Organogenesis and Vertebrate Formation

10. A general framework for studying class consciousness and class formation In one way or another, most class analysts believe that at the core of class analysis is a relatively simple causal structure that looks something like the diagram in Figure 10.1. There is, of course, much disagreement about precisely how to conceptualize the arrows in this causal stream. Do they mean ``determines'' or ``shapes'' or ``imposes limits upon''? Is there a clear sense in which the horizontal causal stream in this structure is ``more important'' or ``more fundamental'' than the unspeci®ed ``other causes''? At one extreme, orthodox historical materialism claimed that one can broadly read off patterns of class struggle directly from the class structure, and these, in turn, determine the fundamental course of history; in the long run, at least, class structures are thought to determine class struggle and class struggles (in conjunction with the development of the forces of production) to determine trajectories of social change. At the other extreme, most non-Marxist class analysts as well as some Marxists view the class structure as at most providing us with the vocabulary for identifying potential actors in class struggles; class structure does not, however, necessarily have a more powerful role in determining actual patterns of class struggle than many other mechan- isms (ideology, the state, ethnicity, etc.), and class struggles are only one among a host of change-producing factors. In this chapter we will explore the elements on the left hand side of Figure 10.1: ``Class structure ? class struggle.'' I will propose a general model of the relationship between class structure and class struggle which captures both the core traditional Marxist intuition that class structures are in some sense the fundamental determinant of class struggles, but nevertheless allows other causal factors considerable potential weight in explaining concrete variations across time and place. The core of the model is an attempt to link a micro-conception of the 185 relationship between class location and class consciousness with a more macro-level understanding of the relationship between class structure and class formation. In section 10.1 of this chapter we will set the stage for this model by brie¯y elaborating the contrast between micro- and macro-levels of analysis. Section 10.2 will discuss the de®nitions of a number of the core concepts which we will use, especially class formation and class con- sciousness. This will be followed in section 10.3 by a discussion of the micro-model, the macro-model and their interconnection. 10.1 Micro- and macro-levels of analysis The contrast between micro- and macro-levels of analysis is often invoked in sociology, and much is made about the necessity of ``moving'' back and forth between these levels, but frequently the precise concep- tual status of the distinction is muddled. I will use the terms to designate different units of analysis, in which macro-levels of analysis are always to be understood as ``aggregations'' of relevant micro-units of analysis. The paradigm for this usage is biology: organisms are aggregations of interconnected organs; organs are aggregations of interconnected cells; cells are aggregations of interconnected cellular structures; cellular structures are aggregations of interconnected molecules. The expression ``are aggregations of'' in these statements, of course, Organogenesis and Vertebrate Formation Organogenesis and Vertebrate Formation Bởi: OpenStaxCollege Gastrulation leads to the formation of the three germ layers that give rise, during further development, to the different organs in the animal body This process is called organogenesis Organogenesis is characterized by rapid and precise movements of the cells within the embryo Organogenesis Organs form from the germ layers through the process of differentiation During differentiation, the embryonic stem cells express specific sets of genes which will determine their ultimate cell type For example, some cells in the ectoderm will express the genes specific to skin cells As a result, these cells will differentiate into epidermal cells The process of differentiation is regulated by cellular signaling cascades Scientists study organogenesis extensively in the lab in fruit flies (Drosophila) and the nematode Caenorhabditis elegans Drosophila have segments along their bodies, and the patterning associated with the segment