Discovery, characterization and mechanism of a Microbacterium esterase for key d-biotin chiral intermediate synthesis.

Esterases are crucial biocatalysts in chiral compound synthesis. Herein, a novel esterase EstSIT01 belonging to family V was identified from Microbacterium chocolatum SIT101 through genome mining and phylogenetic analysis. EstSIT01 demonstrated remarkable efficiency in asymmetrically hydrolyzing meso-dimethyl ester [Dimethyl cis-1,3-Dibenzyl-2-imidazolidine-4,5-dicarboxyate], producing over 99% yield and 99% enantiomeric excess (e.e.) for (4S, 5R)-monomethyl ester, a crucial chiral intermediate during the synthesis of d-biotin. Notably, the recombinant E. coli expressing EstSIT01 exhibited over 40-fold higher activity than that of the wild strain. EstSIT01 displays a preference for short-chain p-NP esters. The optimal temperature and pH were 45 °C and 10.0, with Km and kcat values of 0.147 mmol/L and 5.808 s- 1, respectively. Molecular docking and MD simulations suggest that the high stereoselectivity for meso-diester may attribute to the narrow entrance tunnel and unique binding pocket structure. Collectively, EstSIT01 holds great potential for preparing chiral carboxylic acids and esters.

Dual-Channel Prototype Network for Few-Shot Pathology Image Classification.

In the field of pathology, the scarcity of certain diseases and the difficulty of annotating images hinder the development of large, high-quality datasets, which in turn affects the advancement of deep learning-assisted diagnostics. Few-shot learning has demonstrated unique advantages in modeling tasks with limited data, yet explorations of this method in the field of pathology remain in the early stages. To address this issue, we present a dual-channel prototype network (DCPN), a novel few-shot learning approach for efficiently classifying pathology images with limited data. The DCPN leverages self-supervised learning to extend the pyramid vision transformer (PVT) to few-shot classification tasks and combines it with a convolutional neural network to construct a dual-channel network for extracting multi-scale, high-precision pathological features, thereby substantially enhancing the generalizability of prototype representations. Additionally, we design a soft voting classifier based on multi-scale features to further augment the discriminative power of the model in complex pathology image classification tasks. We constructed three few-shot classification tasks with varying degrees of domain shift using three publicly available pathological datasets-CRCTP, NCTCRC, and LC25000-to emulate real-world clinical scenarios. The results demonstrated that the DCPN outperformed the prototypical network across all metrics, achieving the highest accuracies in same-domain tasks-70.86% for 1-shot, 82.57% for 5-shot, and 85.2% for 10-shot setups-corresponding to improvements of 5.51%, 5.72%, and 6.81%, respectively, over the prototypical network. Notably, in the same-domain 10-shot setting, the accuracy of the DCPN (85.2%) surpassed that of the PVT-based supervised learning model (85.15%), confirming its potential to diagnose rare diseases within few-shot learning frameworks.

Non-canonical amino acids uncover the significant impact of Tyr671 on Taq DNA polymerase catalytic activity.

Responsible for synthesizing the complementary strand of the DNA template, DNA polymerase is a crucial enzyme in DNA replication, recombination and repair. A highly conserved tyrosine (Tyr), located at the C-terminus of the O-helix in family A DNA polymerases, plays a critical role in enzyme activity and fidelity. Here, we combined the technology of genetic code extension to incorporate non-canonical amino acids and molecular dynamics (MD) simulations to uncover the mechanisms by which Tyr671 impacts substrate binding and conformation transitions in a DNA polymerase from Thermus aquaticus. Five non-canonical amino acids, namely l-3,4-dihydroxyphenylalanine (l-DOPA), p-aminophenylalanine (pAF), p-acetylphenylalanine (pAcF), p-cyanophenylalanine (pCNF) and p-nitrophenylalanine (pNTF), were individually incorporated at position 671. Strikingly, Y671pAF and Y671DOPA were active, but with lower activity compared to Y671F and wild-type. Y671pAF showed a higher fidelity than the Y671F, despite both possessing lower fidelity than the wild-type. Metadynamics and long-timescale MD simulations were carried out to probe the role of mutations in affecting protein structure, including open conformation, open-to-closed conformation transition, closed conformation, and closed-to-open conformation transition. The MD simulations clearly revealed that the size of the 671 amino acid residue and interactions with substrate or nearby residues were critical for Tyr671 to determine enzyme activity and fidelity.

Optical authentication method based on correspondence ghost imaging.

