RNA-sequencing transcriptome analysis of Avicennia marina (Forsk.) Vierh. leaf epidermis defines tissue-specific transcriptional response to salinity treatment.

Avicennia marina (Forsk.) Vierh. is a typical mangrove plant. Its epidermis contains salt glands, which can secrete excess salts onto the leaf surfaces, improving the salt tolerance of the plants. However, knowledge on the epidermis-specific transcriptional responses of A. marina to salinity treatment is lacking. Thus, physiological and transcriptomic techniques were applied to unravel the salt tolerance mechanism of A. marina. Our results showed that 400 mM NaCl significantly reduced the plant height, leaf area, leaf biomass and photosynthesis of A. marina. In addition, 1565 differentially expressed genes were identified, of which 634 and 931 were up- and down-regulated. Based on Kyoto Encyclopedia of Genes and Genomes metabolic pathway enrichment analysis, we demonstrated that decreased gene expression, especially that of OEE1, PQL2, FDX3, ATPC, GAPDH, PRK, FBP and RPE, could explain the inhibited photosynthesis caused by salt treatment. Furthermore, the ability of A. marina to cope with 400 mM NaCl treatment was dependent on appropriate hormone signalling and potential sulfur-containing metabolites, such as hydrogen sulfide and cysteine biosynthesis. Overall, the present study provides a theoretical basis for the adaption of A. marina to saline habitats and a reference for studying the salt tolerance mechanism of other mangrove plants.

Physiological and transcriptomic analysis dissects the molecular mechanism governing meat quality during postmortem aging in Hu sheep (Ovis aries).

Introduction: Hu sheep, known for its high quality and productivity, lack fundamental scientific research in China. Methods: This study focused on the effects of 24 h postmortem aging on the meat physiological and transcriptomic alteration in Hu sheep. Results: The results showed that the 24 h aging process exerts a substantial influence on the mutton color, texture, and water content as compared to untreated group. Transcriptomic analysis identified 1,668 differentially expressed genes. Functional enrichment analysis highlighted the importance of glycolysis metabolism, protein processing in endoplasmic reticulum, and the FcγR-mediated phagocytosis pathway in mediating meat quality modification following postmortem aging. Furthermore, protein-protein interaction analysis uncovered complex regulatory networks involving glycolysis, the MAPK signaling pathway, protein metabolism, and the immune response. Discussion: Collectively, these findings offer valuable insights into the molecular mechanisms underlying meat quality changes during postmortem aging in Hu sheep, emphasizing the potential for improving quality control strategies in mutton production.

Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats.

Bamboo rats (Rhizomys pruinosus) are among the few mammals that lives on a bamboo-based diet which is mainly composed of lignocellulose. However, the mechanisms of adaptation of their gut microbiome and metabolic systems in the degradation of lignocellulose are largely unknown. Here, we conducted a multi-omics analysis on bamboo rats to investigate the interaction between their gut microbiomes and metabolic systems in the pre- and post-weaning periods, and observed significant relationships between dietary types, gut microbiome, serum metabolome and host gene expression. For comparison, published gut microbial data from the famous bamboo-eating giant panda (Ailuropoda melanoleuca) were also used for analysis. We found that the adaptation of the gut microbiome of the bamboo rat to a lignocellulose diet is related to a member switch in the order Bacteroidales from family Bacteroidaceae to family Muribaculaceae, while for the famous bamboo-eating giant panda, several aerobes and facultative anaerobes increase after weaning. The conversion of bacteria with an increased relative abundance in bamboo rats after weaning enriched diverse carbohydrate-active enzymes (CAZymes) associated with lignocellulose degradation and functionally enhanced the biosynthesis of amino acids and B vitamins. Meanwhile, the circulating concentration of short-chain fatty acids (SCFAs) derived metabolites and the metabolic capacity of linoleic acid in the host were significantly elevated. Our findings suggest that fatty acid metabolism, including linoleic acid and SCFAs, are the main energy sources for bamboo rats in response to the low-nutrient bamboo diet.

