Delineating the biosynthesis of gentamicin x2, the common precursor of the gentamicin C antibiotic complex.

Gentamicin C complex is a mixture of aminoglycoside antibiotics used worldwide to treat severe Gram-negative bacterial infections. Despite its clinical importance, the enzymology of its biosynthetic pathway has remained obscure. We report here insights into the four enzyme-catalyzed steps that lead from the first-formed pseudotrisaccharide gentamicin A2 to gentamicin X2, the last common intermediate for all components of the C complex. We have used both targeted mutations of individual genes and reconstitution of portions of the pathway in vitro to show that the secondary alcohol function at C-3″ of A2 is first converted to an amine, catalyzed by the tandem operation of oxidoreductase GenD2 and transaminase GenS2. The amine is then specifically methylated by the S-adenosyl-l-methionine (SAM)-dependent N-methyltransferase GenN to form gentamicin A. Finally, C-methylation at C-4″ to form gentamicin X2 is catalyzed by the radical SAM-dependent and cobalamin-dependent enzyme GenD1.This work was supported by a project grant from the Medical Research Council, UK (G1001687) to P.F.L.; and by the 973 and 863 programs from the Ministry of Science and Technology of China, National Science Foundation of China, and the Translational Medical Research Fund of Wuhan University School of Medicine to Y.S.; E.M. thanks the Gates Cambridge Trust for a scholarship. We also gratefully acknowledge Dr. Xinzhou Yang, SouthCentral University for Nationalities, for his assistance in separation of gentamicin A2. We thank Dr. Andrew Truman (John Innes Institute) for helpful discussions.This is the final published version. It was originally published in Chemistry and Biology, Volume 22, Issue 2, 19 February 2015, Pages 251–261, doi:10.1016/j.chembiol.2014.12.01

Controlled shaped-charge blasting technology for deep underground tunnel engineering

S brzim razvojem gospodarstva i društva značajno je porasla potražnja za mineralnim sirovinama i energijom. Međutim, teško je poboljšati učinkovitost miniranja i kontrolirati stabilnost okolnih stijena tijekom izrade konstrukcija u dubokom podzemlju. U ovom je radu kao tehnička osnova upotrijebljen duboki podzemni tunel reverzibilne hidroelektrane Tianchi u Kini. Na temelju stanja preraspodjele naprezanja okolnih stijena nakon iskopa miniranjem, teorijskim analizama, numeričkim simulacijama i in situ ispitivanjima istraženi su učinci širenja pukotina i dinamički odziv okolne stijene na temelju različitih metoda miniranja. Provedena je analiza mehanizma usmjerenoga stvaranja pukotina s obzirom na utjecaj razmaka bušotina i in situ naprezanja. Pokazalo se da početno naprezanje tla potiče širenje pukotina pri miniranju u konturnoj bušotini nastaloj glatkim miniranjem u smjeru pravca minske bušotine. Rezultati testiranja pokazali su da je primjenom kontroliranih metoda miniranja kumulativnim nabojem podzemnih tunela moguće povećati stopu iskorištenosti eksploziva, smanjiti vibracije pri miniranju i postići značajan učinak na usmjereno formiranje pukotina. Rezultati istraživanja od velike su važnosti za građevinarstvo jer mogu dovesti do poboljšanja tehnologije miniranja, učinka stvaranja kontura miniranjem i kontrole stabilnosti okolne stijene.With the rapid development of the economy and society, the demand for mineral resources and energy has increased rapidly. However, it is difficult to improve the efficiency of blasting construction and control the stability of the surrounding rock in deep underground engineering. In this study, the deep underground tunnel of the Tianchi pumped-storage hydropower station in China was considered as the engineering background. Based on the stress redistribution state of the surrounding rock after blasting excavation, the crack propagation effect and dynamic response of the surrounding rock under different controlled blasting methods were studied through theoretical analyses, numerical simulations and in situ tests. The mechanism of directional crack formation was analysed by considering the influence of hole spacing and in situ stress. It was shown that the initial ground stress was conducive to the propagation of the blasting crack in the contour hole of smooth blasting towards the direction line of the blast hole. The test results showed that using controlled shaped-charge blasting methods in the blasting excavation of underground tunnels can improve the utilisation rate of explosives, reduce blasting vibration and achieve a significant effect on directional crack formation. The research results have important engineering significance as they can lead to improvements in the blasting technique, a contour-forming effect of the blasting excavation and control of the stability of the surrounding rock

