Quantitative studies on the polarization optical properties of living cells. I. Microphotometric birefringence detection system

A method of polarization optical analysis is described in which phase retardation attributable to birefringence of a minute area in a microscopic object is determined. The optical system consists of a polarizing microscope with "rectified" strain-free lenses, a photoelectric detector to determine the intensity of the light passing through a minute window located at the image plane of the specimen, and a stage that moves the specimen at appropriate velocities for scanning. The error resulting from any flare of light emerging from outside of the area to be measured is minimized by limiting the illuminated area. The specimen can be observed during the measurement of light intensity by illuminating the whole microscope field at a wavelength different from that of the light used for the measurement. The retardation of the specimen is determined by comparing the specimen and background intensities as functions of the azimuth of a Brace-Koherl compensator. Alternatively, retardation is obtained directly from the light intensity at a fixed compensator angle, using the theory of polarization optics. The basal noise level for the present apparatus is approximately 0.03 nm when measuring birefringence of a 4-micron2 area in 0.1 s, using a X 40, NA 0.65 objective. The noise decreases in inverse proportion to the square root of the area times the duration of measurement.     

Photoreduction and Oxidation of Cytochrome f in Bundle Sheath Cells of Maize

The photo-oxidation of cytochrome f (cytochrome c₅₅₄) in bundle sheath cells isolated from leaves of maize (Zea mays var. DS 606A) has been compared with that in intact maize leaf and in isolated pea leaf cells (Pisum sativum L.). In all cases, illumination with red light caused a negative absorbance change at 554 nm which was attributed to the oxidation of cytochrome f. The extent of this change was greater using monochromatic red light at wavelengths above 700 nm compared with wavelengths below 700 nm. 3-(3,4-Dichlorophenyl)-1, 1-dimethylurea abolished this difference in bundle sheath cells. After illumination for 1 minute or longer in bundle sheath cells, reduction of cytochrome f in the dark was rapid only if the wavelength of the illuminating light was below 700 nm. In the presence of 3-(3,4-dichlorophenyl)-1, 1-dimethlyurea, reduction was slow after illumination at all wavelengths.     

Habitat Preferences of the Critically Endangered Greater Bamboo Lemur (Prolemur simus) and Densities of One of Its Primary Food Sources, Madagascar Giant Bamboo (Cathariostachys madagascariensis), in Sites with Different Degrees of Anthropogenic and Natural Disturbance

Understanding the habitat preferences of a species is critical to the management and conservation of its population. The Critically Endangered greater bamboo lemur, Prolemur simus, is patchily distributed across its geographic range, using a very limited fraction of its total area of occurrence. The ecological basis for this patchy distribution remains largely unexplained. We analyzed the local habitat factors affecting the habitat use of Prolemur simus and densities of one of its primary food sources Madagascar giant bamboo, Cathariostachys madagascariensis. We sampled vegetation and site characteristics along belt transects in mid-altitude rain forest areas of the Ankeniheny–Zahamena rain forest corridor in eastern Madagascar, with (N?=?10) and without (N?=?16) evidence of habitat use by Prolemur simus. In our study site the preferred habitat type of Prolemur simus appears to be primary forest stands with moderate to low levels of human disturbance, greater natural disturbance, high densities of large diameter bamboo, and high structural diversity in tree heights. Cathariostachys madagascariensis appears to exploit canopy gaps created by natural disturbances, and similarly often exploits areas of anthropogenic disturbance. We found the highest densities of bamboo to occur in areas of moderate anthropogenic disturbance, whereas larger diameter culms were associated with lower levels of disturbance and smaller culms with areas of high anthropogenic disturbance. Human use of the forest and protection of the habitat of Prolemur simus are not necessarily incompatible, but our data indicate that the severity and frequency of use should probably be relatively low. Our results suggest that in our study site management strategies that minimize human disturbances, promote structural diversity in tree heights, and maintain relatively high densities of large-culmed bamboo may benefit populations of Prolemur simus.     

