Kinds Of Organelles Research Articles

Label-Free SERS Detection of Protein Damage in Organelles under Electrostimulation with 2D AuNPs-based Nanomembranes as Substrates.

Proteins as the material basis of life are the main undertakers of life activities. However, it is difficult to identify the related proteins in organelles during stimuli-induced stress responses in cells and remains a great challenge in early diagnosis and treatment of disease. Here, proteins in the cell nucleus and mitochondria of cells under the electrical stimulation (ES) process were collected and sensitively detected based on label-free surface-enhanced Raman spectroscopy (SERS) by using AuNP-based nanomembranes as high-performance SERS substrates. Due to the existence of rich "hot spots" on the 2D plasmonic sensing platform, high-quality SERS spectra of proteins were obtained with superior sensitivity and repeatability. From the SERS analyses in vitro, it was found that the conformation of some proteins in the two kinds of organelles from cancerous HCT-116 cells (compared with normal NCM-460 cells) changed significantly and the expression levels of tyrosine, phenylalanine, and tryptophan were significantly promoted during the stimulation process. Although currently the exact proteins are still unknown, the damage of proteins in the organelles of cells at the amino acid level under ES can be revealed by the method. The developed plasmonic SERS sensing platform would be promising for bioassay and cell studies.

Multiple organelle-targeted near-infrared fluorescent probes toward pH and viscosity

Organelles, including mitochondria (mito), lysosomes (lyso), endoplasmic reticulum (ER), Golgi apparatus (Golgi), and ribosome et al., play a vital role in maintaining the regular work of the cell. Viscosity is an essential parameter in the cellular microenvironment. Herein, four viscosity-sensitive near-infrared fluorescent probes DMPC, DEPC, DHDM and DHDV that can simultaneously target multiple organelles were synthesized. As the viscosity increased, the fluorescence intensity of the probes gradually increased due to the hindrance of the rotation of the carbon-carbon single bond. The fluorescence intensity of DHDV increased by about 453 times, and the fluorescence quantum yield also increased from 0.051 to 0.681. Cell experiments indicated the probes could simultaneously target four kinds of organelles, and the four probes could also track mitochondria with no dependence on membrane potential. Further experiments showed that the probes could detect viscosity changes in lyso and mito. In addition, the probes also demonstrated the advantages of low cytotoxicity, good anti-interference and stability, providing a simple and effective tool for studying the activity of organelles with changing viscosity signals.

Two reasonably designed polarity-viscosity sensitive fluorescent probes with large Stokes shift for lighting up lipid droplets in cells

Lipid droplets (LDs) are involved in a variety of complex life activities in cells, which are closely related to human diseases including obesity, diabetes and cancer. LDs are generally considered as a kind of organelle with extremely low water content and high viscosity. Herein, two novel probes (E)-2-(3-(2-(7-(diethylamino)-2-oxo-2H-chromen-3-yl)vinyl)-5,5-dimethylcyclohex-2-en-1-ylidene)malononitrile (LDP-1) and (E)-2-(3-(4-(diethylamino)styryl)-5,5-dimethylcyclohex-2-en-1-ylidene)malononitrile (LDP-2) were synthesized, which exhibited large Stokes shifts of 4758 cm−1 and 3986 cm−1 respectively. The two probes emitted strongly in hydrophobic and high viscosity environments. Moreover, bio-probes LDP-1 and LDP-2 exhibited low biological toxicity, and good selectivity. The two probes were also fit for selectively monitoring LDs distribution in living HeLa cells.

Motility Plays an Important Role in the Lifetime of Mammalian Lipid Droplets.