Probing the mode-locking pattern in the parameter space of a Figure-9 laser.

Due to the many available cavity configurations, a generalized approach for identifying the optimal operating state of a Figure-9 mode-locked laser has proved a challenge. In this Letter, we probe the output pulsation states of an exemplar Figure-9 laser by meticulously scanning its parameter space. Regions corresponding to mode-locked operations are identified periodically in the map of the output states. We correlate these regions to a set of band-like cavity transmission functions that fundamentally allow ultra-short pulse formation. Interestingly, a clear correlation between the mode-locking pattern and the cavity configuration is observed. For example, with the decrease of the fiber loop symmetry in the cavity, half of the solutions in the mode-locking pattern are found to transit to forbidden states. Numerical calculations based on the Jones matrix are used to explain the experimental observations. In addition, the dynamic change of the map of output states is illustrated by using a setup with an automatic algorithm. Our results provide a visually-rich yet simple way for evaluating and optimizing a Figure-9 laser.

Hysteresis of a passively mode-locked fiber laser: effects from cavity dispersion.

Hysteresis is a common phenomenon in passively mode-locked lasers and refers to the effect where the thresholds marking transitions between different pulsation states are not the same for an increasing or decreasing pump power. Despite wide presence in experimental observations, the general dynamics of hysteresis remains elusive, largely due to the challenge to acquire the full hysteresis dynamics of a given mode-locked laser. In this Letter, we overcome this technical bottleneck by fully characterizing an exemplar figure-9 fiber laser cavity, which exhibits well-defined mode-locking patterns in its parameter space or "primitive cell." We varied the net cavity dispersion and observed the salient change of hysteresis characteristics. Specifically, transiting from an anomalous to a normal cavity dispersion is found to consistently increase the likelihood of the single-pulse mode-locking regime. To the best of our knowledge, this is the first time that a laser's hysteresis dynamic is fully probed and related to fundamental cavity parameters.

High energy (>40 nJ), sub-100 fs, 950 nm laser for two-photon microscopy.

Compact and high-energy femtosecond fiber lasers operating around 900-950 nm are desirable for multiphoton microscopy. Here, we demonstrate a >40 nJ, sub-100 fs, wavelength-tunable ultrafast laser system based on chirped pulse amplification (CPA) in thulium-doped fiber and second-harmonic generation (SHG) technology. Through effective control of the nonlinear effect in the CPA process, we have obtained 92-fs pulses at 1903 nm with an average power of 0.89 W and a pulse energy of 81 nJ. By frequency doubling, 95-fs pulses at 954 nm with an average power of 0.46 W and a pulse energy of 42 nJ have been generated. In addition, our system can also achieve tunable wavelength from 932 nm to 962 nm (frequency doubled from 1863 nm to 1919 nm). A pulse width of ∼100 fs and sufficient pulse energy are ensured over the entire tuning range. Finally, we applied the laser in a two-photon microscope and obtained superior imaging results. Due to a relatively low repetition rate (∼ 10 MHz), similar imaging quality can be achieved at significantly reduced average power compared with a commercial 80 MHz laser system. At the same time, the lower average power is helpful in limiting the thermal load to the samples. It is believed that such a setup, with its well-balanced optical characteristics and compact footprint, provides an ideal source for two-photon microscopy.

Spatiotemporal Distribution Characteristics of Nutrients in the Drowned Tidal Inlet under the Influence of Tides: A Case Study of Zhanjiang Bay, China.