A NEW METHOD OF POLARIZATION MICROSCOPIC ANALYSIS : I. Scanning with a Birefringence Detection System

A new method of polarized light analysis is described in which a highly sensitive electronic detector specific for birefringence is used to identify the crystalline axes of an object and then measure its phase retardation due to birefringence. The microscopic system employed in the method consists of an electronic birefringence detection system (BDS), a microscope with strain-free lenses, and a driven stage for passing the specimen at appropriate velocities across the image of an aperture placed at the field stop and imaged in the specimen plane by the condenser. The detector registers retardations directly as voltage at a constant deflection sensitivity of ca. 1.1 v per angstrom unit over a range of 120 angstrom units. The basal rms noise level is 0.002 A for a spot 36 µ in diameter formed by a 95 x, N. A. 1.25 objective pair, and increases in proportion to the reciprocal of the diameter of the scanning spot. The increase in noise with high resolution scanning can be offset by increasing the instrumental time constant, which is adjustable in decades between 0.004 and 0.4 seconds. A number of difficult problems in high extinction polarization microscopy are avoided by the use of modulated light and a rapid electronic detector. For example: (a) The measured distribution of birefringence is unaffected by the usual diffraction anomaly; therefore polarization rectifiers are not required. (b) The detector is selective for birefringence, so that there is no problem in separating contrast due to different optical properties (e.g. dichroism, light scattering). (c) The speed and sensitivity are both increased by between one and two orders of magnitude over that attainable by visual or photographic methods, thereby rendering a vast number of weakly birefringent, light-scattering, and motile objects readily analyzable for the first time with polarized light.     

Characterization of the simian virus 40-specific messenger RNAs isolated from HeLa cells infected with the non-defective adenovirus 2-simian virus 40 hybrid viruses Ad2+ND2 and Ad2+ND4

Previous work has shown that cells infected with the non-defective adenovirus 2-simian virus 40 hybrid viruses, Ad2⁺ND2 and Ad2⁺ND4 synthesize more than one SV40⁴ large T antigen-related protein. These proteins overlap in amino acid sequence and have their carboxy-terminal sequences in common (Mann et al., 1977). We have characterized the messenger RNAs coding for these SV40-specific proteins. By translating in vitro SV40-specific mRNA isolated from cells infected with these viruses we have shown that each SV40-specific protein can incorporate ³⁵S-labeled formyl methionine at its N-terminus donated by [³⁵S]-fmet-tRNA_f^met, demonstrating that each protein results from a de novo initiation event. Furthermore, analysis of the N-terminal tryptic peptides of these proteins indicates that each protein has a unique N-terminal peptide and therefore a unique initiation site for protein synthesis, with the possible exception of the 74,000 and 95,000 molecular weight proteins, which may have the same N-terminal sequence. Therefore, these proteins cannot be derived by proteolytic cleavage of a large precursor protein.The messenger activities for many of the hybrid virus proteins can be resolved by gel electrophoresis, demonstrating the presence of multiple SV40-specific mRNA species. This result is consistent with the possibility that each SV40-specific protein is coded by a distinct species of RNA.     

New information on body size and cranial display structures of Pterodactylus antiquus, with a revision of the genus

Pterodactylus antiquus has long been thought to have been quite small (~50 cm wingspan) and to have differed from P. longicollum, Ctenochasma, Germanodactylus, and Gnathosaurus in lacking a bony cranial crest, though a soft tissue crest and occipital lappet have been described. This article describes a new specimen of P. antiquus larger than all previously known specimens, which demonstrates that the species exceeded 1 m in wingspan and had a low bony cranial crest. A smaller, incipient crest was identified on the holotype specimen. Additional specimens, including the counterpart of Wellnhofer’s original occipital lappet specimen, provide evidence of the occipital lappet and the soft tissue crest extending upward above the naso-antorbital fenestra and orbit. In order to provide a proper taxonomic context for the findings, the recent synonymization of the species Pterodactylus antiquus and P. kochi on the basis of shared correlation of tooth number and skull length despite perceived differences in dentition and skull, neck, and trunk proportions is reviewed. A measurement error that had made it appear that P. antiquus differed significantly from P. kochi in proportions is documented, and after correction of the measurement error and reevaluation of the dental evidence there are no significant differences between the two nominal species. Thus, the synonymization of P. antiquus and P. kochi was appropriate, and a revised diagnosis is presented. In addition, the species P. longicollum and P. micronyx, which for some years have been viewed as not congeneric with P. antiquus, are placed in a new genus and transferred to Aurorazhdarcho, respectively.     

