Embryonic development of Xenopus studied in a cell culture system with tissue-specific monoclonal antibodies

An in vitro microculture system of early gastrula cells of Xenopus laevis has been developed; deep layer cells from the lateral marginal zone (prospective somite region) or ventral ectoderm (prospective epidermis region) were fully dissociated, and the desired number of each (1-100) was distributed into a microculture well and cultured under appropriate conditions. When examined with the tissue-specific Mabs (Mu1 for muscle and E3 for epidermis, respectively), a substantial portion of the deep layer cells from the two regions followed their respective normal embryonic fates. It was found that reproducible cellular differentiation was dependent on the intimate reaggregation of dissociated cells and on the size of the resultant aggregate. About 20 lateral marginal zone cells were found to be sufficient, when put into a culture well, for supporting successful muscle differentiation, whereas about 100 ventral ectoderm cells were necessary for epidermal differentiation.     

Evolutionary conservation of tissue-specific lymphocyte-endothelial cell recognition mechanisms involved in lymphocyte homing

Tissue-specific interactions with specialized high endothelial venules (HEV) direct the homing of lymphocytes from the blood into peripheral lymph nodes, mucosal lymphoid organs, and tissue sites of chronic inflammation. These interactions have been demonstrated in all mammalian species examined and thus appear highly conserved. To assess the degree of evolutionary divergence in lymphocyte-HEV recognition mechanisms, we have studied the ability of lymphocytes to interact with HEV across species barriers. By using an in vitro assay of lymphocyte binding to HEV in frozen sections of lymphoid tissues, we confirm that mouse, guinea pig, and human lymphocytes bind to xenogeneic as well as homologous HEV. In addition, we show that mouse and human lymphoid cell lines that bind selectively to either peripheral lymph node or mucosal vessels (Peyer's patches, appendix) in homologous lymphoid tissues exhibit the same organ specificity in binding to xenogeneic HEV. Furthermore, monoclonal antibodies that recognize lymphocyte "homing receptors" and block homologous lymphocyte binding to peripheral lymph node or to mucosal HEV, also inhibit lymphocyte interactions with xenogeneic HEV in a tissue-specific fashion. Similarly, anti-HEV antibodies against organ-specific mouse high endothelial cell "addressins" involved in lymphocyte homing to peripheral lymph node or mucosal lymphoid organs, not only block the adhesion of mouse lymphocytes but also of human lymphocytes to target mouse HEV. The results illustrate a remarkable degree of functional conservation of elements mediating these cell-cell recognition events involved in organ-specific lymphocyte homing.     

Rice chitinases: sugar recognition specificities of the individual subsites

Sugar recognition specificities of class III (OsChib1a) and class I (OsChia1cDeltaChBD) chitinases from rice, Oryza sativa L., were investigated by analyzing (1)H- and (13)C-nuclear magnetic resonance spectra of the enzymatic products from partially N-acetylated chitosans. The reducing end residue of the enzymatic products obtained by the class III enzyme was found to be exclusively acetylated, whereas both acetylated and deacetylated units were found at the nearest neighbor to the reducing end residue. Both acetylated and deacetylated units were also found at the nonreducing end residue and its nearest neighbor of the class III enzyme products. Thus, only subsite (-1) among the contiguous subsites (-2) to (+2) of the class III enzyme was found to be specific to an acetylated residue. For the class I enzyme, the reducing end residue was preferentially acetylated, although the specificity was not absolute. The nearest neighbor to the acetylated reducing end residue was specifically acetylated. Moreover, the nonreducing end residue produced by the class I enzyme was exclusively acetylated, although there was a low but significant preference for deacetylated units at the nearest neighbor to the nonreducing end. These results suggest that the three contiguous subsites (-2), (-1), and (+1) of the class I enzyme are specific to three consecutive GlcNAc residues of the substrate. In rice plants, the target of the class I enzyme might be a consecutive GlcNAc sequence probably in the cell wall of fungal pathogen, whereas the class III enzyme might act toward an endogenous complex carbohydrate containing GlcNAc residue.     

