Evolutionary engineering of methylotrophic E. coli enables fast growth on methanol.

As methanol can be derived from either CO2 or methane, methanol economy can play an important role in combating climate change. In this scenario, rapid utilization of methanol by an industrial microorganism is the first and crucial step for efficient utilization of the C1 feedstock chemical. Here, we report the development of a methylotrophic E. coli strain with a doubling time of 3.5 hours under optimal conditions, comparable or faster than native model methylotrophs Methylorubrum extorquens AM1 (Td~4hr) and Bacillus methanolicus at 37°C (Td~5hr). To accomplish this, we develop a bacterial artificial chromosome (BAC) with dynamic copy number variation (CNV) to facilitate overcoming the formaldehyde-induced DNA-protein cross-linking (DPC) problem in the evolution process. We track the genome variations of 75 cultures along the evolution process by next-generation sequencing, and identified the features of the fast-growing strain. After stabilization, the final strain (SM8) grows to 20 g/L of cell mass within 77 hrs in a bioreactor. This study illustrates the potential of dynamic CNV as an evolution tool and synthetic methylotrophs as a platform for sustainable biotechnological applications.

Investigating the effects of thermal processing on bitter substances in atemoya (Annona cherimola × Annona squamosa) through sensory-guided separation.

Atemoya (Annona cherimola × Annona squamosa) is a specialty crop in Taiwan. Thermal treatment induces bitterness, complicating seasonal production adjustments and surplus reduction. In this research, sensory-guided separation, metabolomics, and orthogonal partial least squares discrimination analysis (OPLS-DA) are used for identifying the bitterness in atemoya which originates from catechins, epicatechin trimers, and proanthocyanidins. Different thermal treatments (65 °C, 75 °C, and 85 °C) revealed that the glucose and fructose contents in atemoya significantly decreased, while total phenols, flavonoids, and tannins significantly increased. The concentration of 5-hydroxymethylfurfural (5-HMF) increased from 23.16 ng/g in untreated samples to 400.71 ng/g (AP-65), 1208.59 ng/g (AP-75), and 2838.51 ng/g (AP-85). However, these levels are below the 5-HMF bitterness threshold of 3780 ng/g. Combining mass spectrometry analysis with sensory evaluation, OPLS-DA revealed that atemoya treated at 65 °C, 75 °C, and 85 °C exhibited significant bitterness, with the main bitter components being proanthocyanidin dimers and trimers.

Core antibiotic resistance genes mediate gut microbiota to intervene in the treatment of major depressive disorder.

INTRODUCTION: The relationship between depression and gut microbiota remains unclear, but an important role of gut microbiota has been verified. The relationship between gut microbiota and antibiotic resistance genes (ARGs) may be a potential new explanatory pathway. METHODS: We collected samples from 63 depressed patients and 30 healthy controls for metagenomic sequencing. The two groups' microbiota characteristics, functional characteristics, and ARG differences were analyzed. RESULTS: We obtained 30 differential KEGG orthologs (KOs) and their producers in 5 genera and 7 species by HUMAnN3. We found 6 KOs from Weissella_cibaria and Lactobacillus_plantaru are potentially coring functional mechanism of gut microbiota. Different metabolites including sphingolipids, pyrans, prenol lipids, and isoflavonoids also showed significance between MDD and HC. We detected 48 significantly different ARGs: 5 ARGs up-regulated and 43 ARGs down-regulated in MDD compared to HC. Based on Cox model results, Three ARGs significantly affected drug efficacy (ARG29, ARG105, and ARG111). Eggerthella, Weissella, and Lactobacillus were correlated with different core ARGs, which indicated different mechanisms in affecting MDD. LIMITATIONS: The present study needs to be replicated in different ethnic groups. At the same time, a larger Chinese cohort study and detailed experimental verification are also the key to further discussion. CONCLUSION: Our findings suggest that ARGs play a role in the interplay between major depressive disorder and gut microbiota. The role of ARGs should be taken into account when understanding the relationship between depression and gut microbiota.

Seasonality can override the effects of anthropogenic activities on microplastic presence in invertebrate deposit feeders in an urban river system.

