Mitochondrial mechanisms in Treg cell regulation: Implications for immunotherapy and disease treatment

Regulatory T cells (Tregs) play a critical role in maintaining immune homeostasis and preventing autoimmune diseases. Recent advances in immunometabolism have revealed the pivotal role of mitochondrial dynamics and metabolism in shaping Treg functionality. Tregs depend on oxidative phosphorylation (OXPHOS) and fatty acid oxidation (FAO) to support their suppressive functions and long-term survival. Mitochondrial processes such as fusion and fission significantly influence Treg activity, with mitochondrial fusion enhancing bioenergetic efficiency and reducing reactive oxygen species (ROS) production, thereby promoting Treg stability. In contrast, excessive mitochondrial fission disrupts ATP synthesis and elevates ROS levels, impairing Treg suppressive capacity. Furthermore, mitochondrial ROS act as critical signaling molecules in Treg regulation, where controlled levels stabilize FoxP3 expression, but excessive ROS leads to mitochondrial dysfunction and immune dysregulation. Mitophagy, as part of mitochondrial quality control, also plays an essential role in preserving Treg function. Understanding the intricate interplay between mitochondrial dynamics and Treg metabolism provides valuable insights for developing novel therapeutic strategies to treat autoimmune disorders and enhance immunotherapy in cancer.

Engineering of LOV-domains for their use as protein tags

Light-Oxygen-Voltage (LOV) domains are the protein-based light switches used in nature to trigger and regulate various processes. They allow light signals to be converted into metabolic signaling cascades. Various LOV-domain proteins have been characterized in the last few decades and have been used to develop light-sensitive tools in cell biology research. LOV-based applications exploit the light-driven regulation of effector elements to activate signaling pathways, activate genes, or locate proteins within cells. A relatively new application of an engineered small LOV-domain protein called miniSOG (mini singlet oxygen generator) is based on the light-induced formation of reactive oxygen species (ROS). The first miniSOG was engineered from a LOV domain from Arabidopsis thaliana. This engineered 14 kDa light-responsive flavin-containing protein can be exploited as protein tag for the light-triggered localized production of ROS. Such tunable ROS production by miniSOG or similarly redesigned LOV-domains can be of use in studies focused on subcellular phenomena but may also allow new light-fueled catalytic processes. This review provides an overview of the discovery of LOV domains and their development into tools for cell biology. It also highlights recent advancements in engineering LOV domains for various biotechnological applications and cell biology studies.

The Drosophila RNA binding protein Hrp48 binds a specific RNA sequence of the msl-2 mRNA 3' UTR to regulate translation

Repression of msl-2 mRNA translation is essential for viability of Drosophila melanogaster females to prevent hypertranscription of both X chromosomes. This translational control event is coordinated by the female-specific protein Sex-lethal (Sxl) which recruits the RNA binding proteins Unr and Hrp48 to the 3' untranslated region (UTR) of the msl-2 transcript and represses translation initiation. The mechanism exerted by Hrp48 during translation repression and its interaction with msl-2 are not well understood. Here we investigate the RNA binding specificity and affinity of the tandem RNA recognition motifs of Hrp48. Using NMR spectroscopy, molecular dynamics simulations and isothermal titration calorimetry, we identified the exact region of msl-2 3' UTR recognized by Hrp48. Additional biophysical experiments and translation assays give further insights into complex formation of Hrp48, Unr, Sxl and RNA. Our results show that Hrp48 binds independent of Sxl and Unr downstream of the E and F binding sites of Sxl and Unr to msl-2.

The life cycle of feline immunodeficiency virus

Feline immunodeficiency virus (FIV) is a retrovirus of worldwide distribution that can cause an acquired immunodeficiency disease in domestic cats. FIV and the primate lentiviruses, human and simian immunodeficiency viruses (HIV and SIV, respectively) share structural and biological features but also exhibit important differences, which reflect both their evolutionary relationship and divergence. Given that FIV is not only an important cat pathogen but also a useful model for certain aspects of HIV-1 infections in humans, the study of FIV biology is highly relevant. In this review we provide an updated description of the molecular mechanisms involved in each stage of the FIV life cycle.

Mechanical causes and implications of repetitive DNA motifs

Experimental research suggests that local patterns in DNA sequences can result in stiffer or more curved structures, potentially impacting chromatin formation, transcription regulation, and other processes. However, the effect of sequence variation on DNA geometry and mechanics remains relatively underexplored. Using rigid base pair models to aid rapid computation, we investigated the sample space of 100 bp DNA sequences to identify mechanical extrema based on metrics such as static persistence length, global bend, or angular deviation. Our results show that repetitive DNA motifs are overrepresented in these extrema. We identified specific extremal motifs and demonstrated that their geometric and mechanical properties significantly differ from standard DNA through hierarchical clustering. We provide a mathematical argument supporting the presence of DNA repeats in extremizing sequences. Finally, we find that repetitive DNA motifs with extreme mechanical properties are prevalent in genetic databases and hypothesize that their unique mechanical properties could contribute to this abundance.

Human-unique brain cell clusters are associated with learning disorders and human episodic memory activity

The advanced evolution of the human cerebral cortex forms the basis for our high-level cognitive functions. Through a comparative analysis of single-nucleus transcriptome data from the human neocortex and that of chimpanzees, macaques, and marmosets, we discovered 20 subgroups of cell types unique to the human brain, which include 11 types of excitatory neurons. Many of these human-unique cell clusters exhibit significant overexpression of genes regulated by human-specific enhancers. Notably, these specific cell clusters also express genes associated with disease risk, particularly those related to brain dysfunctions like learning disorders. Furthermore, genes linked to cortical thickness and human episodic memory encoding activities show heightened expression within these cell subgroups. These findings underscore the critical role of human brain-unique cell clusters in the evolution of human brain functions.

Quercetin ameliorates senescence and promotes osteogenesis of BMSCs by suppressing the repetitive element‑triggered RNA sensing pathway

Cell senescence impedes the self‑renewal and osteogenic capacity of bone marrow mesenchymal stem cells (BMSCs), thus limiting their application in tissue regeneration. The present study aimed to elucidate the role and mechanism of repetitive element (RE) activation in BMSC senescence and osteogenesis, as well as the intervention effect of quercetin. In an H2O2‑induced BMSC senescence model, quercetin treatment alleviated senescence as shown by a decrease in senescence‑associated β‑galactosidase (SA‑β‑gal)‑positive cell ratio, increased colony formation ability and decreased mRNA expression of p21 and senescence‑associated secretory phenotype genes. DNA damage response marker γ‑H2AX increased in senescent BMSCs, while expression of epigenetic markers methylation histone H3 Lys9, heterochromatin protein 1α and heterochromatin‑related nuclear membrane protein lamina‑associated polypeptide 2 decreased. Quercetin rescued these alterations, indicating its ability to ameliorate senescence by stabilizing heterochromatin structure where REs are primarily suppressed. Transcriptional activation of REs accompanied by accumulation of cytoplasmic double‑stranded (ds)RNA, as well as triggering of the RNA sensor retinoic acid‑inducible gene I (RIG‑I) receptor pathway in H2O2‑induced senescent BMSCs were shown. Similarly, quercetin treatment inhibited these responses. Additionally, RIG‑I knockdown led to a decreased number of SA‑β‑gal‑positive cells, confirming its functional impact on senescence. Induction of senescence or administration of dsRNA analogue significantly hindered the osteogenic capacity of BMSCs, while quercetin treatment or RIG‑I knockdown reversed the decline in osteogenic function. The findings of the current study demonstrated that quercetin inhibited the activation of REs and the RIG‑I RNA sensing pathway via epigenetic regulation, thereby alleviating the senescence of BMSCs and promoting osteogenesis.