The lipid droplet is a kind of organelle that stores neutral lipids in cells. Recent studies have found that in addition to energy storage, lipid droplets also play an important role in biological processes such as resistance to stress, immunity, cell proliferation, apoptosis, and signal transduction. Lipid droplets are formed at the endoplasmic reticulum, and mature lipid droplets participate in various cellular processes. Lipid droplets are decomposed by lipase and lysosomes. In the life of a lipid droplet, the most important thing is to interact with other organelles, including the endoplasmic reticulum, mitochondria, peroxisomes, and autophagic lysosomes. The interaction between lipid droplets and other organelles requires them to be close to each other, which inevitably involves the motility of lipid droplets. In fact, through many microscopic observation techniques, researchers have discovered that lipid droplets are highly dynamic organelles that move quickly. This paper reviews the process of lipid droplet motility, focusing on explaining the molecular basis of lipid droplet motility, the factors that regulate lipid droplet motility, and the influence of motility on the formation and decomposition of lipid droplets. In addition, this paper also proposes several unresolved problems for lipid droplet motility. Finally, this paper makes predictions about the future research of lipid droplet motility.

The Role of the Signaling Pathways Involved in the Effects of Hydrogen Sulfide on Endoplasmic Reticulum Stress

Endoplasmic reticulum (ER) is a kind of organelle with multiple functions including protein synthesis, modification and folding, calcium storage, and lipid synthesis. Under stress conditions, ER homeostasis is disrupted, which is defined as ER stress (ERS). The accumulation of unfolded proteins in the ER triggers a stable signaling network named unfolded protein response (UPR). Hydrogen sulfide is an important signal molecule regulating various physiological and pathological processes. Recent studies have shown that H2S plays an important role in many diseases by affecting ERS, but its mechanism, especially the signaling pathways, is not fully understood. Therefore, in this review, we summarize the recent studies about the signaling pathways involved in the effects of H2S on ERS in diseases to provide theoretical reference for the related in-depth researches.

Quantitative Imaging of Biochemistry in Situ and at the Nanoscale.

Biochemical reactions in eukaryotic cells occur in subcellular, membrane-bound compartments called organelles. Each kind of organelle is characterized by a unique lumenal chemical composition whose stringent regulation is vital to proper organelle function. Disruption of the lumenal ionic content of organelles is inextricably linked to disease. Despite their vital roles in cellular homeostasis, there are large gaps in our knowledge of organellar chemical composition largely from a lack of suitable probes. In this Outlook, we describe how, using organelle-targeted ratiometric probes, one can quantitatively image the lumenal chemical composition and biochemical activity inside organelles. We discuss how excellent fluorescent detection chemistries applied largely to the cytosol may be expanded to study organelles by chemical imaging at subcellular resolution in live cells. DNA-based reporters are a new and versatile platform to enable such approaches because the resultant probes have precise ratiometry and accurate subcellular targeting and are able to map multiple chemicals simultaneously. Quantitatively mapping lumenal ions and biochemical activity can drive the discovery of new biology and biomedical applications.

DeepRibSt: a multi-feature convolutional neural network for predicting ribosome stalling

Ribosomes are a kind of organelle in cells, which are mainly involved in the translation process of genetic materials, but the underlying mechanisms associated with ribosome stalling are not fully understood. Thanks to the development of biological experimental techniques, many ribosome footprintings are generated, which can help us to study ribosome stalling. Effectively obtaining a precise ribosome stalling site will be helpful for the treatment of the related diseases, however there is still much room for the improvement of ribosome stalling prediction. In this study, we propose a new deep neural network model named DeepRibSt for the prediction of ribosome stalling sites. We first process the ribosome footprinting data to the training set. Then three new features, including evolutionary conservation, hydrophobicity, and amino dissociation constant, along with the previous sequence features, are extracted as input to the network. To improve the performance of the algorithm in ribosome stalling prediction, we use two convolutional layers and three fully connected layers to design a new network architecture. To verify the validity of our proposed DeepRibSt, we compare DeepRibSt with four popular deep neural networks, i.e., AlexNet, LeNet, ResNet, and LSTM on human (i.e., Battle2015 and Stumpf13) and yeast (i.e., Pop2014, Young15, and Brar12) data. To further demonstrate the effectiveness of DeepRibS, we compare DeepRibSt with the state-of-the-art method. The experimental results show that DeepRibSt outperforms all other methods and achieves the state-of-the-art performance in accuracy, recall, specificity, F1-score, and the area under the receiver operating characteristic curve (AUC).

