal transduction and metabolism and highlights its potential role in improving stem cell applications.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13287-022-02799-y.

A brief review of mRNA therapeutics and delivery for bone tissue engineering

The therapeutics for bone tissue regeneration requires constant advancements owing to the steady increase in the number of patients suffering from bone-related disorders, and also to find efficient and cost-effective treatment modalities. One of the major advancements in the field of therapeutics is the development of mRNAs. mRNAs, which have been extensively tested for the vaccines, could be very well utilized as a potential inducer for bone regeneration. The ability of mRNAs to enter the cells and instruct the cellular machinery to produce the required native proteins such as BMP or VEGF is a great way to avoid the issues faced with growth factor deliveries such as the production cost, loss of biological function etc. However, there have been a few hurdles for using mRNAs as an effective therapeutic agent, such as proper dosing, tolerating the degradation by RNases, improving the half-life, controlling the spatio-temporal release and reducing the off-target effects. This brief review discusses the various developments in the field of mRNA therapeutics especially for bone tissue engineering, how nano-formulations are being developed to effectively deliver the mRNAs into the cells by evading the immune responses, how researchers have developed certain strategies to increase the half-life, to successfully deliver the mRNAs to specific bone defect area and bring about effective bone regeneration.

Synthesis of Oligosaccharides Resembling the Streptococcus suis Serotype 18 Capsular Polysaccharide as a Basis for Glycoconjugate Vaccine Development

Here we report the first total synthesis of several oligosaccharides resembling the capsular polysaccharide of swine pathogen S. suis serotype 18 repeating unit [→3)-d-GalNAc(α1-3)[d-Glc(β1-2)]-d-GalA4OAc(β1-3)-d-GalNAc(α1-3)-d-BacNAc4NAc(α1→]_n. Access to the pentasaccharide repeating unit antigen proved to be very challenging due to the poor reactivity in the context of the trisaccharide. The challenge was overcome by the creation of a galacturonic acid in a late stage of the synthesis.

The Effect of Anti-browning Agent Activated Carbon and Polyvinyl Pyrrolidone on the Rooting of Embryo Seedlings of "FengDan" and Its Transcriptome Analysis

Peony is an excellent ornamental, medicinal, and oily plant. Its traditional seed propagation methods have the disadvantages of low propagation coefficient, long seedling cycle, and low seedling emergence rate, which severely restrict the supply of seedlings for the peony industry. Efficient tissue culture technology is an important basis for accelerating its breeding and reproduction, and in vitro seed embryo culturing into seedlings can also effectively avoid the above problems. However, the browning phenomenon caused by man-made damage in the process of seed embryo stripping leads to problems such as low induction rate and difficulty in rooting, and the relationship between anti-browning agents and seed embryo root formation is still unclear. This study intends to improve the induction rate of peony seedlings by using different anti-browning agents and different combinations and to clarify the relationship between anti-browning agents and seedling rooting using transcriptome sequencing methods. The results show that both anti-browning agents, activated carbon (AC) and polyvinyl pyrrolidone (PVP), can increase the germination rate of seed embryos. Testing with 0.9 g/L of AC showed excellent performance of peony rooting rate and seedling growth, but only AC and the combination of AC and PVP can further promote rooting development. Through transcriptome analysis, we found that the AC vs. control check (CK), AC vs. PVP, and PVP vs. AC and PVP groups have significantly more differentially expressed genes than the AC vs. AC and PVP groups. Pathway enrichment analysis shows that "phenylpropanoid biosynthesis"/"cutin, suberin, and wax biosynthesis" is significantly enriched in these groups, while the AC vs. AC and PVP groups are mainly enriched in "cytochrome P450," indicating that AC may promote the further development of roots into seedlings by stimulating "phenylpropanoid biosynthesis" and biosynthesis of stratum cutin and suberin. This study can lay the foundation for understanding the potential molecular mechanism of the anti-browning agent promoting the rooting of seed embryo seedlings and also provide a theoretical basis for perfecting the construction of the peony tissue culture and rapid propagation system.