Molecular underpinnings of aging contributing to systemic sclerosis pathogenesis

PURPOSE OF REVIEW

Systemic sclerosis (SSc) is a systemic autoimmune disease characterized by diffuse organ fibrosis and vasculopathy. Aberrant aging has been increasingly implicated in fibrotic diseases of the lung and other organs. The aim of this review is to summarize the established mechanisms of aging and how they may contribute to the pathogenesis of SSc.

RECENT FINDINGS

Shortened telomeres are present in SSc patients with interstitial lung disease (SSc-ILD) and associate with disease severity and mortality. Although the cause of telomere length shortening is unknown, immune mechanisms may be at play. Senescent cells accumulate in affected organs of SSc patients and contribute to a pathologic cellular phenotype that can be profibrotic and inflammatory. In addition to identifying patients with a more severe phenotype, biomarkers of aging may help identify patients who have worse outcomes with immunosuppression.

SUMMARY

Aging mechanisms, including telomere dysfunction and cellular senescence, likely contribute to the progressive fibrosis, vasculopathy, and immune dysfunction of SSc. Further work is needed to understand whether aberrant aging is an initiator or perpetuator of disease, and whether this is cell or organ specific. A better understanding of the role aging mechanisms play in SSc will contribute to our understanding of the underlying pathobiology and may also influence management of patients exhibiting the aging phenotype.

Golden Gate Cloning of Synthetic CRISPR RNA Spacer Sequences

Prokaryotes use CRISPR-Cas systems to interfere with viruses and other mobile genetic elements. CRISPR arrays comprise repeated DNA elements and spacer sequences that can be engineered for custom target sites. These arrays are transcribed into precursor CRISPR RNAs (pre-crRNAs) that undergo maturation steps to form individual CRISPR RNAs (crRNAs). Each crRNA contains a single spacer that identifies the target cleavage site for a large variety of Cas protein effectors. Precise manipulation of spacer sequences within CRISPR arrays is crucial for advancing the functionality of CRISPR-based technologies. Here, we describe a protocol for the design and creation of a minimal, plasmid-based CRISPR array to enable the expression of specific, synthetic crRNAs. Plasmids contain entry spacer sequences with two type IIS restriction sites and Golden Gate cloning enables the efficient exchange of these spacer sequences. Factors that influence the compatibility of the CRISPR arrays with native or recombinant Cas proteins are discussed.

CCT39-COMT1/BGLU18-2 module promotes lignin biosynthesis in poplar

Lignin is a crucial constituent of cell walls and plays a pivotal role in plant growth and development. However, the transcriptional regulatory network governing lignin biosynthesis is not fully understood. In this study, we observed that PpnCCT39 overexpression resulted in greener stems, larger basal diameters, and increased stem dry weight. Additionally, the secondary xylem of lines overexpressing PpnCCT39 was wider, had larger xylem fiber cell areas, and thicker cell walls, compared to those of wild-type plants. Furthermore, PpnCCT39 overexpression led to elevated lignin content and enhanced the rigidity of secondary cell walls. RNA-seq and ChIP-seq association analyses identified 826 potential regulatory target genes of PpnCCT39 that were upregulated and expressed in 1-month-old PpnCCT39 overexpression lines. Gene enrichment analyses revealed enrichment in pathways related to cell wall formation, xylem and phloem development, and the phenylpropanoid pathway. Two genes involved in lignin biosynthesis, PagCOMT1 and PagBGLU18-2, exhibited significantly increased expression in stems of lines overexpressing PpnCCT39, as demonstrated by high FPKM values and RT-qPCR results. Further investigations using yeast one-hybrid, dual-luciferase assays, and electrophoretic mobility shift assays demonstrated that PpnCCT39 directly activates the transcription of PagCOMT1 and PagBGLU18-2, thereby promoting lignin biosynthesis. This study elucidated the transcriptional regulatory mechanism of PpnCCT39 in poplars and revealed its role in activating the expression of key lignin biosynthesis genes. PpnCCT39 facilitates lignin biosynthesis and secondary growth processes, offering a novel theoretical framework for modulating lignin biosynthesis and enhancing timber yield through molecular design.

Cell fate determination during sexual plant reproduction

The flowering plant life cycle is completed by an alternation of diploid and haploid generations. The diploid sporophytes produce initial cells that undergo meiosis and produce spores. From haploid spores, male or female gametophytes, which produce gametes, develop. The union of gametes at fertilization restores diploidy in the zygote that initiates a new cycle of diploid sporophyte development. During this complex process, cell fate determination occurs at each of the critical stages and necessarily underpins successful plant reproduction. Here, we summarize available knowledge on the regulatory mechanism of cell fate determination at these critical stages of sexual reproduction, including sporogenesis, gametogenesis, and early embryogenesis, with particular emphasis on regulatory pathways of both male and female gametes before fertilization, and both apical and basal cell lineages of a proembryo after fertilization. Investigations reveal that cell fate determination involves multiple regulatory factors, such as positional information, differential distribution of cell fate determinants, cell-to-cell communication, and cell type-specific transcription factors. These factors temporally and spatially act for different cell type differentiation to ensure successful sexual reproduction. These new insights into regulatory mechanisms underlying sexual cell fate determination not only updates our knowledge on sexual plant reproduction, but also provides new ideas and tools for crop breeding.

Same, yet different: towards understanding nutrient use in hemp- and drug-type Cannabis

Cannabis sativa L., one of the oldest cultivated crops, has a complex domestication history due to its diverse uses for fibre, seed, oil, and drugs, and its wide geographic distribution. This review explores how human selection has shaped the biology of hemp and drug-type Cannabis, focusing on acquisition and utilization of nitrogen and phosphorus, and how resulting changes in source-sink relations shape their contrasting phenology. Hemp has been optimized for rapid, slender growth and nutrient efficiency, whereas drug-type cultivars have been selected for compact growth with large phytocannabinoid-producing female inflorescences. Understanding these nutrient use and ontogenetic differences will enhance our general understanding of resource allocation in plants. Knowledge gained in comparison with other model species, such as tomato, rice, or Arabidopsis can help inform crop improvement and sustainability in the cannabis industry.

Deciphering the acidophilia and acid resistance in Acetilactobacillus jinshanensis dominating baijiu fermentation through multi-omics analysis

Lactic acid bacteria (LAB) are pivotal in constructing the intricate bio-catalytic networks underlying traditional fermented foods such as Baijiu. However, LAB and their metabolic mechanisms are partially understood in Moutai flavor Baijiu fermentation. Here, we found that Acetilactobacillus jinshanensis became the· dominant species with relative abundance reaching 92%, where the acid accumulated rapidly and peaked at almost 30 g/kg in Moutai flavor Baijiu. After separation, purification, and cultivation, A. jinshanensis exhibited pronounced acidophilia and higher acid resistance compared to other LAB. Further integrated multi-omics analysis revealed that fatty acid synthesis, cell membrane integrity, pHi and redox homeostasis maintenance, protein and amide syntheses were possibly crucial acid-resistant mechanisms in A. jinshanensis. Structural proteomics indicated that the surfaces of A. jinshanensis proteases contained more positively charged amino acid residues to maintain protein stability in acidic environments. The genes HSP20 and acpP were identified as acid-resistant genes for A. jinshanensis by heterologous expression analysis. These findings not only enhance our understanding of LAB in Baijiu, providing a scientific basis for acid regulation for production process, but also offer valuable insights for studying core species in other fermentation systems.