formation has allowed scientists to study which genes play important roles in organogenesis along the length of the embryo at different time points The nematode C.elegans has roughly 1000 somatic cells and scientists have studied the fate of each of these cells during their development in the nematode life cycle There is little variation in patterns of cell lineage between individuals, unlike in mammals where cell development from the embryo is dependent on cellular cues In vertebrates, one of the primary steps during organogenesis is the formation of the neural system The ectoderm forms epithelial cells and tissues, and neuronal tissues During the formation of the neural system, special signaling molecules called growth factors signal some cells at the edge of the ectoderm to become epidermis cells The remaining cells in the center form the neural plate If the signaling by growth factors were disrupted, then the entire ectoderm would differentiate into neural tissue 1/5 Organogenesis and Vertebrate Formation The neural plate undergoes a series of cell movements where it rolls up and forms a tube called the neural tube, as illustrated in [link] In further development, the neural tube will give rise to the brain and the spinal cord The central region of the ectoderm forms the neural tube, which gives rise to the brain and the spinal cord The mesoderm that lies on either side of the vertebrate neural tube will develop into the various connective tissues of the animal body A spatial pattern of gene expression reorganizes the mesoderm into groups of cells called somites with spaces between them The somites, illustrated in [link] will further develop into the ribs, lungs, and segmental (spine) muscle The mesoderm also forms a structure called the notochord, which is rodshaped and forms the central axis of the animal body 2/5 Organogenesis and Vertebrate Formation In this five-week old human embryo, somites are segments along the length of the body (credit: modification of work by Ed Uthman) Vertebrate Axis Formation Even as the germ layers form, the ball of cells still retains its spherical shape However, animal bodies have lateral-medial (left-right), dorsal-ventral (back-belly), and anteriorposterior (head-feet) axes, illustrated in [link] Animal bodies have three axes for symmetry (credit: modification of work by NOAA) How are these established? In one of the most seminal experiments ever to be carried out in developmental biology, Spemann and Mangold took dorsal cells from one embryo and transplanted them into the belly region of another embryo They found that the transplanted embryo now had two notochords: one at the dorsal site from the original 3/5 Organogenesis and Vertebrate Formation cells and another at the transplanted site This suggested that the dorsal cells were genetically programmed to form the notochord and define the axis Since then, researchers have identified many genes that are responsible for axis formation Mutations in these genes leads to the loss of symmetry required for organism development Animal bodies have externally visible symmetry However, the internal organs are not symmetric For example, the heart is on the left side and the liver on the right The formation of the central left-right axis is an important process during development This internal asymmetry is established very early during development and involves many genes Research is still ongoing to fully understand the developmental implications of these genes Section Summary Organogenesis is the formation of organs from the germ layers Each germ layer gives rise to specific tissue types The first stage is the formation of the neural system in the ectoderm The mesoderm gives rise to somites and the notochord Formation of vertebrate axis is another important developmental stage Review Questions Which of the following gives rise to the skin cells? ectoderm endoderm mesoderm none of the above A The ribs form from the ... 11. Class structure, class consciousness and class formation in Sweden, the United States and Japan This chapter will try to apply some of the elements of the models elaborated in the previous chapter to the empirical study of class formation and class consciousness in three developed capitalist countries ± the United States, Sweden and Japan. 