Epidemiological investigation of coccidiosis and associated risk factors in broiler chickens immunized with live anticoccidial vaccines in China.

Coccidiosis is a costly intestinal disease of chickens caused by Eimeria species. This infection is associated with high mortality, reduced feed efficiency, and slowed body weight gain. The diagnosis and control of coccidiosis becomes challenging due to the fact that chickens can be infected by seven different Eimeria species and often occur mixed-species co-infections. Grasping the epidemiology of Eimeria species is crucial to estimate the efficiency of poultry management. This study aimed to explore the distribution of Eimeria species in broiler chickens in China after administering live anticoccidial vaccines. A total of 634 samples were obtained, and the survey results showed that the prevalence of Eimeria was 86.12% (546/634), and the most common species were E. acervulina (65.62%), E. necatrix (50.95%), E. mitis (50.79%), E. tenella (48.42%), and E. praecox (41.80%). Most samples indicated mixed-species infections (an average of 3.29 species per positive sample). Notably, 63.98% of samples contain 3 to 5 Eimeria species within a single fecal sample. The most prevalent combinations were E. acervulina-E. tenella (38.96%) and E. acervulina-E. necatrix (37.22%). Statistical analysis showed that flocks vaccinated with trivalent vaccines were significantly positive for E. necatrix in grower chickens (OR = 3.30, p < 0.05) compared with starter chickens, and tetravalent vaccinated flocks showed that starter chickens demonstrated a higher susceptibility to E. tenella-E. brunetti (OR = 2.03, p < 0.05) and E. acervulina-E. maxima (OR = 2.05, p < 0.05) compared with adult chickens. Geographically, in the case of tetravalent vaccine-immunized flocks, a substantial positive association was observed between E. necatrix infection rates and flocks from eastern (OR = 3.88, p < 0.001), central (OR = 2.65, p = 0.001), and southern China (OR = 3.17, p < 0.001) compared with southwestern China. This study also found a positive association between E. necatrix (OR = 1.64, p < 0.05), E. acervulina (OR = 1.59, p < 0.05), and E. praecox (OR = 1.81, p < 0.05) infection and coccidiosis occurrence compared with non-infected flocks in tetravalent vaccinated flocks. This molecular epidemiological investigation showed a high prevalence of Eimeria species in the field. The emergent species, E. brunetti and E. praecox, might be incorporated into the widely-used live vaccines in the future. These insights could be useful in refining coccidiosis control strategies in the poultry industry.

Establishment and Application Prospect of Reverse Transcriptase Recombinase-Aided Amplification Assay for Subgroup C Avian Metapneumovirus.

Among broilers, the main pathogen that leads to swollen head syndrome (SHS) is the subgroup C avian metapneumovirus (aMPV-C). The aMPV-C infection can lead to an upsurge in the rate of soft-shell eggs, resulting in reduced egg production and seriously affecting the economy of the livestock industry. Therefore, a rapid method for aMPV-C detection needs to be invented. According to the N gene of aMPV-C, we designed the specific probe and primer and created a reverse transcription recombinase-aided amplification assay (RT-RAA) for the detection of aMPV-C. aMPV-C could be detected quickly and specifically by this method at 41 °C for 30 min. The sensitivity assay inferred that the minimum detection threshold of RT-RAA was 3.38 × 101 copies/µL. A specificity assay showed that the RT-RAA method did not cross-react with other subgroups (aMPV-A, aMPV-B, aMPV-D) or other viruses (H9N2, NDV, IBV, IBDV). Forty samples of known clinical background were tested by RT-RAA and RT-qPCR. The two approaches had a 100% correlation rate. In conclusion, this research successfully created an RT-RAA assay for aMPV-C.

Wavelength-tunable Tm:Y2O3 ceramic vortex laser with a changeable orbital angular momentum state.

Wavelength-tunable orbital angular momentum (OAM) lasers with controllable topological charges have the potential for serving as light sources for large-capacity optical communication by combining conventional wavelength division multiplexing (WDM) with OAM mode-division multiplexing (OAM-MDM). In this study, we demonstrate a wavelength-tunable Tm-bulk laser that can control OAM states in the 2-µm spectral range. The excitation conditions for different Laguerre-Gaussian (L G 0,l ) modes in a bulk laser cavity are theoretically determined by measuring the spatial propagation dynamics of the annular pump beam. As a proof-of-principle study, we experimentally generate OAM states of |ℏ| and |2ℏ| from a T m:Y 2 O 3 ceramic laser with a tunable emission wavelength using a Lyot filter (LF). The spatial properties of the scalar optical vortices are well conserved during wavelength tuning, indicating the feasibility of our approach for producing wavelength-tunable structured light. These OAM laser sources, which are characterized by their robustness and compactness, have potential applications in various areas such as optical communications, quantum optics, super-resolution microscopes, and more.

