Chromosome recombination and modification by LoxP-mediated evolution in Vibrio natriegens using CRISPR-associated transposases

Chromosome rearrangement by LoxP-mediated evolution has emerged as a powerful approach to studying how chromosome architecture impacts phenotypes. However, it relies on the in vitro synthesis of artificial chromosomes. The recently reported CRISPR-associated transposases (CASTs) held great promise for the efficient insertion of abundant LoxP sites directly onto the genome of wild-type strains. In this study, with the fastest-growing bacterium Vibrio natrigens (V. natriegens) as an object, a multiplex genome integration tool derived from CASTs was employed to achieve the insertion of cargo genes at eight specific genomic loci within 2 days. Next, we introduced 30 LoxP sites onto chromosome 2 (Chr2) of V. natriegens. Rigorously induced Cre recombinase was used to demonstrate Chromosome Rearrangement and Modification by LoxP-mediated Evolution (CRaMbLE). Growth characterization and genome sequencing showed that the ~358 kb fragment on Chr2 was accountable for the rapid growth of V. natriegens. The enabling tools we developed can help identify genomic regions that influence the rapid growth of V. natriegens without a prior understanding of genome mechanisms. This groundbreaking demonstration may also be extended to other organisms such as Escherichia coli, Pseudomonas putida, Bacillus subtilis, and so on.

Rapid Growth of Metal-Metal Oxide Core-Shell Structures through Joule Resistive Heating: Morphological, Structural, and Luminescence Characterization

The aim of this study is to prove that resistive heating enables the synthesis of metal/metal oxide composites in the form of core-shell structures. The thickness and morphology of the oxide layer depends strongly on the nature of the metal, but the influences of parameters such as the time and current profiles and the presence of an external field have also been investigated. The systems chosen for the present study are Zn/ZnO, Ti/TiO2, and Ni/NiO. The characterization of the samples was performed using techniques based on scanning electron microscopy (SEM). The thicknesses of the oxide layers varied from 10 μm (Zn/ZnO) to 50 μm (Ni/NiO). In the case of Zn- and Ti-based composites, the growth of nanostructures on the oxide layer was observed. Micro- and nanoneedles formed on the ZnO layer while prism-like structures appeared on the TiO2. In the case of the NiO layer, micro- and nanocrystals were observed. Applying an external electric field seemed to align the ZnO needles, whereas its effect on TiO2 and NiO was less appreciable, principally affecting the shape of their grain boundaries. The chemical compositions were analysed using X-ray spectroscopy (EDX), which confirmed the existence of an oxide layer. Structural information was obtained by means of X-ray diffraction (XRD) and was later checked using Raman spectroscopy. The oxide layers seemed to be crystalline and, although some non-stoichiometric phases appeared, the stoichiometric phases were predominant; these were wurtzite, rutile, and cubic for Zn, Ti, and Ni oxides, respectively. The photoluminescence technique was used to study the distribution of defects on the shell, and mainly visible bands (2-2.5 eV), attributed to oxygen vacancies, were present. The near-band edges of ZnO and TiO2 were also observed around 3.2-3.3 eV.

Effects of genetic selection for fast growth on the development of wooden breast myopathy in broilers

1. This study investigated the physiological and molecular mechanisms leading to wooden breast (WB) by comparing growth parameters, oxygen consumption rate, thyroid hormone and gene expression patterns in fast- versus slow-growing broiler lines (Cobb500 and L1986, respectively).2. WB was observed in Cobb500 broilers only and was first diagnosed on d 21 post-hatch. Compared to the slow-growing L1986, Cobb500 showed a significantly higher growth rate, relative breast weight, breast thickness, meat pH and water-retention capacity (drip loss). Correspondingly, there was significantly lower relative heart weight, relative right ventricular weight, triiodothyronine and thyroxine concentrations and oxygen consumption rate.3. Compared to No-WB Cobb500, the WB-affected samples exhibited higher relative breast weight, breast thickness and drip loss and lower plasma total thyroxine (T4) concentrations.4. Selection for fast growth was associated with differential expression of genes involved in hypoxia (PLOD2), energy metabolism (FABP3, FABP4, CD36, and LPL), endoplasmic reticulum stress, muscle regeneration (CSRP3) and fibre-type switching (ANKRD1). WB-affected samples exhibited an upregulation of CSRP3, PLOD2 and ANKRD1, while CD36 was downregulated. Taken together, selection for fast growth and muscle gain is not matched by adequate cardiac and metabolic support systems.