1 More speci®cally, the investiga- tion has three main objectives: ®rst, to examine the extent to which the overall relationship between class locations and class consciousness is broadly consistent with the logic of the class structure analysis we have been using throughout this book; second to compare the patterns of class formation in the three countries; and third to examine the ways in which the micro, multivariate models of consciousness formation vary across the three countries. The ®rst of these tasks centers on exploring the ``class location 7limits? class consciousness'' segment of the model, the second focuses on the ``class structure 7limits? class formation'' segment, and the third centers on the ``macro 7mediates? micro'' aspect of the model. In the next section we will discuss the strategy we will deploy for measuring class consciousness. This will be followed in section 11.2 with a more detailed discussion of the empirical agenda and the strategies of data analysis. Sections 11.3 to 11.5 will then present the results of the data analysis. 1 In the original edition of Class Counts, there are two additional empirical chapters on problems of class consciousness, the ®rst dealing with the interaction between class and state employment in shaping class consciousness, and the second on the relationship between individual class biographies and class consciousness. These had to be dropped from the present edition because of space constraints. 216 11.1 Measuring class consciousness Class consciousness is notoriously hard to measure. The concept is meant to denote subjective properties which impinge on conscious choosing activity which has a class content. The question then arises whether or not the subjective states which the concept taps are really only ``activated'' under conditions of meaningful choice situations, which in the case of class consciousness would imply above all situations of class struggle. There is no necessary reason to assume that these subjective states will be the same when respondents are engaged in the kind of conscious choosing that occurs in an interview. Choosing responses on a survey is a different practice from choosing how to relate to a shop¯oor con¯ict, and the forms of subjectivity which come into play are quite different. The interview setting is itself, after all, a social relation, and this relation may in¯uence the responses of respondents out of deference, or hostility or some other reaction. Furthermore, it is always possible that there is not simply slippage between the way people respond to the arti®cial choices of a survey and the real choices of social practices, but that there is a systematic inversion of responses. As a result, it has been argued by some (e.g. Marshall 1983) that there is little REVIEW ARTICLE Membrane targeting and pore formation by the type III secretion system translocon Pierre-Jean Matteı ¨ 1 , Eric Faudry 2 , Viviana Job 1 , Thierry Izore ´ 1 , Ina Attree 2 and Andre ´ a Dessen 1 1 Bacterial Pathogenesis Group, Institut de Biologie Structurale, UMR 5075 (CNRS ⁄ CEA ⁄ UJF), Grenoble, France 2 Bacterial Pathogenesis and Cellular Responses Team, Centre National de la Recherche Scientifique (CNRS), Universite ´ Joseph Fourier (UJF), LBBSI, iRTSV, CEA, Grenoble, France Introduction Type III secretion systems (T3SS) are complex macro- molecular machineries employed by a number of bac- teria to inject toxins and effectors directly into the cytoplasm of eukaryotic cells. Pathogens carrying this system, which include Pseudomonas, Yersinia, Salmo- nella and Shigella spp., as well as clinical Escherichia coli isolates, can translocate between four and 20 effec- tors with dramatic effects on the target cell, leading, for example, to cytoskeleton rearrangement, membrane disruption or the initiation of apoptosis [1–3]. T3SS are composed of at least twenty distinct pro- teins that assemble into three major parts. The basal body of the system, composed of two main ring-like structures, spans both the inner and outer bacterial membranes (Fig. 1) [4–7]. This multi-protein structure is associated with an ATPase, which itself is mem- brane-associated and faces the bacterial cytoplasm, and is suggested to be involved in facilitating the entry of export substrates into the secretion system [8–10]. The basal body of the T3SS is also associated with a proteinaceous needle that extends outwards from the bacterial surface and is assumed to act as a conduit for effector secretion [6,11–13], although direct evi- dence for this concept is lacking. Because the internal diameter of the needle is relatively small (2.0–2.5 nm), effectors probably travel in unfolded ⁄ semi-unfolded states [11]. Synthesis