Toward synthetic life: Biomimetic synthetic cell communication

Engineering synthetic minimal cells provide a controllable chassis for studying the biochemical principles of natural life, increasing our understanding of complex biological processes. Recently, synthetic cell engineering has enabled communication between both natural live cells and other synthetic cells.A system such as these enable studying interactions between populations of cells, both natural and artificial, and engineering small molecule cell communication protocols for a variety of basic research and practical applications. In this review, we summarize recent progress in engineering communication between synthetic and natural cells, and we speculate about the possible future directions of this work.     

浮游植物细胞自噬作用特点及研究方法

自噬(Autophagy)是真核生物细胞中一类高度保守的、依赖于溶酶体或液泡途径对胞质蛋白和细胞器进行降解的生物学过程。细胞自噬除维持细胞稳态外,在细胞响应各种外界胁迫中也发挥重要作用。近年来,陆续发现浮游植物能够通过细胞自噬应答众多环境胁迫,并在浮游植物细胞中鉴定出了类似于哺乳动物细胞中的核心自噬功能单位。自噬作为一种独特的程序性细胞死亡(PCD)形式,对浮游植物遭受胁迫后的个体存活及种群延续具有至关重要的作用。因此,细胞自噬也将成为浮游植物研究领域的一个新的着力点。主要综述了浮游植物细胞中自噬的保守性、诱导因素、调控机制、自噬与凋亡的交互作用以及浮游植物自噬研究方法等研究进展。     

Cell death in individual freshwater phytoplankton species: relationships with population dynamics and environmental factors

ABSTRACT

Understanding and predicting changes in phytoplankton populations requires knowledge of losses due not only to sedimentation and grazing, but also to intrinsic processes (here, collectively termed ‘cell death’). Cell death is poorly understood, especially in freshwater phytoplankton, but experiments in culture often suggest involvement of abiotic factors (e.g. temperature, light, nutrients). The occurrence of cell death was examined in a simple, natural environment: a small, well-mixed, temperate, urban pond during a period of phytoplankton growth, from mid-July to mid-November. Abundances of 18 phytoplankton taxa were measured weekly and fluorescence microscopy and staining was used to detect dead cells (using SYTOX which measures loss of membrane integrity) and cells undergoing cell death (using Annexin-V, which measures lipid inversions of membranes, an early signal of cell death). Dead and dying cells occurred in most phytoplankton taxa, but incidence and timing varied considerably, e.g. species like the chlorophyte Ankistrodesmus spiralis showed 20–30% of cells staining with SYTOX and Annexin in late autumn when the population was decreasing, while the dinoflagellate Peridinium sp. showed staining of up to 50% of cells with STYOX throughout the period, and the cyanobacterium Microcystis aeruginosa occasionally showed staining of 100% of cells with SYTOX. Overall, there was some association between cell death staining and growth phase with 10–15% of the total community showing SYTOX and Annexin staining in late autumn, when most populations were declining. Cell death could not be correlated with thresholds or rapid changes in abiotic conditions (e.g. temperature, irradiance) or with indicators of nutrient limitation (e.g. N:P ratios). While abiotic factors have been clearly implicated in cell death within unialgal culture experiments, in natural freshwater ecosystems interactions between biotic factors, such as pathogens or allelopathy, may play greater roles in losses related to cell death and be distinct for different taxa.     

Carbon dynamics of logarithmetic and stationary phase phytoplankton as determined by track autoradiography

Track autoradiographic analysis of photosynthetic radiocarbon incorporation at the cellular level indicated that the carbon uptake rate and carbon pool size of exponentially growing (log phase) Scenedesmus cells was threefold that of stationary phase cells, while carbon turnover rates were similar. Carbon fixation was uncoupled from growth and cell division in the stationary phase cells, which were larger and contained less chlorophyll per unit volume than log phase cells. Changes in the temporal pattern of isotope incorporation were evident at the cell level prior to the cessation of division and transition to stationary phase, while bulk carbon fixation responded only the second day after cell division ceased. The carbon uptake patterns of a marine nanoplankter from a nutrient-enriched natural sample resembled that of log phase cells while the control population pattern resembled that of stationary cells. The physical, biochemical, and metabolic differences between log and stationary phase cells are potentially measurable by flow cytometry procedures currently in use and under development. The use of flow cytometry to sort cell types for analysis by track autoradiography and subsequent correlation of metabolic characteristics with flow cytometry signatures is a feasible means of investigating the heterogeneity of phytoplankton metabolic state in the marine environment.     

