Multi-omic Analyses Shed Light on The Genetic Control of High-altitude Adaptation in Sheep.

Sheep were domesticated in the Fertile Crescent and then spread globally, where they have been encountering various environmental conditions. The Tibetan sheep has adapted to high altitudes on the Qinghai-Tibet Plateau over the past 3000 years. To explore genomic variants associated with high-altitude adaptation in Tibetan sheep, we analyzed Illumina short-reads of 994 whole genomes representing ∼ 60 sheep breeds/populations at varied altitudes, PacBio High fidelity (HiFi) reads of 13 breeds, and 96 transcriptomes from 12 sheep organs. Association testing between the inhabited altitudes and 34,298,967 variants was conducted to investigate the genetic architecture of altitude adaptation. Highly accurate HiFi reads were used to complement the current ovine reference assembly at the most significantly associated ß-globin locus and to validate the presence of two haplotypes A and B among 13 sheep breeds. The haplotype A carried two homologous gene clusters: (1) HBE1, HBE2, HBB-like, and HBBC, and (2) HBE1-like, HBE2-like, HBB-like, and HBB; while the haplotype B lacked the first cluster. The high-altitude sheep showed highly frequent or nearly fixed haplotype A, while the low-altitude sheep dominated by haplotype B. We further demonstrated that sheep with haplotype A had an increased hemoglobin-O2 affinity compared with those carrying haplotype B. Another highly associated genomic region contained the EGLN1 gene which showed varied expression between high-altitude and low-altitude sheep. Our results provide evidence that the rapid adaptive evolution of advantageous alleles play an important role in facilitating the environmental adaptation of Tibetan sheep.

Single-cell transcriptomic analysis reveals that the APP-CD74 axis promotes immunosuppression and progression of testicular tumors.

Testicular tumors represent the most common malignancy among young men. Nevertheless, the pathogenesis and molecular underpinning of testicular tumors remain largely elusive. We aimed to delineate the intricate intra-tumoral heterogeneity and the network of intercellular communication within the tumor microenvironment. A total of 40,760 single-cell transcriptomes were analyzed, encompassing samples from six individuals with seminomas, two patients with mixed germ cell tumors, one patient with a Leydig cell tumor, and three healthy donors. Five distinct malignant subclusters were identified in the constructed landscape. Among them, malignant 1 and 3 subclusters were associated with a more immunosuppressive state and displayed worse disease-free survival. Further analysis identified that APP-CD74 interactions were significantly strengthened between malignant 1 and 3 subclusters and 14 types of immune subpopulations. In addition, we established an aberrant spermatogenesis trajectory and delineated the global gene alterations of somatic cells in seminoma testes. Sertoli cells were identified as the somatic cell type that differed the most from healthy donors to seminoma testes. Cellular communication between spermatogonial stem cells and Sertoli cells is disturbed in seminoma testes. Our study delineates the intra-tumoral heterogeneity and the tumor immune microenvironment in testicular tumors, offering novel insights for targeted therapy. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Quantum-Confined Tunable Ferromagnetism on the Surface of a Van der Waals Antiferromagnet NaCrTe2.

The surface of three-dimensional materials provides an ideal and versatile platform to explore quantum-confined physics. Here, we systematically investigate the electronic structure of Na-intercalated CrTe2, a van der Waals antiferromagnet, using angle-resolved photoemission spectroscopy and ab initio calculations. The measured band structure deviates from the calculation of bulk NaCrTe2 but agrees with that of ferromagnetic monolayer CrTe2. Consistently, we observe unexpected exchange splitting of the band dispersions, persisting well above the Néel temperature of bulk NaCrTe2. We argue that NaCrTe2 features a quantum-confined 2D ferromagnetic state in the topmost surface layer due to strong ferromagnetic correlation in the CrTe2 layer. Moreover, the exchange splitting and the critical temperature can be controlled by surface doping of alkali-metal atoms, suggesting the feasibility of tuning the surface ferromagnetism. Our work not only presents a simple platform for exploring tunable 2D ferromagnetism but also provides important insights into the quantum-confined low-dimensional magnetic states.

The uncertainties and certainties of gene transcription in a human tumor cell.

