Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history.

A cattle pangenome representation was created based on the genome sequences of 898 cattle representing 57 breeds. The pangenome identified 83 Mb of sequence not found in the cattle reference genome, representing 3.1% novel sequence compared with the 2.71-Gb reference. A catalog of structural variants developed from this cattle population identified 3.3 million deletions, 0.12 million inversions, and 0.18 million duplications. Estimates of breed ancestry and hybridization between cattle breeds using insertion/deletions as markers were similar to those produced by single nucleotide polymorphism-based analysis. Hundreds of deletions were observed to have stratification based on subspecies and breed. For example, an insertion of a Bov-tA1 repeat element was identified in the first intron of the APPL2 gene and correlated with cattle breed geographic distribution. This insertion falls within a segment overlapping predicted enhancer and promoter regions of the gene, and could affect important traits such as immune response, olfactory functions, cell proliferation, and glucose metabolism in muscle. The results indicate that pangenomes are a valuable resource for studying diversity and evolutionary history, and help to delineate how domestication, trait-based breeding, and adaptive introgression have shaped the cattle genome.

Experimental evidence of ß-relaxation and its structural origin in ZIF-62 glass.

Intrinsic relaxation processes determine the crucial properties of glass, yet their underlying mechanisms are far from well understood. The brand-new glass-forming metal-organic frameworks (MOFs) provide desirable opportunities for looking inside glass relaxation, especially the secondary ß-relaxation phenomenon and mechanism. For a representative zeolitic imidazolate framework-62 (ZIF-62) glass, reliable and fine powder mechanical spectroscopy was performed based on home-made mountings combined with a commercial dynamical mechanical analyzer. For the first time, ß-relaxation was observed in a MOF glass besides the primary α-relaxation. The pronounced ß-relaxation was well demonstrated by a number of characteristics including an excess wing and the full width at half maximum (W) of the α-relaxation peaks, which deviated from the time-temperature superposition. The stretched exponent ß of ZIF-62 glass is 0.71 in the supercooled region. The W of ZIF-62 glass is the maximum among all known glassy materials. The structural origin of α- and ß-relaxation can be attributed to an increase of density, as observed using nuclear magnetic resonance (NMR). A general linear and broad correlation of fragility and stretched exponent ß with W of the α-relaxation peaks was established. When compared with traditional glass-formers, the resulting principles indicate a shared origin for the stretched exponent ß, W, and ß-relaxation in the case of ZIF-62 glass. The presented findings offer an effective new method to explore the glass/liquid transition of MOF glasses, which helps to obtain a deeper insight into the hierarchical relaxation dynamics of the glass transition.

Comparative analyses of copy number variations between swamp buffaloes and river buffaloes.

As an important source of genomic variation, copy number variation (CNV) contributes to environmental adaptation in worldwide buffaloes. Despite this importance, CNV divergence between swamp buffaloes and river buffaloes has not been studied previously. Here, we report 21 152 CNV regions (CNVRs) in 141 buffaloes of 20 breeds detected through multiple CNV calling strategies. Only 248 CNVRs were shared between river buffalo and swamp buffalo, reflecting great variation of CNVRs between the two subspecies. Population structure analysis based on CNVs successfully separated the two buffalo subspecies. We further assessed CNV divergence by calculating FST for genome-wide CNVs. Totally, we identified 110 significantly divergent CNV segments and 44 putatively selected genes between river buffaloes and swamp buffaloes. In particular, LALBA, a key gene controlling milk production in cattle, presented a highly differentiated CNV in the promoter region, which makes it a strong functional candidate gene for differences between swamp buffaloes and river buffaloes in traits related to milk production. Our study provides useful information of CNVs in buffaloes, which may help explain the genetic differences between the two subspecies.

Melatonin improves the quality of rotenone-exposed mouse oocytes through association with histone modifications.

