Combination Of Morphological Analyses Research Articles

Lampbrush chromosomes of Danio rerio.

Danio rerio, commonly known as zebrafish, is an established model organism for the developmental and cell biology studies. Although significant progress has been made in the analysis of the D. rerio genome, cytogenetic studies face challenges due to the unclear identification of chromosomes. Here, we present a novel approach to the study of the D. rerio karyotype, focusing on the analysis of lampbrush chromosomes isolated from growing oocytes. Lampbrush chromosomes, existing during diplotene, serve as a powerful tool for high-resolution mapping and transcription analysis due to their profound decondensation and remarkable lateral loops decorated by RNA polymerases and ribonucleoprotein (RNP) matrix. In D. rerio, lampbrush chromosomes are about 20 times longer than corresponding metaphase chromosomes. We found that the lampbrush chromosome stage karyotype of D. rerio is generally undifferentiated, except for several bivalents bearing distinct marker structures, including loops with complex RNP matrix and locus-associated nuclear bodies. Locus-associated nuclear bodies were enriched for coilin and snRNAs; the loci where they formed presumably correspond to the histone gene clusters. Further, we observed the accumulation of splicing factors in giant terminal RNP aggregates on one bivalent. DAPI staining of Danio rerio lampbrush chromosomes revealed large and small chromomeres non-uniformly distributed along the axis. For example, D. rerio lampbrush chromosome 4, comprising the sex-determining region, is divided into two halves-with small chromomeres bearing long lateral loops and with large dense chromomeres bearing no or very tiny lateral loops. As centromeres were not distinguishable, we identified centromeric regions in all bivalents by FISH mapping of pericentromeric RFAL1, RFAL2, and RFAM tandem repeats. Through a combination of morphological analysis, immunostaining of marker structures, and centromere mapping, we developed cytological maps of D. rerio lampbrush chromosomes. Finally, by RNA FISH we revealed transcripts of pericentromeric and telomeric tandemrepeats at the lampbrush chromosome stage.

COMBINED DECISION SUPPORT MODEL FOR DEVELOPMENT PRIORITIES OF THE KYIV CAR TUNNEL NETWORK

An analysis is conducted for the opportunities to reduce climate (ecological), technogenic and safety risks in the Kyiv transport infrastructure in case of construction of the car tunnel system envisioned in the Kyiv city General plan. The involved structural and functional factors included district type in the potential tunnel’s area, downtown factor, population density, daily pendular movement, arterial network density, aver-age traffic speed at peak hours, surface connectivity of the exits (portals) of the tunnel by automobile roads, surface road throughput, criticalness of the transport infrastructure object, and vulnerability in case of military attacks or terrorist acts. The modified morphological analysis method was applied in the research, that con-sidered groups of climate (ecological) and techogenic risks, and also the military (terrorist) threats. This be-came the basis for construction of the decision support model regarding the evaluation of priorities and rank-ings (rational order) of tunnel construction. Additionally, a combination of morphological analysis with analyt-ical hierarchy process was proposed that provided alternative viewpoints with a different ranking compared to the basic model, depending on the given priorities (weights) of risk factors during decision making. This approach may be useful for development of the transport policy with the goal of approaching climate neutrality for big cities, as well as maximum protection of urban transport infrastructure in conditions of wartime threats.Using the developed system tools and combined models, the urban society can become safer and more resilient, managing transport policies on the basis of the system approach, and multi-criteria analysis of im-pact factors.

Managing the noise environment in the context of densification: Issues, expertise, methods, and limits

Urban densification is often proposed as a solution to ecological problems. Various densification models are studied in the literature, but noise aspects are often neglected. Based on a case study in Quebec City, environmental noise assessment methods (manual and automatic surveys, simulation, etc.) have been explored to identify the skills, expertise, and data needed to integrate the noise dimension into densification projects, and how to choose a model suited to the urban planning context. The availability and quality of data will also be assessed to identify any gaps. Using a combination of morphological analysis and sound simulations, the results will provide a better understanding of the influence of sound quality on densification choices. A discussion about the implications for sustainable urban planning and residents' quality of life, as well as the criteria to be considered in densification strategies to integrate the noise environment effectively. This project will provide answers on the impact of densification models on the noise environment and urban quality of life and allow the development of a framework for improved urban practices.