Microplastic pollution is an urgent threat to the biota of aquatic ecosystems and is generally recognized as a global issue. Identifying the sources of microplastics is acknowledged as the most effective approach for mitigating microplastic pollution. However, the factors that regulate the spatiotemporal dynamics of microplastics in urban river networks, such as microplastic sources and other variables, have not been studied together at the watershed scale, let alone regarding their impact on internal microplastics. Here, we define "internal microplastics" as microplastics in biota, either in the digestive system or internal organs of organisms. We estimated the effects of anthropogenic activities (land cover and wastewater treatment plants) and seasonality on the concentration of internal microplastics in midge larvae (Diptera: Chironomidae) in an urban river system at a watershed scale in Taiwan. Agricultural activities, but not industrial activities, had a significant negative nonlinear effect on microplastic concentration. However, seasonality was the most crucial factor, as the microplastic concentration was significantly lower during the wet season. Although the presence of a wastewater treatment plant significantly increased the microplastic concentration at downstream sampling sites, its effect appeared to be minor. We conclude that seasonality overrides the effects of anthropogenic activities on the variation in the concentration of internal microplastics in midge larvae in an urban river system.

A Mini-Review of Strategies for Quantifying Anthropogenic Activities in Microplastic Studies in Aquatic Environments.

Microplastic pollution is no longer neglected worldwide, as recent studies have unveiled its potential harm to ecosystems and, even worse, to human health. Numerous studies have documented the ubiquity of microplastics, reflecting the necessity of formulating corresponding policies to mitigate the accumulation of microplastics in natural environments. Although anthropogenic activities are generally acknowledged as the primary source of microplastics, a robust approach to identify sources of microplastics is needed to provide scientific suggestions for practical policymaking. This review elucidates recent microplastic studies on various approaches for quantifying or reflecting the degree to which anthropogenic activities contribute to microplastic pollution. Population density (i.e., often used to quantify anthropogenic activities) was not always significantly correlated with microplastic abundance. Furthermore, this review argues that considering potential sources near sample sites as characteristics that may serve to predict the spatial distribution of microplastics in aquatic environments is equivocal. In this vein, a watershed-scale measure that uses land-cover datasets to calculate different percentages of land use in the watershed margins delineated by using Geographic Information System (GIS) software is discussed and suggested. Progress in strategies for quantifying anthropogenic activities is important for guiding future microplastic research and developing effective management policies to prevent microplastic contamination in aquatic ecosystems.

Epidermal Growth Factor Receptor (EGFR) Gene Polymorphism May be a Modifier for Cadmium Kidney Toxicity.

The results of many studies indicate that cadmium (Cd) exposure is harmful to humans, with the proximal tubule of the kidney being the main target of Cd accumulation and toxicity. Studies have also shown that Cd has the effect of activating the pathway of epidermal growth factor receptor (EGFR) signaling and cell growth. The EGFR is a family of transmembrane receptors, which are widely expressed in the human kidney. The aim of this study was to investigate the kidney function estimated glomerular filtration rate (eGFR), and its relationship with plasma Cd level and EGFR gene polymorphism. Using data from Academia Sinica Taiwan biobank, 489 subjects aged 30-70 years were analyzed. The demographic characteristics was determined from questionnaires, and biological sampling of urine and blood was determined from physical examination. Kidney function was assessed by the eGFR with CKD-EPI formula. Plasma Cd (ug/L) was measured by inductively coupled plasma mass spectrometry. A total of 97 single-nucleotide polymorphisms (SNPs) were identified in the EGFR on the Taiwan biobank chip, however 4 SNPs did not pass the quality control. Multiple regression analyses were performed to achieve the study aim. The mean (±SD) plasma Cd level of the study subjects was 0.02 (±0.008) ug/L. After adjusting for confounding variables, rs13244925 AA, rs6948867 AA, rs35891645 TT and rs6593214 AA types had higher eGFR (4.89 mL/min/1.73 m2 (p = 0.035), 5.54 mL/min/1.73 m2 (p = 0.03), 4.96 mL/min/1.73 m2 (p = 0.048) and 5.16 mL/min/1.73 m2 (p = 0.048), respectively). Plasma cadmium and rs845555 had an interactive effect on eGFR. In conclusion, EGFR polymorphisms could be modifiers of Cd kidney toxicity, in which rs13244925 AA, rs6948867 AA, rs35891645 TT and rs6593214 AA may be protective, and Cd interacting with rs845555 may affect kidney function.

Effects of anthropogenic activities on microplastics in deposit-feeders (Diptera: Chironomidae) in an urban river of Taiwan.

