Glutathione peroxidase activity in cell cultures from different regions of human epididymis

Aim: To study the secretory activity and androgen regulation of glutathione peroxidase (GPx) in epithelial cell cultures from human epididymis. Methods: Tissue was obtained from patients undergoing therapeutic orchidectomy for prostatic cancer. Epithelial cell cultures were obtained from the caput, corpus and cauda epididymides. Enzymatic activity was measured in conditioned media by colorimetric methods in absence or presence of 1, 10 or 100 nrnoI.L^(-1) testosterone. The effect of 1 μmol.L^(-1) flutamide was also evaluated. Results: GPx activity was higher in cultures from corpus and cauda than caput epididymidis. The presence of different concentrations of testosterone increase enzyme activity in cell cultures from all epididymal regions. Addition of flutamide reverses the androgen dependent increase of GPx activity. Conclusion: GPx activity is secreted from human epididymal cells in a region dependent manner and is regulated by androgens.

Altered expression patterns of syndecan-1 and ,2 predicl biochemical recurrence in prostate cancer

The clinical features of prostate cancer do not provide an accurate determination of patients undergoing biochemical relapse and are therefore not suitable as indicators of prognosis for recurrence. New molecular markers are needed for proper pre-treatment risk stratification of patients. Our aim was to assess the value of altered expression of syndecan-1 and -2 as a marker for predicting biochemical relapse in patients with clinically localized prostate cancer treated by radical prostatectomy. The expression of syndecan-1 and -2 was examined by immunohistochemical staining in a series of 60 paraffin-embedded tissue samples from patients with localized prostate cancer. Ten specimens from patients with benign prostatic hyperplasia were used as non-malignant controls. Semiquantitative analysis was performed to evaluate the staining patterns. To investigate the prognostic value, Kaplan-Meier survival curves were performed and compared by a log-rank test. In benign samples, syndecan-1 was expressed in basal and secretory epithelial cells with basolateral membrane Iocalisation, whereas syndecan-2 was expressed preferentially in basal cells. In prostate cancer samples, the expression patterns of both syndecans shifted to granular-cytoplasmic Iocalisation. Survival analysis showed a significant difference （P〈0.05） between normal and altered expression of syndecan-1 and -2 in free prostate-specific antigen recurrence survival curves. These data suggest that the expression of syndecan-1 and -2 can be used as a prognostic marker for patients with clinically localized orostate cancer, improving the larostate-specific antigen recurrence risk stratification.

Network models for molecular kinetics and their initial applications to human health

Molecular kinetics underlies all biological phenomena and, like many other biological processes, may best be understood in terms of networks. These networks, called Markov state models （MSMs）, are typically built from physical simulations. Thus, they are capable of quantitative prediction of experiments and can also provide an intuition for complex couformational changes. Their primary application has been to protein folding; however, these technologies and the insights they yield are transferable. For example, MSMs have already proved useful in understanding human diseases, such as protein misfolding and aggregation in Alzheimer＇s disease.

Osteogenesis imperfecta mutations in plastin 3 lead to impaired calcium regulation of actin bundling

Mutations in actin-bundling protein plastin 3(PLS3)emerged as a cause of congenital osteoporosis,but neither the role of PLS3 in bone development nor the mechanisms underlying PLS3-dependent osteoporosis are understood.Of the over 20 identified osteoporosis-linked PLS3 mutations,we investigated all five that are expected to produce full-length protein.One of the mutations distorted an actin-binding loop in the second actin-binding domain of PLS3 and abolished F-actin bundling as revealed by cryo-EM reconstruction and protein interaction assays.Surprisingly,the remaining four mutants fully retained F-actin bundling ability.However,they displayed defects in Ca2+sensitivity:two of the mutants lost the ability to be inhibited by Ca2+;while the other two became hypersensitive to Ca2a.Each group of the mutants with similar biochemical properties showed highly characteristic cellular behavior.Wild-type PLS3 was distributed between lamellipodia and focal adhesions.In striking contrast,the Ca2+-hyposensitive mutants were not found at the leading edge but localized exclusively at focal adhesions/stress fibers,which displayed reinforced morphology.Consistently,the Ca2+-hypersensitive PLS3 mutants were restricted to lamellipodia,while chelation of Ca2+caused their redistribution to focal adhesions.Finally,the bundling-deficient mutant failed to co-localize with any F-actin structures in cells despite a preserved F-actin binding through a non-mutation-bearing actin-binding domain.Our findings revealed that severe osteoporosis can be caused by a mutational disruption of the Ca2+-controlled PLS3’s cycling between adhesion complexes and the leading edge.Integration of the structural,biochemical,and cell biology insights enabled us to propose a molecular mechanism of plastin activity regulation by Ca2+.