DNA-binding affinities and sequence specificities of protoberberine alkaloids and their demethylated derivatives: a comparative study

Berberrubine (1a), jatrorubine (2a), and palmatrubine (3a) have been chemically prepared by partial demethylation of berberine (1), jatrorrhizine (2), and palmatine (3), respectively. Their interactions with calf thymus (CT) DNA, poly(dA-dT)poly(dA-dT), poly(dG-dC)poly(dG-dC), and eight AT-rich 12-mer double-stranded DNAs have been investigated by means of competitive ethidium bromide (EB) displacement experiments. The results showed that DNA-binding affinities of these protoberberine alkaloids have been significantly improved by partial demethylation, and that all of these alkaloids have the preferable binding affinities with AT-rich DNA. Especially, the sequence specificities of DNA-binding of demethylated derivatives 1a, 2a, and 3a had changed to a certain extent when compared with the parent alkaloids 1, 2, and 3, respectively. The binding mode of these alkaloids was further confirmed by UV spectroscopic titration experiments. All the compounds bind to double-stranded DNA most probably via an intercalating mode.     

Evolution of divergent DNA recognition specificities in VDE homing endonucleases from two yeast species

Homing endonuclease genes (HEGs) are mobile DNA elements that are thought to confer no benefit to their host. They encode site-specific DNA endonucleases that perpetuate the element within a species population by homing and disseminate it between species by horizontal transfer. Several yeast species contain the VMA1 HEG that encodes the intein-associated VMA1-derived endonuclease (VDE). The evolutionary state of VDEs from 12 species was assessed by assaying their endonuclease activities. Only two enzymes are active, PI-ZbaI from Zygosaccharomyces bailii and PI-ScaI from Saccharomyces cariocanus. PI-ZbaI cleaves the Z.bailii recognition sequence significantly faster than the Saccharomyces cerevisiae site, which differs at six nucleotide positions. A mutational analysis indicates that PI-ZbaI cleaves the S.cerevisiae substrate poorly due to the absence of a contact that is analogous to one made in PI-SceI between Gln-55 and nucleotides +9/+10. PI-ZbaI cleaves the Z.bailii substrate primarily due to a single base-pair substitution (A/T₊₅ → T/A₊₅). Structural modeling of the PI-ZbaI/DNA complex suggests that Arg-331, which is absent in PI-SceI, contacts T/A₊₅, and the reduced activity observed in a PI-ZbaI R331A mutant provides evidence for this interaction. These data illustrate that homing endonucleases evolve altered specificity as they adapt to recognize alternative target sites.     

cMyc increases cell number through uncoupling of cell division from cell size in CHO cells

Background  

Over the past decades, the increase in maximal cell numbers for the production of mammalian derived biologics has been in a large part due to the development of optimal feeding strategies. Engineering of the cell line is one of probable approaches for increasing cell numbers in bioreactor.     

Harnessing pluripotency from differentiated cells: a regenerative source for tissue-specific stem cell therapies

Processes involving conversion of mature adult cells into undifferentiated cells have tremendous therapeutic potential in treating a variety of malignant and non-malignant disorders, including degenerative diseases. This can be achieved in autologous or allogeneic settings, by replacing either defective cells or regenerating those that are in deficit through reprogramming more committed cells into stem cells. The concept behind reprogramming differentiated cells to a stem cell state is to enable the switching of development towards the required cell lineage that is capable of correcting the underlying cellular dysfunction. The techniques by which differentiated cells can reverse their development, become pluripotent stem cells and transdifferentiate to give rise to new tissue or an entire organism are currently under intense investigation. Examples of reprogramming differentiation in mature adult cells include nuclear reprogramming of more committed cells using the cytoplasm of empty oocytes obtained from a variety of animal species, or cell surface contact of differentiated cells through receptor ligand interaction. Such ligands include monoclonal antibodies, cytokines or synthetic chemical compounds. Despite controversies surrounding such techniques, the concept behind identification and design/screening of biological or pharmacological compounds to enable re-switching of cell fate in-vivo or ex-vivo is paramount for current drug therapies to be able to target more specifically cellular dysfunction at the tissue/organ level. Herein, this review discusses current research in cellular reprogramming and its potential application in regenerative medicine.     

