Protein language models-assisted optimization of a uracil-N-glycosylase variant enables programmable T-to-G and T-to-C base editing.

Current base editors (BEs) use DNA deaminases, including cytidine deaminase in cytidine BE (CBE) or adenine deaminase in adenine BE (ABE), to facilitate transition nucleotide substitutions. Combining CBE or ABE with glycosylase enzymes can induce limited transversion mutations. Nonetheless, a critical demand remains for BEs capable of generating alternative mutation types, such as T>G corrections. In this study, we leveraged pre-trained protein language models to optimize a uracil-N-glycosylase (UNG) variant with altered specificity for thymines (eTDG). Notably, after two rounds of testing fewer than 50 top-ranking variants, more than 50% exhibited over 1.5-fold enhancement in enzymatic activities. When eTDG was fused with nCas9, it induced programmable T-to-S (G/C) substitutions and corrected db/db diabetic mutation in mice (up to 55%). Our findings not only establish orthogonal strategies for developing novel BEs but also demonstrate the capacities of protein language models for optimizing enzymes without extensive task-specific training data.

Fertilizer management for global ammonia emission reduction.

Crop production is a large source of atmospheric ammonia (NH3), which poses risks to air quality, human health and ecosystems1-5. However, estimating global NH3 emissions from croplands is subject to uncertainties because of data limitations, thereby limiting the accurate identification of mitigation options and efficacy4,5. Here we develop a machine learning model for generating crop-specific and spatially explicit NH3 emission factors globally (5-arcmin resolution) based on a compiled dataset of field observations. We show that global NH3 emissions from rice, wheat and maize fields in 2018 were 4.3 ± 1.0 Tg N yr-1, lower than previous estimates that did not fully consider fertilizer management practices6-9. Furthermore, spatially optimizing fertilizer management, as guided by the machine learning model, has the potential to reduce the NH3 emissions by about 38% (1.6 ± 0.4 Tg N yr-1) without altering total fertilizer nitrogen inputs. Specifically, we estimate potential NH3 emissions reductions of 47% (44-56%) for rice, 27% (24-28%) for maize and 26% (20-28%) for wheat cultivation, respectively. Under future climate change scenarios, we estimate that NH3 emissions could increase by 4.0 ± 2.7% under SSP1-2.6 and 5.5 ± 5.7% under SSP5-8.5 by 2030-2060. However, targeted fertilizer management has the potential to mitigate these increases.

Ordered and tunable Majorana-zero-mode lattice in naturally strained LiFeAs.

Majorana zero modes (MZMs) obey non-Abelian statistics and are considered building blocks for constructing topological qubits1,2. Iron-based superconductors with topological bandstructures have emerged as promising hosting materials, because isolated candidate MZMs in the quantum limit have been observed inside the topological vortex cores3-9. However, these materials suffer from issues related to alloying induced disorder, uncontrolled vortex lattices10-13 and a low yield of topological vortices5-8. Here we report the formation of an ordered and tunable MZM lattice in naturally strained stoichiometric LiFeAs by scanning tunnelling microscopy/spectroscopy. We observe biaxial charge density wave (CDW) stripes along the Fe-Fe and As-As directions in the strained regions. The vortices are pinned on the CDW stripes in the As-As direction and form an ordered lattice. We detect that more than 90 per cent of the vortices are topological and possess the characteristics of isolated MZMs at the vortex centre, forming an ordered MZM lattice with the density and the geometry tunable by an external magnetic field. Notably, with decreasing the spacing of neighbouring vortices, the MZMs start to couple with each other. Our findings provide a pathway towards tunable and ordered MZM lattices as a platform for future topological quantum computation.

Roton pair density wave in a strong-coupling kagome superconductor.

The transition metal kagome lattice materials host frustrated, correlated and topological quantum states of matter1-9. Recently, a new family of vanadium-based kagome metals, AV3Sb5 (A = K, Rb or Cs), with topological band structures has been discovered10,11. These layered compounds are nonmagnetic and undergo charge density wave transitions before developing superconductivity at low temperatures11-19. Here we report the observation of unconventional superconductivity and a pair density wave (PDW) in CsV3Sb5 using scanning tunnelling microscope/spectroscopy and Josephson scanning tunnelling spectroscopy. We find that CsV3Sb5 exhibits a V-shaped pairing gap Δ ~ 0.5 meV and is a strong-coupling superconductor (2Δ/kBTc ~ 5) that coexists with 4a0 unidirectional and 2a0 × 2a0 charge order. Remarkably, we discover a 3Q PDW accompanied by bidirectional 4a0/3 spatial modulations of the superconducting gap, coherence peak and gap depth in the tunnelling conductance. We term this novel quantum state a roton PDW associated with an underlying vortex-antivortex lattice that can account for the observed conductance modulations. Probing the electronic states in the vortex halo in an applied magnetic field, in strong field that suppresses superconductivity and in zero field above Tc, reveals that the PDW is a primary state responsible for an emergent pseudogap and intertwined electronic order. Our findings show striking analogies and distinctions to the phenomenology of high-Tc cuprate superconductors, and provide groundwork for understanding the microscopic origin of correlated electronic states and superconductivity in vanadium-based kagome metals.