Assessment of mRNA Decay and Calculation of Codon Occurrence to mRNA Stability Correlation Coefficients after 5-EU Metabolic Labeling

mRNA translation and decay are tightly connected. This chapter describes a method to assess the influence of each codon identity on mRNA stability in cultured cells. The technique involves metabolic labeling of the nascent mRNAs by addition of the nucleoside analog 5-ethynyluridine (5-EU), purification of the RNA at different time-points after chase of the 5-EU, then biotinylation with Click chemistry, pull-down, and sequencing. The transcripts' half-lives are calculated from the expression level of each mRNA at the different time-points. Finally, the method describes the calculation of the Codon occurrence to mRNA Stability correlation Coefficient, or CSC, as a correlation between the codon occurrence in a transcript and the transcript half-life, for each codon.

Endogenous retroelements in hematological malignancies: From epigenetic dysregulation to therapeutic targeting

Endogenous retroelements (EREs), which comprise half of the human genome, play a pivotal role in genome dynamics. Some EREs retained the ability to encode proteins, although most degenerated or served as a source for novel genes and regulatory elements during evolution. Despite ERE repression mechanisms developed to maintain genome stability, widespread pervasive ERE activation is observed in cancer including hematological malignancies. Challenging the perception of noncoding DNA as "junk," EREs are underestimated contributors to cancer driver mechanisms as well as antitumoral immunity by providing innate immune ligands and tumor antigens. This review highlights recent progress in understanding ERE co-option events in cancer and focuses on the controversial debate surrounding their causal role in shaping malignant phenotype. We provide insights into the rapidly evolving landscape of ERE research in hematological malignancies and their clinical implications in these cancers.

Structure, function and formation of the amniote skin pattern

From feather and hair dotted arrays to pigmented stripes and spots, the spatial distribution of skin appendages and colouration often forms visible ornaments crucial for fitness in the coat of birds and mammals. These geometrical motifs are extremely diverse in nature. Yet, phenotypic surveys evidenced common themes in variation: the orientation, appendage-specificity or pigmentation of a given region may be conserved across groups or species. Here, we review naturalist observations of natural variation in the anatomy and ecological function of the skin pattern in amniotes. We then describe several decades of genetics, mathematical modelling and experimental embryology work aiming at understanding the molecular and morphogenetic mechanisms responsible for pattern formation. We discuss how these studies provided evidence that the morphological trends and differences representative of the phenotypic landscape of skin patterns in wild amniote species is rooted in the mechanisms controlling the production of distinct compartments in the embryonic skin.

Computational Prediction of Gene Regulation by lncRNAs

High-throughput sequencing technologies and innovative bioinformatics tools discovered that most of the genome is transcribed into RNA. However, only a fraction of the RNAs in cell translates into proteins, while the majority of them are categorized as noncoding RNAs (ncRNAs). The ncRNAs with more than 200 nt without protein-coding ability are termed long noncoding RNAs (lncRNAs). Hundreds of studies established that lncRNAs are a crucial RNA family regulating gene expression. Regulatory RNAs, including lncRNAs, modulate gene expression by interacting with RNA, DNA, and proteins. Several databases and computational tools have been developed to explore the functions of lncRNAs in cellular physiology. This chapter discusses the tools available for lncRNA functional analysis and provides a detailed workflow for the computational analysis of lncRNAs.

Enhancing multiplex detection capabilities of the Cas12a/blocker DNA system

In the field of molecular diagnostics, the demand for multiplex detection, aimed at reducing overall analysis costs and streamlining procedures, is on the rise, prompting ongoing developments in various technologies. In this study, we developed a novel system, the split T7 promoter-based three-way junction-transcription, coupled with Cas12a/Blocker DNA (T3-CaB), for the multiplex detection of target nucleic acids. The T3-CaB system builds upon the foundation of the T3 system, generating numerous RNA transcripts upon encountering target nucleic acids. Subsequently, these RNA transcripts displace the blocker DNA from reporter DNA, allowing active Cas12a to engage in efficient trans-cleavage reaction on the reporter DNA, resulting in a strong fluorescence signal. Importantly, the proposed system operates at the isothermal condition (37 °C), with the entire analysis completed within 90 min. Further, the detection performance of the proposed system surpasses that of the preceding Cas12a/Blocker DNA system. Model targets, namely the 16S rRNA of Staphylococcus aureus and Escherichia coli, were selected, and a successful demonstration of multiplex detection was achieved. This technology holds promise for broadening the applicability of CRISPR/Cas-based diagnostics, especially in settings necessitating multiplex detection capabilities.

Overexpression of GFP Fusions of Regulators of the SAC from Arabidopsis thaliana

Cell division is a fundamental biological process, essential for sustaining life on Earth. Accurate replication followed by uniform segregation of the genome is required to ensure cell division is sustainable and reduces the likelihood of aneuploidy. The cell cycle has various checkpoints to safeguard proper replication, for example, the spindle assembly checkpoint (SAC) which ensures that all chromosomes are correctly aligned and attached to the spindle, before the transition to anaphase. The precise function of the SAC and SAC components in plants is so far unclear. First, the high level of polyploidy in plants raises concerns about the efficacy of the SAC. Second, many plant SAC components are implicated in other cellular processes, such as MAD1, which has been implicated in the reproductive transition of Arabidopsis thaliana. Overexpression of GFP fusions of core SAC components provides a key route to establish the functions of the different SAC components in plants. Here we describe two methods for agrobacterium-mediated transformation of plants.

Characterization, expression, and polymorphism of MHC II α and MHC II β in Sichuan taimen (Hucho bleekeri)

The major histocompatibility complex (MHC) is involved in antigen presentation and plays an essential role in regulating immune function. In the present study, we identified two MHC class II genes and investigated their potential roles in Hucho bleekeri. The MHC II α and MHC II β of H. bleekeri had typical leading peptides, extracellular domains, connecting peptides, transmembrane region, and cytoplasmic region. Amino acid sequence comparison revealed that MHC II of H. bleekeri has high homology with other vertebrates, among which homology with salmonid fish was the highest. Phylogenetic analysis showed that H. bleekeri MHC II clustered with salmonid fish; moreover they clustered with orthologous genes of other fish, whereas mammalian MHC II clustered into a separate branch. Tissue distribution analysis revealed MHC II was widely expressed in all tested tissues, with both MHC II α and MHC II β highly expressed in the spleen, gill, kidney, and hindgut. After lipopolysaccharide (LPS) and polyinosinic:polycytidylic acid (poly(I:C)) stimulation, the expression of MHC II in the head kidney and spleen of H. bleekeri was significantly upregulated. Compared with MHC II α, MHC II β acted faster in response to the stimulation. Polymorphism analysis of MHC II revealed that all the different alleles belonged to the same major type, and very limited polymorphisms were found in H. bleekeri MHC II α and II β. Selection pressure analysis showed signs of weak and non-significant positive selection in the MHC II α and MHC II β extracellular region. Our study reveals the potential role of MHC II in the immune response of H. bleekeri and provides a reference for studying the evolutionary model of teleost MHC II.

