Combining genome-wide association study and transcriptome analysis to identify molecular markers and genetic basis of population-asynchronous ovarian development in Coilia nasus

Coilia nasus,a migratory fish species found in the middle and lower reaches of the Yangtze River and along offshore areas of China,possesses considerable aquacultural and economic potential.However,the species faces challenges due to significant variation in the gonadal development rate among females,resulting in inconsistent ovarian maturation times at the population level,an extended reproductive period,and limitations on fish growth rate due to ovarian prematurity.In the present study,we combined genome-wide association study(GWAS)and comparative transcriptome analysis to investigate the potential single nucleotide polymorphisms(SNPs)and candidate genes associated with population-asynchronous ovarian development in C.nasus.Genotyping of the female population based on whole-genome resequencing yielded 2120695 high-quality SNPs,39 of which were suggestively associated with ovarian development.Of note,a significant SNP peak on LG21 containing 30 suggestively associated SNPs was identified,with cpne5a determined as the causal gene of the peak.Therefore,single-marker and haplotype association analyses were performed on cpne5a,revealing four genetic markers(P<0.05)and seven haplotypes(r2>0.9)significantly associated with the phenotype.Comparative transcriptome analysis of precociously and normally maturing individuals screened out 29 and 426 overlapping differentially expressed genes in the brain and ovary,respectively,between individuals of different body sizes.Integrating the GWAS and transcriptome analysis results,this study identified genes and pathways related to hypothalamic-pituitary-gonadal axis hormone secretion,extracellular matrix,angiogenesis,and gap junctions involved in population-asynchronous ovarian development.The insights gained from this study provide a basis for a deeper understanding of the molecular mechanisms underlying ovarian development in fish and may facilitate the genetic breeding of C.nasus strains exhibiting population-synchronous ovarian development in the future.

Identification of a three-gene prognostic signature for radioresistant esophageal squamous cell carcinoma

BACKGROUND Esophageal squamous cell carcinoma(ESCC)is causing a high mortality rate due to the lack of efficient early prognosis markers and suitable therapeutic regimens.The prognostic role of genes responsible for the acquisition of radioresistance in ESCC has not been fully elucidated.AIM To establish a prognostic model by studying gene expression patterns pertinent to radioresistance in ESCC patients.METHODS Datasets were obtained from the Gene Expression Omnibus and The Cancer Genome Atlas databases.The edgeR,a Bioconductor package,was used to analyze mRNA expression between different groups.We screened genes specifically responsible for radioresistance to estimate overall survival.Pearson correlation analysis was performed to confirm whether the expression of those genes correlated with each other.Genes contributing to radioresistance and overall survival were assessed by the multivariate Cox regression model through the calculation ofβi and risk score using the following formula:∑^(n)_(i=1)βi×PSI.RESULTS We identified three prognostic mRNAs(cathepsin S[CTSS],cluster of differentiation 180[CD180],and SLP adapter and CSK-interacting membrane protein[SCIMP])indicative of radioresistance.The expression of the three identified mRNAs was related to each other(r>0.70 and P<0.05).As to 1-year and 3-year overall survival prediction,the area under the time-dependent receiver operating characteristic curve of the signature consisting of the three mRNAs was 0.716 and 0.841,respectively.When stratifying patients based on the risk score derived from the signature,the high-risk group exhibited a higher death risk and shorter survival time than the low-risk group(P<0.0001).Overall survival of the low-risk patients was significantly better than that of the highrisk patients(P=0.018).CONCLUSION We have developed a novel three-gene prognostic signature consisting of CTSS,CD180,and SCIMO for ESCC,which may facilitate the prediction of early prognosis of this malignancy.

Strain compensated type Ⅱ superlattices grown by molecular beam epitaxy

We investigate a strain compensation method for the growth of complex interband cascade laser structures. For thick In As/Al Sb superlattice clad layers, the sublayer thicknesses were adjusted so that the tensile strain energy in the In As sublayer was equal to the compressive strain energy in the Al Sb sublayer. For the four-constituent active region, as the compressive strain in the Ga0.65In0.35Sb alloy layer was large, a tensile strain was incorporated in the chirped In As/Al Sb superlattice region for strain compensation to the Ga0.65In0.35Sb alloy. A laser structure of thickness 6 μm was grown on the Ga Sb substrate by molecular beam epitaxy. The wafer exhibited good surface morphology and high crystalline quality.

