He–Ne laser (632.8 nm) pre‐irradiation gives protection against DNA damage induced by a near‐infrared trapping beam

We report the results of a study carried out to investigate the effect of He–Ne laser (632.8 nm) pre‐irradiation on DNA damage induced by continuous wave 1064 nm trapping beam exposure in MCF‐7 cells. A significant decrease in % tail DNA (p < 0.05) was observed in MCF‐7 cells pre‐exposed to He–Ne laser beam. The dependence of the induced protection against 1064 nm trapping beam irradiation induced DNA damage on the time interval between the two irradiations as well as the He–Ne laser pre‐irradiation parameters is presented. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Laser tweezers as a biophotonic tool to investigate the efficacy of living sickle red blood cells in response to optical deformation

A laser tweezer technique based on single and/or dual-laser beams is proposed as a biophotonic tool to trap single cells and investigate their biophysical and biomechanical characteristics. Optical deformability and changes in size and cellular morphology of living and nonliving cells can be measured using the proposed technique. Representative results of red blood cell (RBC) optical deformability of 20 homozygous patients with sickle cell disease, including follow-up patients after treating with hydroxyurea (HU) for at least 3 months and 20 healthy control groups, are presented and compared. Shape recovery of deformed RBCs and relaxation time are recorded for each RBC. Results showed that healthy blood and patients treated with HU demonstrate significantly higher optical deformability and degree of optical elongation with morphological change of RBCs than untreated patients. Moreover, the healthy control group and patients treated with HU exhibited faster relaxation time for RBCs than untreated patients. A trapping power that reaches 180 mW caused no observable photo-damage at a wavelength 1064 nm.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12551-021-00790-0.     

Microdissection of plant chromosomes by argon-ion laser beam

Summary Rice and barley chromosomal samples were prepared both on a polyester membrane and on an ordinary glass slide and subjected to microdissection by an argon-ion laser. The intensity and the position of the laser beam were controlled by a microcomputer. The most suitable intensity to obtain chromosomal fragments was determined experimentally. As a result, specific regions of the centromere, satellite, short arm, or long arm, of the barley and rice chromosomes were dissected out from the chromosomal spreads. Chromosomal fragments were also successfully transferred from the sample into an Eppendorf tube.     

Ultrasensitive detection of proteins and antibodies by absorption-based laser wave-mixing detection using a chromophore label

Nonlinear laser wave mixing is presented as an ultrasensitive absorption-based method for the detection of proteins and antibodies using a nonfluorescing chromophore label, Coomassie Brilliant Blue (CBB). The complexes are flowed through a 150-μm (i.d.) capillary cell and detected using a low-power He-Ne laser. The wave-mixing signal is detected after 10 min of room temperature incubation for the antibody complex and after 18 min for the protein complex. All solutions are prepared in an aqueous buffer without the addition of organic modifiers. Concentration detection limits of 3.4 × 10^-19 and 6.4 × 10^-14 M (signal-to-noise ratio [S/N] = 2) are determined for bovine serum albumin (BSA) and human papillomavirus (HPV) antibody, respectively. Based on the small laser probe volume used (i.e., overlap volume of the two input beams), mass detection limits of 1.7 × 10^-22 and 2.6 × 10^-17 mol are determined for BSA and HPV antibody, respectively.     

Laser-based micromanipulation for separation and identification of individual Frankia vesicles

In studies of symbiotic efficiency it is of great importance to identify and separate individual Frankia strains from a nodule. Therefore, a new laser-based micromanipulation technique has been developed in which individual vesicles from root nodules of two Frankia-Alnus symbioses have been successfully cut loose and separated from clusters of vesicles in sterile conditions under light microscopy using a laser scalpel and optical tweezers. Vesicles from the Alnus incana-Frankia AvCI1 symbiosis were successfully isolated and grown in culture using this technique. The DNA from both Frankia sources was amplified by polymerase chain reaction (PCR). The work shows that a combination of laser-based manipulation techniques and PCR can be used for the separation and study of individual vesicles. This novel laser-based micromanipulation technique opens up various new possibilities, for instance, to study whether several Frankia strains can grow simultaneously in the same root nodule.     

