Uncommon multivariate statistical methods for environmental studies: A review

In this paper we describe the characteristics and the applications of the multivariate methods for spectroscopic and chromatographic techniques independent component analysis (ICA) and two-dimensional correlation spectroscopy (2DCOS) focused to their use in environmental studies. In our opinion, these methods are important because they allow to characterize environmental samples with different aims and scopes from those generally obtained by means of more common multivariate methods such as principal component analysis (PCA) and partial least squares (PLS). The new insights of these methods in recent environmental studies are reviewed and debated.     

Unveil the potential function of CD in surfactant systems

CDs may have promising functions in surfactant systems far beyond simply being disadvantageous to the formation of micelles. In this paper we review the recent literature and our work on the interesting effect of CDs on amphiphilic systems, especially on the concentrated single surfactant systems and catanionic surfactant mixed systems, both of them have been scarcely focused upon in the literature. In concentrated single surfactant systems, the 2:1 surfactant-CD inclusion complexes may form hierarchical self-assemblies such as lamellae, microtubes, and vesicles which are driven by hydrogen bonding. In nonstoichiometrically mixed catanionic surfactant systems, CDs behave as a stoichiometry booster that always selectively binds to the excess component so as to shift the mixing ratio to electro-neutral in the aggregates. In this way, CDs reduce the electrorepulsion in the aggregates and trigger their growth. Upon analysis of literature work and our own results, we expect that a new era focusing on the new function of CDs on surfactant systems will come.     

On application of directons to functional classification of genes in prokaryotes

Functional classification of genes represents one of the most basic problems in genome analysis and annotation. Our analysis of some of the popular methods for functional classification of genes shows that these methods are not always consistent with each other and may not be specific enough for high-resolution gene functional annotations. We have developed a method to integrate genomic neighborhood information of genes with their sequence similarity information for the functional classification of prokaryotic genes. The application of our method to 93 proteobacterial genomes has shown that (i) the genomic neighborhoods are much more conserved across prokaryotic genomes than expected by chance, and such conservation can be utilized to improve functional classification of genes; (ii) while our method is consistent with the existing popular schemes as much as they are among themselves, it does provide functional classification at higher resolution and hence allows functional assignments of (new) genes at a more specific level; and (iii) our method is fairly stable when being applied to different genomes.     

Expedient Synthesis of Lupulones and Their Derivatization to 2,8-7H-Dihydrochromen-7-ones

A convenient and improved method for the synthesis of beta acids or lupulones, which are known to possess e. g. anti-cancer, anti-inflammatory, anti-oxidative and antimicrobial activity, has been developed successfully. Further derivatization of these complex structures to the corresponding dihydrochromen-7-ones, including the natural product machuone, was realized to simplify their analysis and to confirm their molecular structure. In addition to practical and safe laboratory procedures, the advantages associated with this new approach involve the use of water as a solvent and the direct crystallization of lupunones from acetonitrile, rendering our strategy more efficient and benign as compared to available methods.     

A new hydrophobic linker effective for the in situ synthesis of DNA-CPG conjugates as tools for SNP analysis

DNA chips consisting of DNA oligonucleotide probes immobilized on the surface of solid supports are very powerful tools for rapid analysis of multiple samples. In this Letter we describe a new method for the efficient synthesis of DNA probes without their serious elimination by use of a new hydrophobic 16-hyroxydecanoic linker and a new non-aqueous reagent of MeNH₂/THF for the deprotection of the base and phosphate protecting groups on CPG resins. The elimination of DNA probes in this new method could be suppressed more than 20-fold compared with the previous method using a hexaethylene glycol linker and concd NH₄OH. Moreover, we carried out SNPs detection by use of our DNA-CPG conjugate to show the utility of our new linker and deprotection conditions.     

Molecular design of anticancer drug leads based on three-dimensional quantitative structure-activity relationship

Heat shock protein 90 (Hsp90) takes part in the developments of several cancers. Novobiocin, a typically C-terminal inhibitor for Hsp90, will probably used as an important anticancer drug in the future. In this work, we explored the valuable information and designed new novobiocin derivatives based on a three-dimensional quantitative structure-activity relationship (3D QSAR). The comparative molecular field analysis and comparative molecular similarity indices analysis models with high predictive capability were established, and their reliabilities are supported by the statistical parameters. Based on the several important influence factors obtained from these models, six new novobiocin derivatives with higher inhibitory activities were designed and confirmed by the molecular simulation with our models, which provide the potential anticancer drug leads for further research.     