Isolectins from Solanum tuberosum with different detailed carbohydrate binding specificities: unexpected recognition of lactosylceramide by N-acetyllactosamine-binding lectins

Glycosphingolipid recognition by two isolectins from Solanum tuberosum was compared by the chromatogram binding assay. One lectin (PL-I) was isolated from potato tubers by affinity chromatography, and identified by MALDI-TOF mass spectrometry as a homodimer with a subunit molecular mass of 63,000. The other (PL-II) was a commercial lectin, characterized as two homodimeric isolectins with subunit molecular masses of 52,000 and 55,000, respectively. Both lectins recognized N-acetyllactosamine-containing glycosphingolipids, but the fine details of their carbohydrate binding specificities differed. PL-II preferentially bound to glycosphingolipids with N-acetyllactosamine branches, as Galbeta4GlcNAcbeta6(Galbeta4GlcNAcbeta3)Galbeta4Glcbeta1C er. PL-I also recognized this glycosphingolipid, but bound equally well to the linear glycosphingolipid Galbeta4GlcNAcbeta3Galbeta4GlcNAcbeta3Galbeta4Glcbeta1Cer. Neolactotetraosylceramide and the B5 pentaglycosylceramide were also bound by PL-I, while other glycosphingolipids with only one N-acetyllactosamine unit were non-binding. Surprisingly, both lectins also bound to lactosylceramide, with an absolute requirement for sphingosine and non-hydroxy fatty acids. The inhibition of binding to both lactosylceramide and N-acetyllactosamine-containing glycosphingolipids by N-acetylchitotetraose suggests that lactosylceramide is also accomodated within the N-acetylchitotetraose/N-acetyllactosamine-binding sites of the lectins. Through docking of glycosphingolipids onto a three-dimensional model of the PL-I hevein binding domain, a Galbeta4GlcNAcbeta3Galbeta4 binding epitope was defined. Furthermore, direct involvement of the ceramide in the binding of lactosylceramide was suggested.     

CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data

RNA-binding proteins (RBPs) bind to their target RNA molecules by recognizing specific RNA sequences and structural contexts. The development of CLIP-seq and related protocols has made it possible to exhaustively identify RNA fragments that bind to RBPs. However, no efficient bioinformatics method exists to reveal the structural specificities of RBP–RNA interactions using these data. We present CapR, an efficient algorithm that calculates the probability that each RNA base position is located within each secondary structural context. Using CapR, we demonstrate that several RBPs bind to their target RNA molecules under specific structural contexts. CapR is available at https://sites.google.com/site/fukunagatsu/software/capr.     

Embryonic stem cell differentiation: A chromatin perspective

Embryonic stem (ES) cells hold immense promise for the treatment of human degenerative disease. Because ES cells are pluripotent, they can be directed to differentiate into a number of alternative cell-types with potential therapeutic value. Such attempts at "rationally-directed ES cell differentiation" constitute attempts to recapitulate aspects of normal development in vitro. All differentiated cells retain identical DNA content, yet gene expression varies widely from cell-type to cell-type. Therefore, a potent epigenetic system has evolved to coordinate and maintain tissue-specific patterns of gene expression. Recent advances show that mechanisms that govern epigenetic regulation of gene expression are rooted in the details of chromatin dynamics. As embryonic cells differentiate, certain genes are activated while others are silenced. These activation and silencing events are exquisitely coordinated with the allocation of cell lineages. Remodeling of the chromatin of developmentally-regulated genes occurs in conjunction with lineage commitment. Oocytes, early embryos, and ES cells contain potent chromatin-remodeling activities, an observation that suggests that chromatin dynamics may be especially important for early lineage decisions. Chromatin dynamics are also involved in the differentiation of adult stem cells, where the assembly of specialized chromatin upon tissue-specific genes has been studied in fine detail. The next few years will likely yield striking advances in the understanding of stem cell differentiation and developmental biology from the perspective of chromatin dynamics.     

