Mechanistic insight into how multidrug resistant Acinetobacter baumannii response regulator AdeR recognizes an intercistronic region

AdeR-AdeS is a two-component regulatory system, which controls expression of the adeABC efflux pump involved in Acinetobacter baumannii multidrug resistance. AdeR is a response regulator consisting of an N-terminal receiver domain and a C-terminal DNA-binding-domain. AdeR binds to a direct-repeat DNA in the intercistronic region between adeR and adeABC. We demonstrate a markedly high affinity binding between unphosphorylated AdeR and DNA with a dissociation constant of 20 nM. In addition, we provide a 2.75 angstrom crystal structure of AdeR DNA-binding-domain complexed with the intercistronic DNA. This structure shows that the alpha 3 and beta hairpin formed by beta 5-beta 6 interacts with the major and minor groove of the DNA, which in turn leads to the introduction of a bend. The AdeR receiver domain structure revealed a dimerization motif mediated by a gearwheel-like structure involving the D108F109-R122 motif through cation pi stack interaction. The structure of AdeR receiver domain bound with magnesium indicated a conserved Glu19Asp20-Asp63 magnesium-binding motif, and revealed that the potential phosphorylation site Asp63(OD1) forms a hydrogen bond with Lys112. We thus dissected the mechanism of how AdeR recognizes the intercistronic DNA, which leads to a diverse mode of response regulation. Unlocking the AdeRS mechanism provides ways to circumvent A. baumannii antibiotic resistance

From GPT-4 to Gemini and Beyond: Assessing the Landscape of MLLMs on Generalizability, Trustworthiness and Causality through Four Modalities

Multi-modal Large Language Models (MLLMs) have shown impressive abilities in generating reasonable responses with respect to multi-modal contents. However, there is still a wide gap between the performance of recent MLLM-based applications and the expectation of the broad public, even though the most powerful OpenAI's GPT-4 and Google's Gemini have been deployed. This paper strives to enhance understanding of the gap through the lens of a qualitative study on the generalizability, trustworthiness, and causal reasoning capabilities of recent proprietary and open-source MLLMs across four modalities: ie, text, code, image, and video, ultimately aiming to improve the transparency of MLLMs. We believe these properties are several representative factors that define the reliability of MLLMs, in supporting various downstream applications. To be specific, we evaluate the closed-source GPT-4 and Gemini and 6 open-source LLMs and MLLMs. Overall we evaluate 230 manually designed cases, where the qualitative results are then summarized into 12 scores (ie, 4 modalities times 3 properties). In total, we uncover 14 empirical findings that are useful to understand the capabilities and limitations of both proprietary and open-source MLLMs, towards more reliable downstream multi-modal applications

On-site quantitation of morphine in urine by fast derivatization and miniature mass spectrometry analysis

Analysis of drugs in urine is particularly useful for screening of public safety issues, monitoring of medicine appliance and detection of drugs of abuse. Tandem mass spectrometry (MS/MS) of morphine usually produces clusters of fragments, hindering accurate quantitation of morphine in biological samples by fast sampling and direct MS/MS method. In this work, we developed a method that enabled determination and quantitation of morphine in urine in 3 min. It consisted of a simple extraction process, a fast dansyl-derivatization process, and direct analysis by a miniature mass spectrometer. MS/MS of derivatized morphine produced a highly abundant product at m/z 285 in positive ion mode, significantly enhancing the sensitivity by more than 10 times. Quantitation of morphine in urine was achieved by in-trap collision-induced dissociation on the miniature mass spectrometer, with the limit of detection of 50 ng/mL and the limit of quantitation of 100 ng/mL. The performance of the method was also evaluated with a standard liquid chromatography-MS method, showing comparable quantitative accuracy. Finally, the method has applied into quantitation of morphine in real urine samples from individuals suspected to have used opioids

Ecological restoration approaches for degraded muddy coasts: Recommendations and practice

Scientific selection of an ecological restoration approach from among the three common approaches: natural restoration, assisted restoration, and ecological reconstruction is the first step to successful ecological restoration. This study chose the appropriate ecological restoration approach for the study area from the following two perspectives. The threshold effect considers the degree of damage to the muddy coast and makes an estimate of its resilience. The development needs of the coastal zone consider the needs of muddy coasts for ecological protection, safety, and culture and aesthetics; development planning aims to determine the priority of these three needs. This study also assessed common technical measures for ecological restoration of muddy coasts and analyzed the applicability and advantages and disadvantages of each perspective to assist in the selection of specific ecological restoration measures suited to local conditions. The target area for ecological restoration was the muddy coastal area around Yundanmen Island, Sansha Bay, Ningde City, China, which had been degraded by reclamation and aquaculture. Based on conceptual models for selection, ecological restoration approaches for the study area were determined, technical measures were selected, and the plan was developed and implemented. We analyzed the initial effects of ecological restoration on birds, vegetation, and benthic organisms to verify the effectiveness of the chosen ecological restoration approach. This study provides scientific support for rationally planning the ecological restoration of muddy coasts and a reference for the selection of other coastal ecological restoration approaches and technical measures