Urinary metabolomics reveals the biological characteristics of early pregnancy in pigs

Background

Embryo implantation in sows is an important event during pregnancy. During this process, blastocysts undergo dramatic morphologic changes, and the endometrium becomes receptive. Studies have shown that developmental changes associated with the crosstalk between peri-implantation embryos and embryo-uterine are driven by various biomolecules secreted by the endometrium and embryos. In sows, changes in the uterus are also reflected in circulating body fluids and urine. Metabolomics reveals the metabolic state of cells, tissues, and organisms. In this study, we collected urine samples from large white sows during the peri-implantation period. The levels of urinary metabolites at different periods were analyzed using ultra-performance liquid chromatography/tandem mass spectrometry (UPLC–MS/MS) analysis techniques.

Results

A total of 32 samples were collected from 8 sows during the estrus period and at each phase of early pregnancy (9, 12, and 15 days of gestation). A total of 530 metabolites were identified with high confidence in all samples. Compared with samples collected during the estrus phase, 269 differential metabolites were found in samples obtained during early pregnancy.

Conclusions

The identified metabolites included lipids and lipid-like molecules, organic acids and their derivatives, organic oxygen compounds, organoheterocyclic compounds, benzenoids, among others. Metabolites, such as choline and pregnanediol-3-glucuronide, play important roles in pregnancy in sows and other animals. These results reveal the metabolic changes in urine of sows during early pregnancy phase. The differential urinary metabolites can be used for assessing peri-implantation status in sows. Understanding these metabolic changes may promote the management of pregnant sows through various interventions such as provision of proper nutrition.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40813-022-00256-z.

Inner nuclear membrane protein TMEM201 maintains endothelial cell migration and angiogenesis by interacting with the LINC complex

The nuclear envelope comprises the outer nuclear membrane (ONM), inner nuclear membrane (INM), and nucleopore. Although ∼60 INM proteins have been identified, only a few of them have been well characterized, revealing their crucial roles. Our group focused on the INM protein transmembrane protein 201 (TMEM201), whose role in cellular function remains to be defined. In this study, we investigated the role of TMEM201 in endothelial cell migration and angiogenesis. Depletion of TMEM201 expression by short hairpin RNA-mediated interference impeded human umbilical vein endothelial cell (HUVEC) angiogenic behavior in tube formation and fibrin gel bead sprouting assays. Meanwhile, TMEM201-deficient HUVEC exhibited impaired migration ability. We next explored the underlying mechanism and found that the N-terminal of TMEM201 interacted with the linker of nucleoskeleton and cytoskeleton (LINC) complex and was required for regulating endothelial cell migration and angiogenesis. The above in vitro findings were further confirmed by using in vivo models. In Tmem201-knockout mice, retinal vessel development was arrested and aortic ring sprouting was defective. In addition, loss of tmem201 impaired zebrafish intersegmental vessel development. In summary, TMEM201 was shown to regulate endothelial cell migration and control the process of angiogenesis. This study is the first to reveal the role of INM proteins in the vascular system and angiogenesis.

DaXi-high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy

The promise of single-objective light-sheet microscopy is to combine the convenience of standard single-objective microscopes with the speed, coverage, resolution and gentleness of light-sheet microscopes. We present DaXi, a single-objective light-sheet microscope design based on oblique plane illumination that achieves: (1) a wider field of view and high-resolution imaging via a custom remote focusing objective; (2) fast volumetric imaging over larger volumes without compromising image quality or necessitating tiled acquisition; (3) fuller image coverage for large samples via multi-view imaging and (4) higher throughput multi-well imaging via remote coverslip placement. Our instrument achieves a resolution of 450 nm laterally and 2 μm axially over an imaging volume of 3,000 × 800 × 300 μm. We demonstrate the speed, field of view, resolution and versatility of our instrument by imaging various systems, including Drosophila egg chamber development, zebrafish whole-brain activity and zebrafish embryonic development – up to nine embryos at a time.

