Human sperm rotate with a conserved direction during free swimming in four dimensions.

Head rotation in human spermatozoa is essential for different swimming modes and fertilisation, as it links the molecular workings of the flagellar beat with sperm motion in three-dimensional (3D) space over time. Determining the direction of head rotation has been hindered by the symmetry and translucent nature of the sperm head, and by the fast 3D motion driven by the helical flagellar beat. Analysis has been mostly restricted to two-dimensional (2D) single focal plane image analysis, which enables tracking of head centre position but not tracking of head rotation. Despite the conserved helical beating of the human sperm flagellum, human sperm head rotation has been reported to be uni- or bi-directional, and even to intermittently change direction in a given cell. Here, we directly measure the head rotation of freely swimming human sperm using multi-plane 4D (3D+t) microscopy and show that: (1) 2D microscopy is unable to distinguish head rotation direction in human spermatozoa; (2) head rotation direction in non-capacitating and capacitating solutions, for both aqueous and viscous media, is counterclockwise (CCW), as seen from head to tail, in all rotating spermatozoa, regardless of the experimental conditions; and (3) head rotation is suppressed in 36% of spermatozoa swimming in non-capacitating viscous medium, although CCW rotation is recovered after incubation in capacitating conditions within the same viscous medium, possibly unveiling an unexplored aspect of the essential need of capacitation for fertilisation. Our observations show that the CCW head rotation in human sperm is conserved. It constitutes a robust and persistent helical driving mechanism that influences sperm navigation in 3D space over time, and thus is of critical importance in cell motility, propulsion of flagellated microorganisms, sperm motility assessments, human reproduction research, and self-organisation of flagellar beating patterns and swimming in 3D space.

A bioinformatic workflow for in silico secretome prediction with the lignocellulose degrading ascomycete fungus Parascedosporium putredinis NO1.

The increasing availability of microbial genome sequences provides a reservoir of information for the identification of new microbial enzymes. Genes encoding proteins engaged in extracellular processes are of particular interest as these mediate the interactions microbes have with their environments. However, proteomic analysis of secretomes is challenging and often captures intracellular proteins released through cell death and lysis. Secretome prediction workflows from sequence data are commonly used to filter proteins identified through proteomics but are often simplified to a single step and are not evaluated bioinformatically for their effectiveness. Here, a workflow to predict a fungal secretome was designed and applied to the coding regions of the Parascedosporium putredinis NO1 genome. This ascomycete fungus is an exceptional lignocellulose degrader from which a new lignin-degrading enzyme has previously been identified. The 'secretome isolation' workflow is based on two strategies of localisation prediction and secretion prediction each utilising multiple available tools. The workflow produced three final secretomes with increasing levels of stringency. All three secretomes showed increases in functional annotations for extracellular processes and reductions in annotations for intracellular processes. Multiple sequences isolated as part of the secretome lacked any functional annotation and made exciting candidates for novel enzyme discovery.

Optimized configuration for liquid crystal Stokes polarimeters in the presence of fast-axis orientation errors.

We present an optimal configuration for Stokes polarimeters based on liquid crystal variable retarders, with the minimum number of measurements. Due to the inherent variations of the director orientation of the liquid crystal molecules, we propose a configuration that minimizes the sensibility of the polarimeter to fast-axis variations. For the optimization we consider a scheme that maximizes the volume of a tetrahedron inscribed in the Poincare sphere, to address additive and Poisson noise, with one of the vertices invariant to changes in the axis positions. We provide numerical simulations, considering misalignment errors, to analyze the robustness of the configuration. The results show that the proposed configuration helps to maintain the volume enclosed by the tetrahedron with high tolerance to fast-axis orientation errors. The condition number will remain below 3.07 for common misalignment errors and below 1.88 for more controlled liquid crystals. This optimization will improve the performance of liquid crystals polarimeters, with a more robust configuration that also considers misalignment errors, beyond additive and Poisson noise.

Controlling In Planta Gold Nanoparticle Synthesis and Size for Catalysis.