Ultrafast Antisolvent Growth of Single-Crystal CsPbBr3 Microcavity for Whispering-Gallery-Mode Lasing

In recent years, all-inorganic cesium lead bromide (CsPbBr₃) perovskites have garnered considerable attention for their prospective applications in green photonics and optoelectronic devices. However, the development of efficient and economical methods to obtain high-quality micron-sized single-crystalline CsPbBr₃ microplatelets (MPs) has become a challenge. Here, we report the synthesis of CsPbBr₃ MPs on Si/SiO₂ substrate by optimizing the ultrafast antisolvent method (FAS). This technique is able to produce well-dispersed, uniformly sized, and morphologically regular tetragonal phase single crystals, which can give strong green emission at room temperature, with excellent stability and excitonic character. Moreover, the crystals demonstrated lasing with a whispering gallery mode with a low threshold. These results suggest that the single-crystalline CsPbBr₃ MPs synthesized by this method are of high optical quality, holding vast potential for future applications in photonic devices.

Ultrafast One-Step Deposition Route to Fabricate Single-Crystal CsPbX3 (X = Cl, Cl/Br, Br, and Br/I) Photodetectors

Inorganic perovskites have received much attention due to their stability and high performance in luminescence, photoelectric conversion, and photodetection. However, perovskite optoelectronic devices prepared by the solution technique are still suffering from time-consuming and complex operations. In this paper, a single-crystal perovskite-based photodetector (PD) is prepared by very fast one-step deposition of synthesizing microplatelets (MPs) on the electrode directly. The saturated precursor is carefully optimized by adding appropriate antisolvent chlorobenzene (CB) to fabricate the MPs with their PL wavelength ranging from 418 to 600 nm. Furthermore, the PDs with a low dark current on order of nanoangstroms, high responsivity and detectivity of up to 10.7 A W^-1 and 10¹² Jones, respectively, and an ultrafast response rate featured by 278/287 μs (rise/decay time) are achieved. These all-inorganic perovskite PDs with a simple fabricating process and tunable detection wavelength meet the evolution tendency of PDs toward low cost and high performance, which is a high-profile strategy to realize high-performance perovskite PDs.

Comparative Genomic and Transcriptomic Analysis Reveals Specific Features of Gene Regulation in Kluyveromyces marxianus

Kluyveromyces marxianus is a promising host for producing bioethanol and heterologous proteins. It displays many superior traits to a conventional industrial yeast species, Saccharomyces cerevisiae, including fast growth, thermotolerance and the capacity to assimilate a wider variety of sugars. However, little is known about the mechanisms underlying the fast-growing feature of K. marxianus. In this study, we performed a comparative genomic analysis between K. marxianus and other Saccharomycetaceae species. Genes involved in flocculation, iron transport, and biotin biosynthesis have particularly high copies in K. marxianus. In addition, 60 K. marxianus specific genes were identified, 45% of which were upregulated during cultivation in rich medium and these genes may participate in glucose transport and mitochondrion related functions. Furthermore, the transcriptomic analysis revealed that under aerobic condition, normalized levels of genes participating in TCA cycles, respiration chain and ATP biosynthesis in the lag phase were higher in K. marxianus than those in S. cerevisiae. Levels of highly copied genes, genes involved in the respiratory chain and mitochondrion assembly, were upregulated in K. marxianus, but not in S. cerevisiae, in later time points during cultivation compared with those in the lag phase. Notably, during the fast-growing phase, genes involved in the respiratory chain, ATP synthesis and glucose transport were co-upregulated in K. marxianus. A few shared motifs in upstream sequences of relevant genes might result in the co-upregulation. Specific features in the co-regulations of gene expressions might contribute to the fast-growing phenotype of K. marxianus. Our study underscores the importance of genome-wide rewiring of the transcriptional network during evolution.

Biochemical Characteristics and a Genome-Scale Metabolic Model of an Indian Euryhaline Cyanobacterium with High Polyglucan Content

Marine cyanobacteria are promising microbes to capture and convert atmospheric CO₂ and light into biomass and valuable industrial bio-products. Yet, reports on metabolic characteristics of non-model cyanobacteria are scarce. In this report, we show that an Indian euryhaline Synechococcus sp. BDU 130192 has biomass accumulation comparable to a model marine cyanobacterium and contains approximately double the amount of total carbohydrates, but significantly lower protein levels compared to Synechococcus sp. PCC 7002 cells. Based on its annotated chromosomal genome sequence, we present a genome scale metabolic model (GSMM) of this cyanobacterium, which we have named as iSyn706. The model includes 706 genes, 908 reactions, and 900 metabolites. The difference in the flux balance analysis (FBA) predicted flux distributions between Synechococcus sp. PCC 7002 and Synechococcus sp. BDU130192 strains mimicked the differences in their biomass compositions. Model-predicted oxygen evolution rate for Synechococcus sp. BDU130192 was found to be close to the experimentally-measured value. The model was analyzed to determine the potential of the strain for the production of various industrially-useful products without affecting growth significantly. This model will be helpful to researchers interested in understanding the metabolism as well as to design metabolic engineering strategies for the production of industrially-relevant compounds.