DrugAssist: A Large Language Model for Molecule Optimization

Recently, the impressive performance of large language models (LLMs) on a wide range of tasks has attracted an increasing number of attempts to apply LLMs in drug discovery. However, molecule optimization, a critical task in the drug discovery pipeline, is currently an area that has seen little involvement from LLMs. Most of existing approaches focus solely on capturing the underlying patterns in chemical structures provided by the data, without taking advantage of expert feedback. These non-interactive approaches overlook the fact that the drug discovery process is actually one that requires the integration of expert experience and iterative refinement. To address this gap, we propose DrugAssist, an interactive molecule optimization model which performs optimization through human-machine dialogue by leveraging LLM's strong interactivity and generalizability. DrugAssist has achieved leading results in both single and multiple property optimization, simultaneously showcasing immense potential in transferability and iterative optimization. In addition, we publicly release a large instruction-based dataset called MolOpt-Instructions for fine-tuning language models on molecule optimization tasks. We have made our code and data publicly available at https://github.com/blazerye/DrugAssist, which we hope to pave the way for future research in LLMs' application for drug discovery.Comment: Geyan Ye and Xibao Cai are equal contributors; Longyue Wang is corresponding autho

BLSP: Bootstrapping Language-Speech Pre-training via Behavior Alignment of Continuation Writing

The emergence of large language models (LLMs) has sparked significant interest in extending their remarkable language capabilities to speech. However, modality alignment between speech and text still remains an open problem. Current solutions can be categorized into two strategies. One is a cascaded approach where outputs (tokens or states) of a separately trained speech recognition system are used as inputs for LLMs, which limits their potential in modeling alignment between speech and text. The other is an end-to-end approach that relies on speech instruction data, which is very difficult to collect in large quantities. In this paper, we address these issues and propose the BLSP approach that Bootstraps Language-Speech Pre-training via behavior alignment of continuation writing. We achieve this by learning a lightweight modality adapter between a frozen speech encoder and an LLM, ensuring that the LLM exhibits the same generation behavior regardless of the modality of input: a speech segment or its transcript. The training process can be divided into two steps. The first step prompts an LLM to generate texts with speech transcripts as prefixes, obtaining text continuations. In the second step, these continuations are used as supervised signals to train the modality adapter in an end-to-end manner. We demonstrate that this straightforward process can extend the capabilities of LLMs to speech, enabling speech recognition, speech translation, spoken language understanding, and speech conversation, even in zero-shot cross-lingual scenarios

Methyltransferases of gentamicin biosynthesis

Gentamicin C complex from Micromonospora echinospora remains a globally important antibiotic, and there is revived interest in the semisynthesis of analogs that might show improved therapeutic properties. The complex consists of five components differing in their methylation pattern at one or more sites in the molecule. We show here, using specific gene deletion and chemical complementation, that the gentamicin pathway up to the branch point is defined by the selectivity of the methyltransferases GenN, GenD1, and GenK. Unexpectedly, they comprise a methylation network in which early intermediates are ectopically modified. Using whole-genome sequence, we have also discovered the terminal 6'-N-methyltransfer required to produce gentamicin C2b from C1a or gentamicin C1 from C2, an example of an essential biosynthetic enzyme being located not in the biosynthetic gene cluster but far removed on the chromosome. These findings fully account for the methylation pattern in gentamicins and open the way to production of individual gentamicins by fermentation, as starting materials for semisynthesis.This work was supported by National Natural Science Foundation of China Grant 31470186; by the 973 Program Grant 2012CB721005 from the Ministry of Science and Technology of China; by Open Project Grant MMLKF15-12 from the State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University (to Y.S.); by Medical Research Council (MRC) Grants G1001687 and MR/M019020/1 (to P.F.L.); and by an MRC postgraduate studentship (1343325) (to A.R.)