and assembly of the T3SS itself are induced once the bacterium is physically associated Keywords bacterial infection; injection; membrane; pore formation; secretion; toxin Correspondence A. Dessen, Bacterial Pathogenesis Group, Institut de Biologie Structurale, UMR 5075 (CNRS ⁄ CEA ⁄ UJF), 41 rue Jules Horowitz, 38027 Grenoble, France Fax: +33 4 38 78 54 94 Tel: +33 4 38 78 95 90 E-mail: andrea.dessen@ibs.fr (Received 21 September 2010, revised 4 November 2010, accepted 26 November 2010) doi:10.1111/j.1742-4658.2010.07974.x The type III secretion system (T3SS) is a complex macromolecular machin- ery employed by a number of Gram-negative species to initiate infection. Toxins secreted through the system are synthesized in the bacterial cyto- plasm and utilize the T3SS to pass through both bacterial membranes and the periplasm, thus being introduced directly into the eukaryotic cytoplasm. A key element of the T3SS of all bacterial pathogens is the translocon, which comprises a pore that is inserted into the membrane of the target cell, allowing toxin injection. Three macromolecular partners associate to form the translocon: two are hydrophobic and one is hydrophilic, and the latter also associates with the T3SS needle. In this review, we discuss recent advances on the biochemical and structural characterization of the proteins involved in translocon formation, as well as their participation in the modi- fication of intracellular signalling pathways upon infection. Models of tran- slocon assembly and regulation are also discussed. Abbreviations EHEC, enterohaemorrhagic; EPEC, enteropathogenic; IFN, interferon; Comparative studies on the functional roles of N- and C-terminal regions of molluskan and vertebrate troponin-I Hiroyuki Tanaka 1 , Yuhei Takeya 1 , Teppei Doi 1 , Fumiaki Yumoto 2,3 , Masaru Tanokura 3 , Iwao Ohtsuki 2 , Kiyoyoshi Nishita 1 and Takao Ojima 1 1 Laboratory of Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, Japan 2 Laboratory of Physiology, The Jikei University School of Medicine, Tokyo, Japan 3 Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Japan Troponin is a Ca 2+ -dependent regulatory protein com- plex, which constitute thin filaments together with actin and tropomyosin [1]. It is composed of three dis- tinct subunits: troponin-C (TnC), which binds Ca 2+ , troponin-T (TnT), which binds tropomyosin, and trop- onin-I (TnI), which binds actin and inhibits actin–myo- sin interaction [2–4]. In relaxed muscle, TnI binds to actin and inhibits contraction. Upon muscle stimula- tion, Ca 2+ binds to TnC and induces the release of the inhibition by TnI, resulting in muscle contraction. To understand the molecular mechanisms of this Ca 2+ switching, extensive studies of the structure, function, and Ca 2+ -dependent conformational changes of tropo- nin subunits have been carried out. In vertebrate muscles, TnC has a dumbbell-like shape with the N- and C-terminal globular domains linked by a central helix [5,6]. Each domain contains two EF-hand Ca 2+ -binding motifs [7], thus TnC has four possible Ca 2+ -binding sites, sites I and II in the N-domain and sites III and IV in the C-domain [8,9]. Keywords invertebrate; mollusk; regulatory mechanism; troponin; troponin-I Correspondence Takao Ojima, Laboratory of Biochemistry and Biotechnology, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido 041–8611, Japan Tel ⁄ Fax: +81 138 408800 E-mail: ojima@fish.hokudai.ac.jp Note The nucleotide sequences of cDNAs enco- ding Akazara scallop 52K-TnI and 19K-TnI are available in DDBJ ⁄ EMBL ⁄ GenBank databases under accession numbers, AB206837 and AB206838, respectively (Received 24 March 2005, revised 13 June 2005, accepted 15 July 2005) doi:10.1111/j.1742-4658.2005.04866.x Vertebrate troponin regulates muscle contraction through alternative bind- ing of the C-terminal region of the inhibitory subunit, troponin-I (TnI), to actin or troponin-C (TnC) in a Ca 2+ -dependent manner. To elucidate the molecular mechanisms of this regulation by molluskan troponin, we com- pared the functional properties of the recombinant fragments of Akazara scallop TnI and rabbit fast skeletal TnI. The C-terminal fragment of Akaz- ara scallop TnI (ATnI 232)292 ), which contains the inhibitory region (resi- dues 104–115 of rabbit TnI) and the regulatory TnC-binding site (residues 116–131), bound actin-tropomyosin and inhibited actomyosin-tropomyosin Mg-ATPase. However, it did not interact with TnC, even in the presence of Ca 2+ . These results indicated