Lineage structure of the human antibody repertoire in response to influenza vaccination

The adaptive immune system produces a large and diverse set of antibodies,each with an individual evolutionary and clonal history.This so called"antibody repertoire"protects each individual against insults such as infection and cancer,and responds to vaccination with B cell proliferation in response to the antigenic stimulation.Hybridomas and antigen-specific FACSbased analysis have given us much insight on how the immune system generates the complex and diverse immune response required to protect the body from the wide variety of potential pathogens.However,these methods have not been sufficient to make global and unbiased characterizations of the clonal structure of the immune system of a particular individual。

Additive nanomanufacturing of lab-on-a-chip fluorescent peptide nanoparticle arrays for Alzheimer＇s disease diagnosis

This paper proposes an additive nanomanufacturing approach to fabricate a personalized lab-on-a-chip fluorescent peptide nanoparticles （f-PNPs） array for simultaneous multi-biomarker detection that can be used in Alzheimer＇s disease （AD） diagnosis. We will discuss optimization techniques for the additive nanomanufacturing process in terms of reliability, yield and manufacturing efficiency. One contribution of this paper lies in utilization of additive nanomanufacturing techniques to fabricate a patient-specific customize-designed lab-on-a-chip device for personalized AD diagnosis, which remains a major challenge for biomedical engineering. Through the integrated bio-design and bio-manufacturing process, doctor＇s check- up and computer-aided customized design are integrated into the lab-on-a-chip array for patient-specific AD diagnosis. In addition, f-PNPs with targeting moieties for personalized AD biomarkers will be self-assembled onto the customized lab-on-a- chip through the additive nanomanufacturing process, which has not been done before. Another contribution of this research is the personalized lab-on-a-chip f-PNPs array for AD diagnosis utilizing limited human blood. Blood-based AD assessment has been described as ＂the holy grail＂ of early AD detection. This research created the computer-aided design, fabrication through additive nanomanufacturing, and validation of the f-PNPs array for AD diagnosis. This is a highly interdisciplinary research contributing to nanotechnology, biomaterials, and biomedical engineering for neurodegenerative disease. The conceptual work is preliminary with intent to introduce novel techniques to the application. Large-scale manufacturing based on the proposed framework requires extensive validation and optimization.

McSNAC:A software to approximate first-order signaling networks from mass cytometry data

Background:Mass cytometry(CyTOF)gives unprecedented opportunity to simultaneously measure up to 40 proteins in single cells,with a theoretical potential to reach 100 proteins.This high-dimensional single-cell information can be very useful in dissecting mechanisms of cellular activity.In particular,measuring abundances of signaling proteins like phospho-proteins can provide detailed information on the dynamics of single-cell signaling processes.However,computational analysis is required to reconstruct such networks with a mechanistic model.Methods:We propose our Mass cytometry Signaling Network Analysis Code(McSNAC),a new software capable of reconstructing signaling networks and estimating their kinetic parameters from CyTOF data.McSNAC approximates signaling networks as a network of first-order reactions between proteins.This assumption often breaks down as signaling reactions can involve binding and unbinding,enzymatic reactions,and other nonlinear constructions.Furthermore,McSNAC may be limited to approximating indirect interactions between protein species,as cytometry experiments are only able to assay a small fraction of protein species involved in signaling.Results:We carry out a series of in silico experiments here to show(1)McSNAC is capable of accurately estimating the ground-truth model in a scalable manner when given data originating from a first-order system;(2)McSNAC is capable of qualitatively predicting outcomes to perturbations of species abundances in simple second-order reaction models and in a complex in silico nonlinear signaling network in which some proteins are unmeasured.Conclusions:These findings demonstrate that McSNAC can be a valuable screening tool for generating models of signaling networks from time-stamped CyTOF data.