Industrial Applications of Selected JFS Articles

Industrial Applications of Selected <i>JFS</i> Articles

Fast uncoiling kinetics of F1C pili expressed by uropathogenic Escherichia coli are revealed on a single pilus level using force-measuring optical tweezers

Uropathogenic Escherichia coli (UPEC) express various kinds of organelles, so-called pili or fimbriae, that mediate adhesion to host tissue in the urinary tract through specific receptor-adhesin interactions. The biomechanical properties of these pili have been considered important for the ability of bacteria to withstand shear forces from rinsing urine flows. Force-measuring optical tweezers have been used to characterize individual organelles of F1C type expressed by UPEC bacteria with respect to such properties. Qualitatively, the force-versus-elongation response was found to be similar to that of other types of helix-like pili expressed by UPEC, i.e., type 1, P, and S, with force-induced elongation in three regions, one of which represents the important uncoiling mechanism of the helix-like quaternary structure. Quantitatively, the steady-state uncoiling force was assessed as 26.4 ±1.4 pN, which is similar to those of other pili (which range from 21 pN for S(I) to 30 pN for type 1). The corner velocity for dynamic response (1,400nm/s) was found to be larger than those of the other pili (400-700nm/s for S and P pili, and 6nm/s for type 1). The kinetics were found to be faster, with a thermal opening rate of 17Hz, a few times higher than S and P pili, and three orders of magnitude higher than type 1. These data suggest that F1C pili are, like P and S pili, evolutionarily selected to primarily withstand the conditions expressed in the upper urinary tract.

Pathological Changes on Human Breast Cancer Specimens Ablated in vitro with High-Intensity Focused Ultrasound

The purpose of this study was to evaluate the pathologic changes of human breast cancer specimens ablated with high-intensity focused ultrasound (HIFU) in vitro. Twenty specimens of pathologically confirmed breast cancer tissue were ablated with ultrasound-guided HIFU. The evaluation methods include histopathologic observation using hematoxylin-eosin staining, electron microscopic imaging, enzyme histochemical and immunohistochemical examination on tumor antigens. Vacuole-like structures in cytoplasm were observed by histopathologic observation but there were no significant changes in cell morphology and nucleus karyotype. Typical phenomena related to coagulation necrosis were observed in electron microscopic studies; the contour of cell structure was still preserved but the structures of cell (all kinds of organelles and nucleus) were damaged or disappeared. Acid phosphatase and succinate dehydrogenase staining showed that tumor cells were inactivated. In immunohistochemical evaluations, estrogen receptor, progesterone receptor, cerbB-2 and P53 expression changed from 85%, 82%, 75% and 80% in nonablation tissue to no expression in ablated tumor tissue, respectively. We, therefore, conclude that breast cancer cells appear normal contour immediately after ablation with HIFU under light microscopic but they were evaluated to be dead by electron microscopic imaging, enzyme histochemical and immunohistochemical examinations. (E-mail: wangzbpaper@haifu.com.cn)

The peroxisome: a production in four acts

A cell regulates the number, size, and kind of each organelle it possesses in response to its particular role in an environment or tissue. Yet we still know little about how the molecular signaling networks within each cell perform such regulation. In this issue, Saleem et al. (Saleem, R.A., B. Knoblach, F.D. Mast, J.J. Smith, J. Boyle, C.M. Dobson, R. Long-O'Donnell, R.A. Rachubinski, and J.D. Aitchison. 2008. J. Cell Biol. 181:281–292) show for the first time how groups of kinases and phosphatases are organized to control when and how a cell assembles one kind of organelle, the peroxisome.