The GATA transcription factor GNC plays an important role in photosynthesis and growth in poplar

GATA transcription factors are involved in the regulation of diverse growth processes and environmental responses in Arabidopsis and rice. In this study, we conducted a comprehensive bioinformatic survey of the GATA family in the woody perennial Populus trichocarpa. Thirty-nine Populus GATA genes were classified into four subfamilies based on gene structure and phylogenetic relationships. Predicted cis-elements suggested potential roles of poplar GATA genes in light, phytohormone, development, and stress responses. A poplar GATA gene, PdGATA19/PdGNC (GATA nitrate-inducible carbon-metabolism-involved), was identified from a fast growing poplar clone. PdGNC expression was significantly up-regulated in leaves under both high (50 mM) and low (0.2 mM) nitrate concentrations. The CRISPR/Cas9-mediated mutant crispr-GNC showed severely retarded growth and enhanced secondary xylem differentiation. PdGNC-overexpressing transformants exhibited 25-30% faster growth, 20-28% higher biomass accumulation, and ~25% increase in chlorophyll content, photosynthetic rate, and plant height, compared with the wild type. Transcriptomic analysis showed that PdGNC was involved in photosynthetic electron transfer and carbon assimilation in the leaf, cell division and carbohydrate utilization in the stem, and nitrogen uptake in the root. These data indicated that PdGNC plays a crucial role in plant growth and is potentially useful in tree molecular breeding.

Characterization of the developmental dynamics of the elongation of a bamboo internode during the fast growth stage

Previous studies on the fast growth of bamboo shoots mainly focused on the entire culm. No work about the fast elongation of a single internode, which is the basic unit for the fast growth of bamboo shoots, has been reported so far according to our knowledge. In this study, we have systematically investigated the regulating mechanisms underlying the fast growth of a single bamboo internode of Bambusa multiplex (Lour.) Raeusch. ex Schult. We discovered that the growth of the internode displays a logistic pattern, and the two sections located in the bottom of the internode, one for cell division and, another for cell elongation, each with an ~1-cm length, comprise the effective zones for the internode growth. RNA-Seq analysis identified a number of genes potentially involved in regulating the fast growth of bamboo internode such as those that have positive roles in promoting cell growth or division, which were dramatically down-regulated in the internode at fast growth decreasing stage. Further analysis revealed that sugar plays an important role in promoting the fast growth of bamboo internodes through inhibition of BmSnf1. Mechanical stress is found to be involved in the triggering of the internode growth decrease through activation of the generation of reactive oxygen species by upregulating Calmodulins. These results provide systematic insight into the biological mechanisms underlying the fast growth of bamboo shoots based on the behavior of a single internode.

Morphological dissection and cellular and transcriptome characterizations of bamboo pith cavity formation reveal a pivotal role of genes related to programmed cell death

Pith cavity formation is critical for bamboo to overcome the bending force during its fast growth; however, the underlying molecular mechanisms remain largely unknown. Multiple approaches, including anatomical dissection, mathematical modelling and transcriptome profiling, were employed in this study to investigate the biology of pith cavity formation in bamboo Pseudosasa japonica. We found that the corruption of pith tissue occurred sequentially and asymmetrically from the top-centre of the internode down to the bottom, which might be caused by the combined effects of asymmetrical radial and axial tensile forces during shoot-wall cell elongation and spiral growth of bamboo internodes. Programmed cell death (PCD) in pitch manifested by TUNEL positive nuclei, DNA cleavage and degraded organelles, and potentially regulated by ethylene and calcium signalling pathway, ROS burst, cell wall modification, proteolysis and nutrient recycle genes, might be responsible for pith tissue corruption of Ps. japonica. Although similar physiological changes and transcriptome profiles were found in different bamboo species, different formation rates of pith cavity were observed, which might be caused by different pith cells across the internode that were negatively correlated with the culm diameter. These findings provided a systematical view on the formation of bamboo pith cavity and revealed that PCD plays an important role in the bamboo pith cavity formation.