Palmitoylation of NLRP3 Modulates Inflammasome Activation and Inflammatory Bowel Disease Development.

Aberrant activity of NLRP3 has been shown associations with severe diseases. Palmitoylation is a kind of protein post-translational modification, which has been shown to regulate cancer development and the innate immune system. Here, we showed that NLRP3 is palmitoylated at Cys419 and that palmitoyltransferase ZDHHC17 is the predominant enzyme that mediates NLRP3 palmitoylation and promotes NLRP3 activation by interacting with NLRP3 and facilitating NIMA-related kinase 7 (NEK7)-NLRP3 interactions. Blockade of NLRP3 palmitoylation by a palmitoylation inhibitor, 2-bromopalmitate, effectively inhibited NLRP3 activation in vitro. Also, in a dextran sulfate sodium-induced colitis model in mice, 2-bromopalmitate application could attenuate weight loss, improve the survival rate, and rescue pathological changes in the colon of mice. Overall, our study reveals that palmitoylation of NLPR3 modulates inflammasome activation and inflammatory bowel disease development. We propose that drugs targeting NLRP3 palmitoylation could be promising candidates in the treatment of NLRP3-mediated inflammatory diseases.

Tailam paramyxovirus C protein inhibits viral replication.

Jeilongviruses are emerging single-stranded negative-sense RNA viruses in the Paramyxoviridae family. Tailam paramyxovirus (TlmPV) is a Jeilongvirus that was identified in 2011. Very little is known about the mechanisms that regulate viral replication in these newly emerging viruses. Among the non-structural viral proteins of TlmPV, the C protein is predicted to be translated from an open reading frame within the phosphoprotein gene through alternative translation initiation. Though the regulatory roles of C proteins in virus replication of other paramyxoviruses have been reported before, the function of the TlmPV C protein and the relevant molecular mechanisms have not been reported. Here, we show that the C protein is expressed in TlmPV-infected cells and negatively modulates viral RNA replication. The TlmPV C protein interacts with the P protein, negatively impacting the interaction between N and P, resulting in inhibition of viral RNA replication. Deletion mutagenesis studies indicate that the 50 amino-terminal amino acid residues of the C protein are dispensable for its inhibition of virus RNA replication and interaction with the P protein.IMPORTANCETailam paramyxovirus (TlmPV) is a newly identified paramyxovirus belonging to the Jeilongvirus genus, of which little is known. In this work, we confirmed the expression of the C protein in TlmPV-infected cells, assessed its function, and defined a potential mechanism of action. This is the first time that the existence of a Jeilongvirus C protein has been confirmed and its role in viral replication has been reported.

A conserved methyltransferase active site residue of Zika virus NS5 is required for the restriction of STING activation and interferon expression.

Zika virus (ZIKV) is a re-emerging RNA virus and causes major public health events due to its link to severe neurological complications in foetuses and neonates. The cGAS-STING signalling pathway regulates innate immunity and plays an important role in the invasion of DNA and RNA viruses. This study reveals a distinct mechanism by which ZIKV restricts the cGAS-STING signalling to repress IFN-ß expression. ZIKV attenuates IFN-ß expression induced by DNA viruses (herpes simplex virus type 1, HSV-1) or two double-stranded DNAs (dsDNA90 and HSV120) in mouse embryonic fibroblasts (MEFs). Notably, ZIKV NS5, the viral RNA-dependent RNA polymerase, was responsible for the repression of IFN-ß. NS5 interacts with STING in the cytoplasm, suppresses IRF3 phosphorylation and nucleus localization and promotes the cleavage of STING K48-linked polyubiquitination. Furthermore, the NS5 methyltransferase (MTase) domain interacts with STING to restrict STING-induced IFN-ß expression. Interestingly, point mutation analyses of conserved methyltransferase active site residue D146 indicate that it is critical for repressing IFN-ß expression induced by STING stimulation in cGAS-STING signalling.