The presence of microplastics (MPs) in the environment has generated global concerns. However, the explicit assessment of the effect of multiple anthropogenic activities on the existence of MPs in the freshwater system is scarcely reported. This study quantified anthropogenic activities and analyzed their relationship with MPs on a freshwater organism: the midge larvae (Diptera: Chironomidae). The study took place in an urban river and consisted of comparing the abundance and types of MPs. Our results highlight that, while industrial area was the most important variable contributing to the total MP concentration in midge larvae, residential area also influenced the concentration of microfibers in midge larvae. The impact of a residential area on the relative abundance of microfibers in each sample site was diluted by the proximity to an industrial area. In conclusion, we suggest that industrial areas are a potential source of MP pollution in river sediment, and midge larvae can be a good indicator of the MP concentrations in urban river systems. Quantifying anthropogenic activities can help discern their effects on MP concentration in a river system and promote management strategies.

APE1 distinguishes DNA substrates in exonucleolytic cleavage by induced space-filling.

The exonuclease activity of Apurinic/apyrimidinic endonuclease 1 (APE1) is responsible for processing matched/mismatched terminus in various DNA repair pathways and for removing nucleoside analogs associated with drug resistance. To fill in the gap of structural basis for exonucleolytic cleavage, we determine the APE1-dsDNA complex structures displaying end-binding. As an exonuclease, APE1 does not show base preference but can distinguish dsDNAs with different structural features. Integration with assaying enzyme activity and binding affinity for a variety of substrates reveals for the first time that both endonucleolytic and exonucleolytic cleavage can be understood by an induced space-filling model. Binding dsDNA induces RM (Arg176 and Met269) bridge that defines a long and narrow product pocket for exquisite machinery of substrate selection. Our study paves the way to comprehend end-processing of dsDNA in the cell and the drug resistance relating to APE1.

V- and W-band microwave generation and modulation using semiconductor lasers at period-one nonlinear dynamics.

Microwave generation and modulation over the V- and W-bands are investigated using a semiconductor laser subject to both comb-like optical injection and direct modulation. The former not only excites period-one (P1) nonlinear dynamics for tunable microwave generation but also improves the stability and purity of such generated microwaves. The latter upconverts data onto the generated microwaves by superimposing the data effectively only onto the lower oscillation sideband of the P1 dynamics, which prevents the data from dispersion-induced degradation over fiber distribution. As a result, microwaves that are continuously tunable from 40 to 110 GHz with a 3-dB linewidth of less than 1 Hz and with phase noise better than -95dBc/Hz at 10-kHz offset are generated. A bit-error ratio better than the forward error correction limit, 3.8×10-3, is achieved for 12-Gb/s 16-quadrature amplitude modulation data after 25-km fiber distribution.

The effect of Xenopus laevis egg extracts with/without BRG1 on the development of preimplantation cloned mouse embryos.

SummaryMuch effort has been devoted to improving the efficiency of animal cloning. The aim of this study was to investigate the effect of BRG1 contained in Xenopus egg extracts on the development of cloned mouse embryos. The results showed that mouse NIH/3T3 cells were able to express pluripotent genes after treatment with egg extracts, indicating that the egg extracts contained reprogramming factors. After co-injection of Xenopus egg extracts and single mouse cumulus cells into enucleated mouse oocytes, statistically higher pronucleus formation and development rates were observed in the egg Extract- co-injected group compared with those in the no egg extract-injected (NT) group (38-66% vs 18-34%, P<0.001). Removal of BRG1 protein from Xenopus egg extracts was conducted, and the BRG1-depleted extracts were co-injected with single donor cells into recipient oocytes. The results showed that the percentages of pronucleus formation were significantly higher in both BRG1-depleted and BRG1-intact groups than that in the nuclear transfer (NT) group (94, 64% vs 50%, P<0.05). Furthermore, percentages in the BRG1-depleted group were even higher than in the BRG1-intact group (94% vs 64%). More confined expression of Oct4 in the inner cell mass (ICM) was observed in the blastocyst derived from the egg extract-injected groups. However, Nanog expression was more contracted in the ICM of cloned blastocysts in the BRG1-depleted group than in the BGR1-intact group. Based on the present study, BRG1 might not play an essential role in reprogramming, but the factors enhancing pronucleus formation and development of cloned mouse embryos are contained in Xenopus egg extracts.