Multipotent epithelial cells in the process of regeneration and asexual reproduction in colonial tunicates

The cellular and molecular features of multipotent epithelial cells during regeneration and asexual reproduction in colonial tunicates are described in the present study. The epicardium has been regarded as the endodermal tissue-forming epithelium in the order Enterogona, because only body fragments having the epicardium exhibit the regenerative potential. Epicardial cells in Polycitor proliferus have two peculiar features; they always accompany coelomic undifferentiated cells, and they contain various kinds of organelles in the cytoplasm. During strobilation a large amount of organelles are discarded in the lumen, and then, each tissue-forming cell takes an undifferentiated configuration. Septum cells in the stolon are also multipotent in Enterogona. Free cells with a similar configuration to the septum inhabit the hemocoel. They may provide a pool for epithelial septum cells. At the distal tip of the stolon, septum cells are columnar in shape and apparently undifferentiated. They are the precursor of the stolonial bud. In Pleurogona, the atrial epithelium of endodermal origin is multipotent. In Polyandrocarpa misakiensis, it consists of pigmented squamous cells. The cells have ultrastructurally fine granules in the cytoplasm. During budding, coelomic cells with similar morphology become associated with the atrial epithelium. Then, cells of organ placodes undergo dedifferentiation, enter a cell division cycle, and commence morphogenesis. Retinoic acid-related molecules are involved in this dedifferentiation process of multipotent cells. We conclude that in colonial tunicates two systems support the flexibility of tissue remodeling during regeneration and asexual reproduction; dedifferentiation of epithelial cells and epithelial transformation of coelomic free cells.

The effect of α-tocopherol on lipid peroxidation of microsomes and mitochondria from rat testis

The testis is a remarkably active metabolic organ; hence it is suitable not only for studies of lipid metabolism in the organ itself but also for the study of lipid peroxidation processes in general. The content of fatty acids in testis is high with a prevalence of polyunsaturated fatty acids (PUFA) which renders this tissue very susceptible to lipid peroxidation. Studies were carried out to evaluate the effect of α-tocopherol in vitro on ascorbate-Fe ++ lipid peroxidation of rat testis microsomes and mitochondria. Chemiluminescence and fatty acid composition were used as an index of the oxidative destruction of lipids. Special attention was paid to the changes produced on the highly PUFA [C20:4 n6] and [C22:5 n6]. Lipid peroxidation of testis microsomes or mitochondria induced a significant decrease of both fatty acids. Total chemiluminescence was similar in both kinds of organelles when the peroxidized without (control) and with ascorbate-Fe ++ (peroxidized) groups were compared. Arachidonic acid was protected more efficiently than docosapentaenoic acid at all α-tocopherol concentrations tested when rat testis microsomes or mitochondria were incubated with ascorbate-Fe ++. The maximal percentage of inhibition in both organelles was approximately 70%; corresponding to an α-tocopherol concentration between 1 and 0.25 mM. IC50 values from the inhibition of α-tocopherol on the chemiluminescence were higher in microsomes (0.144 mM) than mitochondria (0.078 mM). The protective effect observed by α-tocopherol in rat testis mitochondria was higher compared with microsomes, associated with the higher amount of [C20:4 n6]+[C22:5 n6] in microsomes that in mitochondria. It is propossed that the vulnerability to lipid peroxidation of rat testis microsomes and mitochondria is different because of the different proportion of PUFA in these organelles The peroxidizability index (PI) was positively correlated with the level of long chain fatty acids. The results demonstrated the protective effect of α-tocopherol on lipid peroxidation in microsomes and mitochondria from rat testis.