Flat Top Optical Frequency Combs Based on a Single-Core Quantum Cascade Laser at Wavelength of~8.7μm

We present optical frequency combs with a spectral emission of 48 cm-1and an output power of 420 m W based on a single-core quantum cascade laser at λ ~ 8.7μm. A flat top spectrum sustains up to 130 comb modes delivering ~ 3.2 m W of optical power per mode, making it a valuable tool for dual comb spectroscopy. The homogeneous gain medium, relying on a slightly diagonal bound-to-continuum structure, promises to provide a broad and stable gain for comb operating. Remarkably, the dispersion of this device is measured within 300 fs2/mm to ensure stable comb operation over 90% of the total current range. The comb is observed with a narrow beatnote linewidth around 2 k Hz and has weak dependence on the applied current for stable comb operation.

Tunable characteristic of phase-locked quantum cascade laser arrays

A multimode interference(MMI)structure is designed to simplify the fabrication of quantum cascade laser(QCL)phase-locked arrays.The MMI geometry is optimized with a sufficient output channel distance to accommodate conventional photolithography and wet etching process by which power amplifier array is fabricated without using the complicated two-step etching-regrowth or dry etching technique.The far-field pattern with periodically modulated peaks reveals that the beams from the arrays are phase-locked.Furthermore,the frequency tuning performance of the MMI-based phase-locked arrays is studied using the Littrow-configuration external cavity structure.A wavelength tuning range of more than 60 cm^(−1) is demonstrated,which will eventually realize the high power,frequency tunable,large-scale phase-locked arrays,and their application in spectroscopy.

Broad gain,continuous-wave operation of InP-based quantum cascade laser atλ~11.8μm

We demonstrate a broad gain,continuous-wave(CW)operation InP-based quantum cascade laser(QCL)emitting at 11.8μm with a modified dual-upper-state(DAU)and diagonal transition active region design.A 3 mm cavity length,16.5μm average ridge wide QCL with high-reflection(HR)coatings demonstrates a maximum peak power of 1.07 W at 283 K and CW output power of 60 m W at 293 K.The device also shows a broad and dual-frequency lasing spectrum in pulsed mode and a maximum average power of 258.6 mW at 283 K.Moreover,the full width at half maximum(FWHM)of the electroluminescent spectrum measured at subthreshold current is 2.37μm,which indicates a broad gain spectrum of the materials.The tuning range of 1.38μm is obtained by a grating-coupled external cavity(EC)Littrow configuration,which is beneficial for gas detection.

Beam steering characteristics in high-power quantum-cascade lasers emitting at∼4.6µm

A beam steering effect of high-power quantum cascade(QC) lasers emitting at 4.6 μm was investigated. The continuous wave(CW) output power of an uncoated, 6-mm-long, 7.5-μm-wide buried-heterostructure QC laser at 25℃ was as high as 854.2 m W. The maximum beam steering angle was offset by ±14.2° from the facet normal(0°) in pulsed mode. The phenomenon was judged explicitly by combining the diffraction limit theory and Fourier transform of the spectra. It was also verified by finite element method software simulation and the calculation of two-dimensional(2 D)effective-index model. The observed steering is consistent with a theory for coherence between the two lowest order lateral modes. Therefore, we have established an intrinsic linkage between the spectral instabilities and the beam steering by using the Fourier transform of the spectra, and further presented an extremely valid method to judge the beam steering. The content of this method includes both three equidistant peak positions in the Fourier transform of the spectra and the beam quality located between once the diffraction limit(DL) and twice the DL.

Systemic Signaling and Local Sensing of Phosphate in Common Bean： Cross-Talk between Photosynthate and MicroRNA399

Shoot-to-root communication is crucial for plant acclimation to phosphorus （P）-deficiency. Both sugars and miRNAs have been implicated as potential signal molecules transported through phloem from shoot to root for the reg- ulation of gene expression and Pi uptake in the root. By studying the expression patterns of both a serine/threonine phos- phatase gene （PvHAD1） and microRNA399 （miR399） in common bean （Phaseolus vulgaris L.）, we provide evidence for the interaction between light, phloem transport, and miR399 in the systemic regulation of gene expression under P-deficiency. Especially, miR399 expression in both the shoot and the root requires photosynthetic carbon assimilation during the onset of P-deficiency. In contrast to systemic signaling, local sensing was the primary causal factor for rapid down-regulation of PvHAD1 by Pi prior to the reduction of miR399 level in P-deficient roots. Furthermore, this initial response to Pi in P-de- ficient root was also mimicked by the Pi analog, phosphonate （Phi）. Our current findings suggest that plants have developed a highly coordinated dual regulatory pathway, namely long-distance signaling of P-deficiency from shoot to root versus local sensing of Pi in the root.