ISOLATION AND SELECTION OF YEAST STRAINS CAPABLE OF FERMENTING ORANGE JUICE

This research aims to isolate and select native yeast strains on oranges, capable of fermenting orange juice. Six types of fresh oranges from the Hanoi market were used as samples to isolate yeasts. By morphological observation, eight isolates were confirmed to be yeast strains. Hoa Binh orange juice was used to test the capability of alcoholic fermentation for each of the isolated yeast strains. The chemical composition of the obtained drink after wine distillation was analyzed and the sensory properties of the distillate were evaluated. The result showed that the strain HB2 had the best production capacity of alcohol among the tested strains, the sensory score reached 16.0, which is in the good category. Through a combination of morphological analysis, culture characteristics on agar and liquid media, and MALDI-TOF techniques, the HB2 strain was identified as Saccharomyces cerevisiae.

Hypogene speleogenesis and paragenesis in the Dolomites

The Dolomites of northern Italy feature some of the most intensively studied carbonate rocks worldwide. Yet, little is known about the long karst history of this mountain range dating back to the Miocene. This study scrutinizes three caves (F10, Milchloch and Cioccherloch) in the Fanes-Sennes-Prags Nature Park (Province of South Tyrol) and the adjacent Fosses area in the Natural Park of Ampezzo Dolomites (Province of Belluno, Veneto). Paleo-phreatic passages of these limestone caves mostly follow a NW-SE orientation, similar to the nearby Val Salata fault. A multi-method approach including cave morphological and isotopic analyses of wall-rock cores was applied to reconstruct the multi-stage speleogenetic history of these cavities. Clastic sediments partly cemented to the cave walls and paragenetic features such as ceiling channels and solutional ramps are present in all studied caves. F10 cave shows widespread laughöhle geometries, including inverted cone chambers and horizontal passages with trapezoid cross sections, characteristic of slow water convection in a hypogene regime. Drill cores in F10 cave exhibit a systematic depletion in both oxygen and carbon isotopes close to the cave wall. The thickness of this isotopically altered zone ranges from a few mm to 4 cm and alteration can sometimes also be macroscopically identified. The amplitude of the isotopic shift ranges from 2.0 to 5.0‰ for δ13C and from 1.9 to 4.9‰ for δ18O. One of the wall rock cores from Cioccherloch also shows a thin isotopic halo, while no evidence of isotopic alteration was found in Milchloch. Our results provide strong geochemical evidence of wall rock alteration driven by hypogene water-rock interaction in at least two of the caves. We propose an early hypogene speleogenetic phase, followed by uplift and denudation resulting in the opening of these cavities to the surface that allowed clastic sediment influx. The sediment infill in combination with the abundant paragenetic features records a second phase in the karst evolution. This paragenetic phase did not involve hypogene waters, as indicated by the lack of isotopic alteration in the wall rock of paragenetic features. The latest phase of speleogenesis is represented by vadose morphologies and vadose speleothems locally dating back to at least 650 ka. This study demonstrates that the combination of morphological analyses and geochemical fingerprinting represents a powerful approach to decipher the commonly complex speleogenetic history of limestone caves.

Molecular and morphological characterisation of a new root-lesion nematode, Pratylenchus horti n. sp. (Tylenchomorpha: Pratylenchidae), from Ghent University Botanical Garden

Summary Root-lesion nematodes, Pratylenchus spp., are one of the most important nematode groups in economic terms. The combination of morphological analyses and molecular analyses based on D2-D3 of 28S rDNA, ITS rDNA, and COI mtDNA regions supported the establishment of a new Pratylenchus species, making a total of 103 valid Pratylenchus species. The females of P. horti n. sp. are characterised by the following traits: low labial region with two annuli continuous to the body, en face form belonging to group II sensu Corbett & Clark (1983) with submedian triangular-shaped segments fused with the oral disc and separated from the lateral segments, lateral field with four incisures at vulval level and lacking areolation, robust stylet 15-17 μm long with rounded knobs, and subcylindrical tail with smooth tail tip. The males are largely similar to the females but differ from the females by the partially areolated lateral field, slightly ventrally arcuate and weakly cephalated spicules (15-19 μm), and ventrally curved elongate conical tail with a poorly protruding, crenate bursa. The new species was recovered from soil and root samples from the rhizosphere of Hedychium greenii growing in the Botanical Garden, Ghent University, Belgium.