The tidal dynamics and the characteristics of pollutant migration in the drowned-valley tidal inlet, a typical unit of coastal tidal inlets, are strongly influenced by geomorphological features. Along with the development of society and the economy, the hydrodynamic and water quality environment of the tidal inlet is also becoming more disturbed by human activities, such as reclamation of the sea and the construction of large bridges. In this study, a typical drowned-valley tidal inlet, Zhanjiang Bay (ZJB), was selected for the establishment of a model via coupling of a tidal hydrodynamic model and water quality numerical model. This model can be used to simulate the migration and diffusion of pollutants in ZJB. The spatial and temporal variation processes of water quality factors of the bay under the influence of special geomorphic units was simulated at the tidal-inlet entrance, the flood/ebb tidal delta, and the tidal basin. The results show that ZJB has strong tidal currents that are significantly affected by the terrain. Under the influence of the terrain and tidal currents, the phosphorus and nitrogen concentration at the flood-tide and ebb-tide moments showed obvious temporal and spatial differences in the ebb-tide delta, tidal-inlet entrance, flood-tide delta, and tidal basin. In this study, we analyzed the response mechanism of the water quality environment to the drowned-valley tidal inlet, and this can provide theoretical guidance and a basis for decision-making toward protecting the ecology and water security of ZJB.

Parallel isotope differential modeling for instationary 13C fluxomics at the genome scale.

BACKGROUND: A precise map of the metabolic fluxome, the closest surrogate to the physiological phenotype, is becoming progressively more important in the metabolic engineering of photosynthetic organisms for biofuel and biomass production. For photosynthetic organisms, the state-of-the-art method for this purpose is instationary 13C fluxomics, which has arisen as a sibling of transcriptomics or proteomics. Instationary 13C data processing requires solving high-dimensional nonlinear differential equations and leads to large computational and time costs when its scope is expanded to a genome-scale metabolic network. RESULT: Here, we present a parallelized method to model instationary 13C labeling data. The elementary metabolite unit (EMU) framework is reorganized to allow treating individual mass isotopomers and breaking up of their networks into strongly connected components (SCCs). A variable domain parallel algorithm is introduced to process ordinary differential equations in a parallel way. 15-fold acceleration is achieved for constant-step-size modeling and ~ fivefold acceleration for adaptive-step-size modeling. CONCLUSION: This algorithm is universally applicable to isotope granules such as EMUs and cumomers and can substantially accelerate instationary 13C fluxomics modeling. It thus has great potential to be widely adopted in any instationary 13C fluxomics modeling.

Assessing Seasonal Nitrate Contamination by Nitrate Dual Isotopes in a Monsoon-Controlled Bay with Intensive Human Activities in South China.

Nitrate (NO3-) dual isotope analysis was performed in Zhanjiang Bay, which is a closed bay with intensive human activities in South China, to investigate seasonal changes in the main NO3- sources and their biogeochemical processes in the monsoon-controlled climate. The relatively low N/P ratios in Zhanjiang Bay suggests that nitrogen (N) is a limiting nutrient, which indicates that the increase of N is favorable for phytoplankton proliferation. However, a sufficient amount of ammonium was found in our study area owing to intensive human activities, which can support biological processes. Thus, less NO3- biological processes were found, indicating that NO3- isotopic characteristics may reveal details of the mixing from various sources. The Bayesian mixing model showed that NO3- in the upper bay originated from manure (43%), soil N (30%), N fertilizer (17%), and N precipitation (10%) during winter, which reflects the local human activities; while NO3- sources during summer were mainly N fertilizer (36%), soil N (32%), and manure (31%), indicating the source as the runoff from the upper river basin. Our results suggest that nitrate dual-isotope was very useful for tracing the main NO3- sources in the condition of the sufficient ammonium, and runoff exerted an important impact on the shift in NO3- sources between both the local source and the source from the upper river basin during the two seasons in this monsoon-controlled bay.

Spatial and Seasonal Variations of Sedimentary Organic Matter in a Subtropical Bay: Implication for Human Interventions.