The C-Terminal 300 Amino Acid Residues of the G Protein and Putative Open Reading Frame X of the G Gene of Tailam Paramyxovirus (TlmPV) Are Not Required for Replication in Tissue Culture Cells.

Tailam paramyxovirus (TlmPV) was identified in Sikkim Rats in Hong Kong, China in 2011. Its negative sense RNA genome is similar to J paramyxovirus (JPV) and Beilong paramyxovirus (BeiPV), the prototypes of the recently established genus Jeilongvirus. TlmPV genome is predicted to have eight genes in the order 3'-N-P/V/C-M-F-SH-TM-G/X-L-5'. The predicted size of the TlmPV G protein is 1,052 amino acid (aa) residues and much larger than G proteins of typical paramyxoviruses, which are often less than 800 aa. In addition to G open reading frame (ORF) in the G gene, another ORF, termed ORF-X exists in the G gene transcript. Similar ORF-X exists in JPV and BeiPV G gene, but their expression in virus-infected cells has not been confirmed. In this study, we generated infectious TlmPV using a newly developed reverse genetics system. We have found that the G protein of TlmPV is truncated in cultured cells: stop codons emerged in the G open reading frame, resulting in deletions of amino acid residues beyond residue 732. We have obtained infectious TlmPV lacking the C-terminal 307 aa (rTlmPV-G745) and TlmPV lacking the C-terminal 306 aa and the ORF-X (rTlmPV-GΔ746-X). The recombinant TlmPVs lacking the C-terminal 300 aa reach a higher peak viral titer and have improved genome stability in tissue cultured cells. The work indicates that the C-terminal of the G protein of TlmPV and ORF-X are not required for replication in tissue culture cells, and the deletion of the C-terminal confers a growth advantage in tissue culture cells. IMPORTANCE TlmPV is a member of the recently established genus Jeilongvirus. TlmPV encodes a large G protein and its G gene contains ORF-X. In this work, infectious TlmPV was recovered using reverse genetics. Using this system, we have demonstrated that 300 aa of C-terminal of G and the ORF-X are not required for viral replication in tissue culture cells.

Quantitative 2D Digital Subtraction Venography for Venous Interventions: Validation in Phantom and In Vivo Porcine Models.

PURPOSE: To determine the feasibility of using a 2D quantitative digital subtraction venography (qDSV) technique that employs a temporally modulated contrast injection to quantify blood velocity in phantom, normal, and stenotic porcine iliac vein models. MATERIALS AND METHODS: Blood velocity was calculated using qDSV following temporally-modulated, pulsed injections of iodinated contrast medium, and compared to Doppler ultrasound (US) measurements (phantom: in-line sensor, in vivo: diagnostic linear probe). Phantom evaluation was performed in a compliant polyethylene tube phantom with simulated venous flow. In vivo evaluation of qDSV was performed in normal (n=7) and stenotic (n=3) iliac vein models. Stenoses were created using endovenous radiofrequency ablation and blood velocities were determined at baseline, post-stenosis, post-venoplasty and post-stent placement. RESULTS: In the phantom model, qDSV-calculated blood velocities (12-50 cm/s) had very strong correlations with US-measured velocities (13-51 cm/s) across a range of baseline blood velocities and injection protocols (slope=[1.01-1.13], R2=[0.96-0.99]). qDSV velocities were similar to US regardless of injection method: custom injector, commercial injector, or hand injection. In the normal in vivo model, qDSV-calculated velocities (5-18 cm/s) had strong correlation (slope=1.22, R2=0.90) with US (3-20 cm/s). In the stenosis model, blood velocity at baseline, post-stenosis, post-venoplasty, and post-stent placement were similar on qDSV and US at all time points. CONCLUSION: Venous blood velocity was accurately quantified in a venousphantom and in vivo porcine models using qDSV. Intra-procedural changes in porcine iliac vein blood velocity were quantified with qDSV after creation of a stenosis and subsequently treating it with venoplasty and stent placement.

Estrogens rapidly shape synaptic and intrinsic properties to regulate the temporal precision of songbird auditory neurons.

