A Highly Automated Mobile Laboratory for On-site Molecular Diagnostics in the COVID-19 Pandemic.

BACKGROUND: Infectious disease outbreaks such as the COVID-19 (coronavirus disease 2019) pandemic call for rapid response and complete screening of the suspected community population to identify potential carriers of pathogens. Central laboratories rely on time-consuming sample collection methods that are rarely available in resource-limited settings. METHODS: We present a highly automated and fully integrated mobile laboratory for fast deployment in response to infectious disease outbreaks. The mobile laboratory was equipped with a 6-axis robot arm for automated oropharyngeal swab specimen collection; virus in the collected specimen was inactivated rapidly using an infrared heating module. Nucleic acid extraction and nested isothermal amplification were performed by a "sample in, answer out" laboratory-on-a-chip system, and the result was automatically reported by the onboard information platform. Each module was evaluated using pseudovirus or clinical samples. RESULTS: The mobile laboratory was stand-alone and self-sustaining and capable of on-site specimen collection, inactivation, analysis, and reporting. The automated sampling robot arm achieved sampling efficiency comparable to manual collection. The collected samples were inactivated in as short as 12 min with efficiency comparable to a water bath without damage to nucleic acid integrity. The limit of detection of the integrated microfluidic nucleic acid analyzer reached 150 copies/mL within 45 min. Clinical evaluation of the onboard microfluidic nucleic acid analyzer demonstrated good consistency with reverse transcription quantitative PCR with a κ coefficient of 0.979. CONCLUSIONS: The mobile laboratory provides a promising solution for fast deployment of medical diagnostic resources at critical junctions of infectious disease outbreaks and facilitates local containment of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) transmission.

OncoPDSS: an evidence-based clinical decision support system for oncology pharmacotherapy at the individual level.

BACKGROUND: Precision oncology pharmacotherapy relies on precise patient-specific alterations that impact drug responses. Due to rapid advances in clinical tumor sequencing, an urgent need exists for a clinical support tool that automatically interprets sequencing results based on a structured knowledge base of alteration events associated with clinical implications. RESULTS: Here, we introduced the Oncology Pharmacotherapy Decision Support System (OncoPDSS), a web server that systematically annotates the effects of alterations on drug responses. The platform integrates actionable evidence from several well-known resources, distills drug indications from anti-cancer drug labels, and extracts cancer clinical trial data from the ClinicalTrials.gov database. A therapy-centric classification strategy was used to identify potentially effective and non-effective pharmacotherapies from user-uploaded alterations of multi-omics based on integrative evidence. For each potentially effective therapy, clinical trials with faculty information were listed to help patients and their health care providers find the most suitable one. CONCLUSIONS: OncoPDSS can serve as both an integrative knowledge base on cancer precision medicine, as well as a clinical decision support system for cancer researchers and clinical oncologists. It receives multi-omics alterations as input and interprets them into pharmacotherapy-centered information, thus helping clinicians to make clinical pharmacotherapy decisions. The OncoPDSS web server is freely accessible at https://oncopdss.capitalbiobigdata.com .

Inhibition of immune pathway-initiating hemolymph protease-14 by Manduca sexta serpin-12, a conserved mechanism for the regulation of melanization and Toll activation in insects.

A network of serine proteases (SPs) and their non-catalytic homologs (SPHs) activates prophenoloxidase (proPO), Toll pathway, and other insect immune responses. However, integration and conservation of the network and its control mechanisms have not yet been fully understood. Here we present evidence that these responses are initiated through a conserved serine protease and negatively regulated by serpins in two species, Manduca sexta and Anopheles gambiae. We have shown that M. sexta serpin-12 reduces the proteolytic activation of HP6, HP8, proPO activating proteases (PAPs), SPHs, and POs in larval hemolymph, and we hypothesized that these effects are due to the inhibition of the immune pathway-initiating protease HP14. To test whether these changes are due to HP14 inhibition, we isolated a covalent complex of HP14 with serpin-12 from plasma using polyclonal antibodies against the HP14 protease domain or against serpin-12, and confirmed formation of the complex by 2D-electrophoresis, immunoblotting, and mass spectrometry. Upon recognition of bacterial peptidoglycans or fungal ß-1,3-glucan, the zymogen proHP14 became active HP14, which formed an SDS-stable complex with serpin-12 in vitro. Activation of proHP21 by HP14 was suppressed by serpin-12, consistent with the decrease in steps downstream of HP21, proteolytic activation of proPAP3, proSPH1/2 and proPO in hemolymph. Guided by the results of phylogenetic analysis, we cloned and expressed A. gambiae proSP217 (an ortholog of HP14) and core domains of A. gambiae serpin-11 and -17. The recombinant SP217 zymogen became active during expression, with cleavage between Tyr394 and Ile395. Both MsHP14 and AgSP217 cleaved MsSerpin-12 and AgSRPN11 at Leu*Ser (P1*P1') and formed complexes in vitro. ProPO activation in M. sexta plasma increased after recombinant AgSP217 had been added, indicating that it may function in a similar manner as the endogenous initiating protease HP14. Based on these data, we propose that inhibition of an initiating modular protease by a serpin may be a common mechanism in holometabolous insects to regulate proPO activation and other protease-induced immune responses.