From population ecology to metabolism: growth of Trypanosoma evansi,and implications of glucose depletion,in a live host

Little attention has been paid to the potential top-down effects of population ecology on metabolism. Because it is capable of a fast growth that dramatically modifies its blood environment, the parasitic protozoan, Trypanosoma evansi, is a promising model for the study of density-dependent metabolic processes. We assess the in vivo growth rate, doubling time, biomass yield, glycolytic flux, and enzyme expression of T. evansi. Then, we explore the metabolic changes likely occurring during its growth. At low T. evansi densities, most host glucose is used to produce energy, which results in the release of pyruvate. Part of glucose is used for NADPH production through the pentose phosphate pathway. At high T. evansi densities, fructose, mannose, and glycerol become additional energy sources. Part of host glucose is used for biosynthesis and for NADPH production through alternative metabolic pathways, which results in the release of succinate, alanine, and acetate. The ability of organisms to adjust to resource changes is crucial to their survival. Irrespective if the triggering mechanism is direct (nutrient limitation) or indirect (a pheromone-like factor), nutrient availability is necessarily the main evolutionary factor responsible for the density-dependent metabolic properties of trypanosome populations.     

Glycosylation Is Dispensable for Sorting of Synaptotagmin 1 but Is Critical for Targeting of SV2 and Synaptophysin to Recycling Synaptic Vesicles

Glycosylation is a major form of post-translational modification of synaptic vesicle membrane proteins. For example, the three major synaptic vesicle glycoproteins, synaptotagmin 1, synaptophysin, and SV2, represent ∼30% of the total copy number of vesicle proteins. Previous studies suggested that glycosylation is required for the vesicular targeting of synaptotagmin 1, but the role of glycosylation of synaptophysin and SV2 has not been explored in detail. In this study, we analyzed all glycosylation sites on synaptotagmin 1, synaptophysin, and SV2A via mutagenesis and optical imaging of pHluorin-tagged proteins in cultured neurons from knock-out mice lacking each protein. Surprisingly, these experiments revealed that glycosylation is completely dispensable for the sorting of synaptotagmin 1 to SVs whereas the N-glycans on SV2A are only partially dispensable. In contrast, N-glycan addition is essential for the synaptic localization and function of synaptophysin. Thus, glycosylation plays distinct roles in the trafficking of each of the three major synaptic vesicle glycoproteins.     

Ontogeny of hypoxic modulation of cardiac performance and its allometry in the African clawed frog Xenopus laevis