Melatonin preserves arachidonic and docosapentaenoic acids during ascorbate-Fe2+ peroxidation of rat testis microsomes and mitochondria

The pineal hormone melatonin (N-acetyl, 5-methoxytryptamine) was recently accepted to act as an antioxidant under both in vivo and in vitro conditions. In this study, we examined the possible preventive effect of melatonin on ascorbate-Fe2+ lipid peroxidation of rat testis microsomes and mitochondria. Special attention was paid to the changes produced on the highly polyunsaturated fatty acids C20:4 n6 and C22:5 n6. The lipid peroxidation of testis microsomes or mitochondria produced a significant decrease of C20:4 n6 and C22:5 n6. The light emission (chemiluminescence) used as a marker of lipid peroxidation was similar in both kinds of organelles when the control and peroxidized groups were compared. Both long chain polyunsaturated fatty acids were protected when melatonin was incorporated either in microsomes or mitochondria. The melatonin concentration required to inhibit by 100% the lipid peroxidation process was 5.0 and 1.0mM in rat testis microsomes and mitochondria, respectively. IC 50 values calculated from the inhibition curve of melatonin on the chemiluminescence rates were higher in microsomes (4.98mM) than in mitochondria (0.67mM). The protective effect observed by melatonin in rat testis mitochondria was higher than that observed in microsomes which could be explained if we consider that the sum of C20:4 n6+C22:5 n6 in testis microsomes is two-fold greater than present in mitochondria.

The molecular mechanism of organelle transport along microtubules: the identification and characterization of KIFs (kinesin superfamily proteins).

In the cells various kinds of organelles are transported and distributed to their proper destinations in the cell. Organelle transports are very important for cellular morphogenesis and functions, with the conveying and targeting of essential materials to their correct destination being conducted, often at considerable velocities. Recently we have identified at least 10 new microtubule-associated motor proteins named as KIFs (kinesin superfamily proteins). Their characterization reveals that each member can convey a specific organelle or cargo, although there is some redundancy. It has also become clear that there are distinct subclasses of KIFs that form monomeric, heterodimeric and homodimeric motors. Molecular cell biological approaches combining multidisciplinary methods such as new electron microscopy, biochemistry, immunocytochemistry, biophysics, molecular biology and molecular genetics have revealed precise mechanisms of organelle transports in the cells by KIFs.

Ultrastructural changes in micropylar and granulosa cells during in vitro oocyte maturation in the medaka, Oryzias latipes

AbstractUltrastructural changes in micropylar cells during in vitro oogenesis in the medaka, Oryzias latipes, were examined by electron microscopy. In micropylar cells, bundles of microtubules and tonofilaments are well developed by the post‐vitellogenic stage of oogenesis. At the initiation of germinal vesicle breakdown (GVBD), the twisted cytoplasmic protrusion of the enlarged micropylar cell extends to the oocyte surface through the micropylar canal of the chorion. Various kinds of organelles in the cytoplasm of the micropylar cell show a characteristic pattern of distribution. Extensive tonofilaments occupy a large portion of the cytoplasm in the main cell body, while spiraling bundles of both microtubules and tonofilaments are observed along with mitochondria in the cytoplasmic protrusion. About 3 hours after GVBD, the cytoplasmic protrusion begins to shrink and gradually withdraw from the micropylar canal. It has few or no bundles of microtubules and tonofilaments during its withdrawal. The micropylar cell finally becomes oval in shape by 6 hours after the initiation of GVBD as its cytoplasmic protrusion shrinks completely. These observations suggest that these cell organelles are involved in forming, supporting, and/or withdrawing the cytoplasmic protrusion of the micropylar cell. © Wiley‐Liss, Inc.

Filtering Centrifugation Through Two Layers of Silicone Oil: A Method for the Kinetic Analysis of Rapid Metabolite Transport in Organelles.

Kinetic studies of ATP uptake in amyloplasts from sycamore (Acer pseudoplatanus L.) have been performed with a newly developed method of centrifugation through a double layer of silicone oil; the results are compared with the frequently used method of centrifugation through a single layer. The present technique employs two separate silicone layers: the upper one prevents mixing of the organelle preparation with the incubation layer, which contains the metabolites, and the lower one prevents mixing of the incubation and pelleting layers. Incubation of the organelles takes place in the incubation layer after the upper layer of silicone inverts during centrifugation. Depending on the speed of centrifugation, incubation periods as short as 1 sec and as long as 2 min can be achieved. High reproducibility and accuracy, acquisition of multiple data in a single centrifugation, and maintenance of structural integrity and metabolic activity of the organelles make the technique advantageous for the analysis of metabolite transport in amyloplasts and other kinds of organelles.