Sensory neurons parse millisecond-variant sound streams like birdsong and speech with exquisite precision. The auditory pallial cortex of vocal learners like humans and songbirds contains an unconventional neuromodulatory system: neuronal expression of the estrogen synthesis enzyme aromatase. Local forebrain neuroestrogens fluctuate when songbirds hear a song, and subsequently modulate bursting, gain, and temporal coding properties of auditory neurons. However, the way neuroestrogens shape intrinsic and synaptic properties of sensory neurons remains unknown. Here, using a combination of whole-cell patch clamp electrophysiology and calcium imaging, we investigate estrogenic neuromodulation of auditory neurons in a region resembling mammalian auditory association cortex. We found that estradiol rapidly enhances the temporal precision of neuronal firing via a membrane-bound G-protein coupled receptor and that estradiol rapidly suppresses inhibitory synaptic currents while sparing excitation. Notably, the rapid suppression of intrinsic excitability by estradiol was predicted by membrane input resistance and was observed in both males and females. These findings were corroborated by analysis of in vivo electrophysiology recordings, in which local estrogen synthesis blockade caused acute disruption of the temporal correlation of song-evoked firing patterns. Therefore, on a modulatory timescale, neuroestrogens alter intrinsic cellular properties and inhibitory neurotransmitter release to regulate the temporal precision of higher-order sensory neurons.

Strong electron-phonon coupling and multigap superconductivity in 2H/1T Janus MoSLi monolayer.

Two-dimensional (2D) Janus transition metal dichalcogenides MXY manifest novel physical properties owing to the breaking of out-of-plane mirror symmetry. Recently, the 2H phase of MoSH has been demonstrated to possess intrinsic superconductivity, whereas the 1T phase exhibits a charge density waves state. In this paper, we have systematically studied the stability and electron-phonon interaction characteristics of MoSLi. Our results have shown that both the 2H and 1T phases of MoSLi are stable, as indicated by the phonon spectrum and the ab initio molecular dynamics. However, the 1T phase exhibits an electron-phonon coupling constant that is twice as large as that of the 2H phase. In contrast to MoSH, the 1T phase of MoSLi exhibits intrinsic superconductivity. By employing the ab initio anisotropic Migdal-Eliashberg formalism, we have revealed the two-gap superconducting nature of 1T-MoSLi, with a transition temperature (Tc) of 14.8 K. The detailed analysis indicates that the superconductivity in 1T-MoSLi primarily originates from the interplay between the vibration of the phonon modes in the low-frequency region and the dz2 orbital. These findings provide a fresh perspective on superconductivity within Janus structures.

Single-port robotic-assisted laparoscopic synchronous surgery in pediatric patent processus vaginalis.

PURPOSE: Patent processus vaginalis (PPV) is usually observed in pediatric abdominal surgery; however, robotic single-port surgery in repairing processus vaginalis has not been reported in children. Herein, we present our clinical experiences in single-port robotic surgeries for PPV repair to evaluate both efficacy and safety. METHODS: Retrospective analysis of patients underwent single-port robotic-assisted laparoscopic surgery for genitourinary diseases from May 2020 and May 2023 in our center. Among these patients, 21 children had PPV repaired at the same time. The case characteristics and follow-up data were recorded. RESULTS: Twenty-one of the 53 children were found to have PPV during genitourinary surgery. The simultaneous treatment of the primary disease and PPV with a single-port robotic-assisted platform was both convenient and safe. There was no significant increase in total operation time, and no excessive intraoperative hemorrhage was observed in any of the operations. There were no complications observed on follow-up. CONCLUSION: With a high incidence of PPV in children, a single-port robotic-assisted procedure is feasible and effective if simultaneously performed when addressing a primary abdominal disease.

Ultrasensitive, Fast-Responsive, Directional Airflow Sensing by Bioinspired Suspended Graphene Fibers.

The development of high-performance miniaturized and flexible airflow sensors is essential to meet the need of emerging applications. Graphene-based airflow sensors are hampered by the sluggish response and recovery speed and low sensitivity. Here we employ laser-induced graphene (LIG) with poststructural biomimicry for fabricating high-performance, flexible airflow sensors, including cotton-like porous LIG, caterpillar fluff-like vertical LIG fiber, and Lepidoptera scale-like suspended LIG fiber (SLIGF) structures. The structural engineering changes the deformation behavior of LIGs under stress, among which the synchronous propagation of the scale-like structure of SLIGF is the most conducive to airflow sensing. The SLIGF achieves the shortest average response time of 0.5 s, the highest sensitivity of 0.11 s/m, and a record-low detection threshold of 0.0023 m/s, benchmarked against the state-of-the-art airflow sensors. Furthermore, we showcase the SLIGF airflow sensors in weather forecasting, health, and communications applications. Our study will help develop next-generation waterflow, sound, and motion sensors.