The Diagnosis of Choriocarcinoma in Molar Pregnancies: A Revised Approach in Clinical Testing

BackgroundHydatidiform moles occur in approximately 1 in 1,500 pregnancies; however, early miscarriages or spontaneous abortions may not be correctly identified as molar pregnancies due to poor differentiation of chorionic villi.MethodsThe current clinical testing algorithm used for the detection of hydatidiform moles uses a combination of morphological analysis and p57 immunostaining followed by ploidy testing to establish a diagnosis of either a complete or partial molar pregnancy. We review here 198 referrals for fluorescence in situ hybridization (FISH) ploidy testing, where the initial diagnosis based on morphology is compared to the final diagnosis based on a combination of morphology, FISH and p57 immunohistochemical (IHC) staining.ResultsApproximately 40% of cases were determined to be genetically abnormal, but only 28.8% of cases were diagnosed as molar pregnancies. The underestimation of complete molar pregnancies and those with androgenetic inheritance was also found to be likely using conventional diagnostic methods, as atypical p57 staining was observed in approximately 10% of cases.ConclusionsOur findings suggest that a revised approach to testing products of conception is necessary, with cases screened according to their clinical history in order to distinguish molar pregnancy referrals from hydropic pregnancies.

Mechanism for Tuning the Hydrophobicity of Microfibrillated Cellulose Films by Controlled Thermal Release of Encapsulated Wax.

Although films of microfibrillated cellulose (MFC) have good oxygen barrier properties due to its fine network structure, properties strongly deteriorate after absorption of water. In this work, a new approach has been followed for actively tuning the water resistance of a MFC fiber network by the inclusion of dispersed organic nanoparticles with encapsulated plant wax. The modified pulp suspensions have been casted into films and were subsequently cured at 40 to 220 °C. As such, static water contact angles can be specifically tuned from 120 to 150° by selection of the curing temperature in relation with the intrinsic transition temperatures of the modified pulp, as determined by thermal analysis. The appearance of encapsulated wax after curing was followed by a combination of morphological analysis, infrared spectroscopy and Raman mapping, showing balanced mechanisms of progressive release and migration of wax into the fiber network controlling the surface properties and water contact angles. Finally, the appearance of nanoparticles covered with a thin wax layer after complete thermal release provides highest hydrophobicity.

Lipid mapping of colonic mucosa by cluster TOF-SIMS imaging and multivariate analysis in cftr knockout mice

The cftr knockout mouse model of cystic fibrosis (CF) shows intestinal obstruction; malabsorption and inflammation; and a fatty acid imbalance in intestinal mucosa. We performed a lipid mapping of colon sections from CF and control (WT) mice by cluster time of flight secondary-ion mass spectrometry (TOF-SIMS) imaging to localize lipid alterations. Data were processed either manually or by multivariate statistical methods. TOF-SIMS analysis showed a particular localization for cholesteryl sulfate at the epithelial border, C16:1 fatty acid in Lieberkühn glands, and C18:0 fatty acid in lamina propria and submucosa. Significant increases in vitamin E (vE) and C16:0 fatty acid in the epithelial border of CF colon were detected. Principal component analysis (PCA) and partitioning clustering allowed us to characterize different structural regions of colonic mucosa according to variations in C14:0, C16:0, C16:1, C18:0, C18:1, C18:2, C20:3, C20:4, and C22:6 fatty acids; phosphatidylethanolamine, phosphatidylcholine, and phosphatidylinositol glycerolipids; cholesterol; vitamin E; and cholesteryl sulfate. PCA on spectra from Lieberkühn glands led to separation of CF and WT individuals. This study shows for the first time the spatial distribution of lipids in colonic mucosa and suggests TOF-SIMS plus multivariate analyses as a powerful tool to investigate disease-related tissue spatial lipid signatures.