一类蛋白质相互作用网络比对的线性规划算法

随着越来越多的蛋白质相互作用数据被公布,网络比对在预测蛋白质的新功能和推测蛋白质网络进化历史上发挥着越来越重要的作用。但是,目前主要的网络比对方法要么忽略蛋白质的同源信息或蛋白质网络的结构信息,要么采用启发式算法。文章作者通过将网络比对转化为线性规划问题给出了一个精确的网络比对算法,并且针对水痘病毒和卡波济(氏)肉瘤病毒的蛋白质相互作用数据进行了比对分析。     

Alignment of protein sequences by their profiles

The accuracy of an alignment between two protein sequences can be improved by including other detectably related sequences in the comparison. We optimize and benchmark such an approach that relies on aligning two multiple sequence alignments, each one including one of the two protein sequences. Thirteen different protocols for creating and comparing profiles corresponding to the multiple sequence alignments are implemented in the SALIGN command of MODELLER. A test set of 200 pairwise, structure-based alignments with sequence identities below 40% is used to benchmark the 13 protocols as well as a number of previously described sequence alignment methods, including heuristic pairwise sequence alignment by BLAST, pairwise sequence alignment by global dynamic programming with an affine gap penalty function by the ALIGN command of MODELLER, sequence-profile alignment by PSI-BLAST, Hidden Markov Model methods implemented in SAM and LOBSTER, pairwise sequence alignment relying on predicted local structure by SEA, and multiple sequence alignment by CLUSTALW and COMPASS. The alignment accuracies of the best new protocols were significantly better than those of the other tested methods. For example, the fraction of the correctly aligned residues relative to the structure-based alignment by the best protocol is 56%, which can be compared with the accuracies of 26%, 42%, 43%, 48%, 50%, 49%, 43%, and 43% for the other methods, respectively. The new method is currently applied to large-scale comparative protein structure modeling of all known sequences.     

Opto-mechanical characterization of sclera by polarization sensitive optical coherence tomography

Polarization sensitive optical coherence tomography (PSOCT) is an interferometric technique sensitive to birefringence. Since mechanical loading alters the orientation of birefringent collagen fibrils, we asked if PSOCT can be used to measure local mechanical properties of sclera.Infrared (1300 nm) PSOCT was performed during uniaxial tensile loading of fresh scleral specimens of rabbits, cows, and humans from limbal, equatorial, and peripapillary regions. Specimens from 8 human eyes were obtained. Specimens were stretched to failure at 0.01 mm/s constant rate under physiological conditions of temperature and humidity while birefringence was computed every 117 ms from cross-sectional PSOCT. Birefringence modulus (BM) was defined as the rate of birefringence change with strain, and tensile modulus (TM) as the rate of stress change between 0 and 9% strain.In cow and rabbit, BM and TM were positively correlated with slopes of 0.17 and 0.10 GPa, and with correlation coefficients 0.63 and 0.64 (P < 0.05), respectively, following stress-optic coefficients 4.69, and 4.20 GPa⁻¹. In human sclera, BM and TM were also positively correlated with slopes of 0.24 GPa for the limbal, 0.26 GPa for the equatorial, and 0.31 GPa for the peripapillary regions. Pearson correlation coefficients were significant at 0.51, 0.58, and 0.69 for each region, respectively (<0.001). Mean BM decreased proportionately to TM from the limbal to equatorial to peripapillary regions, as stress-optic coefficients were estimated as 2.19, 2.42, and 4.59 GPa⁻¹, respectively.Since birefringence and tensile elastic moduli correlate differently in cow, rabbit, and various regions of human sclera, it might be possible to mechanically characterize the sclera in vivo using PSOCT.     

Phagocytosis of Dictyostelium discoideum studied by the particle-tracking method

Single phagocytic events of cellular slime mold Dictyostelium discoideum were studied by the method of particle tracking. A 2-microm polystyrene bead, which had been covalently coated with folate, was attached to the advancing edge of a Dictyostelium ameba with the aid of an optical trap. The bead was transported backward on the cell surface. Forty-five percent of the transported beads were internalized. The bead motion was analyzed by determining every 33 ms the x-y coordinate of the centroid of the phase-contrast image of the bead. The x(t) and y(t) traces were smoothed over 1 s and the difference between the smoothed (x(t) and y(t)) and the original traces, delta(x) identical with x(t) - x(t) and delta(y) identical with y(t) - y(t), were calculated, which represented relatively rapid components of the bead motion. The plot of delta(2) = (delta(x)(2) + delta(y)(2)) against time could be divided into three phases on the basis of the variance of delta(2). Comparison of the plot with the video sequence indicated that the first phase corresponded to the transport, the second phase to the internalization, and the third phase to the postinternalization process (intracellular movement). Cytochalasin A at 5 microM completely inhibited phagocytosis without affecting the binding of bead to the cell surface, indicating the importance of actin cytoskeleton in all the phases. At 1 microM cytochalasin A the variance of the postinternalization process decreased, and the duration of the transport phase increased. At 0.25 microM cytochalasin A the duration of the internalization phase exhibited a significant increase, but other parameters did not change appreciably. The complex and differential effects of cytochalasin A on the parameters characterizing the three phases in the phagocytic process indicate that various aspects of actin dynamics are involved in the individual process of phagocytosis.     