Structural insights into the duplex DNA processing of TREX2.

The three prime repair exonuclease 2 (TREX2) is an essential 3'-to-5' exonuclease that functions in cell proliferation, genome integrity and skin homeostasis maintenance. The abnormal expression level of TREX2 can result in broken chromosome, increased susceptibility to skin carcinogenesis and Psoriasis. However, the molecular mechanisms of how TREX2 binds and processes its natural substrates, dsDNA or chromosomal DNA, to maintain genome stability remain unclear. In this study, we present four new crystal structures: apo-TREX2, TREX2 in complex with two different dsDNA substrates, and TREX2 in complex with a processed dsDNA product. Analysis of the structures reveals that TREX2 stacks with the 5'-terminal of dsDNA by a Leu20-Pro21-Asn22 cluster for precisely trimming the 3'-overhang. In addition, TREX2 specifically interacts with the non-scissile strand of dsDNA by an α-helix-loop region. The unique interaction patterns of the TREX2-dsDNA complex highlight the requirement of long double-stranded region for TREX2 binding and provide evidence of the functional role of TREX2 in processing chromosomal DNA. Moreover, the non-processive property of TREX2 is elucidated by the structure of TREX2-product complex. Our work discloses the first structural basis of the molecular interactions between TREX2 and its substrates and unravels the mechanistic actions of TREX2.

Long-reach 60-GHz MMWoF link with free-running laser diodes beating.

With the remote beating of two mutually incoherent laser carriers, the local-oscillator-free long-reach millimeter-wave over fiber (MMWoF) link at 60-GHz band is demonstrated. The unique schemes of the proposed MMWoF are the wavelength-locked colorless laser diode (CLD) modulator, the mutually incoherent optical carrier for heterodyne MMW generation, and the square-law power envelope detection at receiving end. By directly encoding the single-mode with the CLD modulator, the single-carrier modulated QAM-OFDM data is achieved to release the RF power fading after fiber transmission. The mutually incoherent laser beating enables the optical heterodyne MMW generation with two independent optical carriers, which provides the advantages of local-oscillator-free operation and rules out the requirement of dual-mode optical carrier delivery from central office. At the wireless receiving end, the received QAM-OFDM data is self-down-converted to the baseband by employing the square-law power envelope detection. This eliminates the requirement of local oscillator and rules out the influence of the MMW carrier frequency fluctuation between two mutually incoherent lasers (used at central office and remote node), which effectively provides the MMW carrier immunity against the down-conversion instability caused by clock jitter or carrier incoherence. This architecture ensures the transmission of 16.5-Gbit/s 32-QAM OFDM data over 50 km in SMF and 3 m in free-space with the FEC certificated error vector magnitude of 12%, signal-to-noise ratio (SNR) of 18.4 dB, and bit error rate of 3.8 × 10-3. For multi-channel DWDM-PON applications, the proposed local-oscillator-free MMWoF link can successfully perform 11 DWDM channels of 32-QAM OFDM data access at 16.5 Gbit/s per channel via the wavelength controlling of the CLD modulation stage and the detuning of the beating carrier at remote node.

On channel estimation schemes for APD-based DDM-OFDM-PONs under sub-Nyquist sampling.

Implementing preprocessing in a delay-division multiplexing (DDM) orthogonal frequency-division multiplexing (OFDM) passive optical network (PON) requires a priori knowledge of channel responses, which need to be estimated under the constraint of sub-Nyquist analog-to-digital sampling. The localized approach allocates subcarriers in different frequency zones to training symbols in different time slots for channel estimation without spectral overlap. Unfortunately, the localized scheme is susceptible to inaccurate estimation when using an avalanche photodiode (APD), due to variations in APD saturation associated with different training symbols. Instead of localizing all subcarriers of a training symbol in a single frequency zone, we propose distributing training subcarriers through various frequency zones. This distributed scheme would prevent spectral overlap and also reduce the degree of variation in APD saturation, thereby improving the accuracy of channel estimation. Alternatively, we propose an orthogonal scheme in which each training symbol uses all of the subcarriers simultaneously. The orthogonality specified among consecutive training symbols should make it possible to estimate the channel response with low computational complexity. We conducted experiments to compare various schemes used for channel estimation in a 25-Gbps APD-based OFDM-PON. Our results revealed that the orthogonal scheme achieved the best results, and the localized scheme provided the worst channel estimates. We demonstrate the application of the orthogonal scheme in a penalty-free DDM system at 1/32 of the Nyquist rate, which provided a loss budget of 28 dB after fiber transmission over a distance of 25 km.