Rotenone, an insecticide that inhibits mitochondrial complex I and generates oxidative stress, is responsible for neurological disorders and affects the female reproductive system. However, the underlying mechanism is not fully understood. Melatonin, a potential free-radical scavenger, has been shown to protect the reproductive system from oxidative damage. In this study, we investigated the impact of rotenone on mouse oocyte quality and evaluated the protective effect of melatonin on oocytes exposed to rotenone. Our results showed that rotenone impaired mouse oocyte maturation and early embryo cleavage. However, melatonin prevented these negative effects by ameliorating rotenone-induced mitochondrial dysfunction and dynamic imbalance, intracellular Ca2+ homeostasis damage, ER stress, early apoptosis, meiotic spindle formation disruption, and aneuploidy in oocytes. Additionally, RNA sequencing analysis showed that rotenone exposure changed the expression of multiple genes involved in histone methylation and acetylation modifications that result in mouse meiotic defects. However, melatonin partially rescued these defects. These findings suggest that melatonin has protective effects against rotenone-induced mouse oocyte defects.

Characterization of extrachromosomal circular DNA in cattle using 676 whole genome sequencing datasets.

Extrachromosomal circular DNA (eccDNA) is an important fraction of the genome. Recent studies proved that eccDNA plays important roles in genetic variation, aging and environmental adaptation, which have drawn wide attention. However, the characteristics of eccDNA in cattle remain unclear. Here, we studied eccDNAs from 676 cattle of 58 breeds using whole genome sequencing datasets. In total, 47 355 high-confidence eccDNAs were identified and covered 4.6% of the cattle autosomes in length. Similarly to other species, the cattle eccDNA preferentially located in the genic and repeat sequences. Cattle eccDNAs contained complete sequences of 661 genes, which were significantly (p < 0.05) enriched in immunity-related functions. The eccDNA was further proved to have inverted repeats on the boundaries, which contained a high proportion of A/T and ranged from 4 to 17 bp. Interestingly, we successfully separated animals according to their geographical distributions and their tissues where DNA was isolated. This implied possible roles for eccDNA in cattle selection and tissue development. Our study supplies basic knowledges on eccDNAs in cattle, which will promote understanding of extrachromosomal DNA.

Modeling for COVID-19 with the contacting distance.

COVID-19 is a public health emergency for human beings and brings some very harmful consequences in social and economic fields. In order to model COVID-19 and develop the effective control measures, this paper proposes an SEIR-type epidemic model with the contacting distance between the healthy individuals and the asymptomatic or symptomatic infected individuals, and the immigration rate of the healthy individuals since the contacting distance and the immigration rate are two critical factors which determine the transmission of COVID-19. Firstly, the threshold values of the contacting distance and the immigration rate are obtained to analyze the presented model. Secondly, based on the data from January 10, 2020, to March 18, 2020, for Wuhan city, all parameters are estimated. Finally, based on the estimated parameters, the sensitivity analysis and the numerical study are conducted. The results show that the contacting distance and the immigration rate play an important role in controlling COVID-19. Meanwhile, the extinct lag decreases as the contacting distance increases and/or the immigration rate decreases. Our study could give some reasonable suggestions for the health officials and the public and provide a theoretical issue for globally controlling the COVID-19 pandemic.

Tunable, Sheathless Focusing of Diamagnetic Particles in Ferrofluid Microflows with a Single Set of Overhead Permanent Magnets.

There has been increasing interest in the use of magnetic fluids to manipulate diamagnetic particles in microfluidic devices. Current methods for diamagnetic-particle focusing in magnetic fluids require either a pair of repulsive magnets or a diamagnetic sheath flow. We demonstrate herein a tunable, sheathless focusing of diamagnetic particles in a microchannel ferrofluid flow with a single set of overhead permanent magnets. Particles are focused into a single stream near the bottom wall of a straight rectangular microchannel, where a magnetic-field minimum is formed as a result of the magnetization of the ferrofluid. This focusing can be readily switched off and on by removing and replacing the permanent magnets. More importantly, the particle-focusing position can be tuned by shifting the magnets with respect to the microchannel. We perform a systematic experimental study of the parametric effects of the fluid-particle-channel system on diamagnetic-particle focusing in terms of a defined particle-focusing effectiveness.

Mechanical Behaviors of Polymer-Based Composite Reinforcements within High-Field Pulsed Magnets.