The DaXi single-objective light-sheet microscope achieves fast, high-quality imaging of large volumes. DaXi’s design allows increased scanning range without sacrificing imaging speed or quality, multiview imaging and versatile sample mounting.

Social Determinants of Inter-Individual Variability and Vulnerability: The Role of Dopamine

Individuals differ in their traits and preferences, which shape their interactions, their prospects for survival and their susceptibility to diseases. These correlations are well documented, yet the neurophysiological mechanisms underlying the emergence of distinct personalities and their relation to vulnerability to diseases are poorly understood. Social ties, in particular, are thought to be major modulators of personality traits and psychiatric vulnerability, yet the majority of neuroscience studies are performed on rodents in socially impoverished conditions. Rodent micro-society paradigms are therefore key experimental paradigms to understand how social life generates diversity by shaping individual traits. Dopamine circuitry is implicated at the interface between social life experiences, the expression of essential traits, and the emergence of pathologies, thus proving a possible mechanism to link these three concepts at a neuromodulatory level. Evaluating inter-individual variability in automated social testing environments shows great promise for improving our understanding of the link between social life, personality, and precision psychiatry – as well as elucidating the underlying neurophysiological mechanisms.

Fibroblast activation protein activated antifibrotic peptide delivery attenuates fibrosis in mouse models of liver fibrosis

In liver fibrosis, activated hepatic stellate cells are known to overexpress fibroblast activation protein. Here we report a targeted antifibrotic peptide-delivery system in which fibroblast activation protein, which is overexpressed in fibrotic regions of the liver, liberates the antifibrotic peptide melittin by cleaving a fibroblast activation protein-specific site in the peptide. The promelittin peptide is linked to pegylated and maleimide-functionalized liposomes, resulting in promelittin-modified liposomes. The promelittin-modified liposomes were effective in reducing the viability of activated hepatic stellate cells but not that of control cells. In three types of liver fibrosis mouse models, intravenously administered promelittin-modified liposomes significantly reduces fibrotic regions. In addition, in the bile duct ligation mouse model promelittin-modified liposome-treatment increases overall survival. Although this peptide-delivery concept was tested for liver fibrosis, it can potentially be adapted to other fibrotic diseases.

Activated hepatic stellate cells contribute towards the pathogenesis of liver fibrosis, and overexpress fibroblast activation protein. Here the authors report a targeted peptide-delivery system in which fibroblast activation protein liberates the antifibrotic peptide melittin, and demonstrate the approach attenuates fibrosis in mouse models of liver fibrosis.

Combinatorial Effects of the Natural Products Arctigenin, Chlorogenic Acid, and Cinnamaldehyde Commit Oxidation Assassination on Breast Cancer Cells

Major obstacles in current breast cancer treatment efficacy include the ability of breast cancer cells to develop resistance to chemotherapeutic drugs and the off-target cytotoxicity of these drugs on normal cells, leading to debilitating side effects. One major difference between cancer and normal cells is their metabolism, as cancer cells acquire glycolytic and mitochondrial metabolism alterations throughout tumorigenesis. In this study, we sought to exploit this metabolic difference by investigating alternative breast cancer treatment options based on the application of phytochemicals. Herein, we investigated three phytochemicals, namely cinnamaldehyde (CA), chlorogenic acid (CGA), and arctigenin (Arc), regarding their anti-breast-cancer properties. These phytochemicals were administered alone or in combination to MCF-7, MDA-MB-231, and HCC1419 breast cancer or normal MCF-10A and MCF-12F breast cells. Overall, our results indicated that the combination treatments showed stronger inhibitory effects on breast cancer cells versus single treatments. However, only treatments with CA (35 μM), CGA (250 μg/mL), and the combination of CA + CGA (35 μM + 250 μg/mL) showed no significant cytotoxic effects on normal mammary epithelial cells, suggesting that Arc was the driver of normal cell cytotoxicity in all other treatments. CA + CGA and, to a lesser extent, CGA alone effectively induced breast cancer cell death accompanied by decreases in mitochondrial membrane potential, increased mitochondrial superoxide, reduced mitochondrial and glycolytic ATP production, and led to significant changes in cellular and mitochondrial morphology. Altogether, the combination of CA + CGA was determined as the best anti-breast-cancer treatment strategy due to its strong anti-breast-cancer effects without strong adverse effects on normal mammary epithelial cells. This study provides evidence that targeting the mitochondria may be an effective anticancer treatment, and that using phytochemicals or combinations thereof offers new approaches in treating breast cancer that significantly reduce off-target effects on normal cells.

