Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation.

Transposable elements (TEs) exert significant influence on plant genomic structure and gene expression. Here, we explored TE-related aspects across 14 Rosaceae genomes, investigating genomic distribution, transposition activity, expression patterns, and nearby differentially expressed genes (DEGs). Analyses unveiled distinct long terminal repeat retrotransposon (LTR-RT) evolutionary patterns, reflecting varied genome size changes among nine species over the past million years. In the past 2.5 million years, Rubus idaeus showed a transposition rate twice as fast as Fragaria vesca, while Pyrus bretschneideri displayed significantly faster transposition compared with Crataegus pinnatifida. Genes adjacent to recent TE insertions were linked to adversity resistance, while those near previous insertions were functionally enriched in morphogenesis, enzyme activity, and metabolic processes. Expression analysis revealed diverse responses of LTR-RTs to internal or external conditions. Furthermore, we identified 3695 pairs of syntenic DEGs proximal to TEs in Malus domestica cv. 'Gala' and M. domestica (GDDH13), suggesting TE insertions may contribute to varietal trait differences in these apple varieties. Our study across representative Rosaceae species underscores the pivotal role of TEs in plant genome evolution within this diverse family. It elucidates how these elements regulate syntenic DEGs on a genome-wide scale, offering insights into Rosaceae-specific genomic evolution.

Origin and early divergence of tandem duplicated sorbitol transporter genes in Rosaceae: insights from evolutionary analysis of the SOT gene family in angiosperms.

Sorbitol is a critical photosynthate and storage substance in the Rosaceae family. Sorbitol transporters (SOTs) play a vital role in facilitating sorbitol allocation from source to sink organs and sugar accumulation in sink organs. While prior research has addressed gene duplications within the SOT gene family in Rosaceae, the precise origin and evolutionary dynamics of these duplications remain unclear, largely due to the complicated interplay of whole genome duplications and tandem duplications. Here, we investigated the synteny relationships among all identified Polyol/Monosaccharide Transporter (PLT) genes in 61 angiosperm genomes and SOT genes in representative genomes within the Rosaceae family. By integrating phylogenetic analyses, we elucidated the lineage-specific expansion and syntenic conservation of PLTs and SOTs across diverse plant lineages. We found that Rosaceae SOTs, as PLT family members, originated from a pair of tandemly duplicated PLT genes within Class III-A. Furthermore, our investigation highlights the role of lineage-specific and synergistic duplications in Amygdaloideae in contributing to the expansion of SOTs in Rosaceae plants. Collectively, our findings provide insights into the genomic origins, duplication events, and subsequent divergence of SOT gene family members. Such insights lay a crucial foundation for comprehensive functional characterizations in future studies.

Intraoperative microelectrode recording under general anesthesia guided subthalamic nucleus deep brain stimulation for Parkinson's disease: One institution's experience.

Objective: Microelectrode recording (MER) guided subthalamic nucleus deep brain stimulation (STN-DBS) under local anesthesia (LA) is widely applied in the management of advanced Parkinson's disease (PD). Whereas, awake DBS under LA is painful and burdensome for PD patients. We analyzed the influence of general anesthesia (GA) on intraoperative MER, to assess the feasibility and effectiveness of GA in MER guided STN-DBS. Methods: Retrospective analysis was performed on the PD patients, who underwent bilateral MER guided STN-DBS in Wuhan Union Hospital from July 2019 to December 2021. The patients were assigned to LA or GA group according to the anesthetic methods implemented. Multidimensional parameters, including MER signals, electrode implantation accuracy, clinical outcome and adverse events, were analyzed. Results: A total of 40 PD patients were enrolled in this study, including 18 in LA group and 22 in GA group. There were no statistically significant differences in patient demographics and baseline characteristics between two groups. Although, the parameters of MER signal, including frequency, inter-spike interval (ISI) and amplitude, were obviously interfered under GA, the waveforms of MER signals were recognizable and shared similar characteristics with LA group. Both LA and GA could achieve effective electrode implantation accuracy and clinical outcome. They also shared similar adverse events postoperatively. Conclusion: GA is viable and comparable to LA in MER guided STN-DBS for PD, regarding electrode implantation accuracy, clinical outcome and adverse events. Notably, GA is more friendly and acceptable to the patients who are incapable of enduring intraoperative MER under LA.