Gold nanoparticles (Au-NPs) are used as catalysts for a diverse range of industrial applications. Currently, Au-NPs are synthesized chemically, but studies have shown that plants fed Au deposit, this element naturally as NPs within their tissues. The resulting plant material can be used to make biomass-derived catalysts. In vitro studies have shown that the addition of specific, short (∼10 amino acid) peptide/s to solutions can be used to control the NP size and shape, factors that can be used to optimize catalysts for different processes. Introducing these peptides into the model plant species, Arabidopsis thaliana (Arabidopsis), allows us to regulate the diameter of nanoparticles within the plant itself, consequently influencing the catalytic performance in the resulting pyrolyzed biomass. Furthermore, we show that overexpressing the copper and gold COPPER TRANSPORTER 2 (COPT2) in Arabidopsis increases the uptake of these metals. Adding value to the Au-rich biomass offers the potential to make plant-based remediation and stabilization of mine wastes financially feasible. Thus, this study represents a significant step toward engineering plants for the sustainable recovery of finite and valuable elements from our environment.

A multi-omics approach to lignocellulolytic enzyme discovery reveals a new ligninase activity from Parascedosporium putredinis NO1.

Lignocellulose, the structural component of plant cells, is a major agricultural byproduct and the most abundant terrestrial source of biopolymers on Earth. The complex and insoluble nature of lignocellulose limits its conversion into value-added commodities, and currently, efficient transformation requires expensive pretreatments and high loadings of enzymes. Here, we report on a fungus from the Parascedosporium genus, isolated from a wheat-straw composting community, that secretes a large and diverse array of carbohydrate-active enzymes (CAZymes) when grown on lignocellulosic substrates. We describe an oxidase activity that cleaves the major ß-ether units in lignin, thereby releasing the flavonoid tricin from monocot lignin and enhancing the digestion of lignocellulose by polysaccharidase mixtures. We show that the enzyme, which holds potential for the biorefining industry, is widely distributed among lignocellulose-degrading fungi from the Sordariomycetes phylum.

Comparison of two configurations of a Stokes polarimeter measuring three wavelengths simultaneously.

In this paper, we study two configurations of a full-Stokes polarimeter that measures three wavelengths simultaneously. A recently developed fitting calibration process is used to reduce the error in the final Stokes vector. The first configuration uses an optimized setup for the central wavelength that fixes the non-optimized setups for the other two wavelengths. The second configuration is the result of a search for the best simultaneous setups for all three wavelengths. It is found that this second setup gives smaller errors in the measured Stokes parameters before calibration, but the first configuration gives smaller errors after calibration. These results demonstrate the need for a method of finding the best polarimeter configuration for this type of measurement. It seems clear that the condition number by itself is not a metric that provides sufficient information to determine whether a particular configuration is better by giving smaller errors. It is also important to point out that the results presented here are for the particular calibration scheme used. Additionally, it may be that a different calibration method is required to give better results, but that is outside the scope of the present work.

Polarimetric measurement of non-depolarizing optical systems.

The use of polarization measurements has become more common in recent years, as it gives more information than pure intensity measurements. Polarimetric components such as fixed or variable retarders and polarizers must be included in optical systems to obtain the polarization parameters required, and in many cases the optical system also includes other components such as relay and/or imaging optical systems. In this work we present a simple and robust method for the polarimetric characterization of non-depolarizing polarization components and other optical elements in the system, which does not require a full polarimeter. Since there is no depolarization, we represent the components as pure retarders with diattenuation and find their parameters (transmittance for the polarization components, angle of orientation of the fast axis, and retardance), from which we can retrieve their Mueller matrix. Our results show that the proposed method is accurate when compared with results obtained with a Mueller matrix dual-rotating retarder polarimeter calibrated using the eigenvalue calibration method, considered in this work as the gold standard, and is comparatively easier than the latter to implement, particularly for imaging polarimeters.

Spectrally modulated polarimetry with wavelength domain analysis.

Spectrally modulated Stokes polarimeters use a pair of high-order crystal retarders to generate a spectrally dependent modulation of the polarization of light. In these systems, the detected intensity versus wavenumber spectrum is usually referred to as a channeled spectrum, and the Fourier inversion of this spectrum allows the determination of Stokes parameters of light without needing any other mechanical or active device for polarization control. This work proposes a spectrally modulated polarimeter beyond the concept of a channeled wavenumber spectrum, so effectively detaching the spectral modulation from the Fourier analysis technique. The wavelength domain analysis we use is best suited for dispersive spectrometers offering intensity versus wavelength measurements. The technique is illustrated with the measurement of very small optical rotations produced by sucrose solutions. The proposed technique is easily extendable to spectrally modulated Mueller polarimeters.

Effects of typical liquid-crystal retarder errors on optimized Stokes polarimeters.