Sub-60-fs mode-locked Tm,Ho:CaYLuAlO4 laser at 2.05†µm.

Tm,Ho:CaYLuAlO4 (Tm,Ho:CALYLO) crystal has wide emission spectra both for π-polarization and σ-polarization, showing significant potential for the generation of ultrashort pulses. Here, a widely tunable and passively mode-locked laser operation based on Tm,Ho:CALYLO crystal under two polarizations was demonstrated for what we believe to be the first time ever. For π-polarization, a maximum output power of 1.52 W and a tuning range of 255.3 nm were achieved in the continuous wave (CW) regime. In the mode-locked regime, a pulse duration of 68 fs and an average output power of 228 mW were achieved upon GaSb-based semiconductor saturable absorber mirror (SESAM). As for σ-polarization, a broader tuning range of 267.1 nm was realized, leading to the shorter pulse duration of 58 fs at 79.7 MHz repetition rate.

Novel variant infectious bursal disease virus diminishes FAdV-4 vaccination and enhances pathogenicity of FAdV-4.

Infectious bursal disease virus (IBDV) caused an acute and highly contagious infectious disease characterized by severe immunosuppression, causing considerable economic losses to the poultry industry globally. Although this disease was well-controlled under the widely use of commercial vaccines in the past decades, the novel variant IBDV strains emerged recently because of the highly immunized-selection pressure in the field, posting new threats to poultry industry. Here, we reported novel variant IBDV is responsible for a disease outbreak, and assessed the epidemic and pathogenicity of IBDV in this study. Moreover, we constructed a challenge model using Fowl adenovirus serotype 4 (FAdV-4) to study on the immunosuppressive effect. Our findings underscore the importance of IBDV surveillance, and provide evidence for understanding the pathogenicity of IBDV.

Mode-locking of a Tm,Ho:CALYGO laser delivering 50 fs pulses at 2.08 µm.

We study the polarization-dependent laser performance of a novel, to the best of our knowledge, "mixed" Tm,Ho:CaYGdAlO4 crystal in the continuous-wave (CW) and mode-locked regimes. Both in terms of the CW tunability range (261 nm) and the minimum pulse duration (50 fs at 2078 nm, spectral width of 95 nm) in the mode-locked regime, σ-polarization is superior. With extended inhomogeneous spectral broadening due to structural and compositional disorder, Tm,Ho:CaYGdAlO4 is promising for few-optical-cycle pulse generation around 2 µm.

In Situ Atomic-Scale Quantitative Evidence of Plastic Activities Resulting in Reparable Deformation in Ultrasmall-Sized Ag Nanocrystals.

Permanent structural changes in pure metals that are caused by plastic activity are normally irreparable after unloading. Because of the lack of experimental evidence, it is unclear whether the plastic activity can be repaired as the size of the pure metals decreases to several nanometers; it is also unclear how the metals accommodate the plastic deformation. In this study, the in situ atomic-scale loading and unloading of ∼2 nm Ag nanocrystals was investigated, and three modes of plastic deformation were observed: (i) the phase transition from the face-centered cubic (fcc) phase to the hexagonal close-packed (hcp) phase, (ii) stacking faults, and (iii) deformation twin nucleation. We show that all three modes resulted in structural changes that were reparable, and their generation and restoration during loading and unloading were observed in situ. We discovered that the deformation modes of nanosized metals can be predicted from the ratio of the energy barriers of the fcc-hcp phase transition (ΔγH) and the deformation twin nucleation (ΔγT), which differ from those of the theoretical modes of relatively large-sized metals. The proposed ΔγH/ΔγT criterion provides insights into the deformation mechanism of nanometals.

Chemical inhomogeneity-induced profuse nanotwinning and phase transformation in AuCu nanowires.

