Search Results (38)

The recent discovery of TIGR-Tas (Tandem Interspaced Guide RNA-Targeting Systems) marks a major advance in the field of genome editing, introducing a new class of compact, programmable DNA-targeting systems that function independently of traditional CRISPR-Cas pathways. TIGR-Tas effectors use a novel dual-spacer guide RNA (tigRNA) to recognize both strands of target DNA without requiring a protospacer adjacent motif (PAM). These Tas proteins introduce double-stranded DNA cuts with characteristic 8-nucleotide 3′ overhangs and are significantly smaller than Cas9, offering delivery advantages for in vivo editing. Structural analyses reveal homology to box C/D snoRNP proteins, suggesting a previously unrecognized evolutionary lineage of RNA-guided nucleases. This review positions TIGR-Tas at the forefront of a new wave of RNA-programmable genome-editing technologies. In parallel, I provide comparative insight into the diverse and increasingly modular CRISPR-Cas systems, including Cas9, Cas12, Cas13, and emerging effectors like Cas3, Cas10, CasΦ, and Cas14. While the CRISPR-Cas universe has revolutionized molecular biology, TIGR-Tas systems open a complementary and potentially more versatile path for programmable genome manipulation. I discuss mechanistic distinctions, evolutionary implications, and potential applications in human cells, synthetic biology, and therapeutic genome engineering. Full article

Background/Objectives: Truncating mutations in PALB2, a critical component of the BRCA1-PALB2-BRCA2 homologous recombination repair complex, are associated with increased risk and aggressiveness of breast cancer. The consequences of PALB2 truncation on the expression, localization, and functional dynamics of the scaffold protein IQGAP1 were investigated in this study based on two cases of truncated PALB2 human breast invasive ductal carcinoma (IDC), specifically, c.1240C>T (p.Arg414*) and c.2257C>T (p.Arg753*). Methods: Using confocal microscopy, we examined co-expression patterns of IQGAP1 with PALB2, PCNA, CK7, and β-tubulin in tumor tissues from both control cancer and PALB2-mutated cases. Results: In PALB2-truncated tumors, IQGAP1 exhibited enhanced peripheral and plasma membrane localization with elevated co-localization levels compared to controls, suggesting altered cytoskeletal organization. PALB2 truncation increased nuclear and cytoplasmic N-terminal PALB2 immunoreactivity, indicating the presence of truncated isoforms disrupting the homologous recombination repair system. Co-expression analyses with PCNA revealed an inverse expression pattern between IQGAP1 and proliferation markers, suggesting S-phase cell cycle-dependent heterogeneity. Furthermore, the loss of IQGAP1 dominance over CK7 and β-tubulin in mutant tumors, along with persistent intercellular spacing, implied a loss of cell–cell cohesion and the acquisition of invasive traits. Conclusions: These data support a model where PALB2 truncation triggers a reorganization of IQGAP1 that disrupts its canonical structural functions and facilitates tumor progression via enhanced motility and impaired cell–cell interaction. IQGAP1 thus serves as both a functional effector and potential biomarker in PALB2-mutated IDC, opening novel paths for diagnosis and targeted therapeutic intervention. Full article

Group A rotaviruses (RVAs) are a major cause of acute dehydrating diarrhea in infants and young animals worldwide. In rabbits, RVAs are associated with enteric disease, likely in combination with other pathogens. We report the identification and characterization of a lapine RVA strain in an Italian rabbit breeding farm. Increased mortality rates associated with enteric symptoms were reported in the facility in post-weaning rabbits around 40 days of age. By quantitative RT-PCR, an RVA strain was identified in the intestinal contents of deceased rabbits. A PCR-based enrichment protocol coupled with Nanopore sequencing allowed the reconstruction of the nearly complete genome of a rabbit RVA strain, Rabbit-wt/ITA/36-9/2022/G3P[14], with a genotype constellation (G3-P[14]-I2-R2-C2-M3-A9-N2-T6-E5-H3) conserved among lapine RVAs. Each of the 11 gene segments displayed high nucleotide identity and phylogenetic clustering with lapine rotavirus strains, as well as two Belgian human G3P[14] strains, which had been shown to have a zoonotic (lapine) origin. However, the NSP2 gene of strain 36-9 clustered closer with a group of rare human G3P[9] strains, suggesting a common path during their evolution. Gathering sequence data on animal RVAs is pivotal to reconstructing the history of homologous and heterologous RVAs in various mammals, including humans. Full article