Chirped coupled ridge waveguide quantum cascade laser arrays with stable single-lobe far-field patterns

Power scaling in a broad area quantum cascade laser(QCL) tends to deteriorate beam quality with the emission of a multiple-lobe far-field pattern. In this paper, we demonstrate a coupled ridge waveguide QCL array consisting of five elements with chirped geometry. In-phase mode operation is secured by managing supermode loss with properly designed geometries of ridges. A single-lobe lateral far-field with a near diffraction limited beam pattern was obtained in the whole current dynamic range. The devices were fabricated with the wet and dry etching method. The regrowth technique of the In P:Fe insulation layer and In P:Si waveguide layer was employed.Such a structure has the potential to optimize the beam quality of the recently reported high-power broad-area QCL with a reduced cascade number.

Clinicopathological significance of p16, cyclin D1, Rb and MIB-1 levels in skull base chordoma and chondrosarcoma

Objective: To investigate the expression of p16, cyclin D1, retinoblastoma tumor suppressor protein (Rb) and MIB-1 in skull base chordoma and chondrosarcoma tissues, and to determine the clinicopathological significance of the above indexes in these diseases.Methods: A total of 100 skull base chordoma, 30 chondrosarcoma, and 20 normal cartilage tissue samples were analyzed by immunohistochemistry.The expression levels of p16, cyclinD1,Rb and MIB-1 proteins were assessed for potential correlation with the clinicopathological features.Results: As compared to normal cartilage specimen (control), there was decreased expression of p16, and increased expression of cyclin D1, Rb and MIB-1 proteins, in both skull base chordoma and chondrosarcoma specimens.MIB-1 LI levels were significantly increased in skull base chordoma specimens with negative expression of p16, and positive expression of cyclin D1 and Rb (P ＜ 0.05).Significantly elevated MIB-1 LI was also detected in skull base chondrosarcoma tissues, while there was negative expression of p16, cyclin D1 and Rb (P ＜ 0.05).In skull base chordoma, p16 negatively correlated with cyclin D1 and Rb, while cyclin D1 positively correlated with Rb.Additionally, p16, cyclin D1, Rb, or MIB-1 expression showed no correlation with age, gender, or pathological classification of patients with skull base chordoma (P ＞ 0.05).However, p16 and MIB-1 levels correlated with the intradural invasion, and expression of p16, Rb and MIB-1 correlated with the number of tumor foci (P ＜ 0.05).Further, the expression of p16 and MIB-1 appeared to correlate with the prognosis of patients with skull base chordoma.Conclusions: The abnormal expression of p16, cyclin D1 and Rb proteins might be associated with the tumorigenesis of skull base chordoma and chondrosarcoma.

Stable single-mode operation of a distributed feedback quantum cascade laser integrated with a distributed Bragg reflector

We report an index-coupled distributed feedback quantum cascade laser by employing an equivalent phase shift(EPS) of quarter-wave integrated with a distributed Bragg reflector(DBR) at λ~5.03 μm. The EPS is fabricated through extending one sampling period by 50% in the center of a sampled Bragg grating. The key EPS and DBR pattern are fabricated by conventional holographic exposure combined with the optical photolithography technology, which leads to improved flexibility, repeatability, and cost-effectiveness. Stable single-mode emission can be obtained by changing the injection current or heat sink temperature even under the condition of large driving pulse width.

Multi-wavelength sampled Bragg grating quantum cascade laser arrays

A multi-wavelength sampled Bragg grating(SBG) quantum cascade laser array operating between 7.32 and7.85 μm is reported. The sampling grating structure, which can be analyzed as a conventional grating multiplied by a sampling function, is fabricated by holographic exposure combined with optical photolithography. The sampling grating period was varied from 8 to 32 μm, and different sampling order(-1 st,-2 nd, and-3 rd order)modes were achieved. We propose that higher-order modes with optimized duty cycles can be used to take full advantage of the gain curve and improve the wavelength coverage of the SBG array, which will be beneficial to many applications.