Nickel-Catalyzed Arylation of Heteroaryl-containing Diarylmethanes: Exceptional Reactivity of the Ni(NIXANTPHOS)-based Catalyst.

Nickel(0)-catalyzed cross-coupling of heteroaryl-containing diarylmethanes with both aryl bromides and chlorides has been achieved. The success of this reaction relies on the introduction of a unique nickel/NIXANTPHOS-based catalyst system, which provides a direct route to triarylmethanes from heteroaryl-containing diarylmethanes. Reactivity studies indicate the Ni(NIXANTPHOS)-based catalyst exhibits enhanced reactivity over XANTPHOS derivatives and other Ni(phosphine)-based catalysts in the reactions examined.

An α-Keggin polyoxometalate completely constructed from the late transition metal Co(II) as poly atom.

We report a catalytic eight-cobalt-capped α-Keggin polyoxoazocobaltite with a highly symmetric structure completely constructed from the late transition-metal Co(II) as a poly atom, [Co(20)(OH)(24)(MMT)(12)(SO(4))](NO(3))(2)·6H(2)O (1) (MMT: 2-mercapto-5-methyl-1,3,4-thiadiazole). To the best of our knowledge, this is the first homometallic Co(II) magnetic cluster bearing Keggin structure. It can serve as a potential catalyst in the styrene polymerization.

A remarkable member of the polyoxometalates: the eight-nickel-capped alpha-keggin polyoxoazonickelate.

The eight-nickel-capped polyoxoazonickelate, [Ni(20)(OH)(24)(MMT)(12)(SO(4))](NO(3))(2).6H(2)O (1; MMT = 2-mercapto-5-methyl-1,3,4-thiadiazole), has been synthesized, which has an alpha-Keggin structure with eight nickel caps. In this structure, the polyatom is the late transition metal Ni(II); the central heteroatom is S, and the organic terminal ligand becomes the primary part of the Keggin structure. This is a Keplerate-type cluster, which shows a central Ni(II)(12) cuboctahedron formed by the 12 Ni(II) centers of the classical alpha-Keggin core and a Ni(II)(8) hexahedron formed by the eight nickel caps.

Solution structure, antibacterial activity, and expression profile of Manduca sexta moricin.

In response to wounding or infection, insects produce a battery of antimicrobial peptides (AMPs) and other defense molecules to kill the invading pathogens. To study their structures, functions, and transcriptional regulation, we synthesized Manduca sexta moricin, a 42-residue peptide (GKIPVKAIKQAGKVIGKGLRAINIAGTTHDVVSFFRPKKKKH, 4539 Da). The compound exhibited potent antimicrobial activities against a broad spectrum of Gram-positive and Gram-negative bacteria with a minimum inhibitory concentration of 1.4 microM. The mRNA levels of M. sexta moricin increased substantially in fat body and hemocytes after the larvae were challenged with bacterial cells. We determined the solution structure of this AMP by two-dimensional 1H-1H -nuclear magnetic resonance spectroscopy. The tertiary structure is composed of an eight-turn alpha-helix spanning almost the entire peptide. Insights of relationships between the structure and function are also presented.

The solution structure of clip domains from Manduca sexta prophenoloxidase activating proteinase-2.

Clip domains are structural modules found in arthropod serine proteinases and some proteolytically inactive homologues, which mediate extracellular signaling pathways of development and immunity. While little is known about their structures or functions, clip domains are proposed to be sites for interactions of proteinases with their activators, cofactors, and substrates. Here we report the solution structure of dual clip domains from Manduca sexta prophenoloxidase activating proteinase-2. Each domain adopts a new mixed alpha/beta fold (a three-stranded antiparallel beta-sheet flanked by two alpha-helices), and the architecture provides structural information on clip domains from a catalytically active proteinase for the first time. Examination of the structure in conjunction with a multiple sequence alignment of the clip domains from different groups suggests a substrate-binding site, a bacteria-interacting region, and a surface for specific interactions. In summary, our results provide insights into the structural basis of clip domain functions and this structure may represent the prototype of group-2 clip domains.

Exceptional chemical and thermal stability of zeolitic imidazolate frameworks.

Twelve zeolitic imidazolate frameworks (ZIFs; termed ZIF-1 to -12) have been synthesized as crystals by copolymerization of either Zn(II) (ZIF-1 to -4, -6 to -8, and -10 to -11) or Co(II) (ZIF-9 and -12) with imidazolate-type links. The ZIF crystal structures are based on the nets of seven distinct aluminosilicate zeolites: tetrahedral Si(Al) and the bridging O are replaced with transition metal ion and imidazolate link, respectively. In addition, one example of mixed-coordination imidazolate of Zn(II) and In(III) (ZIF-5) based on the garnet net is reported. Study of the gas adsorption and thermal and chemical stability of two prototypical members, ZIF-8 and -11, demonstrated their permanent porosity (Langmuir surface area = 1,810 m(2)/g), high thermal stability (up to 550 degrees C), and remarkable chemical resistance to boiling alkaline water and organic solvents.