The problem of the foul odor caused by H₂S in livestock farms has become a major complaints. In this study, optimal sulfur-oxidizing bacteria (SOB) strains were screened from dairy farm wastewater and the adjacent soil for odor treatment. The strains and physiological functions were determined by identification and genome comparison, and the optimal operating conditions were determined by experiments under different conditions. The identification results showed that the strain that had the highest homology with Halomonas mongoliensis was Halomonas sp. AEB2. The comparative genomic results showed that the average nucleotide identity and DNA–DNA hybridization value were 95.8% and 68.6%, respectively. The optimization results were as follows: sodium succinate-carbon (10 g/L) and ammonium chloride-nitrogen (0.07 g/L). The optimal operating conditions were as follows: seeding rate 4%, temperature 30 °C, stirring speed 90 rpm, and pH 8. The oxidation products of AEB2 were mainly elemental sulfur and tetrathionate, and the metabolic pathway of AEB2 was constructed accordingly. This study suggests a feasible path to reduce H₂S emissions from dairy farms, and it provides theoretical support for the restoration of livestock environment and sustainability. Full article

Vaccination strategies play a pivotal role in achieving broad and robust immune protection. With the advent of new technologies and challenges posed by emerging infectious diseases such as SARS-CoV-2, evaluating the efficacy of homologous (matching tracks) and heterologous (mixing paths) vaccination regimens is critical. This article explores mechanistic insights and empirical evidence on the benefits and limitations of these approaches. Full article

Hyperlipidemia is characterized by a high level of blood lipid which poses a serious threat to human health. Coix seed is a traditional crop of medicine and food homology with a wide range of pharmacological actions. To make clear the attenuation effect of coix seed against hyperlipidemia, low and high doses of coix seed extract (CSE) were orally administered to hyperlipidemia model mice developed by high-fat diet (HFD). Our results showed that CSE notably improved liver pathological injury, and oxidative stress, and declined the levels of glucose and lipid in hyperlipidemia mice. Liver metabolomics showed that lipid-related metabolites notably decreased, and pathways of glycolipid metabolism were seriously affected by CSE intervention. Moreover, 16S rRNA sequencing revealed that CSE treatment notably increased the diversity of gut microbiota. Meanwhile, the microbiota with the function of regulating intestinal balance as well as relieving obesity and nervous diseases significantly enhanced while harmful flora notably decreased after CSE intervention. The results of network pharmacology and molecular docking indicated that the PPAR signaling pathway may be the core path of anti-hyperlipidemia for coix seeds. RT-qPCR further verified that the expression levels of genes from the PPAR pathway notably changed by CSE treatment with fat synthesis genes significantly decreased while lipolysis genes notably enhanced. Therefore, coix seed might be a potential candidate for the treatment of hyperlipidemia. Full article

Mung bean (Vigna radiata) plays a significant role in agricultural trade, food processing and utilization, and cropping structure adjustment due to its abundant nutritional components, medicine-food homology, capacity for nitrogen fixation, and soil improvement. The low yield level is a crucial limitation factor in the mung bean industry, while heterosis is an efficient path for increasing crop yields. The flexible utilization of male sterile mung bean materials may solve this pressing demand in the industry. This study identified a completely male-sterile mutant, vrnp 1, in the EMS-mutagenized mung bean cultivar Jilv 10 population, which is controlled by a single recessive nuclear gene. Furthermore, we employed a series of microscopical and histological techniques and observed that the tapetal cells in the vrnp 1 mutant did not perform as expected when reaching stage 8 of anther development, notably exhibiting a delay in entering PCD. This was accompanied by a failure to deposit cell wall components onto the pollen wall, culminating in a complete absence of mature pollen and the manifestation of male sterility. In conclusion, the vrnp 1 mutant could potentially serve as a promising candidate for male sterility in exploiting hybrid vigor in mung bean. Our research may elucidate how the delayed initiation of programmed cell death in tapetal cells contributes to a factor implicated in mung bean male sterility. Furthermore, the phenotypic data collected during pivotal developmental phases may have contributed to a better grasp of mung bean microspores and anther development. Full article