Ultrafast photonic PCR

Nucleic acid amplification and quantification via polymerase chain reaction(PCR)is one of the most sensitive and powerful tools for clinical laboratories,precision medicine,personalized medicine,agricultural science,forensic science and environmental science.Ultrafast multiplex PCR,characterized by low power consumption,compact size and simple operation,is ideal for timely diagnosis at the point-of-care(POC).Although several fast/ultrafast PCR methods have been proposed,the use of a simple and robust PCR thermal cycler remains challenging for POC testing.Here,we present an ultrafast photonic PCR method using plasmonic photothermal light-to-heat conversion via photon–electron–phonon coupling.We demonstrate an efficient photonic heat converter using a thin gold(Au)film due to its plasmon-assisted high optical absorption(approximately 65%at 450 nm,the peak wavelength of heat source light-emitting diodes(LEDs)).The plasmon-excited Au film is capable of rapidly heating the surrounding solution to over 150℃ within 3 min.Using this method,ultrafast thermal cycling(30 cycles;heating and cooling rate of 12.7960.93℃ s^(-1) and 6.660.29℃ s^(-1),respectively)from 55℃(temperature of annealing)to 95℃(temperature of denaturation)is accomplished within 5 min.Using photonic PCR thermal cycles,we demonstrate here successful nucleic acid(λ-DNA)amplification.Our simple,robust and low cost approach to ultrafast PCR using an efficient photonic-based heating procedure could be generally integrated into a variety of devices or procedures,including on-chip thermal lysis and heating for isothermal amplifications.

Low-cost,simple,and scalable self-assembly of DNA origami nanostructures

Despite demonstrating exciting potential for applications such as drug delivery and biosensing,the development of nanodevices for practical applications and broader use in research and education are still hindered by the time,effort,and cost associated with DNA origami fabrication.Simple and robust methods to perform and scale the DNA origami self-assembly process are critical to facilitate broader use and translation to industrial or clinical applications.We report a simple approach to fold DNA origami nanostructures that is fast,robust,and scalable.We demonstrate fabrication at scales approximately 100-1,500-fold higher than typical scales.We further demonstrate an approach we termed low-cost efficient annealing (LEAN) self-assembly involving initial heating at 65 ℃ for 10 min,then annealing at 51 ℃ for 2 h,followed by brief quenching at 4 ℃ that leads to effective assembly of a range of DNA origami structures tested.In contrast to other methods for scaling DNA origami assembly,this approach can be carried out using cheap and widely available equipment (e.g.,hot plates,water baths,and laboratory burners) and uses standard recipes and materials so is readily applied to any existing or new DNA origami designs.We envision these methods can facilitate device development for commercial applications and facilitate broader use of DNA origami in research and education.

Plasmonic bacteria on a nanoporous mirror via hydrodynamic trapping for rapid identification of waterborne pathogens

A rapid,precise method for identifying waterborne pathogens is critically needed for effective disinfection and better treatment.However,conventional methods,such as culture-based counting,generally suffer from slow detection times and low sensitivities.Here,we developed a rapid detection method for tracing waterborne pathogens by an innovative optofluidic platform,a plasmonic bacteria on a nanoporous mirror,that allows effective hydrodynamic cell trapping,enrichment of pathogens,and optical signal amplifications.We designed and simulated the integrated optofluidic platform to maximize the enrichment of the bacteria and to align bacteria on the nanopores and plasmonic mirror via hydrodynamic cell trapping.Gold nanoparticles are self-assembled to form antenna arrays on the surface of bacteria,such as Escherichia coli and Pseudomonas aeruginosa,by replacing citrate with hydroxylamine hydrochloride in order to amplify the signal of the plasmonic optical array.Owing to the synergistic contributions of focused light via the nanopore geometry,self-assembled nanoplasmonic optical antennas on the surface of bacteria,and plasmonic mirror,we obtain a sensitivity of detecting E.coli as low as 102 cells/ml via surface-enhanced Raman spectroscopy.We believe that our label-free strategy via an integrated optofluidic platform will pave the way for the rapid,precise identification of various pathogens.