Structure and reactivity of Ziegler-Natta catalyst intermediates

This paper provides a survey of our recent research on chemistry that occurs among components of Ziegler-Natta catalysts. Since the amount of information regarding this topic is enormous we have focused on alkoxo compounds, which are attracting more and more attention in polymer industry. In this concept article we discuss recent studies on the inherently very complex catalyst system that involve isolation of various solid polynuclear metal-containing species, determination of their structures by X-ray crystallography, and relating their structures to the activity in polymerization. The presented research may be useful in predicting trends for the development of new single-site catalysts as well as new co-catalysts.     

微流控技术在外泌体分离分析中的研究进展

外泌体是一类由细胞分泌的含有脂质、蛋白、核酸等多种物质的纳米级囊泡,主要参与细胞间的物质交换及信息传导,与多种疾病的发生发展密切相关。对外泌体进行深入研究,理解其生物学功能,对疾病诊断与治疗具有重要意义。由于外泌体尺寸较小且密度和体液接近,想要对复杂生物样本中的外泌体进行分离与分析十分困难。传统的外泌体分离方法如超速离心、超滤等大都需要借助大型仪器设备,且耗时长、操作复杂。因此迫切需要开发高效、便捷的外泌体分离检测手段。微流控技术因其微型化、高通量、可集成等特点,为外泌体的分离分析提供了一个新的平台。该文主要对近年来微流控技术在外泌体分离分析相关领域的研究进展进行了综述。重点从外泌体物理特性和生化特性两个角度出发,介绍了微流控芯片技术用于外泌体分离领域的主要原理、策略和方法。此外,还介绍了微流控技术与荧光、电化学传感、表面等离子体共振等多模态检测方法结合,实现外泌体一体化分析的新进展。最后,该文分析了目前微流控技术用于外泌体分离检测存在的挑战,并对其发展趋势和前景进行了展望。随着微流控外泌体分离分析装置的不断微型化、集成化、自动化,微流控芯片技术将在外泌体分离、生化检测、机制研究等方面将发挥越来越重要的作用。     

Perspectives on the use of electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for short tandem repeat genotyping in the post-genome era.

The recent completion of the first rough draft of the human genome has provided fundamental information regarding our genetic make-up; however, the post-genome era will certainly require a host of new technologies to address complex biological questions. In particular, a rapid and accurate approach to characterize genetic markers, including short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) is demanded. STRs are the most informative of the two polymorphisms owing to their remarkable variability and even dispersity throughout eukaryotic genomes. Mass spectrometry is rapidly becoming a significant method in DNA analysis and has high probability of revolutionizing the way in which scientists probe the human genome. It is our responsibility as biomolecular mass spectrometrists to understand the issues in genetic analysis and the capabilities of mass spectrometry so that we may fulfill our role in developing a rapid, reliable technology to answer specific biological questions. This perspective is intended to familiarize the mass spectrometry community with modern genomics and to report on the current state of mass spectrometry, specifically electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry, for characterization of STRs.     

An ensemble method for multi-type Gram-negative bacterial secreted protein prediction by integrating different PSSM-based features

In Gram-negative bacteria, a wide range of proteins are secreted by highly specialized secretion systems. These secreted proteins play essential roles in the response of bacteria to their environment and also in several physiological processes such as adhesion, pathogenicity, adaptation and survival. Therefore, identifying secreted proteins in Gram-negative bacteria may assist in understanding the secretion mechanism and development of new antimicrobial strategies. Considering that a single-feature model is less likely to comprehensively cover this information, three kinds of feature models were used in this paper to represent protein samples by composition analysis, correlation analysis and smoothing encoding method on position-specific scoring matrix profiles. A support vector machine-based ensemble method with these hybrid features was developed to predict multi-type Gram-negative bacterial secreted proteins. Finally, our method achieves overall accuracies of 97.09% and 96.51% using an independent dataset test and jackknife test on a public test dataset, which are 3.49% and 2.32% higher, respectively, than results obtained by other methods. These results show the effectiveness and stability of the proposed ensemble method. It is anticipated that our method will provide useful information for further research on bacterial secreted proteins and secreted systems.     

Molecular mechanics methods for predicting protein-ligand binding

Ligand binding affinity prediction is one of the most important applications of computational chemistry. However, accurately ranking compounds with respect to their estimated binding affinities to a biomolecular target remains highly challenging. We provide an overview of recent work using molecular mechanics energy functions to address this challenge. We briefly review methods that use molecular dynamics and Monte Carlo simulations to predict absolute and relative ligand binding free energies, as well as our own work in which we have developed a physics-based scoring method that can be applied to hundreds of thousands of compounds by invoking a number of simplifying approximations. In our previous studies, we have demonstrated that our scoring method is a promising approach for improving the discrimination between ligands that are known to bind and those that are presumed not to, in virtual screening of large compound databases. In new results presented here, we explore several improvements to our computational method including modifying the dielectric constant used for the protein and ligand interiors, and empirically scaling energy terms to compensate for deficiencies in the energy model. Future directions for further improving our physics-based scoring method are also discussed.     