CRISPR-Cas technology in forensic investigations: Principles, applications, and ethical considerations

CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins) systems are adaptive immune systems originally present in bacteria, where they are essential to protect against external genetic elements, including viruses and plasmids. Taking advantage of this system, CRISPR-Cas-based technologies have emerged as incredible tools for precise genome editing, thus significantly advancing several research fields. Forensic sciences represent a multidisciplinary field that explores scientific methods to investigate and resolve legal issues, particularly criminal investigations and subject identification. Consequently, it plays a critical role in the justice system, providing scientific evidence to support judicial investigations. Although less explored, CRISPR-Cas-based methodologies demonstrate strong potential in the field of forensic sciences due to their high accuracy and sensitivity, including DNA profiling and identification, interpretation of crime scene investigations, detection of food contamination or fraud, and other aspects related to environmental forensics. However, using CRISPR-Cas-based methodologies in human samples raises several ethical issues and concerns regarding the potential misuse of individual genetic information. In this manuscript, we provide an overview of potential applications of CRISPR-Cas-based methodologies in several areas of forensic sciences and discuss the legal implications that challenge their routine implementation in this research field.

Direct quantification of N6-methyladenosine fractions at specific site in RNA based on deoxyribozyme mediated CRISPR-Cas12a platform

As the most abundant modification in eukaryotic messenger RNA (mRNA) and long noncoding RNA (lncRA), N6-methyladenosine (m6A) has been shown to play essential roles in various significant biological processes and attracted growing attention in recent years. To investigate its functions and dynamics, there is a critical need to quantitatively determine the m6A modification fractions at a precise location. Here, we report a deoxyribozyme mediated CRISPR-Cas12a platform (termed "DCAS") that can directly quantify m6A fractions at single-base resolution. DCAS employs a deoxyribozyme (VMC10) to selectively cleave the unmodified adenine (A) in the RNA, allowing only m6A-modified RNA amplified by RT-PCR. Leveraging the CRISPR-Cas12a quantify the PCR amplification products, DCAS can directly determine the presence of m6A at target sites and its fractions. The combination of CRISPR-Cas12a with RT-PCR has greatly improved the sensitivity and accuracy, enabling the detection of m6A-modified RNA as low as 100 aM in 2 fM total target RNA. This robustly represents an improvement of 2-3 orders of magnitude of sensitivity and selectivity compared to traditional standard methods, such as SCARLET and primer extension methods. Therefore, this method can be successfully employed to accurately determine m6A fractions in real biological samples, even in low abundance RNA biomarkers.

Generating Site Saturation Mutagenesis Libraries and Transferring Them to Broad Host-Range Plasmids Using Golden Gate Cloning

Protein engineering is an established method for tailoring enzymatic reactivity. A commonly used method is directed evolution, where the mutagenesis and natural selection process is mimicked and accelerated in the laboratory. Here, we describe a reliable method for generating saturation mutagenesis libraries by Golden Gate cloning in a broad host range plasmid containing the pBBR1 replicon. The applicability is demonstrated by generating a mutant library of the iron nitrogenase gene cluster (anfHDGK) of Rhodobacter capsulatus, which is subsequently screened for the improved formation of molecular hydrogen.

Golden Gate Assembly of Transcriptional Unit Libraries into a Rearrangeable Gene Cluster

Both regulatory sequences and genome organization contribute to the production of diverse transcript isoforms, which can influence how genes, or sets of genes, are expressed. An efficient, modular approach is needed to generate the combinatorial complexity required to empirically test many combinations of different regulatory sequences and different gene orders. Golden Gate assembly provides such a tool for seamless one-pot cleavage and ligation, by using type IIS restriction enzymes, which cleave outside of their recognition site. In addition to reducing the number of steps, this one-pot reaction can improve correct assemblies by the continued cleavage of self-ligation products that retain the recognition site. Switching the specific restriction enzyme used between steps allows for modular assembly of several units. A protocol to perform modular assemblies with two type IIS restriction enzymes, namely BsaI-v2-HF and BsmBI-v2, is described here. This protocol includes a description for generating destination vectors that add loxPsym sites between transcriptional units, allowing for diversification of gene order, orientation, and spacing.

HSF1/HSP25 system protects mitochondria function from heat stress and assists steroidogenesis in MA-10 Leydig cells

Heat shock response is characterized by the induction of heat shock proteins (HSPs) or molecular chaperones that maintain protein homeostasis. Heat shock transcription factor 1 (HSF1) plays a central role in heat shock response in mammalian cells. To investigate the impact of the heat shock response mechanism on steroidogenesis, we generated MA-10 mouse Leydig tumor cells deficient in HSF1 using CRISPR-Cas9 genome editing. Under heat stress conditions, the levels of StAR protein, but not its mRNA, decreased more in HSF1-knockout cells than in wild-type cells, confirming that HSF1 stabilizes StAR protein. Simultaneously, HSP110, HSP70, and HSP25 were markedly upregulated in a manner dependent on HSF1. Mitochondrial membrane potential (MMP) and ATP synthesis were decreased in HSF1-knockout cells under heat stress conditions, and mitochondrial fragmentation was enhanced. Furthermore, treatment with carbonyl cyanide 3-chlorophenylhydrazone (CCCP), a disruptor of MMP, reduced the levels of StAR protein to a greater extent in HSF1-knockout cells than in wild-type cells, which was associated with decreased MMP and ATP synthesis. Unexpectedly, HSP25 expression was markedly increased in wild-type cells following CCCP treatment. HSP25 knockdown reduces MMP under heat stress conditions and decreases StAR protein levels and progesterone synthesis. HSP25 overexpression in HSF1KO cells restored StAR protein levels. These results show that the HSF1/HSP25 pathway protects mitochondrial function and maintains StAR synthesis.

Structural Maintenance of Chromosomes Complexes

The Structural Maintenance of Chromosomes (SMC) protein complexes are DNA-binding molecular machines required to shape chromosomes into functional units and to safeguard the genome through cell division. These ring-shaped multi-subunit protein complexes, which are present in all kingdoms of life, achieve this by organizing chromosomes in three-dimensional space. Mechanistically, the SMC complexes hydrolyze ATP to either stably entrap DNA molecules within their lumen, or rapidly reel DNA into large loops, which allow them to link two stretches of DNA in cis or trans. In this chapter, the canonical structure of the SMC complexes is first introduced, followed by a description of the composition and general functions of the main types of eukaryotic and prokaryotic SMC complexes. Thereafter, the current model for how SMC complexes perform in vitro DNA loop extrusion is presented. Lastly, chromosome loop formation by SMC complexes is introduced, and how the DNA loop extrusion mechanism contributes to chromosome looping by SMC complexes in cells is discussed.