Previously we have identified that the expression number and levels of oncogenes and antioncogenes are highly positively or negatively associated with major cellular progress in a cancer cell. However, we have not defined any cellular potentials of a human tumor cell at the level of the overall gene expression. Here, we counted the overall number of expression genes and overall counts of mRNA in depth and revealed that the expression levels of mRNA were directly associated with the expression number of genes in a human tumor cell. Gene expression networks revealed steady states of tricarboxylic acid (TCA) cycle and ATP production, differentiation potentials that might be disturbed and blocked by uncertain gene expressing networks, and potential capabilities to undergo epithelial-mesenchymal transition (EMT), neurogenesis, angiogenesis, inflammatory response, immune evasion, and metastasis in a human tumor cell. Our analysis identifies unpredictable gene expression characteristics in human tumor cells. The results might profoundly influence mechanisms how a human tumor cell generates and undergoes its progresses.

Corrigendum to "Enterococcus durans 98D alters gut microbial composition and function to improve DSS-induced colitis in mice" [Volume 10, Issue 7, 15 April 2024, e28486].

[This corrects the article DOI: 10.1016/j.heliyon.2024.e28486.].

ImmunoCellCycle-ID: A high-precision immunofluorescence-based method for cell cycle identification.

The cell cycle is a fundamental process essential for cell proliferation, differentiation, and development. It consists of four major phases: G1, S, G2, and M. These phases collectively drive the reproductive cycle and are meticulously regulated by various proteins that play critical roles in both the prevention and progression of cancer. Traditional methods for studying these functions, such as flow cytometry, require a substantial number of cells to ensure accuracy. In this study, we have developed a user-friendly, immunofluorescence-based method for identifying cell cycle stages, providing single-cell resolution and precise identification of G1, early S, late S, early G2, late G2, and each sub-stage of the M phase using fluorescence microscopy. This method provides high-precision cell cycle identification and can serve as an alternative to, or in combination with, traditional flow cytometry to dissect detailed substages of the cell cycle in a variety of cell lines.

Topiramate suppresses peri-infarct spreading depolarization and improves outcomes in a rat model of photothrombotic stroke.

Ischemic stroke can cause depolarized brain waves, termed peri-infarct depolarization (PID). Here, we evaluated whether topiramate, a neuroprotective drug used to treat epilepsy and alleviate migraine, has the potential to reduce PID. We employed a rat model of photothrombotic ischemia that can reliably and reproducibly induce PID and developed a combined electrocorticography-laser speckle contrast imaging (ECoG-LSCI) platform to monitor neuronal activity and cerebral blood flow (CBF) simultaneously. Topiramate administration after photothrombotic ischemia did not rescue CBF but significantly restored somatosensory evoked potentials in the forelimb area of the primary somatosensory cortex. Moreover, infarct volume was investigated by 2,3,5-triphenyltetrazolium chloride (TTC) staining, and neuronal survival was evaluated by Nissl staining. Mechanistically, the levels of inflammatory markers, such as ED1 (CD68), Iba-1, and GFAP, decreased significantly after topiramate administration, as did BDNF expression, while the expression of NeuN and Bcl-2/Bax increased, which is indicative of reduced inflammation and improved neuroprotection.

Precise hourly personalized embryo transfer significantly improves clinical outcomes in patients with repeated implantation failure.

Purpose: This study investigated whether RNA-Seq-based endometrial receptivity test (rsERT)-which provides precision for the optimal hour of the window of implantation (WOI)-can improve clinical outcomes of frozen embryo transfer (FET) cycles in patients with a history of repeated implantation failure (RIF). Methods: Patients with a history of RIF who received at least one autologous high-quality blastocyst during the subsequent FET cycle were retrospectively enrolled and divided into two groups: rsERT and FET, comprising patients who underwent rsERT-guided pET (n=115) and standard FET without rsERT (n=272), respectively. Results: In the rsERT group, 39.1% (45/115) of patients were receptive. rsERT patients showed a higher probability of achieving both positive human chorionic gonadotropin (63.5% vs. 51.5%, P=0.03) and clinical pregnancy (54.8% vs. 38.6%, P=0.003) rates. In subgroup analysis, rsERT patients with non-receptive results had higher clinical pregnancy rates than patients undergoing FET (58.6% vs. 38.6%, P=0.003). rsERT patients with receptive results guided by rsERT with a precise WOI time had higher, although non-significant, clinical pregnancy rates (48.9% vs. 38.6%, P=0.192) than patients who underwent standard-time FET. Conclusion: Hourly precise rsERT can significantly improve the probability of achieving clinical pregnancy in patients with RIF, especially in those with non-receptive rsERT results.

