Ten simple rules for computational biologists collaborating with wet lab researchers.

Computational biologists are frequently engaged in collaborative data analysis with wet lab researchers. These interdisciplinary projects, as necessary as they are to the scientific endeavor, can be surprisingly challenging due to cultural differences in operations and values. In this Ten Simple Rules guide, we aim to help dry lab researchers identify sources of friction and provide actionable tools to facilitate respectful, open, transparent, and rewarding collaborations.

Polydopamine Synergizes with Quercetin Nanosystem to Reshape the Perifollicular Microenvironment for Accelerating Hair Regrowth in Androgenetic Alopecia.

Accumulated reactive oxygen species (ROS) and their resultant vascular dysfunction in androgenic alopecia (AGA) hinder hair follicle survival and cause permanent hair loss. However, safe and effective strategies to rescue hair follicle viability to enhance AGA therapeutic efficiency remain challenging. Herein, we fabricated a quercetin-encapsulated (Que) and polydopamine-integrated (PDA@QLipo) nanosystem that can reshape the perifollicular microenvironment to initial hair follicle regeneration for AGA treatment. Both the ROS scavenging and angiogenesis promotion abilities of PDA@QLipo were demonstrated. In vivo assays revealed that PDA@QLipo administrated with roller-microneedles successfully rejuvenated the "poor" perifollicular microenvironment, thereby promoting cell proliferation, accelerating hair follicle renewal, and facilitating hair follicle recovery. Moreover, PDA@QLipo achieved a higher hair regeneration coverage of 92.5% in the AGA mouse model than minoxidil (87.8%), even when dosed less frequently. The nanosystem creates a regenerative microenvironment by scavenging ROS and augmenting neovascularity for hair regrowth, presenting a promising approach for AGA clinical treatment.

Self-Renewable Tag for Photostable Fluorescence Imaging of Proteins.

We report the development of a self-renewable tag (srTAG) for protein fluorescence imaging. srTAG leverages the "on-protein" fluorophore equilibrium between the fluorescent zwitterion and non-fluorescent spirocyclic form and the reversible fluorescence labeling to enable self-recovery of fluorescence after photobleaching. This small-sized srTAG allows 2-6 times longer imaging duration compared to other commonly used self-labeling tags and is compatible with fluorophores with different spectral properties. This study provides a new strategy for fine tuning of self-labeling tags.

Foldback-crRNA-Enhanced CRISPR/Cas13a System (FCECas13a) Enables Direct Detection of Ultrashort sncRNA.

The CRISPR/Cas13a system has promising applications in clinical small noncoding RNA (sncRNA) detection because it is free from the interference of genomic DNA. However, detecting ultrashort sncRNAs (less than 20 nucleotides) has been challenging because the Cas13a nuclease requires longer crRNA-target RNA hybrids to be activated. Here, we report the development of a foldback-crRNA-enhanced CRISPR/Cas13a (FCECas13a) system that overcomes the limitations of the current CRISPR/Cas13a system in detecting ultrashort sncRNAs. The FCECas13a system employs a 3'-terminal foldback crRNA that hybridizes with the target ultrashort sncRNA, forming a double strand that "tricks" the Cas13a nuclease into activating the HEPN structural domain and generating trans-cleavage activity. The FCECas13a system can accurately detect miRNA720 (a sncRNA currently known as tRNA-derived small RNA), which is only 17 nucleotides long and has a concentration as low as 15 fM within 20 min. This FCECas13a system opens new avenues for ultrashort sncRNA detection with significant implications for basic biological research, disease prognosis, and molecular diagnosis.

Dual-band terahertz absorber based on square ring metamaterial structure.

In this paper, a dual-band terahertz absorber based on metamaterial structure is designed, fabricated, and measured. The metal periodic array is located on the upper surface of a silicon wafer with a metal ground plane, while the metamaterial structure is created utilizing a square metal ring with four T-shaped metal strips loaded inside of the ring. Two absorption peaks are realized at 0.715 and 1.013 THz with high Q-factors of 152.1 and 98.3, respectively, under normal TE and TM polarized incidence. A prototype of the proposed metamaterial absorber is fabricated by electron beam lithography (EBL) and electron beam evaporation (EBE) technology. Furthermore, a terahertz time-domain spectroscopy (TDS) measurement system is employed to test the absorber sample, with good measurement results obtained. This work provides a new option for the design of multi-band terahertz metamaterial absorbers.