The development of pulsed magnets capable of generating magnetic fields exceeding 100 Tesla has been recognized as a crucial pursuit for advancing the scientific research on high magnetic fields. However, the operation of magnets at ultra-high magnetic fields often leads to accidental failures at their ends, necessitating a comprehensive exploration of the underlying mechanisms. To this end, this study investigates, for the first time, the mechanical behaviors of Zylon fiber-reinforced polymers (ZFRPs) within pulsed magnets from a composite perspective. The study begins with mechanical testing of ZFRPs, followed by the development of its constitutive model, which incorporates the plasticity and progressive damage. Subsequently, in-depth analyses are performed on a 95-T double-coil prototype that experienced a failure. The outcomes reveal a notable reduction of approximately 45% in both the radial and axial stiffness of ZFRPs, and the primary reason for the failure is traced to the damage incurred by the end ZFRPs of the inner magnet. The projected failure field closely aligns with the experiment. Additionally, two other magnet systems, achieving 90.6 T and 94.88 T, are analyzed. Finally, the discussion delves into the impact of transverse mechanical strength of the reinforcement and axial Lorentz forces on the structural performance of magnets.

The Changes in Fecal Bacterial Communities in Goats Offered Rumen-Protected Fat.

Leizhou goats are famous for their delicious meat but have inferior growth performance. There is little information on rumen-protected fat (RPF) from the Leizhou goat. Hence, we observed the effects of RPF on growth, fecal short-chain fatty acids, and bacteria community with respect to Leizhou goats. Twelve goats (13.34 ± 0.024 kg) were selected and assigned randomly to one of two treatments: (1) a control diet (CON) and (2) 2.4% RPF with a control diet (RPF). The final body weight and average daily gain (ADG) were greater (p < 0.05), and the dry matter intake (DMI): ADG was lower (p < 0.05) in the RPF group than in the CON group. There were no differences in DMI between the CON and RPF groups. The concentrations of total short-chain fatty acids, acetate, propionate, and butyrate were lower (p < 0.05) in the RPF group than in the CON group. The relative abundances of Ruminococcus, Rikenellaceae_RC9_gut_group, Treponema, norank_f__norank_o__RF39, Eubacterium_siraeum_group, and Ruminococcus_torques_group were lower (p < 0.05) in the RPF group than in the CON group. The relative abundances of Bacteroides, norank_f__norank_o__Clostridia_UCG-014, norank_f__Eubacterium_coprostanoligenes_group, Eubacterium_ruminantium_group, norank_f__Oscillospirale-UCG-010, Oscillospiraceae_UCG-002, and Family_XIII_AD3011_group were greater (p < 0.05) in the RPF group than in the CON group. It was concluded that RPF could improve the goats' growth performance by regulating their fecal bacteria communities.

Enhancing Oocyte Quality in Aging Mice: Insights from Mesenchymal Stem Cell Therapy and FOXO3a Signaling Pathway Activation.

Ovarian aging reduced the quality of oocytes, resulting in age-related female infertility. It is reported that mesenchymal stem cells (MSCs) therapy can improve age-related ovarian function decline and the success rate of in vitro maturation (IVM) in assisted reproductive therapy. In order to investigate the effectiveness and mechanisms of MSCs to enhance oocyte quality of cumulus oocyte complexes (COCs) in advanced age, this study focus on the respective functional improvement of oocytes and granulosa cells (GCs) from aging mice and further to explore and verify the possible mechanisms. Here, we studied a popular but significant protein of follicular development, Forkhead box O-3a (FOXO3a), which is a transcription factor that mediates a variety of cellular processes, but the functions of which in regulating oocyte quality in MSCs therapy still remain inconclusive. In this study, the RNA-seq data of metaphase II (MII) oocytes and GCs isolated from COCs confirmed that, GCs of immature follicles show the most potential to be the targeted cells of bone marrow mesenchymal stem cells (BMSCs) by FOXO3a signaling pathway. Furthermore, we demonstrated the effectiveness of BMSCs co-culture with aging COCs to enhance oocyte quality and found its mechanism to function via ameliorating the biological function of GCs by alleviating FOXO3a levels. These results provide significant fundamental research on MSCs therapy on ovarian aging, as well as offering guidance for raising the success rate of assisted reproductive technology such IVM in clinical and non-clinical settings.