Mechanisms of intestinal DNA damage and inflammation induced by ammonia nitrogen exposure in Litopenaeus vannamei

Ammonia nitrogen, a common aquaculture pollutant, harms crustaceans by causing intestinal inflammation, though its exact mechanisms are unclear. Thus, we exposed shrimp to 0, 2, 10 and 20 mg/L NH4Cl exposure for 0, 3, 6, 12, 24, 48, 72 h, and explored the intestinal stress, apoptosis, proliferation, inflammation and its histopathological changes. This research indicated that ammonia nitrogen exposure heightens plasma dopamine (DA), 5-hydroxytryptamine (5-HT), norepinephrine (NE), and acetylcholine (ACh) levels, alters gene expression of neurotransmitter receptors in the intestine, triggering the PLCCa2+ pathway and induces endoplasmic reticulum stress. Additionally, mitochondrial fission-related genes (Drp1, FIS1) significantly increase, the level of reactive oxygen species (ROS) was significantly elevated in the intestine, which induced DNA damage effects and initiated the DNA repair function, mainly through the base excision repair pathway, but with a low repair efficiency. By determining the expression of key genes of caspase-dependent and non-caspase-dependent apoptotic pathways, it was found that ammonia nitrogen exposure induced apoptosis in intestinal cells, proliferation key signaling pathways such as Wnt, EGFR and FOXO signaling showed an overall decrease after ammonia nitrogen exposure, combined with the gene expression of cell cycle proteins and proliferation markers, indicated that the proliferation of intestinal cells was inhibited. Performing pearson correlation analysis of intestinal cell damage, proliferation, and inflammatory factors, we hypothesized that ammonia nitrogen exposure induces intestinal endoplasmic reticulum stress and mitochondrial fission, induces elevated ROS, leads to DNA damage, and causes inflammation and damage in intestinal tissues by the underlying mechanism of promoting apoptosis and inhibiting proliferation.

4G cloning: rapid gene assembly for expression of multisubunit protein complexes in diverse hosts

Multisubunit protein complexes are central to many cellular processes, and studying their activities and structures in vitro requires reconstitution via recombinant expression and purification. Obtaining targets at sufficient purity and scale typically involves screening several protein variants and expression hosts. Existing cloning strategies enable co-expression but are often time-consuming, labor-intensive, and host-specific, or involve error-prone steps. We present a novel vector set and assembly strategy to overcome these limitations, enabling expression construct generation for multisubunit complexes in a single step. This modular system can be extended to additional hosts or include new tags. We demonstrate its utility by constructing expression vectors for structural maintenance of chromosomes complexes in various hosts, streamlining workflows, and improving productivity.

Structural and spectroscopic characterization of the peridinin-chlorophyll a-protein (PCP) complex from Heterocapsa pygmaea (HPPCP)

Light harvesting proteins are optimized to efficiently collect and transfer light energy for photosynthesis. In eukaryotic dinoflagellates these complexes utilize chlorophylls and a special carotenoid, peridinin, and arrange them for efficient excitation energy transfer. At the same time, the carotenoids protect the system by quenching harmful chlorophyll triplet states. Here we use advanced spectroscopic techniques and X-ray structure analysis to investigate excitation energy transfer processes in the major soluble antenna, the peridinin chlorophyll a protein (PCP) from the free living dinoflagellate Heterocapsa pygmaea. We determined the 3D-structure of this complex at high resolution (1.2 Å). For better comparison, we improved the reference structure of this protein from Amphidinium carterae to a resolution of 1.15 Å. We then used fs and ns time-resolved absorption spectroscopy to study the mechanisms of light harvesting, but also of the photoprotective quenching of the chlorophyll triplet state. The photoprotection site was further characterized by Electron Spin Echo Envelope Modulation (ESEEM) spectroscopy to yield information on water molecules involved in triplet-triplet energy transfer. Similar to other PCP complexes, excitation energy transfer from peridinin to chlorophyll is found to be very efficient, with transfer times in the range of 1.6-2.1 ps. One of the four carotenoids, the peridinin 614, is well positioned to quench the chlorophyll triplet state with high efficiency and transfer times in the range of tens of picoseconds. Our structural and dynamic data further support, that the intrinsic water molecule coordinating the chlorophyll Mg ion plays an essential role in photoprotection.

A recommended sampling strategy for genetic identification of Second World War victims in Slovenia

Skeletonized human remains from Second World War mass graves in Slovenia are a major challenge in genetic identification, and bones with a high DNA yield must be selected for successful identification. The goal of this study was to construct skeletal sampling strategy recommendations through comparison of the most appropriate groups of skeletal elements. Altogether, 566 bones and teeth from the same mass grave were compared, half analyzed in this study and half in previous studies performed by our group. After anthropological examination, mechanical and chemical cleaning was performed, followed by bone and tooth powdering. Total demineralization of 0.5 g of bone and tooth was followed by extraction and purification of DNA with a Biorobot EZ1 device (Qiagen). The qPCR PowerQuant kit (Promega) was used to measure the amount of DNA, and statistical analysis was performed. Skeletal elements were selected according to known better preservation of DNA in the human body, and they were arranged in seven groups: petrous bone, long bones (femur and tibia), torso bones (first rib and 12th vertebra), metacarpals, metatarsals, short and sesamoid bones (talus, navicular, medial cuneiform, cuboid, calcaneus, and patella), and teeth. Sampling strategy recommendations were constructed based on DNA quantity and quality results. The petrous bone group, metacarpal group, torso bone group, and short and sesamoid bone group produced the highest DNA yields. Accordingly, in addition to standard sampling of long bones (femurs and tibias) and teeth, those additional bone types should be collected for Slovenian Second World War victim identification.

Left/right asymmetrically expressed ephrin and Flamingo proteins regulate lateralized axon growth in C. elegans

While the nervous system of bilaterian animals is mainly left-right (L-R) symmetric at the anatomical level, some molecular and functional L-R asymmetries exist. However, the extent of these molecular asymmetries and their functional consequences remain poorly characterized. C. elegans allows to study L-R asymmetries in the nervous system with single-neuron resolution. We have previously shown that a neural bHLH transcription factor, HLH-16/Olig, is L-R asymmetrically expressed in the AIY neuron lineage and regulates AIY axon projections in a L-R asymmetric manner. Here, by combining a candidate approach and single-cell RNA sequencing data analysis, we identify the ephrin protein EFN-2 and the Flamingo protein FMI-1 as downstream targets of HLH-16 that are L-R asymmetrically expressed in the AIY lineage. We show that EFN-2 and FMI-1 collaborate in the L-R asymmetric regulation of axonal growth. EFN-2 may act via a non-canonical receptor of the L1CAM family, SAX-7. Our study reveals novel molecular L-R asymmetries in the C. elegans nervous system and their functional consequences.

Bacterial 5' UTR: A treasure-trove for post-transcriptional regulation

In bacteria, where gene transcription and translation occur concurrently, post-transcriptional regulation is acknowledged to be effective and precise. The 5' untranslated regions (5' UTRs) typically harbor diverse post-transcriptional regulatory elements, like riboswitches, RNA thermometers, small RNAs, and upstream open reading frames, that serve to modulate transcription termination, translation initiation, and mRNA stability. Consequently, exploring 5' UTR-derived regulatory elements is vital for synthetic biology and metabolic engineering. Over the past few years, the investigation of successive mechanisms has facilitated the development of various genetic tools from bacterial 5' UTRs. This review consolidates current understanding of 5' UTR regulatory functions, presents recent progress in 5' UTR-element design and screening, updates the tools and regulatory strategies developed, and highlights the challenges and necessity of establishing reliable bioinformatic analysis methods and non-model bacterial chassis in the future.