De Novo Design of a Highly Stable Ovoid TIM Barrel:Unlocking Pocket Shape towards Functional Design

The ability to finely control the structure of protein folds is an important prerequisite to functional protein design. The TIM barrelfold is an important target for these efforts as it is highly enriched for diverse functions in nature. Although a TIM barrel proteinhas been designed de novo, the ability to finely alter the curvature of the central beta barrel and the overall architecture of the foldremains elusive, limiting its utility for functional design. Here, we report the de novo design of a TIM barrel with ovoid (twofold)symmetry, drawing inspiration from natural beta and TIM barrels with ovoid curvature. We use an autoregressive backbonesampling strategy to implement our hypothesis for elongated barrel curvature, followed by an iterative enrichment sequencedesign protocol to obtain sequences which yield a high proportion of successfully folding designs. Designed sequences arehighly stable and fold to the designed barrel curvature as determined by a 2.1Å resolution crystal structure. The designs showrobustness to drastic mutations, retaining high melting temperatures even when multiple charged residues are buried in thehydrophobic core or when the hydrophobic core is ablated to alanine. As a scaffold with a greater capacity for hosting diversehydrogen bonding networks and installation of binding pockets or active sites, the ovoid TIM barrel represents a major steptowards the de novo design of functional TIM barrels.

Synergistic and non-specific nucleic acid production by T7 RNA polymerase and Bsu DNA polymerase catalyzed by single-stranded polynucleotides

Point-of-care molecular diagnostic tests show great promise for providing accurate,timely results in lowinfrastructure healthcare settings and at home.The design space for these tests is limited by a variety of possible background reactions,which often originate from relatively weak promiscuous activities of the enzymes used for nucleic acid amplification.When this background signal is amplified alongside the signal of the intended biomarker,the dynamic range of the test can be severely compromised.Therefore,a detailed knowledge of potential side reactions arising from enzyme promiscuity can improve rational design of point-of-care molecular diagnostic tests.Towards this end,we report a previously unknown synergistic reaction between T7 RNA polymerase and Bsu DNA polymerase that produces nucleic acid in the presence of single-stranded DNA or RNA.This reaction occurs in the absence of any previously reported substrates for either polymerases and compromises a theoretical microRNA amplification scheme utilizing these polymerases.

Bioinspired optical antennas: gold plant viruses

The ability to capture the chemical signatures of biomolecules(i.e.,electron-transfer dynamics)in living cells will provide an entirely new perspective on biology and medicine.This can be accomplished using nanoscale optical antennas that can collect,resonate and focus light from outside the cell and emit molecular spectra.Here,we describe biologically inspired nanoscale optical antennas that utilize the unique topologies of plant viruses(and thus,are called gold plant viruses)for molecular fingerprint detection.Our electromagnetic calculations for these gold viruses indicate that capsid morphologies permit high amplification of optical scattering energy compared to a smooth nanosphere.From experimental measurements of various gold viruses based on four different plant viruses,we observe highly enhanced optical cross-sections and the modulation of the resonance wavelength depending on the viral morphology.Additionally,in label-free molecular imaging,we successfully obtain higher sensitivity(by a factor of up to 10^(6))than can be achieved using similar-sized nanospheres.By virtue of the inherent functionalities of capsids and the plasmonic characteristics of the gold layer,a gold virus-based antenna will enable cellular targeting,imaging and drug delivery.