Magnetically driven capsules with multimodal response and multifunctionality for biomedical applications.

Untethered capsules hold clinical potential for the diagnosis and treatment of gastrointestinal diseases. Although considerable progress has been achieved recently in this field, the constraints imposed by the narrow spatial structure of the capsule and complex gastrointestinal tract environment cause many open-ended problems, such as poor active motion and limited medical functions. In this work, we describe the development of small-scale magnetically driven capsules with a distinct magnetic soft valve made of dual-layer ferromagnetic soft composite films. A core technological advancement achieved is the flexible opening and closing of the magnetic soft valve by using the competitive interactions between magnetic gradient force and magnetic torque, laying the foundation for the functional integration of both drug release and sampling. Meanwhile, we propose a magnetic actuation strategy based on multi-frequency response control and demonstrate that it can achieve effective decoupled regulation of the capsule's global motion and local responses. Finally, through a comprehensive approach encompassing ideal models, animal ex vivo models, and in vivo assessment, we demonstrate the versatility of the developed magnetic capsules and their multiple potential applications in the biomedical field, such as targeted drug delivery and sampling, selective dual-drug release, and light/thermal-assisted therapy.

Stability and Hopf bifurcation of an SIR epidemic model with density-dependent transmission and Allee effect.

In this paper, an SIR model with a strong Allee effect and density-dependent transmission is proposed, and its characteristic dynamics are investigated. The elementary mathematical characteristic of the model is studied, including positivity, boundedness and the existence of equilibrium. The local asymptotic stability of the equilibrium points is analyzed using linear stability analysis. Our results indicate that the asymptotic dynamics of the model are not only determined using the basic reproduction number ${R_0}$. If ${R_0} < 1$, there are three disease-free equilibrium points, and a disease-free equilibrium is always stable. At the same time, the conditions for other disease-free equilibrium points to be bistable were determined. If ${R_0} > 1$ and in certain conditions, either an endemic equilibrium emerges and is locally asymptotically stable, or the endemic equilibrium becomes unstable. What must be emphasized is that there is a locally asymptotically stable limit cycle when the latter happens. The Hopf bifurcation of the model is also discussed using topological normal forms. The stable limit cycle can be interpreted in a biological significance as a recurrence of the disease. Numerical simulations are used to verify the theoretical analysis. Taking into account both density-dependent transmission of infectious diseases and the Allee effect, the dynamic behavior becomes more interesting than when considering only one of them in the model. The Allee effect makes the SIR epidemic model bistable, which also makes the disappearance of diseases possible, since the disease-free equilibrium in the model is locally asymptotically stable. At the same time, persistent oscillations due to the synergistic effect of density-dependent transmission and the Allee effect may explain the recurrence and disappearance of disease.

Impact of vaccine measures on the transmission dynamics of COVID-19.

In many nations, efforts to prevent and control COVID-19 have been significantly impeded by the SARS-CoV-2 virus ongoing mutation. The Omicron strain, a more recent and prevalent strain, has had more significant detrimental effects in countries worldwide. To investigate the impact of the Omicron BA.2 strain on vaccine efficacy, we proposed a model with vaccination and immunological decline in this research. Then, we fitted our model based on the number of daily new instances reported by the government in Jilin and Shanghai, China. We estimated the effective reproduction number Re = 4.71 for the Jilin and Re = 3.32 for Shanghai. Additionally, we do sensitivity analysis to identify the critical factors affecting the effective reproduction number Re. It was found that vaccination rate, effectiveness rate, and declining rate had a significant effect on Re. Further, we investigate the relevant parameter thresholds that make Re lower than unity. Finally, rich numerical experiments were then carried out. We observed that even when vaccine efficiency was not high, increasing vaccination rates had a significant effect on early disease transmission, that limiting social distance was the most economical and rational measure to control the spread of disease, and that for a short period, reducing immune decline was not significant in curbing disease transmission.