Liquid crystal variable retarders (LCVRs) are often used in Stokes polarimeters as they allow the measurement of different polarization components by applying an electric field that manipulates the induced retardance. However, the optical retardance introduced by these devices is in general not homogenous across the aperture. Another problem with this type of devices is that the fast-axis orientation is not homogenous, and it changes with the applied voltage. For the optimization of polarimeters, in terms of the noise amplification from the intensity measurements to the polarimetric data, the condition number (CN) is often used, but the effects of LCVR spatial variations are not considered. This paper analyzes the impact of errors in LCVRs in a set of optimized Stokes polarimeters simulated by adding errors in the induced retardance and fast-axis orientation. Then, the CN is calculated to observe the effect of these errors on the optimization. We show how errors in the LCVRs lead to different impacts in the polarimetric measurements for different optimized polarimeters, depending on their experimental parameters. Furthermore, we present the propagation error theory to choose the best experimental parameters to reduce the nonideal effects in optimized polarimeters.

Effect of oils on the transmission properties of a terahertz photonic crystal.

The transmission properties of a photonic crystal immersed in several different oils have been characterized using terahertz time domain spectroscopy in the spectral range of 0.3-1.5 THz. As in previous works, oil samples can be distinguished using terahertz transmission measurements. When the same oils are introduced into a photonic crystal, we find that the effective refractive index of the photonic crystal is sensitive to the properties of the oils and shows differences not seen in bulk measurements. These effects are described in detail and have potential applications in both the sensing of very small volumes of oils and in the fine control of the refractive indices of photonic crystals.

Characterisation of the enzyme transport path between shipworms and their bacterial symbionts.

BACKGROUND: Shipworms are marine xylophagus bivalve molluscs, which can live on a diet solely of wood due to their ability to produce plant cell wall-degrading enzymes. Bacterial carbohydrate-active enzymes (CAZymes), synthesised by endosymbionts living in specialised shipworm cells called bacteriocytes and located in the animal's gills, play an important role in wood digestion in shipworms. However, the main site of lignocellulose digestion within these wood-boring molluscs, which contains both endogenous lignocellulolytic enzymes and prokaryotic enzymes, is the caecum, and the mechanism by which bacterial enzymes reach the distant caecum lumen has remained so far mysterious. Here, we provide a characterisation of the path through which bacterial CAZymes produced in the gills of the shipworm Lyrodus pedicellatus reach the distant caecum to contribute to the digestion of wood. RESULTS: Through a combination of transcriptomics, proteomics, X-ray microtomography, electron microscopy studies and in vitro biochemical characterisation, we show that wood-digesting enzymes produced by symbiotic bacteria are localised not only in the gills, but also in the lumen of the food groove, a stream of mucus secreted by gill cells that carries food particles trapped by filter feeding to the mouth. Bacterial CAZymes are also present in the crystalline style and in the caecum of their shipworm host, suggesting a unique pathway by which enzymes involved in a symbiotic interaction are transported to their site of action. Finally, we characterise in vitro four new bacterial glycosyl hydrolases and a lytic polysaccharide monooxygenase identified in our transcriptomic and proteomic analyses as some of the major bacterial enzymes involved in this unusual biological system. CONCLUSION: Based on our data, we propose that bacteria and their enzymes are transported from the gills along the food groove to the shipworm's mouth and digestive tract, where they aid in wood digestion.

Error analysis of channeled Stokes polarimeters.

This work presents an analysis of passive polarimeters with spectral channeling, referred to as Stokes channeled spectropolarimeters (SCS). The SCS setup comprises two thick birefringent retarders, followed by a horizontal linear polarizer. The simulation of these polarimeters and two extraction methods for the incident Stokes vector is presented as well. The effects of different retarders thickness ratios, the global retardance factor, retardance errors, axes alignment error, and Gaussian noise on root mean square (RMS) errors of the recovered Stokes parameters are described. Furthermore, two different, previously published data extraction methods are presented and compared. We found the best polarimeter configurations from the cases studied, and our results suggest that a mixed extraction process, using different extraction methods for different Stokes parameters, could give better results by reducing RMS errors by about a factor of 5. It is worth mentioning that although calibration is needed to account for the effect of errors, this is out of the scope of this work.

Analysis of experimental errors in Mueller matrix channeled polarimeters.