Microbe-derived carbon materials for electrical energy storage and conversion

Microbes are microscopic living organisms that surround us which include bacteria, archaea, most protozoa, and some fungi and algae. In recent years, microbes have been explored as novel precursors to synthesize carbon-based(nano)materials and as substrates or templates to produce carbon-containing(nano)composites. Being greener and more affordable, microbe-derived carbons(MDCs) offer good potential for energy applications. In this review, we describe the unique advantages of MDCs and outline the common procedures to prepare them. We also extensively discuss the energy applications of MDCs including their use as electrodes in supercapacitors and lithium-ion batteries, and as electrocatalysts for processes such as oxygen reduction, oxygen evolution, and hydrogen evolution reactions which are essential for fuel cell and water electrochemical splitting cells. Based on the literature trend and our group's expertise, we propose potential research directions for developing new types of MDCs. This review, therefore, provides the state-of-the-art of a new energy chemistry concept. We expect to stimulate future research on the applications of MDCs that may address energy and environmental challenges that our societies are facing.     

Global analysis of gene expression in cells of the immune system I. Analytical limitations in obtaining sequence information on polypeptides in two-dimensional gel spots

We have outlined various aspects and limitations of the collective analysis of protein species of a cell (lymphocyte). We have indicated research directions that, in to our opinion, deserve more attention. We have evaluated mainly the approach used in our laboratory and we recognize that a bulk of important research on the interface of proteomics and genomics remains to be dealt with. It is of great value that we can proceed in our quest by trial and error. But as much as the human genome initiative was not implemented by trial and error, but by formulating new technological approaches, we hope that our approach can be incorporated in the mainstream of proteomics. We need several integrating research directions, some of which are outlined in this communication, namely the use of ordered cDNA libraries, cell-free expression systems, high density filter hybridization, identification of two-dimensional (2-D) gel spots in terms of their amino acid composition through biosynthetic labeling and identification of restriction sites in the corresponding coding sequences. In the accompanying paper the cDNA ordered library approach will be described in some detail.     

A novel k-word relative measure for sequence comparison

In order to extract phylogenetic information from DNA sequences, the new normalized k-word average relative distance is proposed in this paper. The proposed measure was tested by discriminate analysis and phylogenetic analysis. The phylogenetic trees based on the Manhattan distance measure are reconstructed with k ranging from 1 to 12. At the same time, a new method is suggested to reduce the matrix dimension, can greatly lessen the amount of calculation and operation time. The experimental assessment demonstrated that our measure was efficient. What's more, comparing with other methods’ results shows that our method is feasible and powerful for phylogenetic analysis.     

Proton magnetic resonance investigation of the cotacticity of non-lactonized and the sequence distributions of lactonized (methyl-methacrylate-vinyl chloride) radical copolymers

By PMR analysis, it has been found that in non-lactonized VC-rich (MMA-VC) radical copolymers, the frequencies of the α-Me resonances depend on the weight fractions of isolated MMA and MMA-MMA diads. By our assumption, the isolated MMA units should be preferentially coisotactic. In the lactonized (MMA-VC) copolymers, two new methoxy resonances lines have been observed and their relative intensities are proportional to the weight fractions of (MMA, VC) pentads and hexads.     

Interlaboratory quality audit program for potable water – assessment of method validation done on inductively coupled plasma atomic emission spectrometer (ICP-AES)

In an effort to assess the method validation done using ICP-AES in our laboratory for potable water, an Environmental Laboratory Approval Program organized by New York State Department of Health, Wadsworth Center providing the reference material has been undertaken for 14 trace elements and seven other chemical constituents. The certified means for the reference material and the results obtained in our laboratory are compared. The comparisons helped us assess the quality of our work. All the data from the inductively coupled plasma atomic emission spectrometer (ICP-AES) fall into the ranges specified. These data are intended to depict the quality of chemical analysis being conducted in our laboratory and to increase the level of confidence of our clientele in accepting our test reports. It should be further noted that while the technique may not be new, the model is new and the simultaneous detection of elements required validation for those of our clientele who are only familiar with sequential AAS and AES. Received: 3 April 2002 Accepted: 4 September 2002     

A new approach to untargeted integration of high resolution liquid chromatography–mass spectrometry data