Effects of Copy Number Variations in the Plectin (PLEC) Gene on the Growth Traits and Meat Quality of Leizhou Black Goats.

The plectin (PLEC) gene is crucial in regulating muscle development and maintaining the cytoskeleton. An abnormal expression of PLEC can lead to muscle atrophy and muscular dystrophy. In a previous study, we found that Leizhou black goats exhibit abundant structural variations in the PLEC gene. However, the genetic effects of these variations on growth traits and meat quality in goats are not fully understood. In this study, three PLEC copy number variations (CNVs) were identified in a population of 417 Leizhou black goats, using quantitative polymerase chain reaction (qPCR) technology. Population distribution analysis revealed a high abundance of various types of these three CNVs. PLEC mRNA was found to be highly expressed in muscle tissue and remained consistently high from 1 month to 24 months after birth. Specifically, the gain type of CNV-1 (chr14: 81056401-81064800) showed a significant association with PLEC mRNA expression in muscle tissue (p < 0.01). The sequence of CNV-1 in PLEC shares similarities with three domain superfamilies associated with muscle development and skin disease. Furthermore, there were significant differences in chest circumference, body weight, carcass weight, the cross-sectional area of the longissimus dorsi lumbar muscle, and shear stress between different types of CNV-1 (p < 0.05). Notably, goats with the CNV-1 gain type demonstrated better phenotypic values compared to those with loss and normal types. These findings suggest that PLEC CNV-1 could play a crucial role in the growth and muscle development of Leizhou black goats, making it a potential marker for assisted selection in goat breeding.

Estimation and sensitivity analysis of a COVID-19 model considering the use of face mask and vaccination.

To model the COVID-19 infection and develop effective control measures, this paper proposes an SEIR-type epidemic model considering the impact of face-mask wearing and vaccination. Firstly, the effective reproduction number and the threshold conditions are obtained. Secondly, based on the data of South Korea from January 20, 2022 to March 21, 2022, the model parameters are estimated. Finally, a sensitivity analysis and the numerical study are conducted. The results show that the face-mask wearing is associated with [Formula: see text] and [Formula: see text] reductions in the numbers of cumulative cases and newly confirmed cases, respectively, after a period of 60 days, when the face mask wearing rate increases by [Formula: see text]. Furthermore, the vaccination rate is associated with [Formula: see text] and [Formula: see text] reductions in the numbers of cumulative cases and the newly confirmed cases, respectively, after the same period of 60 days when the vaccination rate is increased by [Formula: see text]. A combined measure involving face-mask wearing and vaccination may be more effective and reasonable in preventing and controlling this infection. It is also suggested that disease control departments should strongly recommended the wearing of face masks s as well as vaccination to prevent the unvaccinated people from becoming infected.

The current-voltage measurements under flat-top pulsed magnetic fields for non-ohmic transport study.

Investigation of the non-ohmic transport behaviors under high magnetic fields can provide a new way to explore novel field-induced phenomena. We present the current-voltage measurements under high magnetic fields based on the flat-top pulsed magnetic field system. Two different measurement strategies were compared, given that the excitation current swept continuously or increased by a series of pulses. For the short duration of the flat-top pulsed field, the continuous current method was adopted and well optimized to reduce the Joule heating and achieve the quasi-static measurements. Finally, the non-ohmic behaviors of a quasi-one-dimensional charge density wave Li0.9Mo6O17 were successfully studied under the magnetic field up to 30 T at 4.2 K, which was the first current-voltage measurements carried out in pulsed magnetic fields.

A low-jitter timing generator based on completely on-chip self-measurement and calibration in a field programmable gate array.

This paper presents a high-stability and low-jitter Arbitrary Timing Generator (ATG) design based on the Xilinx Field Programmable Gate Array (FPGA) and its special integrated delay line. In recent years, FPGA-based or application specific integrated circuit-based delay lines have been used to achieve picosecond-level timing resolution. Devices with pure digital delay methods can only acquire triggers at the clock rising edges when triggered externally. Therefore, there is a large time irregularity caused by the uncertainty of the entry time of the trigger, which is difficult to compensate and leads to a large time jitter of outputs. We describe the design of an ATG that includes jitter self-measurement and calibration methods, which is available for both internal and external trigger modes. This structure is completely based on the FPGA's own resources and has the advantages of being simple and flexible. Experimental results show a sub-nanosecond timing resolution of 78 ± 20 ps with a minimum of 120 ps and a time jitter of 160 ± 20 ps in the external trigger mode after compensation.