This work analyzes the effect of experimental errors and measurement noise on Mueller matrix channeled spectropolarimeters. The main advantage of this type of polarimeter is the independence on temporal resolution, as it can be used as a snapshot polarimeter. The simulation of the polarimeters with experimental errors and two published extraction methods of the sample Mueller matrix are also presented. The Mueller matrix channeled spectropolarimeter (MMCS) setup consists of a mirrored Stokes channeled spectropolarimeter (SCS) as the polarization states generator (PSG) and a SCS as the polarization states analyzer (PSA). The SCS setup comprises two thick birefringent retarders followed by a horizontal linear polarizer. The effects of the thickness ratio of the retarders, the global retardance factor, retardance errors, axes alignment errors, and additive Gaussian noise are further studied to optimize the MMCS setups. In this work, we do not include a calibration procedure to improve the measured Mueller matrix parameters, but we study the sensitivity of the polarimeter to different configurations and error sources.

Rough surface scattering using a source able to produce an incident beam with controlled polarization and coherence.

We present a comparison of the first numerical and experimental results for the scattering of light from rough surfaces using a recently developed variable coherence polarimetry source that permits obtaining information on the object without having to scan over incidence or scatter angle. We present, for the first time, we believe, the application of this source to a 1D rough surface and show how to analyze the scattered field to retrieve useful information about the surface. This source uses a liquid-crystal phase modulator to control the polarization as well as the coherence of the beam illuminating the rough surface. Changing the polarization state distribution at the source plane, by controlling the phase distribution on a spatial light modulator, gives a scan of two source spots over the rough surface. The scattered beam is analyzed with a Stokes polarimeter. The Kirchhoff approximation is used to calculate the scattered Stokes vector using the experimental incident Stokes vector and intensity distribution as a source. Good agreement is obtained between the numerical and experimental results, for a simple calculation of the number of intensity maxima obtained as the two first-order source spots are scanned across the sample.

Calibration and data extraction in a Stokes polarimeter employing three wavelengths simultaneously.

We present a method for calibration and data extraction for a Stokes polarimeter working with three different wavelengths simultaneously. In the Stokes polarimeter considered in this work, we use two liquid crystal variable retarders (LCVRs) combined with a Glan-Thompson linear polarizer. A recently developed fitting calibration procedure is used. We use the same calibration samples and LCVR voltages for all three wavelengths, giving simultaneous measurement and calibration. We compare the performance of the polarimeter, after calibration, using four or six calibration samples in our experiment. To generate the four known calibration beams, we use a linear polarizer oriented at 130° and 30° with respect to the horizontal, a horizontal linear polarizer followed by a half-wave plate (at 632 nm) with its fast axis at 30°, and a horizontal linear polarizer followed by a quarter-wave plate (at 632 nm) with its fast axis at 30°. For calibration with six reference beams, we add two known calibration beams by setting the fast axis of the half- and quarter-wave plates at 130°. Experimental results show good agreement with the expected results, with the fitting calibration procedure giving an approximately 50% reduction in total RMS error with four calibration samples. There is a negligible reduction in the error when six calibration samples are used compared to the case with four samples.

Characterization of retardance spatial variations over the aperture of liquid-crystal variable retarders.

We present a comparison of two experimental methods to measure retardance as a function of applied voltage and as a function of position over the aperture of liquid-crystal variable retarders. These measurements are required for many applications, particularly in polarimetry. One method involves the scan of an unexpanded laser beam over the aperture, and the other uses an expanded beam from a LED and a CCD camera to measure the full aperture with a single measurement. The first method is time consuming, is limited in the measured spatial resolution, and requires more expensive equipment to perform the scan, whereas the second method is low cost, with the spatial resolution of the CCD, and fast, but in principle has variations of the incident beam over the aperture that affect the measured retardance values. The results obtained show good agreement for the average values of retardance for the two methods, but the expanded-beam method shows more noise, particularly close to the voltage values at which the variable-retarder retardance versus voltage curves are unwrapped. These retardance variations can be reduced by smoothing the retardance image, which makes the expanded-beam method an attractive method for polarimetry applications since it gives the complete information in the full aperture of the device with the additional advantages of low cost, simplicity, and being less time consuming.

Genomic analysis of a lignocellulose degrading strain from the underexplored genus Meridianimaribacter.