Ghost imaging technology has a great application potential in optical security because of its non-local characteristics. In this paper, on the basis of computational ghost imaging, an optical authentication scheme is proposed that utilizes the correspondence imaging technique for the preliminary reconstruction of the object image, and then authenticates the image by a nonlinear correlation algorithm. Different from the previous optical authentication schemes that usually adopted random selection of measurements, this authentication method consciously selects the bucket detector measurement values with large fluctuation and can achieve authentication using ultra-low data volumes less than 1% of the Nyquist limit. In brief, this scheme is easy to implement and has a simpler algorithm and higher stability, which is a tremendous advantage in practical optical authentication systems. The simulation and physical experimental results demonstrate the feasibility of the scheme.

Customized multiple sequence alignment as an effective strategy to improve performance of Taq DNA polymerase.

Engineering Taq DNA polymerase (TaqPol) for improved activity, stability and sensitivity was critical for its wide applications. Multiple sequence alignment (MSA) has been widely used in engineering enzymes for improved properties. Here, we first designed TaqPol mutations based on MSA of 2756 sequences from both thermophilic and non-thermophilic organisms. Two double mutations were generated including a variant H676F/R677G showing a decrease in both activity and stability, and a variant Y686R/E687K showing an improved activity, but a decreased stability. Mutations targeted on coevolutionary residues of Arg677 and Tyr686 were then applied to rescue stability or activity loss of the double mutants, which achieved a partial success. Sequence analysis revealed that the two mutations are abundant in non-thermophilic sequences but not in thermophilic homologues. Then, a small-scale MSA containing sequences from only thermophilic organisms was applied to predict 13 single variants and two of them, E507Q and E734N showed a simultaneous increase in both stability and activity, even in sensitivity. A customized MSA was hence more effective in engineering a thermophilic enzyme and could be used in engineering other enzymes. Molecular dynamics simulations revealed the impact of mutations on the protein dynamics and interactions between TaqPol and substrates. KEY POINTS: • The pool of sequence for alignment is critical to engineering Taq DNA polymerase. • The variants with low properties can be rescued by mutations in coevolving network. • Improving binding with DNA can improve DNA polymerase stability and activity.

Bipolar compressive ghost imaging method to improve imaging quality.

Compressive ghost imaging (CGI) can effectively reduce the number of measurements required for ghost imaging reconstruction. In most cases, however, when using illumination patterns as measurement matrices, CGI has not demonstrated the ability to reconstruct high-quality images at an ultra-low sampling rate as perfect as claimed by compressive sensing theory. According to our analysis, the reason is that the non-negative nature of light intensity causes measurement matrix in compressive ghost imaging to be inconsistent with the essential requirements of good measurement matrix in compressive sensing theory, leading to low reconstruction quality. Aiming at this point, we propose a bipolar compressive ghost imaging method to improve the reconstruction quality of ghost imaging. The validity of the proposed method is proven by simulations and experiments.

Two new 3-hexenol glycosides from the calyces of Physalis alkekengi var. franchetii.

Two new hexenol glycosides, (Z)-hex-3-en-1-ol O-ß-d-xylcopyranosyl-(1-6)-ß -d-glucopyranosyl-(1-2)-ß-d-glucopyranoside (1) and (E)-hex-3-en-1-ol O-ß-d-xylcopyranosyl-(1-6)-ß-d-glucopyranosyl-(1-2)-ß-d-glucopyranoside (2), were isolated from the 50% ethanol elution of macroporous resin of Physalis alkekengi var. franchetii. Their structures were established by detailed spectroscopic analysis, including extensive 2D-NMR data. This is the first time to report the (Z) and (E) 3-hexenol glycosides from Physalis alkekengi var. franchetii.

Spectrum Decomposition-Based Orbital Angular Momentum Communication of Acoustic Vortex Beams Using Single-Ring Transceiver Arrays.

The orbital angular momentum (OAM)-based acoustic vortex (AV) communication has been proven to provide a topological spinning characteristics for data transmission with an improved channel capacity, exhibiting good application prospects in underwater acoustic communications. To improve the accuracy and efficiency of data communication, the spectrum decomposition of OAM modes for OAM-multiplexed AV beams is studied with a simplified structure of single-ring transceiver arrays. The principle of spectrum decomposition for the single-OAM or OAM-multiplexed AV beams is derived based on the phase-coded approach and the orthogonal property of AVs. With the single-ring arrays of 16 transducers and 16 receivers, numerical studies and experimental measurements of eight-OAM-multiplexed AV beams transmitting ASCII codes are conducted. The formation of OAM-multiplexed AV beams is demonstrated by the cross-sectional scanning measurements, and the OAM modes are decoded successfully with a 16-point circular sampling. Compared with the traditional orthogonality-based decoding algorithm, the spectrum decomposition can be realized using a rotational measurement without the multiple premeasurements of single-OAM AV beams. The favorable results demonstrate the feasibility of the spectrum decomposition-based OAM communication for AV beams using a simplified structure of single-ring transceiver arrays, which would facilitate the practical application in underwater communications.