As part of improving road safety around trucks, a solution was proposed to reduce the swept path width of a moving tractor–semi-trailer. This article presents a mathematical analysis of the movement of a tractor unit with a traditional semi-trailer with fixed axles and steered wheels. A simulation analysis of both presented vehicles was carried out. The core of the algorithm controlling the steering angle of the semi-trailer wheels is presented. The influence of controlling the semi-trailer’s swivel wheels on the swept path width of a tractor–trailer with a semi-trailer equipped with swivel wheels is discussed. The assumptions for building the control algorithm are presented. The article presents the advantages of the solution used along with the control algorithm. Measurable benefits resulting from the use of the presented solution are presented, such as increasing cargo space, reducing cargo transport costs, and reducing aerodynamic resistance and fuel consumption. It is worth emphasizing that reducing fuel consumption is very important because it reduces the emission of harmful exhaust gases into the atmosphere. The swept path width is important especially in the case of vehicles moving in a limited area, for example in the parking lots of transhipment and logistics centers, between urban buildings. Vehicles admitted to traffic meet the minimum conditions imposed by homologation regulations, but reducing the swept path width allows for improving the operational properties of the tractor–semi-trailer. The use of the proposed control algorithm to control the turn of the semi-trailer’s steered wheels brings tangible benefits both in improving road safety and in reducing the emission of harmful substances into the environment. Full article

Persistent topological Laplacians constitute a new class of tools in topological data analysis (TDA). They are motivated by the necessity to address challenges encountered in persistent homology when handling complex data. These Laplacians combine multiscale analysis with topological techniques to characterize the topological and geometrical features of functions and data. Their kernels fully retrieve the topological invariants of corresponding persistent homology, while their non-harmonic spectra provide supplementary information. Persistent topological Laplacians have demonstrated superior performance over persistent homology in the analysis of large-scale protein engineering datasets. In this survey, we offer a pedagogical review of persistent topological Laplacians formulated in various mathematical settings, including simplicial complexes, path complexes, flag complexes, digraphs, hypergraphs, hyperdigraphs, cellular sheaves, and N-chain complexes. Full article

This study presents a path-planning approach toward efficient obstacle avoidance in dynamic environments. The developed approach features the awareness of the topological structure of the dynamic environment at a planning instant. It is achieved by employing a homology class path planner to generate a set of non-homotopy global paths. The global paths are cast into tree structures separately and optimized by the developed sampling-based path-planning methods. This mechanism can adaptively adjust the optimizing step size according to the change in the dynamic environment, and the sampling module uses the Gaussian Mixture Model (GMM) Optimizer to control the sampling space. The approach seeks the globally optimal path as it maintains and optimizes homology classes of admissible candidate paths of distinctive topologies in parallel. We conduct various experiments in dynamic environments to verify the developed method’s effectiveness and efficiency. It is demonstrated that the developed method can perform better than the state of the art. Full article

Many folding enzymes use separate domains for the binding of substrate proteins and for the catalysis of slow folding reactions such as prolyl isomerization. FKBP12 is a small prolyl isomerase without a chaperone domain. Its folding activity is low, but it could be increased by inserting the chaperone domain from the homolog SlyD of E. coli near the prolyl isomerase active site. We inserted two other chaperone domains into human FKBP12: the chaperone domain of SlpA from E. coli, and the chaperone domain of SlyD from Thermococcus sp. Both stabilized FKBP12 and greatly increased its folding activity. The insertion of these chaperone domains had no influence on the FKBP12 and the chaperone domain structure, as revealed by two crystal structures of the chimeric proteins. The relative domain orientations differ in the two crystal structures, presumably representing snapshots of a more open and a more closed conformation. Together with crystal structures from SlyD-like proteins, they suggest a path for how substrate proteins might be transferred from the chaperone domain to the prolyl isomerase domain. Full article

We demonstrate the equivalence of two different conjectures in the literature for the holographic entanglement negativity in AdS₃/CFT₂, modulo certain constants. These proposals involve certain algebraic sums of bulk geodesics homologous to specific combinations of subsystems, and the entanglement wedge cross section (EWCS) backreacted by a cosmic brane for the conical defect geometry in the bulk gravitational path integral. It is observed that the former conjectures reproduce the field theory replica technique results in the large central charge limit whereas the latter involves constants related to the Markov gap. In this context, we establish an alternative construction for the EWCS of a single interval in a CFT₂ at a finite temperature to resolve an issue for the latter proposal involving thermal entropy elimination for holographic entanglement negativity. Our construction for the EWCS correctly reproduces the corresponding field theory results modulo the Markov gap constant in the large central charge limit. Full article