The genus Meridianimaribacter is one of the least-studied genera within Cytophaga-Flavobacteria. To date, no genomic analysis of Meridianimaribacter has been reported. In this study, Meridianimaribacter sp. strain CL38, a lignocellulose degrading halophile was isolated from mangrove soil. The genome of strain CL38 was sequenced and analyzed. The assembled genome contains 17 contigs with 3.33 Mbp, a GC content of 33.13% and a total of 2982 genes predicted. Lignocellulose degrading enzymes such as cellulases (GH3, 5, 9, 16, 74 and 144), xylanases (GH43 and CE4) and mannanases (GH5, 26, 27 and 130) are encoded in the genome. Furthermore, strain CL38 demonstrated its ability to decompose empty fruit bunch, a lignocellulosic waste residue arising from palm oil industry. The genome information coupled with experimental studies confirmed the ability of strain CL38 to degrade lignocellulosic biomass. Therefore, Meridianimaribacter sp. strain CL38, with its halotolerance, could be useful for seawater based lignocellulosic biorefining.

Robertkochia solimangrovi sp. nov., isolated from mangrove soil, and emended description of the genus Robertkochia.

To date, there is sparse information for the genus Robertkochia with Robertkochia marina CC-AMO-30DT as the only described member. We report here a new species isolated from mangrove soil collected at Malaysia Tanjung Piai National Park and perform polyphasic characterization to determine its taxonomic position. Strain CL23T is a Gram-negative, yellow-pigmented, strictly aerobic, catalase-positive and oxidase-positive bacterium. The optimal growth conditions were determined to be at pH 7.0, 30-37 °C and in 1-2 % (w/v) NaCl. The major respiratory quinone was menaquinone-6 (MK-6) and the highly abundant polar lipids were four unidentified lipids, a phosphatidylethanolamine and two unidentified aminolipids. The 16S rRNA gene similarity between strain CL23T and R. marina CC-AMO-30DT is 96.67 %. Strain CL23T and R. marina CC-AMO-30DT clustered together and were distinguished from taxa of closely related genera in 16S rRNA gene phylogenetic analysis. Genome sequencing revealed that strain CL23T has a genome size of 4.4 Mbp and a G+C content of 40.72 mol%. Overall genome related indexes including digital DNA-DNA hybridization value and average nucleotide identity are 17.70 % and approximately 70%, below the cutoffs of 70 and 95%, respectively, indicated that strain CL23T is a distinct species from R. marina CC-AMO-30DT. Collectively, based on the phenotypic, chemotaxonomic, phylogenetic and genomic evidences presented here, strain CL23T is proposed to represent a new species with the name Robertkochia solimangrovi sp. nov. (KCTC 72252T=LMG 31418T). An emended description of the genus Robertkochia is also proposed.

Genetic modification of western wheatgrass (Pascopyrum smithii) for the phytoremediation of RDX and TNT.

MAIN CONCLUSION: Transgenic western wheatgrass degrades the explosive RDX and detoxifies TNT. Contamination, from the explosives, hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine (RDX), and 2, 4, 6-trinitrotoluene (TNT), especially on live-fire training ranges, threatens environmental and human health. Phytoremediation is an approach that could be used to clean-up explosive pollution, but it is hindered by inherently low in planta RDX degradation rates, and the high phytotoxicity of TNT. The bacterial genes, xplA and xplB, confer the ability to degrade RDX in plants, and a bacterial nitroreductase gene nfsI enhances the capacity of plants to withstand and detoxify TNT. While the previous studies have used model plant species to demonstrate the efficacy of this technology, trials using plant species able to thrive in the challenging environments found on military training ranges are now urgently needed. Perennial western wheatgrass (Pascopyrum smithii) is a United States native species that is broadly distributed across North America, well-suited for phytoremediation, and used by the US military to re-vegetate military ranges. Here, we present the first report of the genetic transformation of western wheatgrass. Plant lines transformed with xplA, xplB, and nfsI removed significantly more RDX from hydroponic solutions and retained much lower, or undetectable, levels of RDX in their leaf tissues when compared to wild-type plants. Furthermore, these plants were also more resistant to TNT toxicity, and detoxified more TNT than wild-type plants. This is the first study to engineer a field-applicable grass species capable of both RDX degradation and TNT detoxification. Together, these findings present a promising biotechnological approach to sustainably contain, remove RDX and TNT from training range soil and prevent groundwater contamination.

Liquid refractive index measured through a refractometer based on diffraction gratings.

We developed two versions of refractometers to measure the refractive index of liquids. One refractometer comprises a glass cell with a surface relief grating on the inner face of one of its walls, while the other one is a microfluidic channel in the form of serpentine that behaves as a grating. Measurements of the liquid refractive index were performed by sensing the first order intensity. Several liquids have been used including an organic one. Calibration plots are shown.