Expression of CD46 in Developing Rat Spermatozoa: Ultrastructural Localization and Utility as a Marker of the Various Stages of the Seminiferous Tubuli1

Identification of the various stages of the seminal tubule epithelium that are important in spermatogenesis in humans and rodents requires considerable expertise for analysis of ultrastructural appearance under light microscopy. Few good stage-specific markers have been reported to facilitate the process. We recently described characterization of the expression of CD46 (membrane cofactor protein) in the rat using a novel monoclonal antibody. Expression of CD46 was restricted to spermatozoa and their immediate precursors in the testis. In the present study, we used a combination of morphological analyses, known acrosome markers, actin staining, direct nuclear staining, and staining for CD46 to delineate precisely the subcellular location of CD46. Staining of CD46 colocalized with known acrosome markers in late spermatids and mature spermatozoa and was confirmed by electron microscopy to be acrosome-restricted. Expression was first detected in step 7 spermatids, whereas known markers were not expressed until step 9. The CD46 staining pattern differed through spermatid development, and distinct patterns of staining could be identified that, when combined with 4'-6-diamino-2-phenylindole-2HCl nuclear staining, enabled the accurate staging of the seminiferous tubule epithelium in different profiles. This detailed description of the spatiotemporal expression patterns of CD46 provides a valuable tool for analysis of spermatogenesis in the rat. Furthermore, this information will aid ongoing studies regarding the roles of CD46 in acrosome-related spermatozoal functions.

Gonad morphology and oocyte development in Pseudocalanus spp. in relation to spawning activity

Gonad maturation processes were studied in Pseudocalanus spp. females from Georges Bank and Cape Cod Bay (northwest Atlantic) using a combination of morphological analysis and experiments. For light microscopy of the oocytes, females of different maturation stages were preserved immediately after capture. The maturation processes during the spawning cycle were described from observations of live females which were exposed to feeding and starvation at two temperatures, 8 and 15°C, for 12 days. The gonad morphology of these females was examined in 24 h intervals, and spawning events were recorded. Both light microscopy and whole animal observation revealed that oocytes during maturation change in shape and size, in the morphology of the nucleus, and in the appearance of the ooplasm. Due to these modifications of oocyte morphology and due to oocyte migration, the morphology of the gonads changed distinctly during a spawning cycle. Five oocyte development stages were identified by light microscopy and related to a macroscopic system of four gonad development stages, that can be applied to whole animals and allows the identification of females ready to spawn. The experiment showed that food and temperature had strong effects on gonad maturation processes. High proportions of mature females were found when food was available, whereas the proportion of immature females increased shortly after exposure to starvation. Compared to 15°C, gonad maturation at 8°C was prolonged and thus spawning frequency was lower. The final maturation processes at food saturated conditions were slower than the embryonic development, and no indication was found that mature oocytes are stored in the diverticula waiting to be released. The duration of the interspawning interval would thus be determined by the duration of final oocyte maturation which is dependent on both temperature and food supply.

The lumenal domain of the integral membrane protein phogrin mediates targeting to secretory granules.

Phogrin, a transmembrane glycoprotein of neuroendocrine cells, is localized to dense-core secretory granules. We have investigated the subcellular targeting of phogrin by analyzing the sorting of a series of deletion mutants to the regulated pathway of secretion in AtT20 cells. The lumenal domain as a soluble protein was efficiently routed to granules, based on a combination of morphological analysis and secretion studies. Sorting was not dependent on a candidate targeting signal consisting of an N-terminal conserved cysteine-rich motif. Both the pro-region and the lumenal domain of mature, post-translationally processed phogrin independently reached the granule, although the pro-region was sorted more efficiently. Once within the regulated secretory pathway, all phogrin lumenal domain proteins were stored in functional granules for extended periods of time. Thus, phogrin possesses several domains contributing to its targeting to the secretory granule. Our findings support a model of granule biogenesis where proteins are sorted on the basis of their biochemical properties rather than via signal-dependent binding to a targeting receptor. Sorting of integral membrane proteins mediated by the lumenal domain may ensure that functionally important transmembrane molecules are included in the forming granule.