How adaptive evolution reshapes metabolism to improve fitness: recent advances and future outlook

Adaptive laboratory evolution (ALE) has emerged as a powerful tool in basic microbial research and strain development. In the context of metabolic science and engineering, it has been applied to study gene knockout responses, expand substrate ranges, improve tolerance to process conditions, and to improve productivity via designed growth coupling. In recent years, advancements in ALE methods and systems biology measurement technologies, particularly genome sequencing and ¹³C metabolic flux analysis (¹³C-MFA), have enabled detailed study of the mechanisms and dynamics of evolving metabolism. In this review, we discuss a range of studies that have applied flux analysis to adaptively evolved strains, as well as modeling frameworks developed to predict and interpret evolved fluxes. These efforts link mutations to fitness-enhanced phenotypes, identify bottlenecks and approaches to resolve them, and address systems concepts such as optimality.

Whole-Genome and Expression Analyses of Bamboo Aquaporin Genes Reveal Their Functions Involved in Maintaining Diurnal Water Balance in Bamboo Shoots

Water supply is essential for maintaining normal physiological function during the rapid growth of bamboo. Aquaporins (AQPs) play crucial roles in water transport for plant growth and development. Although 26 PeAQPs in bamboo have been reported, the aquaporin-led mechanism of maintaining diurnal water balance in bamboo shoots remains unclear. In this study, a total of 63 PeAQPs were identified, based on the updated genome of moso bamboo (Phyllostachys edulis), including 22 PePIPs, 20 PeTIPs, 17 PeNIPs, and 4 PeSIPs. All of the PeAQPs were differently expressed in 26 different tissues of moso bamboo, based on RNA sequencing (RNA-seq) data. The root pressure in shoots showed circadian rhythm changes, with positive values at night and negative values in the daytime. The quantitative real-time PCR (qRT-PCR) result showed that 25 PeAQPs were detected in the base part of the shoots, and most of them demonstrated diurnal rhythm changes. The expression levels of some PeAQPs were significantly correlated with the root pressure. Of the 86 sugar transport genes, 33 had positive co-expression relationships with 27 PeAQPs. Two root pressure-correlated PeAQPs, PeTIP4;1 and PeTIP4;2, were confirmed to be highly expressed in the parenchyma and epidermal cells of bamboo culm, and in the epidermis, pith, and primary xylem of bamboo roots by in situ hybridization. The authors’ findings provide new insights and a possible aquaporin-led mechanism for bamboo fast growth.

Quasi-Two-Dimensional Halide Perovskite Single Crystal Photodetector

The robust material stability of the quasi-two-dimensional (quasi-2D) metal halide perovskites has opened the possibility for their usage instead of three-dimensional (3D) perovskites. Further, devices based on large area single crystal membranes have shown increasing promise for photoelectronic applications. However, growing inch-scale quasi-2D perovskite single crystal membranes (quasi-2D PSCMs) has been fundamentally challenging. Here we report a fast synthetic method for synthesizing inch-scale quasi-2D PSCMs, namely (C₄H₉NH₃) _n(CH₃NH₃) _n-1Pb _nI_{3 n+1} (index n = 1, 2, 3, 4, and ∞), and demonstrate their application in a single-crystal photodetector. A quasi-2D PSCM has been grown at the water-air interface where spontaneous alignment of alkylammonium cations and high chemical potentials enable uniform orientation and fast in-plane growth. Structural, optical, and electrical characterizations have been conducted as a function of quantum well thickness, which is determined by the index n. It is shown that the photodetector based on the quasi-2D PSCM with the smallest quantum well thickness ( n = 1) exhibits a strikingly low dark current of ∼10^-13 A, higher on/off ratio of ∼10⁴, and faster response time in comparison to those of photodetectors based on quasi-2D PSCMs with larger quantum well thickness ( n > 1). Our study paves the way toward the merging the gap between single crystal devices and the emerging quasi-2D perovskite materials.

The association of hormone signalling genes, transcription and changes in shoot anatomy during moso bamboo growth

Moso bamboo is a large, woody bamboo with the highest ecological, economic and cultural value of all the bamboo types and accounts for up to 70% of the total area of bamboo grown. However, the spatiotemporal variation role of moso bamboo shoot during growth period is still unclear. We found that the bamboo shoot growth can be divided into three distinct periods, including winter growth, early growth and late growth based on gene expression and anatomy. In the early growth period, lateral buds germinated from the top of the bamboo joint in the shoot tip. Intercalary meristems grew vigorously during the winter growth period and early growth period, but in the late growth period, mitosis in the intercalary meristems decreased. The expression of cell cycle-associated genes and the quantity of differentially expressed genes were higher in early growth than those in late growth, appearing to be influenced by hormonal concentrations. Gene expression analysis indicates that hormone signalling genes play key roles in shoot growth, while auxin signalling genes play a central role. In situ hybridization analyses illustrate how auxin signalling genes regulate apical dominance, meristem maintenance and lateral bud development. Our study provides a vivid picture of the dynamic changes in anatomy and gene expression during shoot growth in moso bamboo, and how hormone signalling-associated genes participate in moso bamboo shoot growth.