Evidence of strong and mode-selective electron-phonon coupling in the topological superconductor candidate 2M-WS2.

The interaction between lattice vibrations and electrons plays a key role in various aspects of condensed matter physics - including electron hydrodynamics, strange metal behavior, and high-temperature superconductivity. In this study, we present systematic investigations using Raman scattering and angle-resolved photoemission spectroscopy (ARPES) to examine the phononic and electronic subsystems of the topological superconductor candidate 2M-WS2. Raman scattering exhibits an anomalous nonmonotonic temperature dependence of phonon linewidths, indicative of strong phonon-electron scattering over phonon-phonon scattering. The ARPES results demonstrate pronounced dispersion anomalies (kinks) at multiple binding energies within both bulk and topological surface states, indicating a robust and mode-selective coupling between the electronic states and various phonon modes. These experimental findings align with previous calculations of the Eliashberg function, providing a deeper understanding of the highest superconducting transition temperature observed in 2M-WS2 (8.8 K) among all transition metal dichalcogenides as induced by electron-phonon coupling. Furthermore, our results may offer valuable insights into other properties of 2M-WS2 and guide the search for high-temperature topological superconductors.

DHX9 SUMOylation is required for the suppression of R-loop-associated genome instability.

RNA helicase DHX9 is essential for genome stability by resolving aberrant R-loops. However, its regulatory mechanisms remain unclear. Here we show that SUMOylation at lysine 120 (K120) is crucial for DHX9 function. Preventing SUMOylation at K120 leads to R-loop dysregulation, increased DNA damage, and cell death. Cells expressing DHX9 K120R mutant which cannot be SUMOylated are more sensitive to genotoxic agents and this sensitivity is mitigated by RNase H overexpression. Unlike the mutant, wild-type DHX9 interacts with R-loop-associated proteins such as PARP1 and DDX21 via SUMO-interacting motifs. Fusion of SUMO2 to the DHX9 K120R mutant enhances its association with these proteins, reduces R-loop accumulation, and alleviates survival defects of DHX9 K120R. Our findings highlight the critical role of DHX9 SUMOylation in maintaining genome stability by regulating protein interactions necessary for R-loop balance.

Age-specific composition of milk microbiota in Tibetan sheep and goats.

This study investigates the dynamic changes in milk nutritional composition and microbial communities in Tibetan sheep and goats during the first 56 days of lactation. Milk samples were systematically collected at five time points (D0, D7, D14, D28, D56) post-delivery. In Tibetan sheep, milk fat, protein, and casein contents were highest on D0, gradually decreased, and stabilized after D14, while lactose and galactose levels showed the opposite trend. Goat milk exhibited similar initial peaks, with significant changes particularly between D0, D7, D14, and D56. 16S rRNA gene sequencing revealed increasing microbial diversity in both species over the lactation period. Principal coordinates analysis identified distinct microbial clusters corresponding to early (D0-D7), transitional (D14-D28), and mature (D56) stages. Core phyla, including Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, dominated the milk microbiota, with significant temporal shifts. Core microbes like Lactobacillus, Leuconostoc, and Streptococcus were common in both species, with species-specific taxa observed (e.g., Pediococcus in sheep, Shewanella in goats). Furthermore, we observed a highly shared core microbiota in sheep and goat milk, including Lactobacillus, Leuconostoc, and Streptococcus. Spearman correlation analysis highlighted significant relationships between specific microbial genera and milk nutrients. For instance, Lactobacillus positively correlated with total solids, non-fat milk solids, protein, and casein, while Mannheimia negatively correlated with protein content. This study underscores the complex interplay between milk composition and microbial dynamics in Tibetan sheep and goats, informing strategies for livestock management and nutritional enhancement. KEY POINTS: • The milk can be classified into three types based on the microbiota composition • The changes of milk microbiota are closely related to the variations in nutrition • Filter out microbiota with species specificity and age specificity in the milk.

Rare codon recoding for efficient noncanonical amino acid incorporation in mammalian cells.