Nanosized metals usually exhibit ultrahigh strength but suffer from low homogeneous plasticity. The origin of a strength-ductility trade-off has been well studied for pure metals, but not for random solid solution (RSS) alloys. How RSS alloys accommodate plasticity and whether they can achieve synergy between high strength and superplasticity has remained unresolved. Here, we show that face-centered cubic (FCC) RSS AuCu alloy nanowires (NWs) exhibit superplasticity of ~260% and ultrahigh strength of ~6 GPa, overcoming the trade-off between strength and ductility. These excellent properties originate from profuse hexagonal close-packed (HCP) phase generation (2H and 4H phases), recurrence of reversible FCC-HCP phase transition, and zigzag-like nanotwin generation, which has rarely been reported before. Such a mechanism stems from the inherent chemical inhomogeneity, which leads to widely distributed and overlapping energy barriers for the concurrent activation of multiple plasticity mechanisms. This naturally implies a similar deformation behavior for other highly concentrated solid-solution alloys with multiple principal elements, such as high/medium-entropy alloys. Our findings shed light on the effect of chemical inhomogeneity on the plastic deformation mechanism of solid-solution alloys.

Reduction of depolarization loss in a Tm-doped sesquioxide ceramic laser using a ring-shaped pump beam.

We report on a simple method for reduction of the depolarization loss in an end-pumped Tm:Y2O3 ceramic laser by using a near-field ring-shaped pump beam. Initially, we theoretically derive the expression of the depolarization loss in a bulk laser end-pumped with a near-field flat-top-hat or ring-shaped beam, where a significant reduction of depolarization loss in the latter case is presented. Experimental verification is thereafter carried out with a Tm:Y2O3 ceramic laser employing these two different pump configurations. It shows that the experimentally measured depolarization losses are close to the simulated values; the loss in the case of the annular-beam pump is almost 18 times lower than that with a quasi-top-hat beam at a same absorption pump power of 7.4 W. This work, as a proof-of-principle study, indicates that depolarization loss in the end-pumped bulk lasers can be significantly reduced simply by using a ring-shaped pump beam.

Structural basis of the human negative elongation factor NELF-B/C/E ternary complex.

Negative elongation factor (NELF) is a four-subunit transcription elongation factor that mainly functions in maintaining the paused state of RNA polymerase II in eukaryotes. Upon binding to Pol II, NELF works synergistically with DRB sensitivity-inducing factor (DSIF) and inhibits transcription elongation of Pol II, which subsequently retains a stably paused state 20-60 base pairs downstream of the promoter. The promoter-proximal pausing of Pol II caused by NELF is a general mechanism of transcriptional regulation for most signal-responsive genes. To date, structural studies have significantly advanced our understanding of the molecular mechanisms of NELF. However, a high quality structural model clarifying the interaction details of this complex is still lacking. In this study, we solved the high resolution crystal structure of the NELF-B/C/E ternary complex. We observed detailed interactions between subunits and identified residues important for the association between NELF-B and NELF-E. Our work presents a precise model of the NELF complex, which will facilitate our understanding of its in vivo function.

The attenuated live vaccine strain W2512 provides protection against novel variant infectious bursal disease virus.

Infectious bursal disease virus (IBDV) causes an acute and highly contagious infectious disease characterized by severe immunosuppression, causing great economic losses to the poultry industry globally. Over the past 30 years, this disease has been well controlled through vaccination and strict biosafety measures. However, novel variant IBDV strains have emerged in recent years, posing a new threat to the poultry industry. Our previous epidemiological survey showed that few novel variant IBDV strains had been isolated from chickens immunized with the attenuated live vaccine W2512-, suggesting that this vaccine is efficacious against novel variant strains. Here, we report the protective effect of the W2512 vaccine against novel variant strains in SPF chickens and commercial yellow-feathered broilers. We found that W2512 causes severe atrophy of the bursa of Fabricius in SPF chickens and commercial yellow-feathered broilers, induces high levels of antibodies against IBDV, and protects chickens from infection with the novel variant strains via a placeholder effect. This study highlights the protective effect of commercial attenuated live vaccines against the novel IBDV variant and provides guidance for the prevention and control of this disease.

Genomic analysis and characterization of bacteriophage vB_SpuS_NX263 infecting Salmonella enterica subsp. enterica serovar Pullorum.

In this study, a new Salmonella phage, NX263, was isolated from sewage. This phage could lyse 90.57% (48/53) of the bacterial strains tested and showed good activity over a wide range of temperature (up to 60°C) and pH (5-10). Phylogenetic analysis showed that it should be classified as a member of the genus Skatevirus. The genome of phage NX263 is 46,574 bp in length with a GC content of 45.52%. It contains 89 open reading frames and two tRNA genes. No lysogeny, drug resistance, or virulence-associated genes were identified in the genome sequence, suggesting that this phage could potentially be used to treat Salmonella Pullorum infections.