Fast Growth of GaN Epilayers via Laser-Assisted Metal-Organic Chemical Vapor Deposition for Ultraviolet Photodetector Applications

In this study, we successfully developed a carbon dioxide (CO₂)-laser-assisted metal-organic chemical vapor deposition (LMOCVD) approach to fast synthesis of high-quality gallium nitride (GaN) epilayers on Al₂O₃ [sapphire(0001)] substrates. By employing a two-step growth procedure, high crystallinity and smooth GaN epilayers with a fast growth rate of 25.8 μm/h were obtained. The high crystallinity was confirmed by a combination of techniques, including X-ray diffraction, Raman spectroscopy, transmission electron microscopy, and atomic force microscopy. By optimizing growth parameters, the ∼4.3-μm-thick GaN films grown at 990 °C for 10 min showed a smooth surface with a root-mean-square surface roughness of ∼1.9 nm and excellent thickness uniformity with sharp GaN/substrate interfaces. The full-width at half-maximum values of the GaN(0002) X-ray rocking curve of 313 arcsec and the GaN(101̅2) X-ray rocking curve of 390 arcsec further confirmed the high crystallinity of the GaN epilayers. We also fabricated ultraviolet (UV) photodetectors based on the as-grown GaN layers, which exhibited a high responsivity of 0.108 A W^-1 at 367 nm and a fast response time of ∼125 ns, demonstrating its high optical quality with potential in optoelectronic applications. Our strategy thus provides a simple and cost-effective means toward fast and high-quality GaN heteroepitaxy growth suitable for fabricating high-performance GaN-based UV detectors.

Fast Growth and Broad Applications of 25-Inch Uniform Graphene Glass

A unique ethanol-precursor-based LPCVD route is developed for the fast (4 min, improved 20 times) and scalable (25 inch, improved six times) growth of high-quality graphene glass. The obtained graphene glass presents high uniformity across large areas and is demonstrated to be an excellent material for constructing switchable windows and biosensor devices, owing to its excellent transparency and conductivity.

Surface Monocrystallization of Copper Foil for Fast Growth of Large Single-Crystal Graphene under Free Molecular Flow

Wafer-sized single-crystalline Cu (100) surface can be readily achieved on stacked polycrystalline Cu foils via simple oxygen chemisorption-induced reconstruction, enabling fast growth of large-scale millimeter-sized single-crystalline graphene arrays under molecular flow. The maximum growth rate can reach 300 μm min^-1 , several orders of magnitude higher than previously reported values for millimeter-sized single-crystalline graphene growth on Cu foils.

Heterologous expression of chloroplast-localized geranylgeranyl pyrophosphate synthase confers fast plant growth, early flowering and increased seed yield

Geranylgeranyl pyrophosphate synthase (GGPS) is a key enzyme for a structurally diverse class of isoprenoid biosynthetic metabolites including gibberellins, carotenoids, chlorophylls and rubber. We expressed a chloroplast-targeted GGPS isolated from sunflower (Helianthus annuus) under control of the cauliflower mosaic virus 35S promoter in tobacco (Nicotiana tabacum). The resulting transgenic tobacco plants expressing heterologous GGPS showed remarkably enhanced growth (an increase in shoot and root biomass and height), early flowering, increased number of seed pods and greater seed yield compared with that of GUS-transgenic lines (control) or wild-type plants. The gibberellin levels in HaGGPS-transgenic plants were higher than those in control plants, indicating that the observed phenotype may result from increased gibberellin content. However, in HaGGPS-transformant tobacco plants, we did not observe the phenotypic defects such as reduced chlorophyll content and greater petiole and stalk length, which were previously reported for transgenic plants expressing gibberellin biosynthetic genes. Fast plant growth was also observed in HaGGPS-expressing Arabidopsis and dandelion plants. The results of this study suggest that GGPS expression in crop plants may yield desirable agronomic traits, including enhanced growth of shoots and roots, early flowering, greater numbers of seed pods and/or higher seed yield. This research has potential applications for fast production of plant biomass that provides commercially valuable biomaterials or bioenergy.