Ultra-soft Thermal Diodes Enabled by Dual-Alkane-Based Phase Change Composites

Thermal diode, a type of device that allows heat to flow in one direction preferentially, can be employed in many thermal applications. However, if the mechanical compliance of the thermal diode is poor, which prevents its intimate contact with heat source or sink surfaces, the thermal rectification performance cannot be used to its full extent. In this work, we introduce a heterojunction thermal diode made of a phase change material (PCM) consisting of dual alkanes (hexadecane and paraffine wax) and polyurethane. The fabricated thermal diode exhibits an ultra soft mechanical feature, with a low elastic modulus of 0.4 KPa and larger than 300% elongation until failure: the best values reported to date for thermal diodes. The measured thermal rectification factor is as high as 1.42 that in line with the theoretical model prediction. Molecular dynamic simulations reveal that the thermal rectification mechanism of the PCM based thermal diode originates from the crystal-amorphous phase transition of the hexadecane terminal as the temperature bias flips. Therefore, the heat flow in the forward direction is greater than the flux in the reverse direction. A series of experiments and finite element analyses are employed to verify the feasibility of thermal diodes for applications. Our results demonstrate that the fabricated thermal diode can be potentially used in building envelop to help with temperature regulation and thus reduce energy consumption for space cooling or heating

Environmentally sustainable lithium-ion battery cathode binders based on cellulose nanocrystals

Aqueous binders as environmentally sustainable alternatives to conventional polyvinylidene difluoride (PVDF) binders have not yet been successful for cathodes in lithium-ion batteries (LIBs). Here, carboxylic acid functionalized cellulose nanocrystals (CNC-COOHs) have been obtained from Miscanthus × giganteus (M×G) biomass and evaluated as aqueous binders for LIB cathodes

MTHFD2 Overexpression Predicts Poor Prognosis in Renal Cell Carcinoma and is Associated with Cell Proliferation and Vimentin-Modulated Migration and Invasion

Background/Aims: To investigate the role of methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) in the clinical prognosis and cell biology of renal cell carcinoma (RCC). Methods: A total of 137 RCC tissues were evaluated by immunohistochemistry. The relationship between MTHFD2 overexpression and clinical parameters and vimentin expression was assessed. Kaplan-Meier curves and the log-rank test were applied for survival analysis according to MTHFD2 and vimentin expression in RCC tissues. The expression of MTHFD2 mRNA and protein was examined by quantitative reverse transcription PCR and western blotting, respectively. To determine further the biological activity of MTHFD2 in RCC, 786-O cells were transfected with short hairpin RNA specifically targeting MTHFD2 (shMTHFD2) with or without tumor necrosis factor (TNF)-α stimulation. Cell proliferation, cell migration and invasion and drug sensitivity were subsequently assessed using Cell Counting Kit-8, wound healing, and Transwell assays. Results: Immunohistochemical analysis demonstrated that both MTHFD2 and vimentin overexpression was positively associated with clinical staging, pathological grade, and poor overall survival (all P < 0.05). MTHFD2 expression was closely correlated with vimentin overexpression in RCC (r = 0.402, P < 0.001). After knocking down MTHFD2 expression in 786-O cells, decreased cell proliferation, migration, and invasion were observed and accompanied by the reduced expression of vimentin. The effects of MTHFD2 down-regulation could be partially restrained by TNF-α treatment. Vimentin expression and cell migration and invasion, but not cell proliferation, were reversed by TNF-α stimulation. Furthermore, treatment of 786-O cells with shMTHFD2 increased their sensitivity to chemotherapy drugs. Conclusion: The current results demonstrated that MTHFD2 was overexpressed in RCC and associated with poor clinical characteristics, vimentin expression, and cellular features connected to malignant disease, thus, implicating MTHFD2 as a potential target for RCC therapy