Structural Basis of the Transcriptional Elongation Factor Paf1 Core Complex from Saccharomyces eubayanus.

The multicomponent polymerase associated factor 1 (Paf1) complex (PAF1C) is an important transcription elongation factor that upregulates RNA polymerase II-mediated genome-wide transcription. PAF1C can regulate transcription through direct association with the polymerase or by impacting the chromatin structure epigenetically. In recent years, significant progress has been made in understanding the molecular mechanisms of PAF1C. However, high-resolution structures that can clarify the interaction details among the components of the complex are still needed. In this study, we evaluated the structural core of the yeast PAF1C containing the four components Ctr9, Paf1, Cdc73 and Rtf1 at high resolution. We observed the interaction details among these components. In particular, we identified a new binding surface of Rtf1 on PAF1C and found that the C-terminal sequence of Rtf1 dramatically changed during evolution, which may account for its different binding affinities to PAF1C among species. Our work presents a precise model of PAF1C, which will facilitate our understanding of the molecular mechanism and the in vivo function of the yeast PAF1C.

Halostachys caspica pathogenesis-related protein 10 acts as a cytokinin reservoir to regulate plant growth and development.

Pathogenesis-related class 10 (PR-10) proteins play a role in plant growth and development, but the underlying molecular mechanisms are unclear. Here, we isolated a salt-induced PR-10 gene from the halophyte Halostachys caspica and named it HcPR10. HcPR10 was constitutively expressed during development and HcPR10 localized to the nucleus and cytoplasm. HcPR10-mediated phenotypes including bolting, earlier flowering, increased branch number and siliques per plant are highly correlated with increased cytokinin levels in transgenic Arabidopsis. Meanwhile, increased levels of cytokinin in plants is temporally correlated with HcPR10 expression patterns. Although the expression of cytokinin biosynthesis genes validated was not upregulated, cytokinin-related genes including chloroplast-related genes, cytokinin metabolism and cytokinin responses genes and flowering-related genes were significantly upregulated in the transgenic Arabidopsis compared to the wild type by transcriptome deep sequencing. Analysis of the crystal structure of HcPR10 revealed a trans-zeatin riboside (a type of cytokinin) located deep in its cavity, with a conserved conformation and protein-ligand interactions, supporting HcRP10 acts as a cytokinin reservoir. Moreover, HcPR10 in Halostachys caspica predominantly accumulated in vascular tissue, the site of long-distance translocation of plant hormones. Collectively, we draw that HcPR10 as a cytokinin reservoir induces cytokinin-related signal transduction in plants, thereby promoting plant growth and development. These findings could provide intriguing insights into the role of HcPR10 proteins in phytohormone regulation in plants and advance our understanding of cytokinin-mediated plant development and could facilitate the breeding of transgenic crops with earlier mature, higher yielding agronomic traits.

The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain.

The lysine acetyltransferase KAT6A (MOZ, MYST3) belongs to the MYST family of chromatin regulators, facilitating histone acetylation. Dysregulation of KAT6A has been implicated in developmental syndromes and the onset of acute myeloid leukemia (AML). Previous work suggests that KAT6A is recruited to its genomic targets by a combinatorial function of histone binding PHD fingers, transcription factors and chromatin binding interaction partners. Here, we demonstrate that a winged helix (WH) domain at the very N-terminus of KAT6A specifically interacts with unmethylated CpG motifs. This DNA binding function leads to the association of KAT6A with unmethylated CpG islands (CGIs) genome-wide. Mutation of the essential amino acids for DNA binding completely abrogates the enrichment of KAT6A at CGIs. In contrast, deletion of a second WH domain or the histone tail binding PHD fingers only subtly influences the binding of KAT6A to CGIs. Overexpression of a KAT6A WH1 mutant has a dominant negative effect on H3K9 histone acetylation, which is comparable to the effects upon overexpression of a KAT6A HAT domain mutant. Taken together, our work revealed a previously unrecognized chromatin recruitment mechanism of KAT6A, offering a new perspective on the role of KAT6A in gene regulation and human diseases.

Watt-level femtosecond Tm-doped "mixed" sesquioxide ceramic laser in-band pumped by a Raman fiber laser at 1627 nm.