Epigenetic Targeting for Controlling Persistent Neurotropic Infections Caused by Borna Virus and HIV

Long-lasting persistence within infected cells is a major challenge for viral pathogens, as it necessitates an exact regulation of viral replication to reduce viral cytopathic effects. This is particularly challenging for viruses that persistently infect cells with limited renewal capabilities, such as neurons. Accordingly, neurotropic viruses have evolved various specific mechanisms to promote a long-lasting persistent infection in the host cells without inducing an exacerbated cytopathic effect. Borna disease virus (BDV) and Human immunodeficiency virus (HIV) are two neurotropic RNA viruses that, in contrast to other RNA viruses, can establish long-lasting intranuclear infections within the nervous system. These viruses interact with different cellular processes such as epigenetic modifications to develop a successful persistence infection. Studies show that cellular epigenetic mechanisms play a significant role in the pathogenesis of BDV and HIV and their neurological disorders. Hence, targeting these mechanisms by epigenetic modulator agents can be regarded as a novel therapeutic strategy to manage BDV- and HIV-associated neurological diseases. This review provides an overview of different epigenetic modulator compounds as a potential therapeutic target for controlling persistent neurotropic intranuclear infections caused by BDV and HIV.

Intragenic cytosine methylation modification regulates the response of SUCLα1 to lower temperature in Solanaceae

The tricarboxylic acid cycle (TCAC) is a fundamental metabolic process governing matter and energy in plant cells, playing an indispensable role. However, its involvement in responding to low temperature stress in potato remains poorly understood. Previous studies have identified succinyl-CoA ligase (SUCL), which catalyzes the phosphorylation of TCAC substrates, as a gene associated with lower temperatures. Nevertheless, its function in potato's response to lower temperatures remains unclear. Phylogenetic analysis has revealed that Solanum tuberosum possesses α and β subunits of SUCL, which cluster with those of Solanum lycopersicum, Nicotiana tabacum and Nicotiana benthamiana. Further investigation has shown that StSUCLα1 is predominantly located within mitochondria. Low temperatures induce methylation modification alterations at 11 intragenic cytosine sites and lead to changes in StSUCLα1 expression levels. Correlation analysis suggests that alterations in intragenic cytosine methylation sites of SUCLα1 may be associated with MET1. Knocking down NbSUCLα1, the homologous gene of StSUCLα1 in N. benthamiana, results in increased susceptibility to low temperature stress in plants. In summary, we have confirmed that SUCLα1 is a key gene modulated by intragenic cytosine methylation in response to lower temperatures, providing a novel target for genetic breeding aimed at enhancing potato tolerance to low temperature stress.

BET inhibitor and CDK4/6 inhibitor synergistically inhibit breast cancer by suppressing BRD4 stability and DNA damage repair

CDK4/6 inhibitors have shown clinical benefits in hormone receptor positive breast cancer. However, monotonous indications and unclear resistance mechanisms greatly limit the clinical application of these inhibitors. We attempt to improve the therapeutic effect of CDK4/6 inhibitors against breast cancer by combination with BET inhibitors. Although this combination therapy has begun to be studied in recent clinical trials, the mechanism of action is not clear. We provide the evidence that CDK4/6 inhibitor LY2835219 plus BRD4 inhibitor OTX-015 synergistically inhibits both ER positive and triple-negative breast cancer cells growth in vitro and in vivo. Mechanistically, LY2835219 accelerates the degradation of BRD4 through the proteasome pathway via inhibition of CDK4 activity. This instability of BRD4 protein in turn enhances the anti-tumor effect of CDK4/6 inhibitor by suppressing transcription of DNA damage repair gene RAD51, and synergistically promotes γ-H2AX accumulation and DNA double-strand breaks. Overall, we demonstrated the potential combined therapeutic value of CDK4/6 and BRD4 inhibitors and elucidated the mechanisms, which may provide a new rational approach for breast cancer patients.

Quantitative Profiling of Histone Variants and Posttranslational Modifications by Tandem Mass Spectrometry in Arabidopsis

Histone dynamics constitute an important layer of gene regulations associated with development and growth in multicellular eukaryotes. They also stand as key determinants of plant responses to environmental changes. Histone dynamics include the exchange of histone variants as well as post-translational modifications of their amino acid residues (such as acetylation and mono/di/trimethylation), commonly referred to as histone marks. Investigating histone dynamics with a focus on combinatorial changes occurring at their residues will greatly help unravel how plants achieve phenotypic plasticity.Mass spectrometry (MS) analysis offers unequaled resolution of the abundance of histone variants and of their marks. Indeed, relative to other techniques such as western blot or genome-wide profiling, this powerful technique allows quantifying the relative abundances of histone forms, as well as revealing coexisting marks on the same histone molecule. Yet, while MS-based histone analysis has proven efficient in several animals and other model organisms, this method stands out as more challenging in plants. One major challenge is the isolation of sufficient amounts of pure, high-quality histones, likely rendered difficult by the presence of the cell wall, for sufficiently deep and resolutive identification of histone species.In this chapter, we describe a straightforward MS-based proteomic method, implemented to characterize histone marks from Arabidopsis thaliana seedling tissues and cell culture suspensions. After acid extraction of histones, in vitro propionylation of free lysine residues, and digestion with trypsin, a treatment at highly basic pH allows obtaining sharp spectral signals of biologically relevant histone peptide forms.The method workflow described here shall be used to measure changes in histone marks between Arabidopsis thaliana genotypes, along developmental time-courses, or upon various stresses and treatments.

Mutational signatures and their association with cancer survival and gene expression in multiple cancer types

Different endogenous and exogenous mutational processes cause specific patterns of somatic mutations and mutational signatures. Although their biological research has been intensive, there are only rare studies assessing the possible prognostic role of mutational signatures. We used data from The Cancer Genome Atlas to study the associations between the activity of the mutational signatures and four survival endpoints in 18 types of malignancies. We further explored the prognostic differences according to, for example, the HPV status in head and neck squamous cell carcinomas and smoking status in lung cancers. The predictive power of the signatures over time was evaluated with a dynamic area under the curve model, and the links between mutational signature activities and differences in gene expression patterns were analyzed. In 12 of 18 studied cancer types, we identified at least one mutational signature whose activity predicted survival outcomes after adjusting for the established prognostic factors. For example, overall survival was associated with the activity of mutational signatures in nine cancer types and disease-specific survival in seven cancer types. The clock-like signatures SBS5 and SBS40 were most commonly associated with survival endpoints. The genes of the myosin binding protein and melanoma antigen families were among the most substantially dysregulated genes between the signatures of low and high activity. The differences in gene expression also revealed various enriched pathways. Based on these data, specific mutational signatures associate with the gene expression and have the potential to serve as strong prognostic factors in several cancer types.