CD8 T Cell Virus Inhibition Assay Protocol

The human immunodeficiency virus (HIV)-1 viral inhibition assay (VIA) measures CD8⁺ T cell-mediated inhibition of HIV replication in CD4⁺ T cells and is increasingly used for clinical testing of HIV vaccines and immunotherapies. Different VIAs that differ in length of CD8:CD4 T cell culture periods (6-13 days), purity of CD4 cultures [isolated CD4⁺ T cells or CD8⁺ depleted peripheral blood mononuclear cells (PBMCs)], HIV strains (laboratory strains, isolates, reporter viruses) and read-outs of virus inhibition (p24 ELISA, intracellular measurement of p24, luciferase reporter expression, and viral gag RNA) have been reported. Here, we describe multiple modifications to a 7-day VIA protocol, the most impactful being the introduction of independent replicate cultures for both HIV infected-CD4 (HIV-CD4) and HIV-CD4:CD8 T cell cultures. Virus inhibition was quantified using a ratio of weighted averages of p24⁺ cells in replicate cultures and the corresponding 95% confidence intervals. We identify methodological and analysis changes that could be incorporated into other protocols to improve assay reproducibility. We found that in people living with HIV (PLWH) on antiretroviral therapy (ART), CD8 T cell virus inhibition was largely stable over time, supporting the use of this assay and/or analysis methods to examine therapeutic interventions. Graphic abstract.

Pro-Calcific Environment Impairs Ischaemia-Driven Angiogenesis

Peripheral arterial disease (PAD) is characterised by accelerated arterial calcification and impairment in angiogenesis. Studies implicate vascular calcification as a contributor to PAD, but the mechanisms remain unclear. We aimed to determine the effect of calcification on ischaemia-driven angiogenesis. Human coronary artery endothelial cells (ECs) were treated with calcification medium (CM: CaCl₂ 2.7 mM, Na₂PO₄ 2.0 mM) for 24 h and exposed to normoxia (5% CO₂) or hypoxia (1.2% O₂; 5% CO₂ balanced with N₂). In normoxia, CM significantly inhibited tubule formation and migration and upregulated calcification markers of ALP, BMP2, and Runx2. CM elevated levels of calcification-protective gene OPG, demonstrating a compensatory mechanism by ECs. CM failed to induce pro-angiogenic regulators VEGFA and HIF-1α in hypoxia and further suppressed the phosphorylation of endothelial nitric oxide synthase (eNOS) that is essential for vascular function. In vivo, osteoprotegerin-deficient mice (OPG^−/−), a calcification model, were subjected to hind-limb ischaemia (HLI) surgery. OPG^−/− mice displayed elevated serum alkaline phosphatase (ALP) activity compared to wild-type controls. OPG^−/− mice experienced striking reductions in blood-flow reperfusion in both 8-week-old and 6-month-old mice post-HLI. This coincided with significant impairment in tissue ischaemia and reduced limb function as assessed by clinical scoring (Tarlov). This study demonstrated for the first time that a pro-calcific environment is detrimental to ischaemia-driven angiogenesis. The degree of calcification in patients with PAD can often be a limiting factor with the use of standard therapies. These highly novel findings require further studies for full elucidation of the mechanisms involved and have implications for the development of therapies to suppress calcification in PAD.