Mobile anchor-free localization for wireless sensor networks

Localization is a fundamental problem in wireless sensor networks. In this paper, we consider how to localize individual nodes in a wireless sensor network when some subset of the network nodes can be in motion at any given time. For situations in which it is not practical or costefficient to use GPS or anchor nodes, this paper proposes an Anchor-Free (AF) Mobile Geographic Distributed Localization (MGDL) algorithm for wireless sensor networks. Taking advantage of the accelerometers that are present in standard motes, MGDL monitors a moving distance for each node, then uses a procedures to detect any movement of each node. If movement is detected, then the moved node will trigger a series of mobile localization procedures to recalculate and update the location locally, such procedures will be stopped while the node stops moving. Data collected using Tmote Invent nodes (Moteiv Inc.) and simulations show that proposed detection method can efficiently detect the movement, and that the localization is accurate and the communication is efficient in different static and mobile contexts

Providing Anonymity in Wireless Sensor Networks

Abstract—Sensor networks are often used to monitor sensitive information from the environment or track sensitive objects’ movements. Anonymity has become an important problem in sensor networks, and has been widely researched in wireless ad hoc and wired networks. The limited capacity and resources of current sensor networks have brought new challenges to anonymity research. In this paper, two efficient methods are proposed based on using a one-way hash chain to dynamically change the identity of sensor nodes in order to provide anonymity, and their anonymity properties are analyzed and compared. I

Dummy Template-Based Molecularly Imprinted Membrane Coating for Rapid Analysis of Malachite Green and Its Metabolic Intermediates in Shrimp and Fish

A novel malachite green molecularly imprinted membrane (MG-MIM) with specific selectivity for malachite green (MG) and leucomalachite green (LMG) was prepared using a hydrophobic glass fiber membrane as the polymer substrate, methyl violet as a template analog, 4-vinyl benzoic acid as the functional monomer, and ethyleneglycol dimethacrylate as the crosslinking agent. MG-MIM and non-imprinted membrane (NIM) were structurally characterized using scanning electron microscopy, surface area analyzer, Fourier-transform infrared spectrometer and synchronous thermal analyzer. The results showed that MG-MIM possessed a fluffier surface, porous and looser structure, and had good thermal stability. Adsorption properties of MG-MIM were investigated under optimal conditions, and adsorption equilibrium was reached in 20 min. The saturated adsorption capacities for MG and LMG were 24.25 ng·cm−2 and 13.40 ng·cm−2, and the maximum imprinting factors were 2.41 and 3.20, respectively. Issues such as “template leakage” and “embedding” were resolved. The specific recognition ability for the targets was good and the adsorption capacity was stable even after five cycles. The proposed method was successfully applied for the detection of MG and LMG in real samples, and it showed good linear correlation in the range of 0 to 10.0 μg·L−1 (R2 = 0.9991 and 0.9982), and high detection sensitivity (detection limits of MG and LMG of 0.005 μg/kg and 0.02 μg·kg−1 in shrimp, and 0.005 μg/kg and 0.02 μg/kg in fish sample). The recoveries and relative standard deviations were in the range of 76.31–93.26% and 0.73–3.72%, respectively. The proposed method provides a simple, efficient and promising alternative for monitoring MG and LMG in aquatic products

Crystal structure of master biofilm regulator CsgD regulatory domain reveals an atypical receiver domain

The master regulator CsgD switches planktonic growth to biofilm formation by activating synthesis of curli fimbriae and cellulose in Enterobacteriaceae. CsgD was classified to be the LuxR response regulatory family, while its cognate sensor histidine kinase has not been identified yet. CsgD consists of a C-terminal DNA binding domain and an N-terminal regulatory domain that provokes the upstream signal transduction to further modulate its function. We provide the crystal structure of Salmonella Typhimurium CsgD regulatory domain, which reveals an atypical 55 response regulatory receiver domain folding with the 2 helix representing as a disorder loop compared to the LuxR/FixJ canonical response regulator, and the structure indicated a noteworthy 5 helix similar to the non-canonical master regulator VpsT receiver domain 6. CsgD regulatory domain assembles with two dimerization interfaces mainly through 1 and 5, which has shown similarity to the c-di-GMP independent and stabilized dimerization interface of VpsT from Vibrio cholerae respectively. The potential phosphorylation site D59 is directly involved in the interaction of interfaces I and mutagenesis studies indicated that both dimerization interfaces could be crucial for CsgD activity. The structure reveals important molecular details for the dimerization assembly of CsgD and will shed new insight into its regulation mechanism