Analysis of the antigenic and immunogenic properties of the native rabies virus glycoprotein purified by Lens culinaris lectin affinity chromatography

Rabies virus glycoprotein (RABV-G) is responsible for the recognition of specific cell surface receptors and induces the production of neutralizing antibodies (VNA). Since RABV-G is a glycoprotein, this work aimed to evaluate Lens culinaris (LCA) chromatography as a simple and effective purification method. The purity and identification of the protein obtained were analyzed by SDS-PAGE, ELISA and lectin-binding assay. The antigenic properties of the purified RABV-G were evaluated by direct ELISA using human serum samples from individuals who had received rabies pre-exposure vaccination. For the immunogenicity study, Swiss Webster mice were immunized with purified RABV-G and the specific antibodies were measured by direct ELISA and RFFIT. As results, it was observed that the purified protein reveled a molecular mass of 55 kDa and the presence of carbohydrate; additionally, it was recognized by anti-rabies virus glycoprotein monoclonal antibody. Purified RABV-G induced high VNA titers (>50.0 IU/ml) in vivo, as detected by RFFIT, as well as RABV-G specific IgG1 (0.8 mean OD±SD) and IgG2a (0.3 mean OD±SD) antibodies, with a predominance of IgG1 (p< 0.001). In addition, it was observed that RABV-G was efficient in selectively detecting anti- RABV-G IgG in the sera of vaccinated individuals compared to the negative control. Therefore, LCA chromatography was efficient in preserving the native properties of RABV-G that are essential in inducing an adequate humoral immune response. In addition, the purified RABV-G presented analytical potential as an ELISA reagent.

TetR and OmpR family regulators in natural product biosynthesis and resistance

This article provides a comprehensive review and sequence-structure analysis of transcription regulator (TR) families, TetR and OmpR/PhoB, involved in specialized secondary metabolite (SSM) biosynthesis and resistance. Transcription regulation is a fundamental process, playing a crucial role in orchestrating gene expression to confer a survival advantage in response to frequent environmental stress conditions. This process, coupled with signal sensing, enables bacteria to respond to a diverse range of intra and extracellular signals. Thus, major bacterial signaling systems use a receptor domain to sense chemical stimuli along with an output domain responsible for transcription regulation through DNA-binding. Sensory and output domains on a single polypeptide chain (one component system, OCS) allow response to stimuli by allostery, that is, DNA-binding affinity modulation upon signal presence/absence. On the other hand, two component systems (TCSs) allow cross-talk between the sensory and output domains as they are disjoint and transmit information by phosphorelay to mount a response. In both cases, however, TRs play a central role. Biosynthesis of SSMs, which includes antibiotics, is heavily regulated by TRs as it diverts the cell's resources towards the production of these expendable compounds, which also have clinical applications. These TRs have evolved to relay information across specific signals and target genes, thus providing a rich source of unique mechanisms to explore towards addressing the rapid escalation in antimicrobial resistance (AMR). Here, we focus on the TetR and OmpR family TRs, which belong to OCS and TCS, respectively. These TR families are well-known examples of regulators in secondary metabolism and are ubiquitous across different bacteria, as they also participate in a myriad of cellular processes apart from SSM biosynthesis and resistance. As a result, these families exhibit higher sequence divergence, which is also evident from our bioinformatic analysis of 158 389 and 77 437 sequences from TetR and OmpR family TRs, respectively. The analysis of both sequence and structure allowed us to identify novel motifs in addition to the known motifs responsible for TR function and its structural integrity. Understanding the diverse mechanisms employed by these TRs is essential for unraveling the biosynthesis of SSMs. This can also help exploit their regulatory role in biosynthesis for significant pharmaceutical, agricultural, and industrial applications.

Infertility following trisomic pregnancies: A nationwide cohort study

OBJECTIVE

To study whether gynecologic or reproductive disorders show association with trisomic conceptions.

METHODS

This nationwide cohort study utilized the Registry of Congenital Malformations to identify women who had a trisomic pregnancy (n = 5784), either with trisomy 13 (T13; n = 351), trisomy 18 (T18; n = 1065) or trisomy 21 (T21; n = 4369) from 1987 to 2018. We used the Finnish Maternity cohort to match the cases to population controls (n = 34 422) on the age, residence, and timing of pregnancy. These data were cross-linked to the ICD-10 diagnoses of the national Care Registry for Health Care data on specialized health care in Finland during 1996 to 2019. Both inflammatory (ICD-10 diagnoses: N70-N77) and noninflammatory disorders of the genital tract (N80-N98) were studied. Crude odds ratios (ORs) with 95% CIs were calculated for associations between diagnoses and trisomic conceptions.

RESULTS

The diagnosis of female infertility (N97) at any time was associated with trisomic conceptions (OR: 1.19, 95% CI: 1.08-1.32). In the subgroup analysis, this association was found for T18 (OR: 1.29, 95% CI: 1.03-1.61) and T21 (OR: 1.17, 95% CI: 1.04-1.32), but not for T13 (OR: 1.15, 95% CI: 0.75-1.72). When restricting the timing of the diagnosis of female infertility, an elevated OR was found only after the index pregnancy (OR: 1.81, 95% CI: 1.56-2.09). These increased odds for infertility after trisomic conceptions were observed both in women <35 years (T18 OR: 1.91, 95% CI: 1.21-3.00; T21 OR: 1.68, 95% CI: 1.31-2.14) and in women ≥35 years (T18 OR: 2.17, 95% CI: 1.40-3.33; T21 OR: 1.87; 95% CI: 1.47-2.39), but not after T13 conceptions.

CONCLUSION

Our observational data suggest a link between trisomic conceptions and subsequent diagnoses of infertility but do not demonstrate causality. These data implicate that partially similar mechanisms might predispose to trisomy and infertility, regardless of maternal age.

Novel pof1 mutation suppresses the sensitivity to DNA replication inhibitor in fission yeast RecQ helicase mutant

Homologous recombination is vital for DNA double-strand break repair. Dysfunction in homologous recombination can lead to cell death, mutations, and cancer. In fission yeast (Schizosaccharomyces pombe), RecQ helicase Rqh1 resolves recombination intermediates. We found that rqh1-hd strain impaired growth in media containing hydroxyurea and thiabendazole. Using this condition, we identified a novel pof1 mutation (pof1-A81T) that suppress the poor growth of the rqh1-hd strain on the plate containing hydroxyurea and thiabendazole. Compared to rqh1-hd, rqh1-hd pof1-A81T cells displayed reduced Replication Protein A foci on chromosome bridges after hydroxyurea treatment. This suggests that pof1-A81T mutation suppresses the accumulation of recombination intermediates in hydroxyurea-treated rqh1-hd cells. Additionally, pof1-A81T mutation rescued the segregation defect of nucleolar protein Gar2 observed in hydroxyurea-treated rqh1-hd cells, potentially by mitigating recombination intermediate accumulation in rDNA. These results suggest that the pof1-A81T mutation suppresses the accumulation of recombination intermediates, particularly in rDNA, and alleviates the rqh1 deficiency phenotype in S. pombe.

Exploring the complex information processes underlying plant behavior

Newly discovered plant behaviors, linked to historical observations, contemporary technologies, and emerging knowledge of signaling mechanisms, argue that plants utilize complex information processing systems. Plants are goal-oriented in an evolutionary and physiological sense; they demonstrate agency and learning. While most studies on plant plasticity, learning, and memory deal with the responsiveness of individual plants to resource availability and biotic stresses, adaptive information is often perceived from and coordinated with neighboring plants, while competition occurs for limited resources. Based on existing knowledge, technologies, and sustainability principles, climate-smart agricultural practices are now being adopted to enhance crop resilience and productivity. A deeper understanding of the dynamics of plant behavior offers a rich palette of potential amelioration strategies for improving the productivity and health of natural and agricultural ecosystems.