Stirring influences the phytoplankton species composition within enclosed columns of coastal sea water

A brief daily stirring of two enclosed water columns led to the maintenance of larger phytoplankton cells than in two unstirred columns. Small herbivorous copepods, Noctiluca sp., and the ctenophore Pleurobrachia sp. were also maintained over the 6 weeks of the experiment. Grazing pressure appeared to decrease the average size of the phytoplankton cells during periods of low standing stocks.Mechanical stirring is a useful technique for manipulating the phytoplankton species composition and cell size in enclosed water columns where natural mixing processes are greatly reduced. N : P utilization ratios were lower and more similar to the ‘Redfield’ ratio of 15.5 in stirred (16–19) than in unstirred enclosures (25–27). Fluctuations in phytoplankton, small copepods, and Pleurobrachia standing stocks, suggest that stirring may hasten progress to equilibrium among the components of the food web in the enclosures.     

The Role of eNSCs in Neurodegenerative Disease

Recent progress in biology has shown that many if not all adult tissues contain a population of stem cells. It is believed that these cells are involved in the regeneration of the tissue or organ in which they reside as a response to the natural turnover of differentiated cells or to injury. In the adult mammalian brain, stem cells in the subventricular zone and the dentate gyrus may also play a role in the replacement of neurons. A positive beneficial response to injury does not necessarily require cell replacement. New findings suggest that some populations of endogenous neural stem cells in the central nervous system may have adopted a function different from cell replacement and are involved in the protection of neurons in diverse paradigms of disease and injury. In this article, we will focus on the immature cell populations of the central nervous system and the signal transduction pathways that regulate them which suggest new possibilities for their manipulation in injury and disease.     

Stochastic effects in adaptive reconstruction of body damage: implied the creativity of natural selection

After an injury occurs, mechanical/biochemical loads on muscles influence the composition and structure of recovering muscles; this effect likely occurs in other tissues, cells and biological molecules as well owing to the similarity, interassociation and interaction among biochemical reactions and molecules. The ‘damage and reconstruction’ model provides an explanation for how an ideal cytoarchitecture is created by reducing components not suitable for bearing loads; in this model, adaptive changes are induced by promoting the stochasticity of biochemical reactions. Biochemical and mechanical loads can direct the stochasticity of biochemical reactions, which can in turn induce cellular changes. Thus, mechanical and biochemical loads, under natural selection pressure, modify the direction of cell‐ and tissue‐level changes and guide the formation of new structures and traits, thereby influencing microevolution. In summary, the ‘damage and reconstruction’ model accounts for the role of natural selection in the formation of new organisms, helps explain punctuated equilibrium, and illustrates how macroevolution arises from microevolution.     

Medicinal mushroom modulators of molecular targets as cancer therapeutics

Empirical approaches to discover anticancer drugs and cancer treatments have made limited progress in the past several decades in finding a cure for cancer. The expanded knowledge of the molecular basis of tumorigenesis and metastasis, together with the inherently vast structural diversity of natural compounds found in mushrooms, provided unique opportunities for discovering new drugs that rationally target the abnormal molecular and biochemical signals leading to cancer. This review focuses on mushroom low-molecular-weight secondary metabolites targeting processes such as apoptosis, angiogenesis, metastasis, cell cycle regulation, and signal transduction cascades. Also discussed in this review are high-molecular-weight polysaccharides or polysaccharide–protein complexes from mushrooms that appear to enhance innate and cell-mediated immune responses, exhibit antitumor activities in animals and humans, and demonstrate the anticancer properties of selenium compounds accumulated in mushrooms.     

Impact of natural products in modern drug development

Usage of natural substances as therapeutic agents in modern medicine has sharply declined from the predominant position held in the early decades of last century, but search for bioactive molecules from nature (plants, animals, microflora) continues to play an important role in fashioning new medicinal agents. With the advent of modern techniques, instrumentation and automation in isolation and structural characterisation, we have on hand an enormous repository of natural compounds. In parallel to this, biology has also made tremendous progress in expanding its frontiers of knowledge. An interplay of these two disciplines constitutes the modern thrust in research in the realm of compounds elaborated by nature. The purpose of this article is to underline how natural products research continues to make significant contributions in the domain of discovery and development of new medicinal products. It is proposed to present the material under several heads, each of which has made natural products research relevant in the search for new and better medication.     

Drosophila embryonic 'fibroblasts': Extending mutant analysis in vitro

The in vivo analysis of Drosophila using genetics, with almost a hundred year history, has produced an immense body of knowledge about biology. In vitro analysis, while arguably the poor cousin to its in vivo relative, has a utility-in biochemical analyses and in cell-based screening, for example, with RNAi. A major block to the development of in vitro analysis has been the lack of an efficient genetic method to derive cell lines from mutant Drosophila strains. We recently discovered that expression of activated Ras (Ras^V12) provides cells in vitro with both a survival and a proliferative advantage and hence promotes the generation of cell lines.¹ In this addendum, we provide new data describing the genesis of seven cell lines corresponding to a rumi mutant, which demonstrate that the method can be used to derive lines and study genetic mutants in vitro.     