Recycling Valuable Metals from Spent Lithium-Ion Batteries Using Carbothermal Shock Method.

Pyrometallurgy technique is usually applied as a pretreatment to enhance the leaching efficiencies in the hydrometallurgy process for recovering valuable metals from spent lithium-ion batteries. However, traditional pyrometallurgy processes are energy and time consuming. Here, we report a carbothermal shock (CTS) method for reducing LiNi0.3 Co0.2 Mn0.5 O2 (NCM325) cathode materials with uniform temperature distribution, high heating and cooling rates, high temperatures, and ultrafast reaction times. Li can be selectively leached through water leaching after CTS process with an efficiency of >90 %. Ni, Co, and Mn are recovered by dilute acid leaching with efficiencies >98 %. The CTS reduction strategy is feasible for various spent cathode materials, including NCM111, NCM523, NCM622, NCM811, LiCoO2 , and LiMn2 O4 . The CTS process, with its low energy consumption and potential scale application, provides an efficient and environmentally friendly way for recovering spent lithium-ion batteries.

Sodium butyrate exerts antioxidant stress effects and attenuates Aß25-35-induced cytotoxicity in PC12 cells.

Alzheimer's disease (AD), a common neurodegenerative disease, is characterised by the deposition of amyloid-ß (Aß) plaques and neurofibrillary tangles. An increasing number of studies have demonstrated that Aß causes neuronal damage and mitochondrial dysfunction. Herein, we evaluated the neuroprotective effect of sodium butyrate (NaB) against Aß induced neurotoxicity in PC12 cells. The results revealed that 3 mM of NaB promoted the expression of angiotensin-converting enzyme and brain-derived neurotrophic factor, which exert a neuroprotective effect by activating G protein-coupled receptors. Moreover, NaB could significantly improve mitochondrial dysfunction caused by Aß. In conclusion, NaB protected PC12 cells from Aß-induced cell damage, highlighting the potential of NaB in AD treatment.

A smart enzyme reactor based on a photo-responsive hydrogel for purifying water from phenol contaminated sources.

In this paper, a smart enzyme reactor (SER) was synthesized using immobilized tyrosinase (Tyr) in a photo-responsive hydrogel via a polydopamine-assisted self-assembly strategy for purifying water from phenol contaminated water. PDA was not only utilized as a binder between Tyr and the hydrogel to prevent the leakage of Tyr with relatively high enzymatic activity from the SER, but also acted as a light absorber to trigger the hydrophilic/hydrophobic switching of PNIPAm hydrogels to realize the efficient reclamation of clean water. Experimental results showed that the SER maintained a well-defined porous structure with excellent elasticity, which was beneficial for water transport and enzyme accessibility. And the stability and reusability of Tyr in the degradation of phenol were all improved. Furthermore, clean water could be reclaimed completely and facilely by light irradiation after enzymatic remediation in the SER.

Molecular Dynamics Beyond the Monolayer Adsorption as Derived from Langmuir Curve Fitting.

Langmuir adsorption model is a classic physical-chemical adsorption model and is widely used to describe the monolayer adsorption behavior at the material interface in environmental chemistry. Traditional adsorption dynamic modeling solely considered the surface physiochemical interaction between the adsorbent and adsorbate. The surface reaction dynamics resulting from the heterogeneous surface and intrinsic electronic structure of absorbents were rarely considered within the reported adsorption experiments. Herein, by employing the chlorine hybrid graphene oxide (GO-Cl) to adsorb Ag+ in an aqueous solution, complicated molecular dynamics significantly deviated from the monolayer adsorption mechanism, as suggested by Langmuir adsorption curve fitting, has been elucidated down to atomic scale. In the time-dependent Ag adsorption experiments, both Ag single atoms and Ag/AgCl nanoparticle heterostructures are observed to be formed sequentially on GO-Cl. These observations indicate that for the surface adsorption dynamics, not only the surface chemical adsorption process involved but also photoreduction and the C-Cl bond cleavage reaction has been heavily engaged within the GO-Cl interface, suggesting a much more complicated vision rather than the monolayered adsorption algorithm as derived from curve fitting. This study uses GO-Cl as a simple example to disclose the complicated adsorption dynamic process underneath Langmuir adsorption curve fitting. It advocates the necessity of imaging the interfacial atomic-scale dynamic structure with high-resolution microscopy techniques in modern adsorption studies, rather than simply explaining the adsorption dynamics relying on the curve fitting results due to the complicated physiochemical reactivity of the adsorbents.