Mapping the classical cross-bridge theory and backward steps in a three bead laser trap setup

According to the cross-bridge theory (Huxley, 1957) [1], the interaction between myosin and actin is governed by a deterministic process where the myosin molecule pulls the actin filament in one specific direction only. However, studies on single myosin-actin interactions produced displacements of actin not only in the preferred but also in the opposite direction. This phenomenon is typically referred to as backward steps by the myosin head. Molloy et al. (1995) [2] speculated that these backward steps are not caused by the molecular interactions of actin with myosin but are an artifact of the Brownian motion associated with these molecular level experiments. The aim of this study was to investigate, whether a theoretical model can support Molloy’s speculation. We therefore developed a theoretical model of actin-myosin based muscle contraction that was strictly based on Huxley’s assumption of one stepping direction only, but incorporated Brownian motion, as observed in single cross-bridge-actin interactions. The mathematical model is based on Langevin equations describing the classical three-bead laser trap setup and uses a novel semi-analytical approach to study the percentage of backward steps. We analyzed the effects of different initial actin attachment site distribution and laser trap stiffness on the ratio of forward to backward steps. Our results demonstrate that backward steps and the classical cross-bridge theory are perfectly compatible in a three-bead laser trap setup.     

Towards biological applications of nanophotonic tweezers

Optical trapping (synonymous with optical tweezers) has become a core biophysical technique widely used for interrogating fundamental biological processes on size scales ranging from the single-molecule to the cellular level. Recent advances in nanotechnology have led to the development of ‘nanophotonic tweezers,’ an exciting new class of ‘on-chip’ optical traps. Here, we describe how nanophotonic tweezers are making optical trap technology more broadly accessible and bringing unique biosensing and manipulation capabilities to biological applications of optical trapping.     

Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists tree of life based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution.Reviewing Editor: Dr. John Oakeshott     

Structural analysis of microparticles by confocal laser scanning microscopy

This study demonstrates the potential of conforcal laser scanning microscopy (CLSM) as a characterization tool for different types of microparticles. Microparticles were prepared by various methods including complex coacervation, spray drying, double emulsion solvent evaporation technique, and ionotropic gelation. Protein drugs and particle wall polymers were covalently labeled with a fluorescent marker prior to particle preparation, while low molecular weight drugs were labeled by mixing with a fluorescent marker of similar solubility properties. As was demonstrated in several examples, CLSM allowed visualization of the polymeric particle wall composition and detection of heterogeneous polymer distribution or changes in polymer matrix composition under the influence of the drug. Furthermore, CLSM provides a method for three-dimensional reconstruction and image analysis of the microparticles by imaging several coplanar sections throughout the object. In conclusion, CLSM allows the inspection of internal particle structures without prior sample destruction. It can be used to localize the encapsulated compounds and to detect special structural details of the particle wall composition.     

Chromosomal localization of a proinsulin transgene in Japanese quail by laser pressure catapulting

Transgenic avian bioreactors produce therapeutic recombinant proteins in egg white. To date, however, methods for transgenic modification of the avian genome or determining transgenic status of individual birds are scarce. The dual, but interrelated, goals of this research were to: (1) develop a method of detecting stable DNA insertion into Japanese quail; and (2) provide a method for gene location on avian chromosomes. We created Teflon-coated coverslip slides to facilitate laser pressure catapulting of avian chromosomes for DNA amplification and nucleotide sequencing. Transgenic G₂ Japanese quail, containing germline incorporation of proinsulin, were identified by isolation of chromosomes using laser microdissection and laser pressure catapulting. Subsequent amplification of each chromosome identified 2–5 chromosomes with the proinsulin transgene inserted. Nucleotide sequencing of each chromosomal insertion was identical to the proinsulin portion of the original vector. By applying laser pressure catapulting and PCR of individual chromosomes, we were able to determine that the transgene correctly inserted into avian chromosomes and that the majority of the insertions occurred within microchromosomes. Because many potential therapeutic transgenes have similar or nearly identical nucleotide sequence to the host’s native gene, laser microdissection and subsequent analysis may be required for detailed documentation of transgene expression before proceeding with transgenic protein production.     

Alignment of high resolution mass spectra: development of a heuristic approach for metabolomics

One of the challenges of using mass spectrometry for metabolomic analyses of samples consisting of thousands of compounds is that of peak identification and alignment. This paper addresses the issue of aligning mass spectral data from different samples in order to determine average component m/z peak values. The alignment scheme developed takes the instrument m/z measurement error into consideration in order to heuristically align two or more samples using a technique comparable to automated visual inspection and alignment. The results obtained using mass spectral profiles of replicate human urine samples suggest that this heuristic alignment approach is more efficient than other approaches using hierarchical clustering algorithms. The output consists of an average m/z and intensity value for the spectral components together with the number of matches from the different samples. One of the major advantages of using this alignment strategy is that it eliminates the boundary problem that occurs when using predetermined fixed bins to identify and combine peaks for averaging and the efficient runtime allows large datasets to be processed quickly.     