Fine structure of the micropylar cell and its change during oocyte maturation in the chum salmon, Oncorhynchus keta.

In the ovarian follicle, the micropylar cell (MPC) is distinguished from neighboring granulosa cells by its larger cell size and its thick cytoplasmic process. The micropylar cell body fits into a shallow depression (micropylar vestibule) on the outer surface of the egg envelope; its process extends through the micropylar canal, which extends from the bottom of the vestibule through the full thickness of the zona pellucida interna. At its distal end, the cell process expands into a bulb which fits into an indentation of the ooplasmic surface immediately beneath the inner opening of the micropylar canal. Intermediate and desmosomelike junctions establish an intimate association between MPC process and oocyte. Various kinds of organelles and inclusions in the MPC show a characteristic pattern of cytoplasmic distribution; rough endoplasmic reticulum with markedly dilated cisternae is found exclusively in the main cell body, while microtubules and thin filaments are observed in the cytoplasmic process. Immediately before or during the breakdown of the germinal vesicle in the intrafollicular oocyte, the cytoplasmic process of the MPC gradually decreases in length and begins to withdraw from the micropylar canal. At the same time, the ooplasmic surface protrudes outward to form a papilla in the canal. The intimate MPC-oocyte association disappears during formation of the ooplasmic papilla. Hydration of the oocyte apparently occurs at the final stage of maturation and probably participates in papilla formation. Although the MPC undergoes degenerative changes as ovulation draws near, it remains attached to the inner surface of the granulosa cell layer even after its association with the oocyte has completely disappeared. We speculate that the micropyle develops during fish oogenesis through the combined activity of the MPC and neighboring granulosa cells. It appears that the cell body of the micropylar cell and nearby granulosa cells exert mechanical pressure on the external surface of the growing oocyte and thus participate in formation of the micropylar vestibule. The cytoplasmic process of the MPC evidently forms a passive barrier to deposition of material for the egg envelope in the animal pole, thereby resulting in formation of the micropylar canal.

The amniotic, allantoic and yolk sac epithelia of the cat: SEM and TEM studies.

The epithelial layers of the feline allantoamnion and yolk sac between the 23rd day and full term were studied using SEM, TEM, and light microscopical histochemistry. Amniotic, allantoic and yolk sac fluid were analysed. The attenuated and relatively inert amniotic epithelium sloughs off completely around the 54th day, the amniotic cavity is then lined by fibrous connective tissue only. The exocoelomic epithelium is regarded as the source of the abundant macrophages, rich in lysosomal enzymes, that are seen in the allantoamniotic membrane after obliteration of the exocoelomic cleft. The allantoic epithelium has been mistaken for the amniotic one by many authors. Its cuboidal, glycogen-rich cells develop coral-like luminal outgrowths after the 45th day, which contain almost all kinds of organelles. The basal cell poles form large interdigitations, and the nuclei become heavily lobulated. The changes are accompanied by drastic alterations in the ionic composition of the allantoic fluid. The yolk sac endoderm differs greatly from the allantoic endoderm. It is the most active epithelium of the accessory fetal membranes. The yolk sac mesothelium retains many long microvilli over the whole gestational period. The nutritional value of the yolk sac fluid is only higher than that of the amniotic fluid in its glycerol and cholesterol values.

Association of the endoplasmic reticulum and the plastids in Tozzia alpina L. scale leaves

Numerous plastids and some peculiar aggregates of endoplasmic reticulum have been observed in the phloem cells of Tozzia alpina scale leaves; the plastids can be sheathed partly or even completely with smooth endoplasmic reticulum as single cisternae or associated in aggregates of tubular units. Possible functional relationships between the two kinds of organelles and explanation of endoplasmic reticulum proliferation at the periphery of plastids and in the cytoplasm are discussed.