The ontogeny of cardiac hypoxic responses, and how such responses may be modified by rearing environment, are poorly understood in amphibians. In this study, cardiac performance was investigated in Xenopus laevis from 2 to 25 days post-fertilization (dpf). Larvae were reared under either normoxia or moderate hypoxia (PO₂ = 110 mmHg), and each population was assessed in both normoxia and acute hypoxia. Heart rate (f _h ) of normoxic-reared larvae exhibited an early increase from 77 ± 1 beats min^?1 at 2 dpf to 153 ± 1 beats min^?1 at 4 dpf, followed by gradual decreases to 123 ± 3 beats min^?1 at 25 dpf. Stroke volume (SV), 6 ± 1 nl, and cardiac output (CO), 0.8 ± 0.1 μl min^?1, at 5 dpf both increased by more than 40-fold to 25 dpf with rapid larval growth (~30-fold increase in body mass). When exposed to acute hypoxia, normoxic-reared larvae increased f _h and CO between 5 and 25 dpf. Increased SV in acute hypoxia, produced by increased end-diastolic volume (EDV), only occurred before 10 dpf. Hypoxic-reared larvae showed decreased acute hypoxic responses of EDV, SV and CO at 7 and 10 dpf. Over the period of 2–25 dpf, cardiac scaling with mass showed scaling coefficients of ?0.04 (f _h ), 1.23 (SV) and 1.19 (CO), contrary to the cardiac scaling relationships described in birds and mammals. In addition, f _h scaling in hypoxic-reared larvae was altered to a shallower slope of ?0.01. Collectively, these results indicate that acute cardiac hypoxic responses develop before 5 dpf. Chronic hypoxia at a moderate level can not only modulate this cardiac reflex, but also changes cardiac scaling relationship with mass.     

Cell density and amino acid transport in 3T3, SV3T3, and SV3T3 revertant cells

The transport of selected neutral and cationic amino acids has been studied in Balb/c 3T3, SV3T3, and SV3T3 revertant cell lines. After properly timed preincubations to control the size of internal amino acid pools, the activity of systems A, ASC, L, and Ly⁺ has been discriminated by measurements of amino acid uptake (initial entry rate) in the presence and absence of sodium and of transportspecific model substrates. L-Proline, 2-aminoisobutyric acid, and glycine were primarily taken up by system A; L-alanine and L-serine by system ASC; L-phenylalanine by system L; and L-lysine by system Ly⁺ in SV3T3 cells. L-Proline and L-serine were also preferential substrates of systems A and ASC, respectively, in 3T3 and SV3T3 revertant cells. Transport activity of the Na⁺-dependent systems A and ASC decreased markedly with the increase of cell density, whereas the activity of the Na⁺-independent systems L and Ly⁺remained substantially unchanged. The density-dependent change in activity of system A occurred through a mechanism affecting transport maximum (V_max) rather than substrate concentration for half-maximal velocity (K_m). Transport activity of systems A and ASC was severalfold higher in transformed SV3T3 cells than in 3T3 parental cells at all the culture densities that could be compared. In SV3T3 revertant cells, transport activity by these systems remained substantially similar to that observed in transformed SV3T3 cells. The results presented here add cell density as a regulatory factor of the activity of systems A and ASC, and show that this control mechanism of amino acid transport is maintained in SV40 virus-transformed 3T3 cells that have lost density-dependent inhibition of growth, as well as in SV3T3 revertant cells that have resumed it.     

Robust Benchmark Structural Variant Calls of An Asian Using State-of-the-art Long-read Sequencing Technologies

The importance of structural variants(SVs) for human phenotypes and diseases is now recognized.Although a variety of SV detection platforms and strategies that vary in sensitivity and specificity have been developed,few benchmarking procedures are available to confidently assess their performances in biological and clinical research.To facilitate the validation and application of these SV detection approaches,we established an Asian reference material by characterizing the genome of an Epstein-B...     

Cardiovascular responses to sustained maximal isometric contractions of the finger flexors

This study investigated cardiovascular responses to 2 min sustained submaximal (20% MVC) and maximal (100% MVC) voluntary isometric contractions of the finger flexors in healthy young women. Cardiovascular variables investigated were: heart rate (f _c), mean arterial pressure ( _a), and stroke volume (SV). Doppler echocardiography was used to estimate SV from measures of aortic diameter (AD) and time-velocity integrals. Preliminary studies indicated that AD did not change significantly after 2 min sustained 100% MVC. Therefore, pre-exercise AD values were used to calculate SV before, during and after exercise. During the 2-min 100% MVC period, f _c and _aincreased significantly during the first 30 s of contraction. f _c then remained constant during the remainder of the 2-min contraction period, while _acontinued to rise. SV did not change significantly during the 100% MVC task but increased significantly during recovery from sustained 100% MVC. The data suggest that the magnitude of cardiovascular responses to isometric exercise is dependent on the specific task performed, and that there is a different pattern of response for f _c, _a, and SV during 20% and 100% MVC tasks. Unlike f _c and _a, SV did not change significantly during isometric exercise, but increased significantly after sustained 100% MVC.     