The ability to genetically encode noncanonical amino acids (ncAAs) has empowered proteins with improved or previously unknown properties. However, existing strategies in mammalian cells rely on the introduction of a blank codon to incorporate ncAAs, which is inefficient and limits their widespread applications. In this study, we developed a rare codon recoding strategy that takes advantage of the relative rarity of the TCG codon to achieve highly selective and efficient ncAA incorporation through systematic engineering and big data-model predictions. We highlight the broad utility of this strategy for the incorporation of dozens of ncAAs into various functional proteins at the wild-type protein expression levels, as well as the synthesis of proteins with up to six-site ncAAs or four distinct ncAAs in mammalian cells for downstream applications.

Compendium of 5810 genomes of sheep and goat gut microbiomes provides new insights into the glycan and mucin utilization.

BACKGROUND: Ruminant gut microbiota are critical in ecological adaptation, evolution, and nutrition utilization because it regulates energy metabolism, promotes nutrient absorption, and improves immune function. To study the functional roles of key gut microbiota in sheep and goats, it is essential to construct reference microbial gene catalogs and high-quality microbial genomes database. RESULTS: A total of 320 fecal samples were collected from 21 different sheep and goat breeds, originating from 32 distinct farms. Metagenomic deep sequencing and binning assembly were utilized to construct a comprehensive microbial genome information database for the gut microbiota. We successfully generated the largest reference gene catalogs for gut microbiota in sheep and goats, containing over 162 million and 82 million nonredundant predicted genes, respectively, with 49 million shared nonredundant predicted genes and 1138 shared species. We found that the rearing environment has a greater impact on microbial composition and function than the host's species effect. Through subsequent assembly, we obtained 5810 medium- and high-quality metagenome-assembled genomes (MAGs), out of which 2661 were yet unidentified species. Among these MAGs, we identified 91 bacterial taxa that specifically colonize the sheep gut, which encode polysaccharide utilization loci for glycan and mucin degradation. CONCLUSIONS: By shedding light on the co-symbiotic microbial communities in the gut of small ruminants, our study significantly enhances the understanding of their nutrient degradation and disease susceptibility. Our findings emphasize the vast potential of untapped resources in functional bacterial species within ruminants, further expanding our knowledge of how the ruminant gut microbiota recognizes and processes glycan and mucins. Video Abstract.

Observation of Type-II Topological Nodal-Line Fermions in ZrSiSe.

Recently, there has been significant interest in topological nodal-line semimetals due to their linear energy dispersion with one-dimensional nodal lines or loops. These materials exhibit fascinating physical properties, such as drumhead surface states and 3D anisotropic nodal-line structures. Similar to Weyl semimetals, type-II nodal-line semimetals have two crossing bands that are both electron-like or hole-like along a certain direction. However, the direct observation of type-II nodal-line Fermions has been challenging due to the lack of suitable material platforms and the low density of states. Here we present experimental evidence for the coexistence of both type-I and type-II nodal-line Fermions in ZrSiSe, which was obtained through magneto-optical and angle-resolved photoemission spectroscopy (ARPES) measurements. Our density functional theory calculations predict that the type-II nodal-line structure can be developed in the Z-R line of the first Brillouin zone based on the lattice constants of the grown single crystal. Indeed, ARPES measurements reveal the type-II nodal-line band structure. The extracted type-II Landau level transitions from magneto-optical measurements exhibit good agreement with the calculated type-II energy dispersion model based on the band structure. Our experimental results demonstrate that ZrSiSe possesses two types of nodal-line Fermions, distinguishing it from other ZrSiX (X = S, Te) materials and positioning it as an ideal platform for investigating type-II nodal-line semimetals.

Short stature with brachydactyly caused by a novel mutation in the IHH gene and response to 4-year growth hormone therapy: a case report.

Background: The etiology of short stature is heterogeneous. The disturbance of endochondral ossification and cartilage matrix synthesis caused by genetic mutations often causes short height combined with skeletal deformities in children. Some patients with minor skeletal abnormalities, such as short fingers and mild limb shortening, may be overlooked by clinicians and misdiagnosed as idiopathic short stature (ISS) or growth hormone deficiency (GHD). Case Description: We conducted a detailed investigation of laboratory and imaging examinations on a family with short stature and non-classical brachydactyly type A1 (BDA1) and summarized the clinical features. They received whole exome sequencing (WES) to reveal the possible genetic variation. A heterozygous mutation in the Indian hedgehog gene (IHH) (c.387_388insC, p.Thr130Hisfs*18) was found in the two siblings and their mother. The siblings both started recombinant human growth hormone (rhGH) therapy (rhGH: 33 µg/kg/day) and followed up for 4 years. After treatment, the siblings' height improved significantly, and they acquired a significant increase in the height standard deviation score (SDS) (the boy: +2.54, the girl: +1.86) during the 4-year therapy. No noticeable adverse effect was observed during rhGH treatment. Conclusions: We found a novel heterozygous pathogenic mutation in the IHH gene in a family and detailed the phenotype with short stature and non-classical BDA1. The therapy of rhGH showed promising effects. To avoid misdiagnosis, clinicians should not overlook minor skeletal anomalies in patients with short stature, especially those with a family history.

nCas9 Engineering for Improved Target Interaction Presents an Effective Strategy to Enhance Base Editing.