Because of its high sensitivity and specificity, hyphenated mass spectrometry has become the predominant method to detect and quantify metabolites present in bio-samples relevant for all sorts of life science studies being executed. In contrast to targeted methods that are dedicated to specific features, global profiling acquisition methods allow new unspecific metabolites to be analyzed. The challenge with these so-called untargeted methods is the proper and automated extraction and integration of features that could be of relevance. We propose a new algorithm that enables untargeted integration of samples that are measured with high resolution liquid chromatography–mass spectrometry (LC–MS). In contrast to other approaches limited user interaction is needed allowing also less experienced users to integrate their data. The large amount of single features that are found within a sample is combined to a smaller list of, compound-related, grouped feature-sets representative for that sample. These feature-sets allow for easier interpretation and identification and as important, easier matching over samples. We show that the automatic obtained integration results for a set of known target metabolites match those generated with vendor software but that at least 10 times more feature-sets are extracted as well. We demonstrate our approach using high resolution LC–MS data acquired for 128 samples on a lipidomics platform. The data was also processed in a targeted manner (with a combination of automatic and manual integration) using vendor software for a set of 174 targets. As our untargeted extraction procedure is run per sample and per mass trace the implementation of it is scalable. Because of the generic approach, we envision that this data extraction lipids method will be used in a targeted as well as untargeted analysis of many different kinds of TOF-MS data, even CE- and GC–MS data or MRM. The Matlab package is available for download on request and efforts are directed toward a user-friendly Windows executable.     

Two Decades of Laccases: Advancing Sustainability in the Chemical Industry

Given the current state of environmental affairs and that our future on this planet as we know it is in jeopardy, research and development into greener and more sustainable technologies within the chemical and forest products industries is at its peak. Given the global scale of these industries, the need for environmentally benign practices is propelling new green processes. These challenges are also impacting academic research and our reagents of interest are laccases. These enzymes are employed in a variety of biotechnological applications due to their native function as catalytic oxidants. They are about as green as it gets when it comes to chemical processes, requiring O₂ as their only co‐substrate and producing H₂O as the sole by‐product. The following account will review our twenty year journey on the use of these enzymes within our research group, from their initial use in biobleaching of kraft pulps and for fiber modification within the pulp and paper industry, to their current application as green catalytic oxidants in the field of synthetic organic chemistry.     

Fluids in nanospaces: molecular simulation studies to find out key mechanisms for engineering

We have analyzed various phenomena that occur in nanopores, focusing on elucidating their key mechanisms, to advance the effective engineering use of nanoporous materials. As ideal experimental systems, molecular simulations can effectively provide information at the molecular level that leads to mechanistic insight. In this short review, several of our recent results are presented. The first topic is the critical point depression of Lennard-Jones fluid in silica slit pores due to finite size effects, studied by our original Monte Carlo (MC) technique. We demonstrate that the first layers of adsorbed molecules in contact with the pore walls act as a “fluid wall” and impose extra finite size effects on the fluid confined in the central portion of the pore. We next present a new kernel for pore size distribution (PSD) analysis, based entirely on molecular simulation, which consists of local isotherms for nitrogen adsorption in carbon slit pores at 77 K. The kernel is obtained by combining grand canonical Monte Carlo (GCMC) method and open pore cell MC method that was developed in the previous study. We show that overall trends of the PSDs of activated carbons calculated with our new kernel and with conventional kernel from non-local density functional theory are nearly the same; however, apparent difference can be seen between them. As the third topic, we apply a free energy analysis method with the aid of GCMC simulations to investigate the gating behavior observed in a porous coordination polymer, and propose a mechanism for the adsorption-induced structural transition based on both the theory of equilibrium and kinetics. Finally, we construct an atomistic silica pore model that mimics MCM-41, which has atomic-level surface roughness, and perform molecular simulations to understand the mechanism of capillary condensation with hysteresis. We calculate the work required for the gas–liquid transition from the simulation data, and show that the adsorption branch with hysteresis for MCM-41 arise from spontaneous capillary condensation from a metastable state.     

Ionic Liquids for the Chemical Recycling of Polymeric Materials and Control of Their Solubility

Plastics are wonderful materials that have modernized our daily life; however, importance of effective recycling of plastics is gradually recognized widely. In this account, we describe our discovery of new and efficient methods for the chemical recycling of plastics using ionic liquids (ILs). Since the chemical recycling usually requires high temperature conditions to breakdown chemical bonds in polymeric materials, we thought that less-flammability and non-volatility of ionic liquids are the most suitable physical properties for this purpose. Ionic liquids successfully depolymerized polyamides and unsaturated polyesters smoothly and corresponding monomeric materials were obtained in good yields. To the best of our knowledge, this was the first use of Ionic liquids for such reactions. However, we encountered another difficult problem-separation. To solve the problem, we developed solubility-switchable ionic liquids, a new type of ionic liquids in which solubility is readily changed using the chemistry of protective groups. Conversion between hydrophilic and lipophilic forms was readily achieved using a simple chemical treatment under mild conditions, and the complete separation of products was achieved by liquid-liquid-extraction. The robustness of either form unlocks their wide use as reaction solvents.