4CMenB journey to the 10-year anniversary and beyond

The 4-component meningococcal serogroup B (MenB) vaccine, 4CMenB, the first broadly protective, protein-based MenB vaccine to be licensed, is now registered in more than 50 countries worldwide. Real-world evidence (RWE) from the last decade confirms its effectiveness and impact, with infant immunization programs showing vaccine effectiveness of 71-95% against invasive MenB disease and cross-protection against non-B serogroups, including a 69% decrease in serogroup W cases in 4CMenB-eligible cohorts in England. RWE from different countries also demonstrates the potential for additional moderate protection against gonorrhea in adolescents. The real-world safety profile of 4CMenB is consistent with prelicensure reports. Use of the endogenous complement human serum bactericidal antibody (enc-hSBA) assay against 110 MenB strains may enable assessment of the immunological effectiveness of multicomponent MenB vaccines in clinical trial settings. Equitable access to 4CMenB vaccination is required to better protect all age groups, including older adults, and vulnerable groups through comprehensive immunization policies.

Liquid-liquid phase separation of tau and α-synuclein: A new pathway of overlapping neuropathologies

Liquid-liquid phase separation (LLPS) is a critical phenomenon that leads to the formation of liquid-like membrane-less organelles within cells. Advances in our understanding of condensates reveal their significant roles in biology and highlight how their dysregulation may contribute to disease. Recent evidence indicates that the high protein concentration in coacervates may lead to abnormal protein aggregation associated with several neurodegenerative diseases. The presence of condensates containing multiple amyloidogenic proteins may play a role in the co-deposition and comorbidity seen in neurodegeneration. This review first provides a brief overview of the physicochemical bases and molecular determinants of LLPS. It then summarizes our understanding of Tau and α-synuclein (AS) phase separation, key proteins in Alzheimer's and Parkinson's diseases. By integrating recent findings on complex Tau and AS coacervation, this article offers a fresh perspective on how LLPS may contribute to the pathological overlap in neurodegenerative disorders and provide a novel therapeutic target to mitigate or prevent such conditions.

Recent progress in mRNA cancer vaccines

The research and development of messenger RNA (mRNA) cancer vaccines have gradually overcome numerous challenges through the application of personalized cancer antigens, structural optimization of mRNA, and the development of alternative RNA-based vectors and efficient targeted delivery vectors. Clinical trials are currently underway for various cancer vaccines that encode tumor-associated antigens (TAAs), tumor-specific antigens (TSAs), or immunomodulators. In this paper, we summarize the optimization of mRNA and the emergence of RNA-based expression vectors in cancer vaccines. We begin by reviewing the advancement and utilization of state-of-the-art targeted lipid nanoparticles (LNPs), followed by presenting the primary classifications and clinical applications of mRNA cancer vaccines. Collectively, mRNA vaccines are emerging as a central focus in cancer immunotherapy, offering the potential to address multiple challenges in cancer treatment, either as standalone therapies or in combination with current cancer treatments.

Comprehensive physiological and genomic characterization of a potential probiotic strain, Lactiplantibacillus plantarum ILSF15, isolated from the gut of tribes of Odisha, India

Characterizing probiotic features of organisms isolated from diverse environments can lead to the discovery of novel strains with promising functional features and health attributes. The present study attempts to characterize a novel probiotic strain isolated from the gut of the tribal population of Odisha, India. Based on 16S rRNA-based phylogeny, the strain was identified as a species of the Lactiplantibacillus genus and was named Lactiplantibacillus plantarum strain ILSF15. The current investigation focuses on elucidating this strain's genetic and physiological properties associated with probiotic attributes such as biosafety risk, host adaptation/survival traits, and beneficial functional features. The novel strain was observed, in vitro, exhibiting features such as acid/bile tolerance, adhesion to the host enteric epithelial cells, cholesterol assimilation, and pathogen exclusion, indicating its ability to survive the harsh environment of the human GIT and resist the growth of harmful microorganisms. Additionally, the L. plantarum ILSF15 strain was found to harbor genes associated with the metabolism and synthesis of various bioactive molecules, including amino acids, carbohydrates, lipids, and vitamins, highlighting the organism's ability to efficiently utilize diverse resources and contribute to the host's nutrition and health. Several genes involved in host adaptation/survival strategies and host-microbe interactions were also identified from the ILSF15 genome. Moreover, L. plantarum strains, in general, were found to have an open pangenome characterized by high genetic diversity and the absence of specific lineages associated with particular habitats, signifying its versatile nature and potential applications in probiotic and functional food industries.

Application of autophagy in mesenchymal stem cells

In this editorial, we have taken an in-depth look at the article published by Wan et al. The study showed that preconditioning mesenchymal stem cells (MSCs) protected them against programmed cell death, and increased their survival rate and therapeutic potential. Autophagy, a type of programmed cell death, is a major intracellular degradation and recycling pathway that is crucial for maintaining cellular homeostasis, self-renewal, and pluripotency. We have explored the relationship between autophagy and MSCs to determine the role of autophagy in the therapeutic applications of MSCs.

GSK3β phosphorylation catalyzes the aggregation of tau into Alzheimer's disease-like filaments

The pathological deposition of proteins is a hallmark of several devastating neurodegenerative diseases. These pathological deposits comprise aggregates of proteins that adopt distinct structures named strains. However, the molecular factors responsible for the formation of distinct aggregate strains are unknown. Here, we show that the serine/threonine kinase GSK3β catalyzes the aggregation of the protein tau into Alzheimer's disease (AD)-like filaments. We demonstrate that phosphorylation by GSK3β, but not by several other kinases, promotes the aggregation of full-length tau as well as enhances phase separation into gel-like condensate structures. Cryoelectron microscopy further reveals that the fibrils formed by GSK3β-phosphorylated tau adopt a fold comparable to that of paired helical filaments isolated from the brains of AD patients. Our results elucidate the intricate relationship between posttranslational modification and the formation of tau strains in neurodegenerative diseases.

Biofilm formation by Staphylococcus aureus is triggered by a drop in the levels of a cyclic dinucleotide

The bacterial pathogen Staphylococcus aureus forms multicellular communities known as biofilms in which cells are held together by an extracellular matrix principally composed of repurposed cytoplasmic proteins and extracellular DNA. These biofilms assemble during infections or under laboratory conditions by growth on medium containing glucose, but the intracellular signal for biofilm formation and its downstream targets were unknown. Here, we present evidence that biofilm formation is triggered by a drop in the levels of the second messenger cyclic-di-AMP. Previous work identified genes needed for the release of extracellular DNA, including genes for the cyclic-di-AMP phosphodiesterase GdpP, the transcriptional regulator XdrA, and the purine salvage enzyme Apt. Using a cyclic-di-AMP riboswitch biosensor and mass spectrometry, we show that the second messenger drops in abundance during biofilm formation in a glucose-dependent manner. Mutation of these three genes elevates cyclic-di-AMP and prevents biofilm formation in a murine catheter model. Supporting the generality of this mechanism, we found that gdpP was required for biofilm formation by diverse strains of S. aureus. We additionally show that the downstream consequence of the drop in cyclic-di-AMP is inhibition of the "accessory gene regulator" operon agr, which is known to suppress biofilm formation through phosphorylation of the transcriptional regulator AgrA by the histidine kinase AgrC. Consistent with this, an agr mutation bypasses the block in biofilm formation and eDNA release caused by a gdpP mutation. Finally, we report the unexpected observation that GdpP inhibits phosphotransfer from AgrC to AgrA, revealing a direct connection between the phosphodiesterase and agr.