MbHY5-MbYSL7 mediates chlorophyll synthesis and iron transport under iron deficiency in Malus baccata.

Iron (Fe) plays an important role in cellular respiration and catalytic reactions of metalloproteins in plants and animals. Plants maintain iron homeostasis through absorption, translocation, storage, and compartmentalization of iron via a cooperative regulative network. Here, we showed different physiological characteristics in the leaves and roots of Malus baccata under Fe sufficiency and Fe deficiency conditions and propose that MbHY5 (elongated hypocotyl 5), an important transcription factor for its function in photomorphogenesis, participated in Fe deficiency response in both the leaves and roots of M. baccata. The gene co-expression network showed that MbHY5 was involved in the regulation of chlorophyll synthesis and Fe transport pathway under Fe-limiting conditions. Specifically, we found that Fe deficiency induced the expression of MbYSL7 in root, which was positively regulated by MbHY5. Overexpressing or silencing MbYSL7 influenced the expression of MbHY5 in M. baccata.

Design and fabrication of SU-8 polymer arrayed waveguide gratings based on flexible PDMS substrates.

We investigated and fabricated 1×8 and 1×16 traditional/saddle arrayed waveguide grating (AWG) wavelength division multiplexing devices on flexible substrates. The core layer was made of the negative epoxy photoresist SU-8, and polydimethylsiloxane (PDMS) material was selected for the cladding based on the high refractive index difference. A chemical modification method of PDMS was proposed to enhance the film-forming characteristics of the SU-8 core layer on PDMS substrates. After fabricating and characterizing the optical properties of the AWGs, the dimensions of the proposed 1×8 and 1×16 AWGs were 0.9×0.8cm2 and 1.1×0.9cm2, respectively. Experimental results showed that the saddle-type 1×8 and 1×16 AWGs had good signal transmission characteristics, and the insertion losses were only 5.1 dB and 6.8 dB, respectively, which were lower than those of traditional-type AWGs with the same dimensions and number of waveguides.

Identification of PLATZ genes in Malus and expression characteristics of MdPLATZs in response to drought and ABA stresses.

Plant AT-rich sequences and zinc-binding proteins (PLATZ) play crucial roles in response to environmental stresses. Nevertheless, PLATZ gene family has not been systemically studied in Rosaceae species, such as in apple, pear, peach, or strawberry. In this study, a total of 134 PLATZ proteins were identified from nine Rosaceae genomes and were classified into seven phylogenetic groups. Subsequently, the chromosomal localization, duplication, and collinearity relationship for apple PLATZ genes were investigated, and segmental duplication is a major driving-force in the expansion of PLATZ in Malus. Expression profiles analysis showed that PLATZs had distinct expression patterns in different tissues, and multiple genes were significantly changed after drought and ABA treatments. Furthermore, the co-expression network combined with RNA-seq data showed that PLATZ might be involved in drought stress by regulating ABA signaling pathway. In summary, this study is the first in-depth and systematic identification of PLATZ gene family in Rosaceae species, especially for apple, and provided specific PLATZ gene resource for further functional research in response to abiotic stress.

RBP differentiation contributes to selective transmissibility of OPT3 mRNAs.

Long-distance mobile mRNAs play key roles in gene regulatory networks that control plant development and stress tolerance. However, the mechanisms underlying species-specific delivery of mRNA still need to be elucidated. Here, the use of grafts involving highly heterozygous apple (Malus) genotypes allowed us to demonstrate that apple (Malus domestica) oligopeptide transporter3 (MdOPT3) mRNA can be transported over a long distance, from the leaf to the root, to regulate iron uptake; however, the mRNA of Arabidopsis (Arabidopsis thaliana) oligopeptide transporter 3 (AtOPT3), the MdOPT3 homolog from A. thaliana, does not move from shoot to root. Reciprocal heterologous expression of the two types of mRNAs showed that the immobile AtOPT3 became mobile and moved from the shoot to the root in two woody species, Malus and Populus, while the mobile MdOPT3 became immobile in two herbaceous species, A. thaliana and tomato (Solanum lycopersicum). Furthermore, we demonstrated that the different transmissibility of OPT3 in A. thaliana and Malus might be caused by divergence in RNA-binding proteins between herbaceous and woody plants. This study provides insights into mechanisms underlying differences in mRNA mobility and validates the important physiological functions associated with this process.