Somatic polyploidy promotes cell function under stress and energy depletion: evidence from tissue-specific mammal transcriptome

Polyploid cells show great among-species and among-tissues diversity and relation to developmental mode, suggesting their importance in adaptive evolution and developmental programming. At the same time, excessive polyploidization is a hallmark of functional impairment, aging, growth disorders, and numerous pathologies including cancer and cardiac diseases. To shed light on this paradox and to find out how polyploidy contributes to organ functions, we review here the ploidy-associated shifts in activity of narrowly expressed (tissue specific) genes in human and mouse heart and liver, which have the reciprocal pattern of polyploidization. For this purpose, we use the modular biology approach and genome-scale cross-species comparison. It is evident from this review that heart and liver show similar traits in response to polyploidization. In both organs, polyploidy protects vitality (mainly due to the activation of sirtuin-mediated pathways), triggers the reserve adenosine-5′-triphosphate (ATP) production, and sustains tissue-specific functions by switching them to energy saving mode. In heart, the strongest effects consisted in the concerted up-regulation of contractile proteins and substitution of energy intensive proteins with energy economic ones. As a striking example, the energy intensive alpha myosin heavy chain (providing fast contraction) decreased its expression by a factor of 10, allowing a 270-fold increase of expression of beta myosin heavy chain (providing slow contraction), which has approximately threefold lower ATP-hydrolyzing activity. The liver showed the enhancement of immunity, reactive oxygen species and xenobiotic detoxication, and numerous metabolic adaptations to long-term energy depletion. Thus, somatic polyploidy may be an ingenious evolutionary instrument for fast adaptation to stress and new environments allowing trade-offs between high functional demand, stress, and energy depletion.     

Embryonic myocardial cell aggregates: volume and pulsation rate

Spontaneously beating aggregates of myocardial cells from whole heart, atria, and apical portions of the ventricles were prepared by trypsin-dissociation and gyratory reaggregation of 4-, 7-, and 14-day-old chick embryo tissue. Pulsation rate and volume of aggregates were determined. The pulsation rate for a given volume aggregate decreased as the age of the donor embryo increased. Atrial aggregates of a given size beat faster than ventricular aggregates of the same size. However, in all cases the pulsation rate varied inversely with the aggregate volume. These results are not in agreement with the pacemaker concept as generally accepted, which predicts that a mass of heart cells would take on the pulsation rate of the fastest cell or cells within it. Differential composition of large and small aggregates was ruled out as a determining factor in the inverse rate-volume relationship. We suggest that (a) limited diffusion in large aggregates compared to small aggregates or (b) the larger total membrane capacitance of the electrically coupled cells of larger aggregates compared with that of smaller aggregates, plays a major role in setting the pulsation rate.     

Embryonic polarity: protein stability in asymmetric cell division

Recent work on pattern formation in Caenorhabditis elegans has uncovered a new mechanism of asymmetric cell division: the cytoplasm is polarized by cortical proteins, and this polarization then influences the stability of other maternally expressed proteins that in turn determine early embryonic cell fates.     

Alpha 2 beta 1 integrins from different cell types show different binding specificities

Purified alpha 2 beta 1 integrin from human platelets was compared in its function and immunoreactivity to alpha 2 beta 1 from endothelial cells. Both alpha 2 beta 1 integrins bound to type I collagen-Sepharose and had indistinguishable immunoreactivities when analyzed by a panel of monoclonal and polyclonal alpha 2-specific antibodies. However, functional analysis using rechromatography of purified receptors on laminin and collagen-Sepharose showed that endothelial alpha 2 beta 1 was able to bind to laminin, whereas its counterpart from platelets did not. Moreover, a receptor binding assay indicated that, in contrast to platelets, endothelial cells might also use alpha 2 beta 1 to bind to fibronectin. These results suggest that the alpha 2 beta 1 binding specificity may be modulated by cell-type specific factors.     

Pattern recognition receptors: from the cell surface to intracellular dynamics

Detection of potentially infectious microorganisms is essential for plant immunity. Microbial communities growing on plant surfaces are constantly monitored according to their conserved microbe-associated molecular patterns (MAMPs). In recent years, several pattern-recognition receptors, including receptor-like kinases and receptor-like proteins, and their contribution to disease resistance have been described. MAMP signaling must be carefully controlled and seems to involve receptor endocytosis. As a further surveillance layer, plants are able to specifically recognize microbial effector molecules via nucleotide-binding site leucine-rich repeat receptors (NB-LRR). A number of recent studies show that NB-LRR translocate to the nucleus in order to exert their activity. In this review, current knowledge regarding the recognition of MAMPs by surface receptors, receptor activation, signaling, and subcellular redistribution are discussed.