Cowden syndrome (CS) is a rare disease that was first described in 1963 and later included in the large group of genodermatoses. It is the most common syndrome among the PTEN-associated hamartomatous tumor syndromes (PHTS). CS has an autosomal dominant inheritance pattern, with increased penetrance and variable expressivity, making early diagnosis difficult. Mutations in the PTEN gene (phosphatase and TENsin homolog) are involved in its pathogenesis, involving many organs and systems originating in the three embryonic layers (ectodermum, endodermum, and mesodermum). The consequence is the development of hamartomatous lesions in various organs (brain, intestines, thyroid, oropharyngeal cavity, colon, rectum, etc.). Multiple intestinal polyps are common in patients with CS, being identified in over 95% of patients undergoing colonoscopy. The authors describe the case of a patient who presented the first signs of the disease at 3 ½ years (tonsil polyp) but was diagnosed only at the age of 20 following a colonoscopy that revealed hundreds of intestinal polyps, suggesting further molecular testing. A heterozygous frameshift mutation was identified in the PTEN gene, classified as a potentially pathogenic variant (c.762del.p(Val255*)). The authors present this case to highlight the path taken by the patient from the first symptoms to the diagnosis and to emphasize the clinical aspects of this mutational variant that have still not been identified in other patients with this syndrome. Full article

Homologous recombination (HR) is a fundamental process common to all species. HR aims to faithfully repair DNA double strand breaks. HR involves the formation of nucleoprotein filaments on DNA single strands (ssDNA) resected from the break. The nucleoprotein filaments search for homologous regions in the genome and promote strand exchange with the ssDNA homologous region in an unbroken copy of the genome. HR has been the object of intensive studies for decades. Because multi-scale dynamics is a fundamental aspect of this process, studying HR is highly challenging, both experimentally and using computational approaches. Nevertheless, knowledge has built up over the years and has recently progressed at an accelerated pace, borne by increasingly focused investigations using new techniques such as single molecule approaches. Linking this knowledge to the atomic structure of the nucleoprotein filament systems and the succession of unstable, transient intermediate steps that takes place during the HR process remains a challenge; modeling retains a very strong role in bridging the gap between structures that are stable enough to be observed and in exploring transition paths between these structures. However, working on ever-changing long filament systems submitted to kinetic processes is full of pitfalls. This review presents the modeling tools that are used in such studies, their possibilities and limitations, and reviews the advances in the knowledge of the HR process that have been obtained through modeling. Notably, we will emphasize how cooperative behavior in the HR nucleoprotein filament enables modeling to produce reliable information. Full article

A microwave absolute distance measurement method with ten-micron-level accuracy and meter-level range based on frequency domain interferometry is proposed and experimentally demonstrated for the first time. Theoretical analysis indicates that an interference phenomenon occurs instantaneously in the frequency domain when combining two homologous broad-spectrum microwave beams with different paths, and the absolute value of the distance difference between the two paths is only inversely proportional to the period of frequency domain interference fringes. The proof-of-principle experiments were performed to prove that the proposed method can achieve absolute distance measurement in the X-band with standard deviations of 15 μm, 17 μm, and 26 μm and within ranges of 1.69 m, 2.69 m, and 3.75 m. Additionally, a displacement resolution of 100 microns was realized. The multi-target recognition performance was also verified in principle. Furthermore, at the expense of a slight decrease in ranging accuracy, a fast distance measurement with the single measurement time of 20 μs was achieved by using a digitizer combined with a Fourier transform analyzer. Compared with the current microwave precision ranging technologies, the proposed method not only has the advantages of high precision, large range, and rapid measurement capability, but the required components are also easily obtainable commercial devices. The proposed method also has better complex engineering applicability, because the ten-micron-level ranging accuracy is achievable only by using a simple Fourier transform without any phase estimation algorithm, which greatly reduces the requirement for signal-to-noise ratio. Full article