Elemental (total organic carbon (TOC) and total nitrogen (TN)) and stable carbon and nitrogen isotope compositions (δ13C and δ15N, respectively) in the surface sediment of Zhanjiang Bay (ZJB) in spring and summer were measured to study the spatial and seasonal changes of organic matter (OM) and assess the human-induced and environment-induced changes in the area. The OM in the surface sediment of ZJB was a mixture of terrestrial and marine sources, and was dominated by marine OM (54.9% ± 15.2%). Compared to the central ZJB, the channel and coastal ZJB areas had higher δ13C and δ15N values, higher TOC and TN concentrations, and lower TOC/TN ratios, indicating higher primary productivity and higher percentages of marine OM in the latter two subregions. Mariculture activities, sewage inputs, and dredging were responsible for these phenomena. Clear seasonal variations in OM were observed in ZJB. The average proportions of terrestrial OM in summer increased by 10.2% in the ZJB channel and 26.0% in the coastal ZJB area compared with those in spring. Heavy rainfall brought a large amount of terrestrial OM into the channel and coastal ZJB areas, leading to the increase of the terrestrial OM fraction in these two subregions in summer. In summary, anthropogenic influences had a significant influence on the spatial and seasonal variations of sedimentary OM in ZJB.

Slowing down photocarrier relaxation in Dirac semimetal Cd3As2 via Mn doping.

In this Letter, we successfully introduce a long-lived non-radiative photocarrier decay component in a Dirac semimetal Cd3As2 thin film via Mn doping. The long-lived decay component is found to vary between 200 ps and 2.8 ns with different Mn concentrations and probing wavelengths. Most remarkably, the elongated transients persist over the important mid-infrared wavelengths (observed up to 4 µm). Saturable absorption measurement reveals stronger modulation effects for long-width pulses (∼80 ps) from the Mn-doped samples. Our results provide new insights into the effect of transition-metal doping on the ultrafast optical properties of Dirac semimetal Cd3As2 and establish Cd3As2 as a highly amendable material for mid-infrared photonic applications.

Nanotube mode-locked, wavelength and pulsewidth tunable thulium fiber laser.

Mode-locked oscillators with highly tunable output characteristics are desirable for a range of applications. Here, with a custom-made tunable filter, we demonstrate a carbon nanotube (CNT) mode-locked thulium fiber laser with widely tunable wavelength, spectral bandwidth, and pulse duration. The demonstrated laser's wavelength tuning range reached 300 nm (from 1733 nm to 2033 nm), which is the widest-ever that was reported for rare-earth ion doped fiber oscillators in the near-infrared. At each wavelength, the pulse duration can be regulated by changing the filter's bandwidth. For example, at ~1902 nm, the pulse duration can be adjusted from 0.9 ps to 6.4 ps (the corresponding output spectral bandwidth from 4.3 nm to 0.6 nm). Furthermore, we experimentally and numerically study the spectral evolution of the mode-locked laser in presence of a tunable filter, a topic that has not been thoroughly investigated for thulium-doped fiber lasers. The detailed dynamical change of the mode-locked spectra is presented and we observed gradual suppression of the Kelly sidebands as the filter's bandwidth is reduced. Further, using the polarization-maintaiing (PM) cavity ensures that the laser is stable and the output laser's polarization extinction ratio is measured to exceed 20 dB.

Dirac semimetal saturable absorber with actively tunable modulation depth.

In this Letter, we demonstrate an electrically contacted saturable absorber (SA) device based on topological Dirac semimetal Cd3As2. With a current-induced temperature change in the range of 297-336 K, the modulation depth of the device is found to be significantly altered from 33% to 76% (under the irradiation of a 1560 nm femtosecond laser). The broad tuning of the modulation depth is attributed to the strong temperature dependence of the carrier concentration close to room temperature. The simple tuning mechanism uncovered here, together with the compatibility with III-V compounds substrate, such as GaAs, points to the potential of fabricating broadband, electrically tunable, SESAM-like devices based on emerging bulk Dirac materials.

20 GHz actively mode-locked thulium fiber laser.

A high repetition-rate actively mode-locked thulium fiber laser is demonstrated where an electro-optic lithium niobate phase modulator is used to synchronize the longitudinal modes in the cavity. The repetition rate of the actively mode-locked laser is tunable from 14.6 MHz to 19 GHz, where the 19 GHz pulses exhibit a super-mode suppression ratio of 46 dB. Furthermore, the output pulse width could be manipulated through finely controlling the detuning frequency or repetition rate. We have also experimentally observed rational harmonic mode-locking in the laser and obtained 14 GHz and 21 GHz repetition rate pulses using a 7 GHz modulating signal. To the best of our knowledge, we have improved the repetition-rate of actively mode-locked thulium fiber laser by more than one order of magnitude. Such a high repetition source can be readily synchronized to a master clock, which makes it very suitable for high speed optical data processing, communication and remote sensing.