Novel Gold Dendritic Nanoforests Combined with Titanium Nitride for Visible-Light-Enhanced Chemical Degradation.

In this study, gold dendritic nanoforests (Au DNFs)-titanium nitride (TiN) composite was firstly proposed for visible-light photodegradation of pollutants. A high-power impulse magnetron sputtering system was used to coat TiN films on silicon wafers, and a fluoride-assisted galvanic replacement reaction was applied to deposit Au DNFs on TiN/Si substrates. Scanning electron microscope images and X-ray diffraction patterns of TiN/Si, Au DNFs/Si, and Au DNFs/TiN/Si samples verified that this synthesis process was accurately controlled. The average reflectance of Au DNFs/Si and Au DNFs/TiN/Si considerably declined to approximately 10%, because the broadband localized surface plasmon resonances of Au DNFs cause broadband absorbance and low reflectance. In photocatalytic performance, 90.66 ± 1.41% 4-nitrophenol was successfully degraded in 180 min by Au DNFs/TiN/Si under visible-light irradiation. Therefore, Au DNFs/TiN/Si has the chance to be a visible-light photocatalyst for photodegradation of pollutants.

Simultaneous realization of high sensing sensitivity and tunability in plasmonic nanostructures arrays.

A plasmonic nanostructure (PNS) which integrates metallic and dielectric media within a single structure has been shown to exhibit specific plasmonic properties which are considered useful in refractive index (RI) sensor applications. In this paper, the simultaneous realization of sensitivity and tunability of the optical properties of PNSs consisting of alternative Ag and dielectric of nanosphere/nanorod array have been proposed and compared by using three-dimensional finite element method. The proposed system can support plasmonic hybrid modes and the localized surface plasmonic resonances and cavity plasmonic resonances within the individual PNS can be excited by the incident light. The proposed PNSs can be operated as RI sensor with a sensitivity of 500 nm/RIU (RIU = refractive index unit) ranging from UV to the near-infrared. In addition, a narrow bandwidth and nearly zero transmittance along with a high absorptance can be achieved by a denser PNSs configuration in the unit cell of PNS arrays. We have demonstrated the number of modes sustained in the PNS system, as well as, the near-field distribution can be tailored by the dielectric media in PNSs.

DFT/IDFT-free receiving scheme for spread-OFDM signals employing low-sampling-rate ADCs.

This paper presents a DFT/IDFT-free receiving scheme for spread-OFDM signals. Leveraging sub-Nyquist sampling and proper sampling delay, the proposed scheme enables each user to receive the requested data without the need for DFT and IDFT; thus, the complexity at receiver can be greatly reduced. Nonetheless, DC component is altered in an AC coupling system, such that severe waveform distortion is caused when the process of DFT/IDFT is omitted. Thus, a DC-zeroing algorithm is proposed to guarantee constant DC after sub-Nyquist sampling, thereby eliminating such distortion. To experimentally verify the concept of proposed scheme, a 27.15-Gbit/s optical spread-OFDM signal was transmitted over fiber and received by the DFT/IDFT-free scheme with sub-Nyquist sampling. More users will reduce the required sampling rate at receiver; for the case of 16 users, the required sampling rate for the 27.15-Gbit/s signal is as low as 1 GSample/s. The experimental results show that error-free transmission was achievable, and the penalty due to lowering sampling rate (i.e., increasing the number of users) is insignificant.

V-band gapless OFDM RoF system with power detector down-conversion and novel Volterra nonlinear filtering.

This Letter presents a V-band gapless orthogonal frequency division multiplexing (OFDM) RoF system at 60 GHz employing a power detector to support vector signal down-conversion. Additional RF tone is generated and transmitted from a central station to replace the local oscillator at a wireless receiver for power detector down-conversion. To enhance the spectrum efficiency, the gap between the OFDM signal and the RF tone is not needed. However, the down-converted signal will suffer signal-to-signal interference (SSBI). In this Letter, we propose and successfully employ a novel Volterra nonlinear compensation to mitigate SSBI, resulting in a 22% data rate improvement with a bit-loading algorithm.