Cell death in lake phytoplankton communities

1. The fraction of living and dead phytoplankton cells in seven Florida lakes was assessed by using the cell digestion assay, a non‐staining membrane permeability test. The cell digestion assay is an effective method to analyse cell viability in complex natural phytoplankton communities. 2. The lakes examined ranged widely in phytoplankton abundance and community composition. The variability in the percentage of living cells (% LC) was high among the taxonomic groups forming the different phytoplankton communities, ranging from 19.7% to 98% LC. 3. All cells within single cyanobacteria filaments were determined to be either dead or alive, suggesting physiological integration of the cells within colonies. 4. Within each lake, the dominant taxa generally exhibited the highest proportion of living cells. A high proportion of living cells was found to be a characteristic of the different taxa forming the communities of eutrophic lakes. The average value for the % LC for all groups comprising the phytoplankton communities in each of the lakes ranged from 29.9 ± 7.2 to 80.4 ± 4.0 (mean ± SE) and varied strongly and positively with chlorophyll a concentration. 5. These results suggest phytoplankton cell death to be an important process structuring phytoplankton communities in lakes, particularly in oligotrophic ones.     

Separation and concentration of phytoplankton populations using centrifugal elutriation

Centrifugal elutriation is a technique for separating particles on the basis of their sedimentation velocity, an expression of size, shape, and specific gravity. Unialgal cultures, mixtures of two phytoplankton cultures, and natural seawater samples were elutriated to determine the feasibility of this technique for collecting fractions of different cell cycle phases, separating two phytoplankton species, and concentrating cells from dilute samples. Elutriation resulted in the separation of a culture of Dunaliella tertiolecta and Phaeodactylum tricornutum into homogeneous fractions of each species. Cells in the natural seawater sample were concentrated by nearly 2 orders of magnitude. Centrifugal elutriation provides an alternative cell separation and concentration technique when large numbers of cells are required.     

some aspects of the biochemical and mineral composition of marine plankton

A natural population of phytoplankton and two species of zooplankton, Calanus finmarchicus (Gunnerus) (stage V) and Sagitta elegans (Verrill) (mature), were analysed for their biochemical and mineral composition. Comparison with published data for the same categories of plankton shows that the distribution of both organic and mineral fractions is highly variable, the causes of which are not equally understood. The composition of the organic fraction is affected by the duality of function of the biochemical constituents and by the large number of ecological factors which influence their concentration. Whether this applies to the mineral fraction remains uncertain; nevertheless it appears that plankton concentrate trace metals, that phytoplankton has a greater ability to concentrate them than zooplankton, and that the ability of zooplankton to concentrate various metals varies with the species.     

Use of isolated brain capillaries and cultured endothelial cells to study the blood-brain barrier

Brain capillary endothelial cells are responsible for forming the blood-brain barrier (BBB). Methods are now available to isolate microvessels from brain and study their biochemical and transport characteristics. From these investigations, new ideas have been proposed concerning the role of endothelial cells in the function of the BBB. More recently, success in culturing endothelial cells from brain microvessels has opened the way for novel approaches to the study of the regulation of endothelial cell permeability. We anticipate continued rapid progress in this area and expect that this will lead to a better understanding of the mechanisms involved in the regulation of BBB permeability and brain capillary function.     

Phosphate Stress in Cultures and Field Populations of the Dinoflagellate Prorocentrum minimum Detected by a Single-Cell Alkaline Phosphatase Assay

Alkaline phosphatase activity is a common marker of phosphate stress in many phytoplankton, but it has been difficult to attribute alkaline phosphatase activity to specific organisms or groups of phytoplankton in the field with traditional biochemical procedures. A new alkaline phosphatase substrate, ELF-97 (enzyme-labeled fluorescence), shows promise in this regard. When a phosphate group is cleaved from the ELF-97 reagent, the remaining molecule precipitates near the site of enzyme activity, thus fluorescently tagging cells with alkaline phosphatase activity. We characterized ELF-97 labeling in axenic cultures of a common dinoflagellate, Prorocentrum minimum, in order to understand ELF-97 labeling dynamics when phosphate nutrition varies. Enzyme activity, as detected by ELF-97 labeling, appears to be induced in late-log- or early-stationary-phase cultures if cells are grown in low-phosphate media and is lost when phosphate-stressed cells are refed with phosphate. ELF-97 appears to label an inducible intracellular alkaline phosphatase in P. minimum based on confocal microscopy studies. This may limit the use of this reagent to organisms that lack high levels of constitutive intracellular phosphatases. After laboratory cultures were characterized, ELF-97 was used to assay field populations of P. minimum in Narragansett Bay during two 1-week periods, and 12 to 100% of the P. minimum cells were labeled. The level of cell labeling was reduced by 3 days of incubation with added inorganic phosphate. Our results indicate that ELF-97 is an excellent new tool for monitoring phytoplankton phosphate stress in the environment when the data are supported by appropriate laboratory studies.     