Nanoscale Manipulation of Wrinkle-Pinned Vortices in Iron-Based Superconductors.

The controlled manipulation of Abrikosov vortices is essential for both fundamental science and logical applications. However, achieving nanoscale manipulation of vortices while simultaneously measuring the local density of states within them remains challenging. Here, we demonstrate the manipulation of Abrikosov vortices by moving the pinning center, namely one-dimensional wrinkles, on the terminal layers of Fe(Te,Se) and LiFeAs, by utilizing low-temperature scanning tunneling microscopy/spectroscopy (STM/S). The wrinkles trap the Abrikosov vortices induced by the external magnetic field. In some of the wrinkle-pinned vortices, robust zero-bias conductance peaks are observed. We tailor the wrinkle into short pieces and manipulate the wrinkles by using an STM tip. Strikingly, we demonstrate that the pinned vortices move together with these wrinkles even at high magnetic field up to 6 T. Our results provide a universal and effective routine for manipulating wrinkle-pinned vortices and simultaneously measuring the local density of states on the iron-based superconductor surfaces.

Efficacy and Molecular Mechanism of Quercetin on Constipation Induced by Berberine via Regulating Gut Microbiota.

Berberine (BBR) is used to treat cancer, inflammatory conditions, and so on. But the side effects of BBR causing constipation should not be ignored. In clinical application, the combination of Amomum villosum Lour. (AVL) and BBR can relieve it. However, the effective ingredients and molecular mechanism of AVL in relieving constipation are not clear. A small intestine propulsion experiment was conducted in constipated mice to screen active ingredients of AVL. We further confirmed the molecular mechanism of action of the active ingredient on BBR-induced constipation. Quercetin (QR) was found to be the effective ingredient of AVL in terms of relieving constipation. QR can efficiently regulate the microbiota in mice suffering from constipation. Moreover, QR significantly raised the levels of substance P and motilin while lowering those of 5-hydroxytryptamine and vasoactive intestinal peptide; furthermore, it also increased the protein expression levels of calmodulin, myosin light-chain kinase, and myosin light chain. The use of QR in combination with BBR has an adverse effect-reducing efficacy. The study provides new ideas and possibilities for the treatment of constipation induced by BBR.

The Dependence of Solid Electrolyte Interphase on the Crystal Facet of Current Collector in Li Metal Battery.

The continuous electrolyte decomposition and uncontrolled dendrite growth caused by the unstable solid electrolyte interphase (SEI) have largely hindered the development of Li metal batteries. Here, we demonstrate that tuning the facet of current collector can regulate the composition of SEI and the subsequent Li deposition behavior using single-crystal Cu foils as an ideal platform. The theoretical and experimental studies reveal that the (100) facet of Cu possesses strong adsorption to anions, guiding more anions to participate preferentially in the inner Helmholtz plane and further promoting the formation of the stable inorganic-rich SEI. Consequently, the single-crystal Cu foils with a single [100] orientation (s-Cu(100)) achieve the dendrite-free Li deposition with enhanced Li plating/stripping reversibility. Moreover, the Li anode deposited on s-Cu(100) can stabilize the operation of an Ah-level pouch cell (350 Wh kg-1) with a low negative/positive capacity ratio (~2) and lean electrolyte (2.4 g Ah-1) for 150 cycles. Impressively, this strategy demonstrates universality in a series of electrolytes employed different anions. This work provides new insights into the correlation between the SEI and current collector, opening a universal avenue towards high-performance Li metal batteries.

Boosted Second Harmonic Generation of a Chiral Hybrid Lead Halide Resonant to Charge Transfer Exciton from Metal Halide Octahedra to Ligand.

Chiral hybrid organic-inorganic metal halides (HOMHs) offer an ideal platform for the advancement of second-order nonlinear optical (NLO) materials owing to their inherent noncentrosymmetric structures. The enhancement of optical nonlinearity of chiral HOMHs could be achieved by matching the free exciton and/or self-trapped exciton energy levels with desired NLO frequencies. However, the current scarcity of resonance modes and low resonance ratio hamper the further improvements of NLO performance. Herein, we propose a new resonant channel of charge transfer (CT) excited states from metal halide polyhedra to organic ligand to boost the second-order optical nonlinearity of chiral HOMHs. The model lead halide (C7H10N)PbBr3 (C7H10N=1-ethylpyridinium) exhibits a drastically enhanced second harmonic generation in resonance to the deep CT exciton energy, with intensity of up to 111.0 times that of KDP and 10.9 times that of urea. The effective NLO coefficient has been determined to be as high as ~40.2 pm V-1, balanced with a large polarization ratio and high laser damage threshold. This work highlights the contribution of organic ligands in the construction of a resonant channel for enhancing second-order NLO coefficients of metal halides, and thus provides guidelines for designing new chiral HOMHs materials for advanced nonlinear photonic applications.