Silicon Waveguide Integrated with Germanium Photodetector for a Photonic-Integrated FBG Interrogator.

We report a vertically coupled germanium (Ge) waveguide detector integrated on silicon-on-insulator waveguides and an optimized device structure through the analysis of the optical field distribution and absorption efficiency of the device. The photodetector we designed is manufactured by IMEC, and the tests show that the device has good performance. This study theoretically and experimentally explains the structure of Ge PIN and the effect of the photodetector (PD) waveguide parameters on the performance of the device. Simulation and optimization of waveguide detectors with different structures are carried out. The device's structure, quantum efficiency, spectral response, response current, changes with incident light strength, and dark current of PIN-type Ge waveguide detector are calculated. The test results show that approximately 90% of the light is absorbed by a Ge waveguide with 20 µm Ge length and 500 nm Ge thickness. The quantum efficiency of the PD can reach 90.63%. Under the reverse bias of 1 V, 2 V and 3 V, the detector's average responsiveness in C-band reached 1.02 A/W, 1.09 A/W and 1.16 A/W and the response time is 200 ns. The dark current is only 3.7 nA at the reverse bias voltage of -1 V. The proposed silicon-based Ge PIN PD is beneficial to the integration of the detector array for photonic integrated arrayed waveguide grating (AWG)-based fiber Bragg grating (FBG) interrogators.

ERF4 affects fruit firmness through TPL4 by reducing ethylene production.

The firmness of fleshy fruit crops has a significant effect on their quality, consumer preference, shelf life and transportability. In a combined quantitative trait locus and genome-wide association studies study of apple fruit texture, we identified a mutation (C-G) in the ethylene response factor-associated amphiphilic repression (EAR) motif in the coding region of the apple ETHYLENE RESPONSE FACTOR4 (ERF4) gene. Chromatin immunoprecipitation sequencing showed that ERF4 binds to the promoter of ERF3, which is involved in regulation of ethylene biosynthesis. The EAR mutation in ERF4 results in reduced repression of ERF3 expression, which is turn promotes ethylene production and loss of fruit firmness. ERF4 acts as a transcriptional repressor whose activity is modulated by a TOPLESS co-repressor 4 (TPL4)-binding EAR repression motif. Biolayer interferometry analysis showed that the mutation in the EAR motif causes a reduction in the interaction with TPL4. Suppression of ERF4 or TPL4 promoted fruit ripening and ethylene production. Taken together, our results provide insights into how ERF4 allelic variation underlies an important fruit quality trait.

The Structural, Electronic, and Optical Properties of Ge/Si Quantum Wells: Lasing at a Wavelength of 1550 nm.

The realization of a fully integrated group IV electrically driven laser at room temperature is an essential issue to be solved. We introduced a novel group IV side-emitting laser at a wavelength of 1550 nm based on a 3-layer Ge/Si quantum well (QW). By designing this scheme, we showed that the structural, electronic, and optical properties are excited for lasing at 1550 nm. The preliminary results show that the device can produce a good light spot shape convenient for direct coupling with the waveguide and single-mode light emission. The laser luminous power can reach up to 2.32 mW at a wavelength of 1550 nm with a 300-mA current. Moreover, at room temperature (300 K), the laser can maintain maximum light power and an ideal wavelength (1550 nm). Thus, this study provides a novel approach to reliable, efficient electrically pumped silicon-based lasers.

A long non-coding apple RNA, MSTRG.85814.11, acts as a transcriptional enhancer of SAUR32 and contributes to the Fe-deficiency response.