Ximaoornatins A–C, Polyoxygenated Diterpenoids from the Hainan Soft Coral Sinularia ornata

Three complex polyoxygenated diterpenoids possessing uncommon tetradecahydro-2,13:6,9-diepoxybenzo[10]annulene scaffold, namely ximaoornatins A–C (1–3), one new eunicellin-type diterpene, litophynin K (4), and a related known compound, litophynol B (5) were isolated from the South China Sea soft coral Sinularia ornata. The structures and absolute configurations of 1–4 were established by extensive spectroscopic analysis, X-ray diffraction analysis, and/or modified Mosher’s method. A plausible biosynthetic relationship of 1 and its potential precursor 4 was proposed. In a bioassay, none of the isolated compounds showed obvious anti-inflammatory activity on LPS-induced TNF-α release in RAW264.7 macrophages and PTP1B inhibitory effects.

Rif1-Dependent Control of Replication Timing

Successful duplication of the genome requires the accurate replication of billions of base pairs of DNA within a relatively short time frame. Failure to accurately replicate the genome results in genomic instability and a host of diseases. To faithfully and rapidly replicate the genome, DNA replication must be tightly regulated and coordinated with many other nuclear processes. These regulations, however, must also be flexible as replication kinetics can change through development and differentiation. Exactly how DNA replication is regulated and how this regulation changes through development is an active field of research. One aspect of genome duplication where much remains to be discovered is replication timing (RT), which dictates when each segment of the genome is replicated during S phase. All organisms display some level of RT, yet the precise mechanisms that govern RT remain are not fully understood. The study of Rif1, a protein that actively regulates RT from yeast to humans, provides a key to unlock the underlying molecular mechanisms controlling RT. The paradigm for Rif1 function is to delay helicase activation within certain regions of the genome, causing these regions to replicate late in S phase. Many questions, however, remain about the intricacies of Rif1 function. Here, we review the current models for the activity of Rif1 with the goal of trying to understand how Rif1 functions to establish the RT program.

Response mechanism of gut microbiome and metabolism of European seabass (Dicentrarchus labrax) to temperature stress

In animals, the gut microbiome is vital to growth, and changes in the composition of these microbial communities may affect growth and adaptability to the environment. Temperature is another important factor that influences the healthy growth of animals. To date, the mechanism by which juvenile European seabass (Dicentrarchus labrax) and their symbiotic flora adapt to changes in environmental temperature is not well understood. Therefore, we evaluated the effect of temperature on the gut microbiota and metabolism of European seabass juveniles. We used 16S rRNA gene amplicon sequencing and non-targeted liquid chromatography with tandem mass spectrometry (LC-MS/MS)-based metabolomics to study the gut microbes of European seabass after 60 days of rearing of water temperature at 10 °C (T1), 15 °C (T2) and 20 °C (T3). At the phylum level, the abundance of the gut microbiota did not differ significantly among the three groups after 60 days of cultivation. At the genus level, however, the abundance of Faecalibacterium, Filifactor, Butyricicoccus, and Erysipelotrichaceae UCG-006 in the intestines differed significantly among the temperature groups. Compared with T2, the relative abundance of Filifactor in T1 was significantly increased, while Faecalibacterium was significantly decreased, while the relative abundance of Butyricicoccus and Erysipelotrichaceae UCG-006 in T3 was significantly increased. The LC-MS/MS analysis revealed 107 metabolites in the 10 °C group and 68 metabolites in the 20 °C group that differed significantly from those in the intestines of fish in the 15 °C control group. These metabolites are closely related to several metabolic pathways, including amino acid metabolism, glucose and lipid metabolism, and the tricarboxylic acid cycle. Correlation analysis of the Intestine microbiota, metabolic pathways, and metabolites identified metabolic pathways and metabolites that were strongly related to the observed significant differences in the microbiome among the temperature groups. These results show that temperature can induce significant changes in the gut microbiota and metabolism of European seabass juveniles, and that significant changes in metabolites may be mediated through the interaction of the microbiome and metabolic pathways.