We report on a semiconductor saturable absorber mirror mode-locked Tm:(Lu,Sc)2O3 ceramic laser in-band pumped by a Raman fiber laser at 1627 nm. The nonlinear refractive index (n2) of the Tm:(Lu,Sc)2O3 ceramic has been measured to be 4.66 × 10-20 m2/W at 2000 nm. An average output power up to 1.02 W at 2060 nm is achieved for transform-limited 280-fs pulses at a repetition rate of 86.5 MHz, giving an optical efficiency with respect to the absorbed pump power of 36.4%. Pulses as short as 66 fs at 2076 nm are produced at the expense of output power (0.3 W), corresponding to a spectral bandwidth of 69 nm. The present work reveals the potential of Tm3+-doped sesquioxide transparent ceramics for power scaling of femtosecond mode-locked bulk lasers emitting in the 2-µm spectral range.

63 W wing-pumped Tm:YAG single-crystal fiber laser.

We present a high-power continuous-wave (CW) Tm:YAG single-crystal fiber (SCF) laser wing-pumped by laser diodes at 791 nm. A maximum output power of 63.3 W is achieved at ∼ 2.01 µm, corresponding to a slope efficiency of 34.2%. This is, to the best of our knowledge, the highest power obtained from the SCF laser in the 2 µm spectral range. In addition to the wing pumping scheme, the large surface-to-volume ratio of such fiber-geometry crystalline rod with diffusion-bonded undoped YAG end caps are benefited for the spatial uniform distribution of pump intensity and thermal load, and thus improving the power scalability.

SESAM mode-locked Tm:Y2O3 ceramic laser.

We demonstrate a widely tunable and passively mode-locked Tm:Y2O3 ceramic laser in-band pumped by a 1627-nm Raman fiber laser. A tuning range of 318 nm, from 1833 to 2151 nm, is obtained in the continuous-wave regime. The SESAM mode-locked laser produces Fourier-transform-limited pulses as short as 75 fs at ∼ 2.06 µm with an average output power of 0.26 W at 86.3 MHz. For longer pulse durations of 178 fs, an average power of 0.59 W is achieved with a laser efficiency of 29%. This is, to the best of our knowledge, the first mode-locked Tm:Y2O3 laser in the femtosecond regime. The spectroscopic properties and laser performance confirm that Tm:Y2O3 transparent ceramics are a promising gain material for ultrafast lasers at 2 µm.

Molecular Characterization Analysis of Prevalent Infectious Bronchitis Virus and Pathogenicity Assessment of Recombination Strain in China.

Avian coronavirus infectious bronchitis virus (IBV) is a respiratory pathogen of chickens, resulting in severe economic losses in the poultry industry. This study aimed to monitor and isolate the molecular identity of IBV in broiler flocks with respiratory symptoms in eight provinces of China. In total, 910 samples (oropharyngeal and cloacal mixed swabs) from broiler flocks showed IBV positive rates of 17.6% (160/910) using PCR assay. Phylogenetic analysis of the complete S1 genes of 160 IBV isolates was performed and revealed that QX-type (GI-19), TW-type (GI-7), 4/91-type (GI-13), HN08-type (GI-22),TC07-2-type (GVI-1), and LDT3-type (GI-28) exhibited IBV positive rates of 58.15, 25, 8.12, 1.86, 5.62, and 1.25%. In addition, recombination analyses revealed that the four newly IBV isolates presented different recombination patterns. The CK/CH/JS/YC10-3 isolate likely originated from recombination events between strain YX10 (QX-type) and strain TW2575-98 (TW-type), the pathogenicity of which was assessed, comparing it with strain GZ14 (TW-type) and strain CK/CH/GD/JR07-7 (QX-type). The complete S1 gene data from these isolates indicate that IBV has consistently evolved through genetic recombination or mutation, more likely changing the viral pathogenicity and leading to larger outbreaks in chick populations, in China.

The emergence of a disease caused by a mosquito origin Cluster 3.2 Tembusu virus in chickens in China.

In 2021, a chicken Tembusu virus (TMUV) caused outbreaks of a disease characterized by retarded growth and egg production decline in chickens in China. Two TMUV strains SD2021 and GX2021 were isolated from the diseased chickens and phylogenetic analysis of the E gene nucleotide sequence revealed that the chicken TMUV SD2021 and GX2021 were most close to mosquito origin TMUV in Cluster 3.2, which was distinct from the prevalent duck TMUVs in Cluster 2. The TMUV SD2021 caused growth retardation and neurological symptoms in chickens through both intranasal and intramuscular infection routes, but has no direct-contact transmissibility among chickens. The findings of this study highlight the pathogenicity of a chicken adapted mosquito-origin TMUV in chickens in China.