Backbone Engineering of Polymeric Catalysts for High-Performance CO2 Reduction in Bipolar Membrane Zero-Gap Electrolyzer.

Bipolar membranes (BPMs) have emerged as a promising solution for mitigating CO2 losses, salt precipitation and high maintenance costs associated with the commonly used anion-exchange membrane electrode assembly for CO2 reduction reaction (CO2RR). However, the industrial implementation of BPM-based zero-gap electrolyzer is hampered by the poor CO2RR performance, largely attributed to the local acidic environment. Here, we report a backbone engineering strategy to improve the CO2RR performance of molecular catalysts in BPM-based zero-gap electrolyzers by covalently grafting cobalt tetraaminophthalocyanine onto a positively charged polyfluorene backbone (PF-CoTAPc). PF-CoTAPc shows a high acid tolerance in BPM electrode assembly (BPMEA), achieving a high FE of 82.6 % for CO at 100 mA/cm2 and a high CO2 utilization efficiency of 87.8 %. Notably, the CO2RR selectivity, carbon utilization efficiency and long-term stability of PF-CoTAPc in BPMEA outperform reported BPM systems. We attribute the enhancement to the stable cationic shield in the double layer and suppression of proton migration, ultimately inhibiting the undesired hydrogen evolution and improving the CO2RR selectivity. Techno-economic analysis shows the least energy consumption (957 kJ/mol) for the PF-CoTAPc catalyst in BPMEA. Our findings provide a viable strategy for designing efficient CO2RR catalysts in acidic environments.

P2X7 receptor is required for the ototoxicity caused by aminoglycoside in developing cochlear hair cells.

Aminoglycoside antibiotics (AGAs) are widely used in life-threatening infections, but they accumulate in cochlear hair cells (HCs) and result in hearing loss. Increases in adenosine triphosphate (ATP) concentrations and P2X7 receptor expression were observed after neomycin treatment. Here, we demonstrated that P2X7 receptor, which is a non-selective cation channel that is activated by high ATP concentrations, may participate in the process through which AGAs enter hair cells. Using transgenic knockout mice, we found that P2X7 receptor deficiency protects HCs against neomycin-induced injury in vitro and in vivo. Subsequently, we used fluorescent gentamicin-Fluor 594 to study the uptake of AGAs and found fluorescence labeling in wild-type mice but not in P2rx7-/- mice in vitro. In addition, knocking-out P2rx7 did not significantly alter the HC count and auditory signal transduction, but it did inhibit mitochondria-dependent oxidative stress and apoptosis in the cochlea after neomycin exposure. We thus conclude that the P2X7 receptor may be linked to the entry of AGAs into HCs and is likely to be a therapeutic target for auditory HC protection.

Toward large-scale, ordered and tunable Majorana-zero-modes lattice on iron-based superconductors.

Majorana excitations are the quasiparticle analog of Majorana fermions in solid materials. Typical examples are the Majorana zero modes (MZMs) and the dispersing Majorana modes. When probed by scanning tunneling spectroscopy, the former manifest as a pronounced conductance peak locating precisely at zero-energy, while the latter behaves as constant or slowly varying density of states. The MZMs obey non-abelian statistics and are believed to be building blocks for topological quantum computing, which is highly immune to the environmental noise. Existing MZM platforms include hybrid structures such as topological insulator, semiconducting nanowire or 1D atomic chains on top of a conventional superconductor, and single materials such as the iron-based superconductors (IBSs) and 4Hb-TaS2. Very recently, ordered and tunable MZM lattice has also been realized in IBS LiFeAs, providing a scalable and applicable platform for future topological quantum computation. In this review, we present an overview of the recent local probe studies on MZMs. Classified by the material platforms, we start with the MZMs in the iron-chalcogenide superconductors where FeTe0.55Se0.45and (Li0.84Fe0.16)OHFeSe will be discussed. We then review the Majorana research in the iron-pnictide superconductors as well as other platforms beyond the IBSs. We further review recent works on ordered and tunable MZM lattice, showing that strain is a feasible tool to tune the topological superconductivity. Finally, we give our summary and perspective on future Majorana research.