Iron (Fe) is an essential plant nutrient and its deficiency typically limits plant growth. Long non-coding (lnc) RNAs are involved in adaptive responses to nutrient stress; however, it is not known whether they function in the regulation of the canonical Fe-deficiency response. The expression of Malus domestica (apple) lncRNA MSTRG.85814 is induced by Fe deficiency, as identified by high-throughput strand-specific RNA-seq analysis of an apple homograft system. MSTRG.85814 has a complex structure, with 13 predicted RNA sequence variants, four of which are upregulated in the roots of plants experiencing Fe deficiency. We found that one MSTRG.85814 splice variant (MSTRG.85814.11) positively modulated its cis target mRNA derived from the small auxin upregulated gene SAUR32. This in turn promoted the expression of SAUR32 and caused an increase in the expression of a plasma membrane proton ATPase, AHA10. Using a pH imaging technique, a significant decrease in the apoplastic pH was observed to occur in the root tips of MSTRG.85814.11 or SAUR32-overexpressing apple plants. Thus MSTRG.85814.11 was shown to positively promote SAUR32 expression, which then activated proton extrusion involved in the Fe-deficiency response. These results reveal a mechanism by which lncRNA promotes environmental Fe-deficiency stress adaption.

Natural Variation Underlies Differences in ETHYLENE RESPONSE FACTOR17 Activity in Fruit Peel Degreening.

Through natural or human selection, many fleshy fruits have evolved vivid external or internal coloration, which often develops during ripening. Such developmental changes in color are associated with the biosynthesis of pigments as well as with degreening through chlorophyll degradation. Here, we demonstrated that natural variation in the coding region of the gene ETHYLENE RESPONSE FACTOR17 (ERF17) contributes to apple (Malus domestica) fruit peel degreening. Specifically, ERF17 mutant alleles with different serine (Ser) repeat insertions in the coding region exhibited enhanced transcriptional regulation activity in a dual-luciferase reporter assay when more Ser repeats were present. Notably, surface plasmon resonance analysis showed that the number of Ser repeats affected the binding activity of ERF17 to the promoter sequences of chlorophyll degradation-related genes. In addition, overexpression of ERF17 in evergreen apples altered the accumulation of chlorophyll. Furthermore, we demonstrated that ERF17 has been under selection since the origin of apple tree cultivation. Taken together, these results reveal allelic variation underlying an important fruit quality trait and a molecular genetic mechanism associated with apple domestication.

[Investigation on occupational stress of workers in clean workshops of electric company].

OBJECTIVE: The aim is to learn the situation of work stress, burnout and depression in clean workshops of electronic company by investigation, and provide the clues for the further interventions as well as the basic data for the future evaluation. METHODS: The survey was carried out in a electronic company in Xishan,Wuxi city. The subjects including all the 395 employees in clean workshops and 205 in ordinary workshops were asked to fill in an anonymous cross-sectional questionnaire, in which the distributions of age, gender, job duration, working time and working strength were similar between two kinds of workshops. The response rate was 98.9%. RESULTS: There were no significant differences between clean and ordinary workshops in age, gender, smoking, drinking and working hours, except for employed years. It was not found that any differences between two kinds of workshop for the rates of burnout, depression and stress. However, the rates of burnout, depression and stress were 19.7%(77/391), 24.8%(97/391) and 88.5%(346/391) in clean workshops and 19.3%(39/202), 23.8%(48/202) and 84.6%(171/202) in ordinary workshops. There were no significant differences between two workshops for the scores of burnout and depression, but the stress score in clean workshops was higher than that of ordinary workshop (P = 0.015). Further stratified analysis found that stress score of male in clean workshop was higher than that of female (P = 0.002), while it was inverse in ordinary workshops (P = 0.034). In addition, the stress score of male in clean workshops was significantly higher than that of male in ordinary one (P = 0.003). The stress score of workers with age ≥22 year old was higher than that of age <22 in clean workshops, while the stress rate of workers with job duration ≥1.6 years was more than that of those with the shorter job duration. The risk of stress in clean workshops was as 3.78 times as ordinary one and the 95% confidence interval was 1.54∼9.31 after adjusted age and gender. There were negative correlations between stress and society support in both clean and ordinary workshops. CONCLUSION: The levels of work stress, burnout and depression were high in this electronic company. The stress in clean workshops was more serious than that of ordinary ones, especially for the males.