Ultrasound-assisted brain delivery of nanomedicines for brain tumor therapy: advance and prospect.

Nowadays, brain tumors are challenging problems, and the key of therapy is ensuring therapeutic drugs cross the blood-brain barrier (BBB) effectively. Although the efficiency of drug transport across the BBB can be increased by innovating and modifying nanomedicines, they exert insufficient therapeutic effects on brain tumors due to the complex environment of the brain. It is worth noting that ultrasound combined with the cavitation effect of microbubbles can assist BBB opening and enhance brain delivery of nanomedicines. This ultrasound-assisted brain delivery (UABD) technology with related nanomedicines (UABD nanomedicines) can safely open the BBB, facilitate the entry of drugs into the brain, and enhance the therapeutic effect on brain tumors. UABD nanomedicines, as the main component of UABD technology, have great potential in clinical application and have been an important area of interest in the field of brain tumor therapy. However, research on UABD nanomedicines is still in its early stages despite the fact that they have been associated with many disciplines, including material science, brain science, ultrasound, biology, and medicine. Some aspects of UABD theory and technology remain unclear, especially the mechanisms of BBB opening, relationship between materials of nanomedicines and UABD technology, cavitation and UABD nanomedicines design theories. This review introduces the research status of UABD nanomedicines, investigates their properties and applications of brain tumor therapy, discusses the advantages and drawbacks of UABD nanomedicines for the treatment of brain tumors, and offers their prospects. We hope to encourage researchers from various fields to participate in this area and collaborate on developing UABD nanomedicines into powerful tools for brain tumor therapy.

Nanoscale Calculation of Proton-Induced DNA Damage Using a Chromatin Geometry Model with Geant4-DNA.

Monte Carlo simulations can quantify various types of DNA damage to evaluate the biological effects of ionizing radiation at the nanometer scale. This work presents a study simulating the DNA target response after proton irradiation. A chromatin fiber model and new physics constructors with the ELastic Scattering of Electrons and Positrons by neutral Atoms (ELSEPA) model were used to describe the DNA geometry and the physical stage of water radiolysis with the Geant4-DNA toolkit, respectively. Three key parameters (the energy threshold model for strand breaks, the physics model and the maximum distance to distinguish DSB clusters) of scoring DNA damage were studied to investigate the impact on the uncertainties of DNA damage. On the basis of comparison of our results with experimental data and published findings, we were able to accurately predict the yield of various types of DNA damage. Our results indicated that the difference in physics constructor can cause up to 56.4% in the DNA double-strand break (DSB) yields. The DSB yields were quite sensitive to the energy threshold for strand breaks (SB) and the maximum distance to classify the DSB clusters, which were even more than 100 times and four times than the default configurations, respectively.

Total Synthesis of Mulberry Diels-Alder-Type Adducts Kuwanons G and H.

Mulberry Diels-Alder-type adducts (MDAAs) are a group of rare natural polyphenols biosynthetically derived from [4 + 2]-cycloaddition of chalcones and dehydroprenylphenols. In this study, kuwanons G (1) and H (2), two bioactive MDAAs with unique dehydroprenylflavonoid dienes, were totally synthesized for the first time in a biomimetic manner. The key features of the convergent route include the use of the Baker-Venkataraman rearrangement, alkylation of ß-diketone, intramolecular cyclization, and Suzuki-Miyaura coupling to achieve the subunit diene.

Converting Spent LiFePO4 Battery into Zeolitic Phosphate for Highly Efficient Heavy Metal Adsorption.

Developing efficient recycling technologies for large-scale spent batteries is the key to build a zero-waste city. Herein, a [Al8.5Fe0.5P12O48]·[C24H72N16]·[Li·4H2O]·[12H2O] (AlFePO-Li) zeolite, crystallizing in space group I4̅3m with a = 16.6778(3) Å, has been constructed via the hydrothermal treatment of spent LiFePO4 battery. Benefiting from the three-dimensional 12-member-ring channels in its structure and chemical adsorption, excellent Pb2+ removal capacity up to 723.8 mg g-1 has been achieved. Detailed adsorption mechanism study revealed that the cation exchange capacity is significantly contributed by ion exchange of the protonated organic amine cations in the zeolite channel and the protons from the framework dangling phosphate group. This work demonstrates a novel method of reutilizing spent LIBs to construct zeolite for heavy metal removal. It is of great importance to achieve sustainable development based on the "resource utilization" and "trash-to-treasure" strategy.