Identification and Characterization of a Novel Galactofuranose-Specific β-D-Galactofuranosidase from Streptomyces Species

β-D-galactofuranose (Galf) is a component of polysaccharides and glycoconjugates and its transferase has been well analyzed. However, no β-D-galactofuranosidase (Galf-ase) gene has been identified in any organism. To search for a Galf-ase gene we screened soil samples and discovered a strain, identified as a Streptomyces species by the 16S ribosomal RNA gene analysis, that exhibits Galf-ase activity for 4-nitrophenyl β-D-galactofuranoside (pNP-β-D-Galf) in culture supernatants. By draft genome sequencing of the strain, named JHA19, we found four candidate genes encoding Galf-ases. Using recombinant proteins expressed in Escherichia coli, we found that three out of four candidates displayed the activity of not only Galf-ase but also α-L-arabinofuranosidase (Araf-ase), whereas the other one showed only the Galf-ase activity. This novel Galf-specific hydrolase is encoded by ORF1110 and has an optimum pH of 5.5 and a Km of 4.4 mM for the substrate pNP-β-D-Galf. In addition, this enzyme was able to release galactose residue from galactomannan prepared from the filamentous fungus Aspergillus fumigatus, suggesting that natural polysaccharides could be also substrates. By the BLAST search using the amino acid sequence of ORF1110 Galf-ase, we found that there are homolog genes in both prokaryotes and eukaryotes, indicating that Galf-specific Galf-ases widely exist in microorganisms.     

A re-examination of the human fossil specimen from Bački Petrovac (Serbia)

A fragmented human calotte was discovered during the early 1950s near Ba?ki Petrovac (Serbia), in association with Palaeolithic stone tools. After its initial publication, the fossil specimen remained largely unknown outside of the Serbian academe and no detailed comparative study has ever been carried out. Since the whereabouts of the fossil itself are currently unknown, and given its potential significance for the Pleistocene human evolution, we re-examine the data published by 0255 and 0260. Using the original measurements, mostly taken on the frontal bone, and a wide comparative sample of 68 fossil specimens, the fossil was compared and analyzed by statistical multivariate methods. We also conducted a visual examination of the morphology based on the available photographic material. Our analysis reveals phenetic similarity with Middle Pleistocene archaic Homo from Africa and anatomically modern Homo sapiens. However, the absence of primitive cranial traits in Ba?ki Petrovac indicates a clear modern Homo sapiens designation. Although lost at the moment, there is a chance for the re-discovery of the fossil in the years to come. This would give us an opportunity to acquire absolute dates and to study the specimen in a more detailed manner.     

Forced-unfolding and force-quench refolding of RNA hairpins

Nanomanipulation of individual RNA molecules, using laser optical tweezers, has made it possible to infer the major features of their energy landscape. Time-dependent mechanical unfolding trajectories, measured at a constant stretching force (f_S) of simple RNA structures (hairpins and three-helix junctions) sandwiched between RNA/DNA hybrid handles show that they unfold in a reversible all-or-none manner. To provide a molecular interpretation of the experiments we use a general coarse-grained off-lattice Gō-like model, in which each nucleotide is represented using three interaction sites. Using the coarse-grained model we have explored forced-unfolding of RNA hairpin as a function of f_S and the loading rate (r_f). The simulations and theoretical analysis have been done both with and without the handles that are explicitly modeled by semiflexible polymer chains. The mechanisms and timescales for denaturation by temperature jump and mechanical unfolding are vastly different. The directed perturbation of the native state by f_S results in a sequential unfolding of the hairpin starting from their ends, whereas thermal denaturation occurs stochastically. From the dependence of the unfolding rates on r_f and f_S we show that the position of the unfolding transition state is not a constant but moves dramatically as either r_f or f_S is changed. The transition-state movements are interpreted by adopting the Hammond postulate for forced-unfolding. Forced-unfolding simulations of RNA, with handles attached to the two ends, show that the value of the unfolding force increases (especially at high pulling speeds) as the length of the handles increases. The pathways for refolding of RNA from stretched initial conformation, upon quenching f_S to the quench force f_Q, are highly heterogeneous. The refolding times, upon force-quench, are at least an order-of-magnitude greater than those obtained by temperature-quench. The long f_Q-dependent refolding times starting from fully stretched states are analyzed using a model that accounts for the microscopic steps in the rate-limiting step, which involves the trans to gauche transitions of the dihedral angles in the GAAA tetraloop. The simulations with explicit molecular model for the handles show that the dynamics of force-quench refolding is strongly dependent on the interplay of their contour length and persistence length and the RNA persistence length. Using the generality of our results, we also make a number of precise experimentally testable predictions.     