Excitation of magnetic fields by a circularly polarized laser pulse in a plasma channel

The excitation of quasistatic magnetic fields by a circularly polarized laser pulse in a plasma channel is considered. It is shown that, to second order in the amplitude of the electric field of the laser pulse, circular rotation of the plane of polarization of the laser radiation in a radially nonuniform plasma gives rise to a nonlinear azimuthal current and leads to the excitation of the radial and axial components of the magnetic field. The dependence of the magnetic field distribution over the plasma channel on the spatial dimensions of the pulse and on the channel width is investigated for a moderate-power laser pulse. The structure of the magnetic fields excited by a relativistic laser pulse in a wide plasma channel is analyzed.     

Detection of intranuclear forces by the use of laser optics during the recovery process of elongated interphase nuclei in centrifuged protenemal cells ofAdiantum capillus-veneris

For the direct investigation of intranuclear dynamics in living cells, extremely deformed nuclei of basipetally centrifuged protonemal cells of the fernAdiantum capillus-veneris were manipulated by the laser trap and the laser scalpel. Whereas the nucleolus was tightly fixed at the central position inside the non-centrifuged nucleus and proved to be immovable by the optical trap, it could easily be trapped and moved towards three directions inside the bubble-like terminal widening of the basal thread-like extension of centrifuged nuclei. Due to the connection of the nucleolus to the chromatin inside the nuclear thread (NT), moving was not possible against the direction of the nuclear apical main body. Nucleoli in recovered nuclei were again immovable, thus indicating the presence of a dynamic nucleolar anchoring system inside the nucleus. When the nucleolus in the bubble was arrested during the thread shortening process by the optical trap, the acropetal movement of the bubble continued. Probably due to dragging forces, some nucleoli became stretched, and a thick strand of a still unknown composition stretched between the nucleolus and the insertion site of the shortening NT. To assess whether the shrinking of the nuclear envelope (NE) and the shortening of the chromatin inside the NT were independent processes, the chromatin above the bubble was cut inside the NT by the laser scalpel. After severance, a gap between the nucleolus and the end of the chromatin strand in the NT indicated the shortening of the chromatin inside the NT. From these findings it was concluded that a shortening force was existing in the chromatin of the NT and that probably no physical link existed between the chromatin and the NE.     

Unraveling secrets of telomeres: One molecule at a time

Telomeres play important roles in maintaining the stability of linear chromosomes. Telomere maintenance involves dynamic actions of multiple proteins interacting with long repetitive sequences and complex dynamic DNA structures, such as G-quadruplexes, T-loops and t-circles. Given the heterogeneity and complexity of telomeres, single-molecule approaches are essential to fully understand the structure–function relationships that govern telomere maintenance. In this review, we present a brief overview of the principles of single-molecule imaging and manipulation techniques. We then highlight results obtained from applying these single-molecule techniques for studying structure, dynamics and functions of G-quadruplexes, telomerase, and shelterin proteins.     

Gaussian-based Alignment of Protein Structures: Deriving a Consensus Superposition when Alternative Solutions Exist

The use of a Gaussian-based representation of protein structures for evaluating protein-structure similarities and deriving three-dimensional superpositions is presented. The approach, as implemented in the program GAPS, is applied to three pairs of proteins with different topological characteristics (rich -helix, mixed -helix/-strand, and rich -strand), low sequence identities (10–30%), and recognized difficulties to define a unique optimum alignment.Validation of the GAPS superpositions is done by comparison with superpositions obtained by the TOP, GA_FIT, and ALIGN programs and those directly extracted from the FSSP database. Results suggest that a Gaussian-based methodology offers an objective means to, depending on the Gaussian-based representation, derive a consensus three-dimensional superposition when alternative superposition solutions exist.     

Motility of bovine spermatozoa studied by laser light scattering

Laser light scattering has been employed to determine the swimming speed distribution and the fraction of motile cells in samples of bovine spermatozoa. As predicted from theory, average trajectory velocities determined by laser light scattering were approximately four times the average translational speed estimated using light microscopy. The proportion of motile spermatozoa decreased with time at the same rate when samples were prepared in either HEPES or phosphate buffers. However, whereas the mean swimming velocity declined slowly in HEPES buffer, it dropped rapidly when phosphate buffer was used. Dilution (in the range 40–0.4×10⁶ spermatozoa·ml^-1) in either of these two buffers reduced the fraction of motile spermatozoa in the sample, but the mean swimming velocity of the remaining active spermatozoa was unchanged. Lowering the temperature from 37° C to 15° C reduced the mean swimming speed by a factor of 2–3 and the fraction of motile cells by a factor of 4–5.