Base editors (BEs) are a recent generation of genome editing tools that couple a cytidine or adenosine deaminase activity to a catalytically impaired Cas9 moiety (nCas9) to enable specific base conversions at the targeted genomic loci. Given their strong application potential, BEs are under active developments toward greater levels of efficiency and safety. Here, a previously overlooked nCas9-centric strategy is explored for enhancement of BE. Based on a cytosine BE (CBE), 20 point mutations associated with nCas9-target interaction are tested. Subsequently, from the initial positive X-to-arginine hits, combinatorial modifications are applied to establish further enhanced CBE variants (1.1-1.3). Parallel nCas9 modifications in other versions of CBEs including A3A-Y130F-BE4max, YEE-BE4max, CGBE, and split-AncBE4max, as well as in the context of two adenine BEs (ABE), likewise enhance their respective activities. The same strategy also substantially improves the efficiencies of high-fidelity nCas9/BEs. Further evidence confirms that the stabilization of nCas9-substrate interactions underlies the enhanced BE activities. In support of their translational potential, the engineered CBE and ABE variants respectively enable 82% and 25% higher rates of editing than the controls in primary human T-cells. This study thus demonstrates a highly adaptable strategy for enhancing BE, and for optimizing other forms of Cas9-derived tools.

A Disturbance Compensation Control Strategy for Rotational Speed Standard Device Based on AMB System.

The rotational speed standard device that can carry loads is the key device for calibrating passive rotational speed sensors. The rotor of the passive rotational speed sensor is connected to the rotor of the standard speed device through a coupling, and the standard reference speed is provided by the standard device. Due to the rotor eccentricity, the unbalanced force of the rotor occurs, and it can not only affect the rotational speed accuracy but can also damage the mechanical bearings of the standard speed device. To solve this issue, a method for suppressing the unbalanced force of the speed standard device based on an active magnetic bearing (AMB) force compensation system is proposed. First, the overall structure of the system is briefly introduced. Then, the force feedback control system model with the AMB as the force actuator is established, and a PI controller is designed to achieve the disturbed force control. Finally, a semi-physical simulation experimental platform is built to verify the effectiveness of the proposed method. The experimental results show that the AMB force compensation system can reduce 84.4%, 81.6%, and 79.8% of the unbalanced vibration force at the frequency of 30 Hz, 90 Hz, and 150 Hz, respectively.

Temperature and pressure-induced excitation-dependent emissions in zero-dimensional hybrid metal halides with mixed halogens.

Zero-dimensional (0D) hybrid metal halides (HMHs) have emerged as a promising platform for exploring excitation-dependent multicolor luminescent materials owing to their diverse crystal structures and chemical compositions. Nevertheless, understanding the mechanism behind excitation-dependent emissions (EDEs) in 0D HMHs and achieving precise modulation remains challenging. In this work, the delicate regulations on the EDE of 0D (DMEDABr)4SnBr3I3 (DMEDA: N, N'-dimethylethylenediamine) with mixed halogens are achieved under low temperature and high pressure, respectively. The inhomogeneous halogen occupation at the atomic scale leads to the formation of Br-rich and I-rich SnX6 (X = Br, I) octahedra, which act as distinct luminescent centers upon photoexcitation. At low temperatures, the narrowed photoluminescence spectra could distinguish the individual emissions from different luminescent centers, resulting in a pronounced EDE of (DMEDABr)4SnBr3I3. In addition, the contraction and distortion of the luminescent SnX6 (X = Br, I) centers at high pressure further result in different degrees of emission shifts, giving rise to the gradual emergence and disappearance of EDE. This work elucidates the underlying mechanism of EDE in 0D HMHs and highlights the crucial role of halogens in determining the optical properties of metal halides.