[Isolation, identification and prokaryotic expression of a bacteriocin-like substance from Bacillus licheniformis].

The ban on addition of antibiotics in animal feed in China has made the search for new antibiotics substitutes, e.g. bacteriocin, a hot topic in research. The present study successfully isolated an antibacterial substance producing strain of Bacillus sp. from alpaca feces by agar diffusion method, using Escherichia coli, Salmonella enterica, Staphylococcus aureus, Staphylococcus epidermidis, Micrococcus luteus and Listeria monocytogenes as indicator bacteria. The isolated strain was named as B. licheniformis SXAU06 based on colony morphology, Gram staining and 16S rRNA gene sequence. The antibacterial substance was isolated and purified through a series of procedures including (NH4)2SO4 precipitation, chloroform extraction, molecular interception and SDS-PAGE analysis. Bioinformatics analysis of the LC-MS/MS data indicated that the antibacterial substance was a bacteriocin-like substance (BLIS) with an approximate molecular weight of 14 kDa, and it was designated as BLIS_SXAU06. BLIS_SXAU06 exhibited high resistance to treatment of proteinase K, high temperature, high acidity and alkalinity. BLIS_SXAU06 was heterologously expressed in E. coli and the recombinant BLIS_SXAU06 exhibited effective antibacterial activity against S. aureus, S. epidermidis, M. luteus, and L. monocytogenes, showing potential to be investigated further.

Fully redundant auxiliary system for gyrotron-based terahertz sources in long-term operation.

The Wuhan National High Magnetic Field Center is incorporating the flat-top pulsed magnetic field (FTPMF) into pulse gyrotrons. It will be the first chance to make a pulse-magnet gyrotron available for generating a long-pulse radiation of 100 ms or above without affecting its high operating frequency and high radiation power. However, unlike continuous wave gyrotrons, pulse gyrotrons in long-term operation have their own challenges, namely, misalignment caused by concussions, much stronger low-frequency electromagnetic interference from the pulse magnet, and inevitable explosion. This article will focus on the difficulties faced by pulse gyrotrons in years of operation, discuss the protection and restoration from failures, and, consequently, propose a fully redundant, explosion-proof, and quickly recoverable auxiliary system for long-term operation of pulse gyrotrons. This system integrates the control unit of traditional pulsed magnets and superconducting magnets so that it can be compatible with any form of gyrotron facilities. Therefore, once the FTPMF or the superconducting magnet is available, the long-pulse radiation will be obtained. Several experimental results, including the most recent explosion, show the reliability of the proposed system.

Self-Powered Acceleration Sensor Based on Multilayer Suspension Structure and TPU-RTV Film for Vibration Monitoring.

In this paper, we designed a triboelectric acceleration sensor with excellent multiple parameters. To more easily detect weak vibrations, the sensor was founded on a multilayer suspension structure. To effectively improve the electrical properties of the sensor, a surface roughening and internal doping friction film, which was refined with a room temperature vulcanized silicone rubber (RTV) and some thermoplastic polyurethanes (TPU) powder in a certain proportion, was integrated into the structure. It was found that the optimization of the RTV film increases the open circuit voltage and short circuit current of the triboelectric nanogenerator (TENG) by 223% and 227%, respectively. When the external vibration acceleration is less than 4 m/s2, the sensitivity and linearity are 1.996 V/(m/s2) and 0.999, respectively. Additionally, when it is in the range between 4 m/s2 and 15 m/s2, those are 23.082 V/(m/s2) and 0.975, respectively. Furthermore, the sensor was placed in a simulated truck vibration environment, and its self-powered monitoring ability validated by experiments in real time. The results show that the designed sensor has strong practical value in the field of monitoring mechanical vibration acceleration.