Anti-inflammatory effects of vinpocetine in LPS-stimulated microglia via activation of AMPK.

Microglia are the resident immune cells in the central nervous system (CNS), which play important roles in the repair of neuroinflammatory injury. The present study investigated the anti-neuroinflammatory effects of vinpocetine induced by lipopolysaccharide (LPS) in BV2 microglia. BV2 microglia were pretreated with vinpocetine, and then stimulated with LPS (100 ng/mL). The cytotoxicity of BV2 microglia was assessed by MTT assay. The expression levels of nitrite oxide were measured by Griess assay. Proinflammatory cytokines and mediators were determined by Western blot, ELISA, or quantitative real-time PCR. Vinpocetine significantly decreased the generation of nitric oxide-inducible nitric oxide synthase (iNOS), cyclooxygenase- (COX-) 2 in a dose-dependent manner. In addition, vinpocetine decreased the production of pro-inflammatory cytokines such as tumor necrosis factor alpha (TNF-α), interleukin (IL)-6 and IL-1ß. Furthermore, it was observed that phosphorylation levels of AMPK (Thr-172) decreased in LPS-stimulated BV2 microglia. Vinpocetine treatment increased AMPK phosphorylation in LPS-stimulated BV2 microglia. AMPK inhibition by siRNA blocked the anti-inflammatory effects of vinpocetine induced by LPS in BV2 microglia. The overall results demonstrate that vinpocetine has anti-inflammatory effects on LPS-stimulated BV2 microglia via inducing phosphorylation of AMPK, suggesting that vinpocetine is a potential therapeutic agent in neuroinflammatory injury.

Diversity of Conopeptides and Their Precursor Genes of Conus Litteratus.

The venom of various Conus species is composed of a rich variety of unique bioactive peptides, commonly referred to as conotoxins (conopeptides). Most conopeptides have specific receptors or ion channels as physiologically relevant targets. In this paper, high-throughput transcriptome sequencing was performed to analyze putative conotoxin transcripts from the venom duct of a vermivorous cone snail species, Conus litteratus native to the South China Sea. A total of 128 putative conotoxins were identified, most of them belonging to 22 known superfamilies, with 43 conotoxins being regarded as belonging to new superfamilies. Notably, the M superfamily was the most abundant in conotoxins among the known superfamilies. A total of 15 known cysteine frameworks were also described. The largest proportion of cysteine frameworks were VI/VII (C-C-CC-C-C), IX (C-C-C-C-C-C) and XIV (C-C-C-C). In addition, five novel cysteine patterns were also discovered. Simple sequence repeat detection results showed that di-nucleotide was the major type of repetition, and the codon usage bias results indicated that the codon usage bias of the conotoxin genes was weak, but the M, O1, O2 superfamilies differed in codon preference. Gene cloning indicated that there was no intron in conotoxins of the B1- or J superfamily, one intron with 1273-1339 bp existed in a mature region of the F superfamily, which is different from the previously reported gene structure of conotoxins from other superfamilies. This study will enhance our understanding of conotoxin diversity, and the new conotoxins discovered in this paper will provide more potential candidates for the development of pharmacological probes and marine peptide drugs.

Magnetic Drug Targeting: Preclinical in Vivo Studies, Mathematical Modeling, and Extrapolation to Humans.

A sound theoretical rationale for the design of a magnetic nanocarrier capable of magnetic capture in vivo after intravenous administration could help elucidate the parameters necessary for in vivo magnetic tumor targeting. In this work, we utilized our long-circulating polymeric magnetic nanocarriers, encapsulating increasing amounts of superparamagnetic iron oxide nanoparticles (SPIONs) in a biocompatible oil carrier, to study the effects of SPION loading and of applied magnetic field strength on magnetic tumor targeting in CT26 tumor-bearing mice. Under controlled conditions, the in vivo magnetic targeting was quantified and found to be directly proportional to SPION loading and magnetic field strength. Highest SPION loading, however, resulted in a reduced blood circulation time and a plateauing of the magnetic targeting. Mathematical modeling was undertaken to compute the in vivo magnetic, viscoelastic, convective, and diffusive forces acting on the nanocapsules (NCs) in accordance with the Nacev-Shapiro construct, and this was then used to extrapolate to the expected behavior in humans. The model predicted that in the latter case, the NCs and magnetic forces applied here would have been sufficient to achieve successful targeting in humans. Lastly, an in vivo murine tumor growth delay study was performed using docetaxel (DTX)-encapsulated NCs. Magnetic targeting was found to offer enhanced therapeutic efficacy and improve mice survival compared to passive targeting at drug doses of ca. 5-8 mg of DTX/kg. This is, to our knowledge, the first study that truly bridges the gap between preclinical experiments and clinical translation in the field of magnetic drug targeting.