Chemical Composition, Antioxidant, Antimicrobial, and Phytotoxic Potential of Eucalyptus grandis × E. urophylla Leaves Essential Oils.

Eucalyptus grandis × E. urophylla was a unique hybridization in China. However, the chemical and pharmacological properties were rarely reported. Therefore, in this work, we used a steam distillation method to obtain essential oils from leaves of E. grandis × E. urophylla, and further evaluated the antioxidant, antimicrobial, and phytotoxic potential of the essential oil. Gas chromatography mass spectrometry (GC-MS) was applied to investigate the chemical composition of E. grandis × E. urophylla essential oil (EEO) and the results showed that the main components of EEO were monoterpenes followed by sesquiterpenes. Among them, α-pinene accounted about 17.02%. EEO could also well scavenge 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2, 2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) free radicals showing a good free radical clearance ability. In addition, EEO efficiently inhibited the growth of six kinds of bacteria as well as seven kinds of plant pathogens, especially Salmonella typhimurium and Colletotrichum gloeosporioides. Moreover, the seedling germination of Raphanus sativus, Lactuca sativa, Lolium perenne, and Bidens pilosa was significantly suppressed by EEO, thus, indicating essential oils from eucalyptus possessed an excellent phytotoxic activity. This study may give a better understanding on EEO and provide a pharmacological activities analysis contributing to the further research of EEO as a functional drug in agronomic and cosmetic industries.

Mixed Redox-Couple-Involved Chalcopyrite Phase CuFeS2 Quantum Dots for Highly Efficient Cr(VI) Removal.

Iron-based nanosized ecomaterials for efficient Cr(VI) removal are of great interest to environmental chemists. Herein, inspired by the "mixed redox-couple" cations involved in the crystal structure and the quantum confinement effects resulting from the particle size, a novel type of iron-based ecomaterial, semiconducting chalcopyrite quantum dots (QDs), was developed and used for Cr(VI) removal. A high removal capacity up to 720 mg/g was achieved under optimal pH conditions, which is superior to those of the state-of-the-art nanomaterials for Cr(VI) removal. The mechanism of Cr(VI) removal was elucidated down to an atomic scale by combining comprehensive characterization techniques with adsorption kinetic experiments and DFT calculations. The experimental results revealed that the material was a good electron donor semiconductor attributed to the existence of "mixed redox couple of Cu(I)-S-Fe(III)" in the crystal structure. With the size-dependent quantum confinement effect and the high surface area, the semiconducting chalcopyrite QDs could effectively remove Cr(VI) from aqueous solution through a syngenetic photocatalytic reduction and adsorption mechanism. This study not only reports the design histogram of the iron-based CuFeS2 QD ecomaterial for efficient Cr(VI) removal but also paves the way for understanding the atomic-scale mechanism behind the syngenetic effects of using the QD semiconducting material for Cr(VI) removal.

19-nor-, 20-nor-, and tetranor-Halimane-Type Furanoditerpenoids from Croton crassifolius.

The phytochemical investigation of the roots of Croton crassifolius led to the isolation of 16 new halimane furanoditerpenoids, crohalifuranes A-P (1-16), along with 15 known analogues, 17-31. The new structures including their absolute configurations were elucidated by NMR and MS data analysis, comparison of experimental and calculated electronic circular dichroism data, single-crystal X-ray diffraction data, and chemical methods. Crohalifuranes A (1) and B (2) are tetranor- and 19-nor-halimane diterpenoids featuring a rare decahydroacenaphthene core, respectively, which might be derived from the accompanying crassifoliusin A by loss of the furan ring or the C-19 substituent. Crohalifurane C (3) represents the first example of a 20-nor-halimane diterpenoid, and crohalifurane D (4) is characterized by an unusual 6,20-δ-lactone moiety. All compounds were examined for their inhibitory effects on nitric oxide (NO) production induced by lipopolysaccharide in RAW264.7 cells, and 2 and 23 exhibited moderate inhibition on NO production with IC50 values of 17.2 ± 1.3 and 23.7 ± 1.4 µM, respectively.

Euphoresulanes A-M, structurally diverse jatrophane diterpenoids from Euphorbia esula.