Thermophilic xylanases: from bench to bottle

Lignocellulosic biomass is a valuable raw material. As technology has evolved, industrial interest in new ways to take advantage of this raw material has grown. Biomass is treated with different microbial cells or enzymes under ideal industrial conditions to produce the desired products. Xylanases are the key enzymes that degrade the xylosidic linkages in the xylan backbone of the biomass, and commercial enzymes are categorized into different glycoside hydrolase families. Thermophilic microorganisms are excellent sources of industrially relevant thermostable enzymes that can withstand the harsh conditions of industrial processing. Thermostable xylanases display high-specific activity at elevated temperatures and distinguish themselves in biochemical properties, structures, and modes of action from their mesophilic counterparts. Natural xylanases can be further improved through genetic engineering. Rapid progress with genome editing, writing, and synthetic biological techniques have provided unlimited potential to produce thermophilic xylanases in their natural hosts or cell factories including bacteria, yeasts, and filamentous fungi. This review will discuss the biotechnological potential of xylanases from thermophilic microorganisms and the ways they are being optimized and produced for various industrial applications.     

Programmed cell death: a missing link is found

Two families of proteins have advanced our understanding of the molecular basis of programmed cell death (PCD) in animal cells - the caspases and Bcl-2-related proteins. While caspases lie at the heart of the death programme, Bcl-2-related proteins act as key intracellular regulators. Although there has been considerable progress in elucidating the biochemical functions of caspases, how Bcl-2-related proteins regulate caspase activation and thereby PCD, has remained a mystery. One key to resolving this mystery seems to lie with a new third family of proteins related to the Caenorhabditis elegans cell-death protein CED-4, which connects Bcl-2-related proteins to caspases. An important step in defining this new family has been made by the identification of a human CED-4 homologue.     

Dedifferentiated fat cells: A cell source for regenerative medicine

The identification of an ideal cell source for tissue regeneration remains a challenge in the stem cell field. The ability of progeny cells to differentiate into other cell types is important for the processes of tissue reconstruction and tissue engineering and has clinical, biochemical or molecular implications. The adaptation of stem cells from adipose tissue for use in regenerative medicine has created a new role for adipocytes. Mature adipocytes can easily be isolated from adipose cell suspensions and allowed to dedifferentiate into lipid-free multipotent cells, referred to as dedifferentiated fat (DFAT) cells. Compared to other adult stem cells, the DFAT cells have unique advantages in their abundance, ease of isolation and homogeneity. Under proper condition in vitro and in vivo, the DFAT cells have exhibited adipogenic, osteogenic, chondrogenic, cardiomyogenc, angiogenic, myogenic, and neurogenic potentials. In this review, we first discuss the phenomena of dedifferentiation and transdifferentiation of cells, and then dedifferentiation of adipocytes in particular. Understanding the dedifferentiation process itself may contribute to our knowledge of normal growth processes, as well as mechanisms of disease. Second, we highlight new developments in DFAT cell culture and summarize the current understanding of DFAT cell properties. The unique features of DFAT cells are promising for clinical applications such as tissue regeneration.     

Cell biology of stem cells: an enigma of asymmetry and self-renewal

Stem cells present a vast, new terrain of cell biology. A central question in stem cell research is how stem cells achieve asymmetric divisions to replicate themselves while producing differentiated daughter cells. This hallmark of stem cells is manifested either strictly during each mitosis or loosely among several divisions. Current research has revealed the crucial roles of niche signaling, intrinsic cell polarity, subcellular localization mechanism, asymmetric centrosomes and spindles, as well as cell cycle regulators in establishing self-renewing asymmetry during stem cell division. Much of this progress has benefited from studies in model stem cell systems such as Drosophila melanogaster neuroblasts and germline stem cells and mammalian skin stem cells. Further investigations of these questions in diverse types of stem cells will significantly advance our knowledge of cell biology and allow us to effectively harness stem cells for therapeutic applications.