The identification of a serum viability factor for SV3T3 cells as biotin and its possible relationship to the maintenance of Krebs cycle activity

A low-molecular weight-factor (“Peak III”) from calf serum, which enhances the viability (and hence growth) of simian virus 40-transformed 3T3 (SV3T3), but not 3T3, cells when grown in low-serum (0.15–0.30%, $\text{v}\text{v}$) Dulbecco's modified Eagle's medium, has been identified as the vitamin biotin. The extraction procedure involved acidification of the serum to pH 4.5, boiling, ultrafiltration of the supernatant through a Pellicon membrane, and Sephadex G-25 chromatography. Peak III was identified as biotin for the following reasons. (i) The viability/growth activity was completely retained on an avidin-Sepharose but not a Sepharose column. (ii) Peak III preparations contained a compound which reacted with the cyclic ureide-specific reagent, p-dimethyl-aminocinnamaldehyde, and which migrated on thin-layer chromatography with the same R_f as biotin. (iii) Peak III and biotin had the same biological effects on SV3T3 cells, including a reduction in the number of dead cells, a lowering of the amount of lactic acid accumulated, and a synergism with iron in stimulating growth. (iv) They were not additive in their effects at saturating doses. To test the hypothesis that at least part of the biotin viability/growth effect may be due to the maintenance of Krebs cycle intermediate levels through the activation of pyruvate carboxylase, Krebs cycle intermediates were added singly to cells in low-serum medium without biotin. Malate, citrate, isocitrate, and fumarate (but not oxaloacetate, α-ketoglutarate, and succinate) were growth stimulatory for SV3T3 but not 3T3 cells. When added in combinations they were no more effective than alone.     

Harvesting far-red light: Functional integration of chlorophyll f into Photosystem I complexes of Synechococcus sp. PCC 7002

The heterologous expression of the far-red absorbing chlorophyll (Chl) f in organisms that do not synthesize this pigment has been suggested as a viable solution to expand the solar spectrum that drives oxygenic photosynthesis. In this study, we investigate the functional binding of Chl f to the Photosystem I (PSI) of the cyanobacterium Synechococcus 7002, which has been engineered to express the Chl f synthase gene. By optimizing growth light conditions, one-to-four Chl f pigments were found in the complexes. By using a range of spectroscopic techniques, isolated PSI trimeric complexes were investigated to determine how the insertion of Chl f affects excitation energy transfer and trapping efficiency. The results show that the Chls f are functionally connected to the reaction center of the PSI complex and their presence does not change the overall pigment organization of the complex. Chl f substitutes Chl a (but not the Chl a red forms) while maintaining efficient energy transfer within the PSI complex. At the same time, the introduction of Chl f extends the photosynthetically active radiation of the new hybrid PSI complexes up to 750 nm, which is advantageous in far-red light enriched environments. These conclusions provide insights to engineer the photosynthetic machinery of crops to include Chl f and therefore increase the light-harvesting capability of photosynthesis.