Thirteen new jatrophane diterpenoids, euphoresulanes A-M (1-13), and seven known analogues (14-20) were isolated from the whole plants of Euphorbia esula. Their structures were elucidated by extensive spectroscopic analysis, and the absolute configurations of 1, 6, and 10 were confirmed by single crystal X-ray diffraction. Compounds 1-20 were screened for the multidrug resistance (MDR) reversal activity on P-glycoprotein (Pgp)-dependent cancer cell line HepG2/ADR, and 1, 2, 4, 6, and 8 exhibited comparable activity to the positive drugs. Euphoresulane H (8), the most active MDR modulator, could enhance the efficacy of anticancer drug adriamycin to ca. 33 folds at 5 µM. The structure-activity relationship (SAR) study revealed that the acyloxy substitution at C-9 is essential to the activity and presence of H-2 was favorable.

Effects of Ultrasonic-Assisted Extraction on the Yield and the Antioxidative Potential of Bergenia emeiensis Triterpenes.

This study was the first designed to evaluate the extraction and antioxidant ability of triterpenes from Bergenia emeiensis rhizomes. The yield of triterpenes from B. emeiensis was mainly affected by the concentration of ethanol, followed by the extraction time, solvent to sample ratio, and the power of ultrasound. Thus, the response surface method was applied to investigate the interaction between the two factors and to optimize the extraction process. The optimal extraction conditions were 210 W, 75% ethanol, 40 min and 25 mL/g with a maximum yield of 229.37 ± 7.16 mg UAE/g. Moreover, the antioxidant ability of triterpenes from B. emeiensis (TBE) was evaluated by determining the scavenging capacity on free radicals and the protection on CHO cells and Caenorhabditis elegans against oxidative stress. The results showed the triterpenes could clear 2,2-Diphenyl-1-picryl-hydrazyl (DPPH) radicals well and had a strong reducing power. In addition, the survival of CHO cells was higher than that of the control group as a result of reducing the reactive oxygen species (ROS) level and promoting the activities of antioxidant enzymes. In addition, TBE could also enhance the survival of C. elegans under H2O2 conditions. Therefore, triterpenes from B. emeiensis could be developed into a beneficial potential for antioxidants.

Phenolic Composition, Antioxidant and Anticancer Potentials of Extracts from Rosa banksiae Ait. Flowers.

Rosa banksiae Ait. (R. banksiae) is a traditional Chinese folk medicine and an ornamental plant. Most previous studies have focused on cultivation and utilization while there are few research papers on the pharmacological activity of R. banksiae. This study aimed to get a better understanding of R. banksiae by extracting polyphenols with fractionated extraction technology. The results showed that ethyl acetate phase (EAP) contained the most polyphenols, while water phase (WP) had the least. HPLC analysis indicated that rutin and luteolin-4'-O-glucoside existed in the EAP and butanol phase (BP), but quercetin was only detected in the EAP. Six phenolic compositions were not detected in WB. The antioxidant and anti-tumor abilities of the EAP and BP were excellent. The results revealed that R. banksiae possessed a great antioxidant capacity and was rich in polyphenols, thus indicating R. banksiae was suitable for being a natural antioxidant and an abundant source of polyphenols.

In Vivo and In Vitro Antioxidant Activities of Methanol Extracts from Olive Leaves on Caenorhabditis elegans.

The aim of this study was to evaluate the antioxidant activities of extracts from olive leaves (EOL). The main contents of EOL were determined by colorimetric methods. The antioxidant activities were assessed by measuring the scavenging free radicals in vitro. To investigate the antioxidant activity in vivo, we detected the survival of Caenorhabditis elegans, under thermal stress. Subsequently the reactive oxygen species (ROS) level, activities of antioxidant enzymes, the expression of HSP-16.2 and the translocation of daf-16 were measured. The results showed that, polyphenols was the main component. EOL could well scavenge DPPH and superoxide anion radicals in vitro. Compared to the control group, the survival rate of C. elegans treated with EOL was extended by 10.43%, under heat stress. The ROS level was reduced, while the expression of hsp-16.2 was increased to protect the organism against the increasing ROS. The level of malondialdehyde (MDA) also decreased sharply. The activities of inner antioxidant enzymes, such as catalase (CAT), superoxide dismutase (SOD), and glutathione peroxidase (GSH-PX) were potentiated, which might have had a correlation with the DAF-16 transcription factor that was induced-turned into the nuclear. Therefore, EOL showed a strong antioxidant ability in vitro and in vivo. Hence, it could be a potential candidate when it came to medicinal and edible plants.