Comprehensive Analyses of Bone and Cartilage Transcriptomes Evince Ion Transport, Inflammation and Cartilage Development-Related Genes Involved in Chickens’ Femoral Head Separation

Simple Summary

Femoral head necrosis (FHN) and other locomotor problems cause severe impacts on the poultry industry due to huge economic losses and reduced animal welfare. Femoral head separation (FHS), the initial phase of FHN, is usually a subclinical condition characterized by the detachment of articular cartilage from the bone. In this study, we aimed to identify genes and biological processes involved with FHS in broilers. A better understanding of the FHS molecular mechanisms can help to develop strategies to reduce this condition in chickens. Here, we described several genes that have their expression altered in the articular cartilage and femur when normal and FHS-affected animals were compared. Furthermore, genetic variants were found differing between the studied groups. Therefore, performing an integrated analysis of these datasets, we were able to detect genes and variants related to FHS in chickens. Some of them, such as SLC4A1, RHAG, ANK1, MKNK2, SPTB, ADA, C7 and EPB420 genes were highlighted and should be further explored to validate them as candidates to FHS and FHN in chickens and possibly in humans.

Abstract

Femoral head separation (FHS) is usually a subclinical condition characterized by the detachment of articular cartilage from the bone. In this study, a comprehensive analysis identifying shared and exclusive expression profiles, biological processes (BP) and variants related to FHS in the femoral articular cartilage and growth plate in chickens was performed through RNA sequencing analysis. Thirty-six differentially expressed (DE) genes were shared between femoral articular cartilage (AC) and growth plate (GP) tissues. Out of those, 23 genes were enriched in BP related to ion transport, translation factors and immune response. Seventy genes were DE exclusively in the AC and 288 in the GP. Among the BP of AC, the response against bacteria can be highlighted, and for the GP tissue, the processes related to chondrocyte differentiation and cartilage development stand out. When the chicken DE genes were compared to other datasets, eight genes (SLC4A1, RHAG, ANK1, MKNK2, SPTB, ADA, C7 and EPB420) were shared between chickens and humans. Furthermore, 89 variants, including missense in the SPATS2L, PRKAB1 and TRIM25 genes, were identified between groups. Therefore, those genes should be more explored to validate them as candidates to FHS/FHN in chickens and humans.

Single-cell Damagenome Profiling by Linear Copying and Splitting based Whole Genome Amplification (LCS-WGA)

Spontaneous DNA damage frequently occurs on the human genome, and it could alter gene expression by inducing mutagenesis or epigenetic changes. Therefore, it is highly desired to profile DNA damage distribution on the human genome and identify the genes that are prone to DNA damage. Here, we present a novel single-cell whole-genome amplification method which employs linear-copying followed by a split-amplification scheme, to efficiently remove amplification errors and achieve accurate detection of DNA damage in individual cells. In comparison to previous methods that measure DNA damage, our method uses a next-generation sequencing platform to detect misincorporated bases derived from spontaneous DNA damage with single-cell resolution.

DNA-Based Biosensors for the Biochemical Analysis: A Review

In recent years, DNA-based biosensors have shown great potential as the candidate of the next generation biomedical detection device due to their robust chemical properties and customizable biosensing functions. Compared with the conventional biosensors, the DNA-based biosensors have advantages such as wider detection targets, more durable lifetime, and lower production cost. Additionally, the ingenious DNA structures can control the signal conduction near the biosensor surface, which could significantly improve the performance of biosensors. In order to show a big picture of the DNA biosensor's advantages, this article reviews the background knowledge and recent advances of DNA-based biosensors, including the functional DNA strands-based biosensors, DNA hybridization-based biosensors, and DNA templated biosensors. Then, the challenges and future directions of DNA-based biosensors are discussed and proposed.