Three-dimensional Dirac semimetal thin-film absorber for broadband pulse generation in the near-infrared.

In this Letter, the transient nonlinear absorption of three-dimensional (3D) topological Dirac semimetal Cd3As2 thin film was characterized in the near-infrared band. By performing broadband pump-probe measurements, we experimentally proved that molecular beam epitaxy (MBE) grown Cd3As2 exhibits strong and tunable saturable absorption effects across 1-2 µm. By further inserting the Cd3As2 film into the cavities of Tm- and Er-doped fiber lasers, we obtained stable mode-locked operations at 1.96 and 1.56 µm. Our results experimentally establish that Cd3As2 is a promising broadband saturable absorber (SA) for pulsed lasers in the infrared range.

Carbon Nanotube Mode-Locked Thulium Fiber Laser With 200 nm Tuning Range.

We demonstrated a mode-locked thulium/holmium (Tm/Ho) fiber laser continuously tunable across 200 nm (from 1860 nm to 2060 nm), which to the best of our knowledge represents the widest tuning range ever achieved for a passively mode-locked fiber laser oscillator. The combined use of a broadband carbon nanotube (CNT) saturable absorber and a diffraction grating mirror ensures ultra-broad tuning range, superb stability and repeatability, and makes the demonstrated laser a highly practical source for spectroscopy, imaging and optical communications. The laser emits <5 ps pulses with an optical spectral bandwidth of ∼3 nm across the full tuning range. Our results indicate that carbon nanotubes can be an excellent saturable absorber for achieving gain-bandwidth-limited tunable operation for 2 µm thulium fiber lasers.

A robust and tuneable mid-infrared optical switch enabled by bulk Dirac fermions.

Pulsed lasers operating in the mid-infrared (3-20 µm) are important for a wide range of applications in sensing, spectroscopy, imaging and communications. Despite recent advances with mid-infrared gain platforms, the lack of a capable pulse generation mechanism remains a significant technological challenge. Here we show that bulk Dirac fermions in molecular beam epitaxy grown crystalline Cd3As2, a three-dimensional topological Dirac semimetal, constitutes an exceptional ultrafast optical switching mechanism for the mid-infrared. Significantly, we show robust and effective tuning of the scattering channels of Dirac fermions via an element doping approach, where photocarrier relaxation times are found flexibly controlled over an order of magnitude (from 8 ps to 800 fs at 4.5 µm). Our findings reveal the strong impact of Cr doping on ultrafast optical properties in Cd3As2 and open up the long sought parameter space crucial for the development of compact and high-performance mid-infrared ultrafast sources.

Ultrafast nonlinear photoresponse of single-wall carbon nanotubes: a broadband degenerate investigation.

Understanding of the fundamental photoresponse of carbon nanotubes has broad implications for various photonic and optoelectronic devices. Here, Z-scan and pump-probe spectroscopy performed across 600-2400 nm were combined to give a broadband 'degenerate' mapping of the nonlinear absorption properties of single-wall carbon nanotubes (SWNTs). In contrast to the views obtained from non-degenerate techniques, sizable saturable absorption is observed from the visible to the near-infrared range, including the spectral regions between semiconducting excitonic peaks and metallic tube transitions. In addition, the broadband mapping unambiguously reveals a photobleaching to photoinduced absorption transition feature within the first semiconducting excitonic band ∼2100 nm, quantitatively marking the long-wavelength cut-off for saturable absorption of the SWNTs investigated. Our findings present a much clearer physical picture of SWNTs' nonlinear absorption characteristics, and help provide updated design guidelines for SWNT based nonlinear optical devices.