that the mechanism involved in the alter- native binding of this region was not observed in molluskan troponin. On the other hand, ATnI 130)252 , which contains the structural TnC-binding site (residues 1–30 of rabbit TnI) and the inhibitory region, bound strongly to both actin and TnC. Moreover, the ternary complex consisting of this frag- ment, troponin-T, and TnC activated the Stability and fibril formation properties of human and fish transthyretin, and of the Escherichia coli transthyretin-related protein Erik Lundberg 1 , Anders Olofsson 2 , Gunilla T. Westermark 3 and A. Elisabeth Sauer-Eriksson 1 1 Department of Chemistry, Umea ˚ University, Sweden 2 Department of Medical Biochemistry and Biophysics, Umea ˚ University, Sweden 3 Division of Cell Biology, Diabetes Research Centre, Linko ¨ ping University, Sweden Transthyretin (TTR) is a homotetrameric plasma pro- tein that binds and transports the thyroid hormones 3,5,3¢-triiodo-l-thyronine and 3,5,3¢,5¢-tetraiodo-l-thyr- onine (thyroxine) and retinol by binding to the retinol- binding protein when it is loaded with retinol [1]. TTR is mainly expressed in the adult liver, the choroid plexus of the brain, and the retina [2,3]. TTR is involved in three amyloid diseases: familial amyloidotic polyneuropathy, familial amyloidotic cardiomyopathy (FAC), and senile systemic amyloidosis (SSA) [4,5]. Whereas SSA is associated with native TTR, point mutations, of which more than 80 have been identified, cause FAP and FAC [6]. TTR mutations associated with familial amyloid diseases display a wide range of Keywords amyloid; fibril formation; HIU hydrolase; transthyretin; transthyretin-related protein Correspondence A. E. Sauer-Eriksson, Department of Chemistry, Umea ˚ University, SE-90187 Umea ˚ , Sweden Fax: +46 90 7865944 Tel: +46 90 7865923 E-mail: elisabeth.sauer-eriksson@chem. umu.se (Received 7 November 2008, revised 20 January 2009, accepted 26 January 2009) doi:10.1111/j.1742-4658.2009.06936.x Human transthyretin (hTTR) is one of several proteins known to cause amyloid disease. Conformational changes in its native structure result in aggregation of the protein, leading to insoluble amyloid fibrils. The trans- thyretin (TTR)-related proteins comprise a protein family of 5-hydroxyiso- urate hydrolases with structural similarity to TTR. In this study, we tested the amyloidogenic properties, if any, of sea bream TTR (sbTTR) and Escherichia coli transthyretin-related protein (ecTRP), which share 52% and 30% sequence identity, respectively, with hTTR. We obtained filamen- tous structures from all three proteins under various conditions, but, inter- estingly, different structures displayed different tinctorial properties. hTTR and sbTTR formed thin, curved fibrils at low pH (pH 2–3) that bound thioflavin-T (thioflavin-T-positive) but did not stain with Congo Red (CR) (CR-negative). Aggregates formed at the slightly higher pH of 4.0–5.5 had different morphology, displaying predominantly amorphous structures. CR-positive material of hTTR was found in this material, in agreement with previous results. ecTRP remained soluble at pH 2–12 at ambient tem- peratures. By raising of the temperature, fibril formation could be induced at neutral pH in all three proteins. Most of these temperature-induced fibrils were thicker and straighter than the in vitro fibrils seen at low pH. In other words, the temperature-induced fibrils were more similar to fibrils seen in vivo. The melting temperature of ecTRP was 66.7 °C. This is approximately 30 °C lower than the melting temperatures of sbTTR and hTTR. Information from the crystal structures was used to identify possible explanations for the reduced thermostability of ecTRP. Abbreviations AFM, atomic force microscopy; BME, b-mercaptoethanol; CR, Congo Red; DSC, differential scanning calorimetry; ecTRP, Escherichia coli transthyretin-related protein; EM, electron microscopy; FAC, familial amyloidotic cardiomyopathy; ... lungs, and segmental (spine) muscle The mesoderm also forms a structure called the notochord, which is rodshaped and forms the central axis of the animal body 2/5 Organogenesis and Vertebrate Formation. .. original 3/5 Organogenesis and Vertebrate Formation cells and another at the transplanted site This suggested that the dorsal cells were genetically programmed to form the notochord and define.. .Organogenesis and Vertebrate Formation The neural plate undergoes a series of cell movements where it rolls up and forms a tube called the neural tube,